title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2021-05 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The combination of lactoferrin and linolenic acid inhibits colorectal tumor growth through activating AMPK/JNK-related apoptosis pathway link: https://peerj.com/articles/11072 last-modified: 2021-05-31 description: Colorectal cancer is a common cause of death with few available therapeutic strategies, and the preventative complexes in adjunctive therapy are urgently needed. Increasing evidences have shown that natural ingredients, including lactoferrin, oleic acid, docosahexaenoic acid (DHA) and linolenic acid, possess anti-inflammatory and anti-tumor activities. However, investigations and comparisons of their combinations in colorectal tumor model have not been reported, and the mechanism is still unrevealed. In the study, we examined the viability, migration, invasion and apoptosis of HT29 cells to choose the proper doses of these components and to select the effective combination in vitro. BALB/c nude mice bearing colorectal tumor were used to explore the role of selected combination in inhibiting tumor development in vivo. Additionally, metabonomic detection was performed to screen out the specific changed metabolitesand related pathway. The results demonstrated that lactoferrin at 6.25 μM, oleic acid at 0.18 mM, DHA at 0.18 mM, and linolenic acid at 0.15 mM significantly inhibited the viabilities of HT29 cells (p < 0.05). The combination of lactoferrin (6.25 μM) + linolenic acid (0.15 mM) exhibited the strongest activity in inhibiting the migration and invasion of HT29 cells in vivo and suppressing tumor development in vitro (p < 0.05). Furthermore, the lactoferrin + linolenic acid combination activated p-AMPK and p-JNK, thereby inducing apoptosis of HT29 cells (p < 0.05). The present study was the first to show that lactoferrin + linolenic acid combination inhibited HT29 tumor formation by activating AMPK/JNK related pathway. creator: Qianqian Yao creator: Huiying Li creator: Linlin Fan creator: Shengnan Huang creator: Jiaqi Wang creator: Nan Zheng uri: https://doi.org/10.7717/peerj.11072 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yao et al. title: Identification and functional analysis of SWEET gene family in Averrhoa carambola L. fruits during ripening link: https://peerj.com/articles/11404 last-modified: 2021-05-31 description: Sugar Will Eventually be Exported Transporters (SWEETs), a type of sugar efflux transporters, have been extensively researched upon due to their role in phloem loading for distant sugar transport, fruit development, and stress regulation, etc. Several plant species are known to possess the SWEET genes; however, little is known about their presence in Averrhoa Carambola L. (Oxalidaceae), an evergreen fruit crop (star fruit) in tropical and subtropical regions of Southeast Asia. In this study, we established an Averrhoa Carambola L. unigenes library from fruits of ‘XianMiyangtao’ (XM) by RNA sequencing (RNA-seq). A total of 99,319 unigenes, each longer than 200 bp with a total length was 72.00 Mb, were identified. A total of 51,642 unigenes (52.00%) were annotated. Additionally, 10 AcSWEET genes from the Averrhoa Carambola L. unigenes library were identified and classified, followed by a comprehensive analysis of their structures and conserved motif compositions, and evolutionary relationships. Moreover, the expression patterns of AcSWEETs in ‘XM’ cultivars during fruit ripening were confirmed using quantitative real-time PCR (qRT-PCR), combined with the soluble sugar and titratable acids content during ripening, showed that AcSWEET2a/2b and AcSWEET16b might participate in sugar transport during fruit ripening. This work presents a general profile of the AcSWEET gene family in Averrhoa Carambola L., which can be used to perform further studies on elucidating the functional roles of AcSWEET genes. creator: Qihua Lin creator: Qiuzhen Zhong creator: Zehuang Zhang uri: https://doi.org/10.7717/peerj.11404 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Lin et al. title: Teratological changes in postembryos of Eratigena atrica obtained by the application of alternating temperatures on spider embryos link: https://peerj.com/articles/11457 last-modified: 2021-05-31 description: Spider embryonic development depends on several factors, including temperature. Under optimum thermal conditions embryogenesis proceeds undisturbed and embryo mortality is low. On the other hand, dramatic shifts in incubation temperature may cause a range of developmental defects in embryos. It has been confirmed in numerous laboratory experiments that abrupt temperature changes can be a powerful teratogenic factor. Changes in the external structure are frequently reflected in the internal anatomy, and above all, in the central nervous system. In the present teratological study, by exposing spider embryos to the temperatures of 14 °C and 32 °C, changed every 12 hours for the first 10 days of their development, we obtained 74 postembryos of Eratigena atrica with body deformities such as oligomely, heterosymely, schistomely, bicephaly, complex anomalies and others. We selected six spiders to describe and analyze their morphological changes. In one case, that of a spider affected by polymely (the presence of a supernumerary appendage) combined with heterosymely (the fusion of walking legs), we also focused on the structure of the central nervous system. The analysis indicated that this complex anomaly was accompanied by only one change in the central nervous system: the presence of a supernumerary neuropil. Since no fusion of walking leg neuropils was observed, it was concluded that, in this instance, there was no relationship between the fusion of legs and the structure of the central nervous system. creator: Teresa Napiórkowska creator: Julita Templin creator: Paweł Napiórkowski uri: https://doi.org/10.7717/peerj.11457 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Napiórkowska et al. title: New interpretation of the cranial osteology of the Early Cretaceous turtle Arundelemys dardeni (Paracryptodira) based on a CT-based re-evaluation of the holotype link: https://peerj.com/articles/11495 last-modified: 2021-05-31 description: Arundelemys dardeni is an Early Cretaceous paracryptodire known from a single, incomplete, but generally well-preserved skull. Phylogenetic hypotheses of paracryptodires often find Arundelemys dardeni as an early branching baenid. As such, it has a central role in understanding the early evolution of the successful clade Baenidae, which survived the Cretaceous–Paleogene mass extinction, as well as the diversification of Paracryptodira into its subclades, which recent research suggests to perhaps include helochelydrids, compsemydids, pleurosternids, and baenids. Computer tomography scans of the holotype material that were produced for the initial description of Arundelemeys dardeni reveal several errors in the initial anatomical description of the species, which we correct based on element-by-element segmentation. In addition, we provide entirely novel anatomical information, including descriptions of several previously undescribed cranial bones, the endosseous labyrinth, and the cranial scutes, the latter of which are unknown for most paracryptodires. We provide an interpretation of cranial scutes which homologizes the scutes of Arundelemys dardeni with those of other stem turtles. creator: Serjoscha W. Evers creator: Yann Rollot creator: Walter G. Joyce uri: https://doi.org/10.7717/peerj.11495 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Evers et al. title: The effect of staphylococcal mastitis including resistant strains on serum procalcitonin, neopterin, acute phase response and stress biomarkers in Holstein dairy cows link: https://peerj.com/articles/11511 last-modified: 2021-05-31 description: Staphylococcal mastitis (SM) is a frequent disease in the dairy cattle that is costly to treat. This study aimed to investigate the alterations in the levels of procalcitonin (PCT), neopterin (NPT), haptoglobin (HP), serum amyloid A (SAA), proinflammatory cytokines (IL-1β, IL-8, TNF-α, IF-γ) and oxidative stress (OS) biomarkers in Holstein dairy cows with SM under field conditions. In addition, we also evaluated the role of examined biomarkers in disease pathogenesis and their use as diagnostic biomarkers for the disease in dairy cows. Fifty-three dairy cows with SM, including those with infections caused by Staphylococcus aureus (n = 42) and methicillin resistant S. aureus (MRSA) (n = 11) were selected for this study. In addition, 20 healthy dairy cows were enrolled as a control group. Higher serum levels of PCT, NP, IL-1β, IL-8, TNF-α, IF-γ, HP and SAA and a state of OS was detected in SM group in comparison with the controls. Moreover, the levels of all examined biomarkers in mastitic cows with S. aureus when compared with those infected with MRSA was not significantly different. All examined biomarkers demonstrated a significant degree of discrimination between SM cows and healthy controls (the area under the curve (AUC) ranged from 83.6 for SAA to 100 for PCT). Our study showed that SM in dairy cows was associated with substantial changes in serum PCT, NPT, Acute phase proteins (APPs), proinflammatory cytokines, and OS levels. This study demonstrates that clinical examination in tandem with quantification of PCT, NPT, APPs and cytokines, OS biomarkers could be a useful assessment tool for SM in dairy cows. creator: Wael El-Deeb creator: Mahmoud Fayez creator: Naser Alhumam creator: Ibrahim Elsohaby creator: Sayed A. Quadri creator: Hermine Mkrtchyan uri: https://doi.org/10.7717/peerj.11511 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 El-Deeb et al. title: Lipid accumulation of Chlorella sp. TLD6B from the Taklimakan Desert under salt stress link: https://peerj.com/articles/11525 last-modified: 2021-05-31 description: Chlorella has become an important raw material for biodiesel production in recent years, and Chlorella sp. TLD6B, a species with high lipid concentrations and high salt and drought tolerance, has been cultivated on a large scale. To explore the lipid accumulation of Chlorella sp. TLD6B and its relationship to external NaCl concentrations, we performed physiological measurements and genome-wide gene expression profiling under different levels of salt stress. Chlorella sp. TLD6B was able to tolerate high levels of salt stress (0.8 M NaCl addition). Lipid concentrations initially increased and then decreased as salt stress increased and were highest under the addition of 0.2 M NaCl. Comparative transcriptomic analysis revealed that salt stress enhanced the expression of genes related to sugar metabolism and fatty acid biosynthesis (the ACCases BC and BCCP, KAS II, and GPDHs involved in TAG synthesis), thereby promoting lipid accumulation under the addition of 0.2 M NaCl. However, high salinity inhibited cell growth. Expression of three SADs, whose encoded products function in unsaturated fatty acid biosynthesis, was up-regulated under high salinity (0.8 M NaCl addition). This research clarifies the relationship between salt tolerance and lipid accumulation and promotes the utilization of Chlorella sp. TLD6B. creator: Hong Li creator: Jun Tan creator: Yun Mu creator: Jianfeng Gao uri: https://doi.org/10.7717/peerj.11525 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: The immediate effect of a single session of pain neuroscience education on pain and the autonomic nervous system in subjects with persistent pain, a pilot study link: https://peerj.com/articles/11543 last-modified: 2021-05-31 description: BackgroundThe autonomic nervous system is a system that operates at the subconscious level and has been associated with neurobehavioral aspects of pain. Overall, persistent pain has a stimulating effect on the sympathetic nervous system. A promising emerging nonpharmacological treatment to manage persistent pain is neuroscience-based pain education. The overarching goal of neuroscience-based pain education is to change cognitions about pain and the pain experience through education. The aim was to determine the immediate and short-term impact of a neuroscience-based pain education video on the autonomic nervous system and pain in a subgroup of individuals with persistent pain.MethodsA convenience sample of 26 subjects were recruited for this study. Each subject indicated their pain level at the time of testing using a Visual Analogue Scale. Automated pupillometry was utilized to measure pupil diameter. After two minutes of accommodation to the goggles, the pupil was measured continuously for 60 s. Following this a 5-minute video presentation “Understanding Pain” was watched, followed by a continuous pupil measurement for 60 s. Three minutes after this measure, the final pupil diameter measurement was taken for 60 s. After completing the final pupil measure, the subject was asked to fill out a second Visual Analogue Scale and a Global Rate of Change.OutcomesEach subject completed a Global Rating of Change Scale and the mean score was 1.14 (SD = 1.61 and a SEM = 0.), supporting the hypothesis of an overall self-perceived benefit from the intervention. There was a statistically significant difference in pain following the video, P < 0.01. A significant correlation was observed between the self-perceived decrease in pain level and the Global Rating of Change score, p = 0.02. There was no statistically significant difference in the mean pupil diameter following the video with p = 0.76 for the right eye and p = 0.250 for the left eye.DiscussionThis pilot study demonstrated that a 5-minute neuroscience-based pain education video reduced perceived pain in a small sample of subjects with persistent pain. Watching the neuroscience-based pain education video did not seem to result in an immediate generalized autonomic nervous system response. However, it resulted in a different reaction on each eye. This unequal response might be the result of the hemispheric lateralization of the ANS. This study supports the fact that the pain experience is determined by the balance between conscious cognitive processes and subconscious processes based on previous psychological experiences. creator: Rob Sillevis creator: Gabriel Trincado creator: Eric Shamus uri: https://doi.org/10.7717/peerj.11543 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sillevis et al. title: Nutrient criteria to achieve New Zealand’s riverine macroinvertebrate targets link: https://peerj.com/articles/11556 last-modified: 2021-05-31 description: Waterways worldwide are experiencing nutrient enrichment from population growth and intensive agriculture, and New Zealand is part of this global trend. Increasing fertilizer in New Zealand and intensive agriculture have driven substantial water quality declines over recent decades. A recent national directive has set environmental managers a range of riverine ecological targets, including three macroinvertebrate indicators, and requires nutrient criteria be set to support their achievement. To support these national aspirations, we use the minimization-of-mismatch analysis to derive potential nutrient criteria. Given that nutrient and macroinvertebrate monitoring often does not occur at the same sites, we compared nutrient criteria derived at sites where macroinvertebrates and nutrients are monitored concurrently with nutrient criteria derived at all macroinvertebrate monitoring sites and using modelled nutrients. To support all three macroinvertebrate targets, we suggest that suitable nutrient criteria would set median dissolved inorganic nitrogen concentrations at ~0.6 mg/L and median dissolved reactive phosphorus concentrations at ~0.02 mg/L. We recognize that deriving site-specific nutrient criteria requires the balancing of multiple values and consideration of multiple targets, and anticipate that criteria derived here will help and support these environmental goals. creator: Adam D. Canning creator: Michael K. Joy creator: Russell G. Death uri: https://doi.org/10.7717/peerj.11556 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Canning et al. title: Paeoniflorin improves functional recovery through repressing neuroinflammation and facilitating neurogenesis in rat stroke model link: https://peerj.com/articles/10921 last-modified: 2021-05-28 description: BackgroundMicroglia, neuron, and vascular cells constitute a dynamic functional neurovascular unit, which exerts the crucial role in functional recovery after ischemic stroke. Paeoniflorin, the principal active component of Paeoniae Radix, has been verified to exhibit neuroprotective roles in cerebralischemic injury. However, the mechanisms underlying the regulatory function of Paeoniflorin on neurovascular unit after cerebral ischemia are still unclear.MethodsIn this study, adult male rats were treated with Paeoniflorin following transient middle cerebral artery occlusion (tMCAO), and then the functional behavioral tests (Foot-fault test and modified improved neurological function score, mNSS), microglial activation, neurogenesis and vasculogenesis were assessed.ResultsThe current study showed that Paeoniflorin treatment exhibited a sensorimotor functional recovery as suggested via the Foot-fault test and the enhancement of spatial learning as suggested by the mNSS in rat stroke model. Paeoniflorin treatment repressed microglial cell proliferation and thus resulted in a significant decrease in proinflammatory cytokines IL-1β, IL-6 and TNF-α. Compared with control, Paeoniflorin administration facilitated von Willebrand factor (an endothelia cell marker) and doublecortin (a neuroblasts marker) expression, indicating that Paeoniflorin contributed to neurogenesis and vasculogenesis in rat stroke model. Mechanistically, we verified that Paeoniflorin repressed JNK and NF-κB signaling activation.ConclusionsThese results demonstrate that Paeoniflorin represses neuroinflammation and facilitates neurogenesis in rat stroke model and might be a potential drug for the therapy of ischemic stroke. creator: Hongli Tang creator: Leiruo Wu creator: Xixi Chen creator: Huiting Li creator: Baojun Huang creator: Zhenyang Huang creator: Yiyang Zheng creator: Liqing Zhu creator: Wujun Geng uri: https://doi.org/10.7717/peerj.10921 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Tang et al. title: Development of an inexpensive matrix-assisted laser desorption—time of flight mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize link: https://peerj.com/articles/11359 last-modified: 2021-05-28 description: Many endophytes and rhizobacteria associated with plants support the growth and health of their hosts. The vast majority of these potentially beneficial bacteria have yet to be characterized, in part because of the cost of identifying bacterial isolates. Matrix-assisted laser desorption-time of flight (MALDI-TOF) has enabled culturomic studies of host-associated microbiomes but analysis of mass spectra generated from plant-associated bacteria requires optimization. In this study, we aligned mass spectra generated from endophytes and rhizobacteria isolated from heritage and sweet varieties of Zea mays. Multiple iterations of alignment attempts identified a set of parameters that sorted 114 isolates into 60 coherent MALDI-TOF taxonomic units (MTUs). These MTUs corresponded to strains with practically identical (>99%) 16S rRNA gene sequences. Mass spectra were used to train a machine learning algorithm that classified 100% of the isolates into 60 MTUs. These MTUs provided >70% coverage of aerobic, heterotrophic bacteria readily cultured with nutrient rich media from the maize microbiome and allowed prediction of the total diversity recoverable with that particular cultivation method. Acidovorax sp., Pseudomonas sp. and Cellulosimicrobium sp. dominated the library generated from the rhizoplane. Relative to the sweet variety, the heritage variety c ontained a high number of MTUs. The ability to detect these differences in libraries, suggests a rapid and inexpensive method of describing the diversity of bacteria cultured from the endosphere and rhizosphere of maize. creator: Michael G. LaMontagne creator: Phi L. Tran creator: Alexander Benavidez creator: Lisa D. Morano uri: https://doi.org/10.7717/peerj.11359 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 LaMontagne et al. title: Lower cretaceous avian-dominated, theropod, thyreophoran, pterosaur and turtle track assemblages from the Tugulu Group, Xinjiang, China: ichnotaxonomy and palaeoecology link: https://peerj.com/articles/11476 last-modified: 2021-05-28 description: Rich tetrapod ichnofaunas, known for more than a decade, from the Huangyangquan Reservoir (Wuerhe District, Karamay City, Xinjiang) have been an abundant source of some of the largest Lower Cretaceous track collections from China. They originate from inland lacustrine clastic exposures of the 581–877 m thick Tugulu Group, variously divided into four formations and subgroups in the northwestern margin of the Junggar Basin. The large Huangyangquan track assemblages occur in the Lower layer/Subgroup II. Similarly-composed track assemblages also occur at the smaller Asphaltite site in the Upper Layer/Subgroup III. The Huangyangquan assemblages have yielded more than 1,500 identified tracks including abundant tracks of avian and non-avian theropods, pterosaurs and turtles and less abundant tracks of stegosaurs. Previous avian track identifications have been reassessed to conclude that Moguiornipes robustus is a taphotaxon and Koreanaornis dodsoni might be better accommodated in the ichnogenus Aquatilavipes which appears to be the dominant avian ichnotaxon. The avian track Ignotornis is also recognized and represents the first occurrence of this ichnogenus in China. Although the Huangyangquan assemblages lack some of the larger components (e.g., sauropodan and ornithopodan tracks) known from other Lower Cretaceous localities, the association of abundant tracks of smaller tetrapods (avian and non-avian theropods, pterosaurs and turtles) appears to be representative of lacustrine basin faunas of this region, and are an excellent example of the shorebird ichnocoenosis/ichnofacies concept. This is the first comprehensive review and re-analysis of an important Lower Cretaceous ecosystem. creator: Lida Xing creator: Martin G. Lockley creator: Chengkai Jia creator: Hendrik Klein creator: Kecheng Niu creator: Lijun Zhang creator: Liqi Qi creator: Chunyong Chou creator: Anthony Romilio creator: Donghao Wang creator: Yu Zhang creator: W Scott Persons creator: Miaoyan Wang uri: https://doi.org/10.7717/peerj.11476 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Xing et al. title: Using a mobile health app to improve patients’ adherence to hypertension treatment: a non-randomized clinical trial link: https://peerj.com/articles/11491 last-modified: 2021-05-28 description: Poor adherence to hypertension treatment increases complications of the disease and is characterized by a lack of awareness and acceptance of ongoing treatment. Mobile health (mHealth) apps can optimize processes and facilitate access to health information by combining treatment methods with attractive solutions. In this study, we aimed at verifying the influence of using an mHealth app on patients’ adherence to hypertension treatment, also examining how user experience toward the app influenced the outcomes. A total of 49 participants completed the study, men and women, diagnosed with hypertension and ongoing medical treatment. For 12 weeks, the control group continued with conventional monitoring, while the experimental group used an mHealth app. From the experimental group, at baseline, 8% were non-adherent, 64% were partial adherents and 28% were adherent to the treatment. Baseline in the control group indicated 4.2% non-adherents, 58.3% partial adherents, and 37.5% adherents. After follow-up, the experimental group had an increase to 92% adherent, 8% partially adherent, and 0% non-adherent (P < 0.001). In the control group, adherence after follow-up remained virtually the same (P ≥ 0.999). Results of user experience were substantially positive and indicate that the participants in the experimental group had a satisfactory perception of the app. In conclusion, this study suggests that using an mHealth app can empower patients to manage their own health and increase adherence to hypertension treatment, especially when the app provides a positive user experience. creator: Simiane Salete Volpi creator: Daiana Biduski creator: Ericles Andrei Bellei creator: Danieli Tefili creator: Lynn McCleary creator: Ana Luisa Sant’Anna Alves creator: Ana Carolina Bertoletti De Marchi uri: https://doi.org/10.7717/peerj.11491 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Volpi et al. title: Resveratrol improves cardiac function and left ventricular fibrosis after myocardial infarction in rats by inhibiting NLRP3 inflammasome activity and the TGF-β1/SMAD2 signaling pathway link: https://peerj.com/articles/11501 last-modified: 2021-05-28 description: BackgroundSeveral studies have shown that resveratrol (RES), a naturally occurring polyphenol found in many plants, is beneficial for preventing cardiovascular diseases. However, the mechanism underlying the RES-mediated protection against myocardial infarction has not yet been revealed entirely. In this study, we investigated the protective effects of RES on cardiac function in a rat model of acute myocardial infarction (AMI) and the related underlying mechanisms.MethodsMale Sprague-Dawley rats were randomly divided into four groups: Sham (sham operation), Sham-RES, AMI (AMI induction), and AMI-RES. The rat AMI model was established by the permanent ligation of left anterior descending coronary artery method. The rats in the RES-treated groups were gavaged with RES (50 mg/kg/day) daily for 45 days after the Sham operation or AMI induction; rats in the Sham and AMI groups were gavaged with deionized water. Cardiac function was evaluated by echocardiography. Atrial interstitial fibrosis was assessed by hematoxylin-eosin or Masson’s trichrome staining. Real-time PCR and western blotting analyses were performed to examine the levels of signaling pathway components.ResultsRES supplementation decreased the inflammatory cytokine levels, improved the cardiac function, and ameliorated atrial interstitial fibrosis in the rats with AMI. Furthermore, RES supplementation inhibited NLRP3 inflammasome activity, decreased the TGF-β1 production, and downregulated the p-SMAD2/SMAD2 expression in the heart.ConclusionRES shows notable cardioprotective effects in a rat model of AMI; the possible mechanisms underlying these effects may involve the improvement of cardiac function and atrial interstitial fibrosis via the RES-mediated suppression of NLRP3 inflammasome activity and inhibition of the TGF-β1/SMAD2 signaling pathway in the heart. creator: Jinjin Jiang creator: Xiuping Gu creator: Huifeng Wang creator: Shibin Ding uri: https://doi.org/10.7717/peerj.11501 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Jiang et al. title: Establishment of a modified percutaneous CT-guided paraspinal intramuscular VX-2 squamous cell carcinoma dual tumor model in rabbits link: https://peerj.com/articles/11536 last-modified: 2021-05-28 description: BackgroundThe rabbit VX-2 tumor model is a commonly used transplanted tumor model and is widely used in surgical, radiological, and interventional studies. Most of the known tumor models for each site are single solid tumors. This study aimed to establish an accurate and stable intramuscular dual tumor model guided by computed tomography (CT).MethodsIn this study, we compared three different inoculation methods to select the most appropriate dual tumor model. Six New Zealand White rabbits were used as tumor-carrying rabbits for tumor harvesting. Thirty rabbits were divided into three groups as experimental rabbits. Group A applied the tumor cell suspension method, in which the suspension was injected into the designated location with a syringe under CT guidance. Groups B and C used tumor tissue strips obtained in vivo or under direct in vitro vision. The tumor tissue strips were implanted into the designated locations using a guide needle under CT guidance. The differences in tumorigenic rate, the size difference between bilateral tumors, and metastasis between the three methods were compared.ResultsIt was found that group A obtained a 100% tumor survival rate, but the size of the tumor was more variable, and needle tract implantation metastasis occurred in 5 cases. In group B, tumor tissue strips were taken in vivo for implantation, in which one case failed to survive. Tumor tissue strips in group C were obtained in vitro under direct vision. The tumor tissue strips obtained in vitro by puncture using a biopsy needle in group C had a 100% tumorigenicity rate and stable tumor size. No significant needle tract implantation metastases were found in either group B or C. The variance of tumor size obtained in group A was significantly higher than in groups B and C. The variance of tumor size in group C was the smallest. Group C had high tumorigenicity and a more stable size and morphology of the formed tumors.ConclusionThe results showed that the method of obtaining tumor tissue strips using in vitro direct vision puncture and implanting them into the muscle with CT guidance and guide needles can establish an accurate and stable dual tumor model. This dual tumor model can provide substantial support for relevant preclinical studies. creator: Liangliang Meng creator: Husheng Shan creator: Xiaofeng He creator: Jiantao Zhou creator: Jingxiang Huang creator: Xin Zhang creator: Li Ma creator: Xiaodong Xue creator: Zhongliang Zhang creator: Yueyong Xiao uri: https://doi.org/10.7717/peerj.11536 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Meng et al. title: Food insecurity increases energetic efficiency, not food consumption: an exploratory study in European starlings link: https://peerj.com/articles/11541 last-modified: 2021-05-28 description: Food insecurity—defined as limited or unpredictable access to nutritionally adequate food—is associated with higher body mass in humans and birds. It is widely assumed that food insecurity-induced fattening is caused by increased food consumption, but there is little evidence supporting this in any species. We developed a novel technology for measuring foraging, food intake and body mass in small groups of aviary-housed European starlings (Sturnus vulgaris). Across four exploratory experiments, we demonstrate that birds responded to 1–2 weeks of food insecurity by increasing their body mass despite eating less. Food-insecure birds therefore increased their energetic efficiency, calculated as the body mass maintained per unit of food consumed. Mass gain was greater in birds that were lighter at baseline and in birds that faced greater competition for access to food. Whilst there was variation between experiments in mass gain and food consumption under food insecurity, energetic efficiency always increased. Bomb calorimetry of guano showed reduced energy density under food insecurity, suggesting that the energy assimilated from food increased. Behavioural observations of roosting showed inconsistent evidence for reduced physical activity under food insecurity. Increased energetic efficiency continued for 1–2 weeks after food security was reinstated, indicating an asymmetry in the speed of the response to food insecurity and the recovery from it. Future work to understand the mechanisms underlying food insecurity-induced mass gain should focus on the biological changes mediating increased energetic efficiency rather than increased energy consumption. creator: Melissa Bateson creator: Clare Andrews creator: Jonathon Dunn creator: Charlotte B.C.M. Egger creator: Francesca Gray creator: Molly Mchugh creator: Daniel Nettle uri: https://doi.org/10.7717/peerj.11541 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Bateson et al. title: Molecular diversity within the genus Laeonereis (Annelida, Nereididae) along the west Atlantic coast: paving the way for integrative taxonomy link: https://peerj.com/articles/11364 last-modified: 2021-05-27 description: The polychaete genus Laeonereis (Annelida, Nereididae) occurs over a broad geographic range and extends nearly across the entire Atlantic coast of America, from the USA to Uruguay. Despite the research efforts to clarify its diversity and systematics, mostly by morphological and ecological evidence, there is still uncertainty, mainly concerning the species Laeonereis culveri, which constitutes an old and notorious case of taxonomic ambiguity. Here, we revised the molecular diversity and distribution of Laeonereis species based on a multi-locus approach, including DNA sequence analyses of partial segments of the cytochrome c oxidase subunit I (COI), 16S rRNA, and 28S rRNA genes. We examined Laeonereis specimens collected from 26 sites along the American Atlantic coast from Massachusetts (USA) to Mar del Plata (Argentina). Although no comprehensive morphological examination was performed between different populations, the COI barcodes revealed seven highly divergent MOTUs, with a mean K2P genetic distance of 16.9% (from 6.8% to 21.9%), which was confirmed through four clustering algorithms. All MOTUs were geographically segregated, except for MOTUs 6 and 7 from southeastern Brazil, which presented partially overlapping ranges between Rio de Janeiro and São Paulo coast. Sequence data obtained from 16S rRNA and 28S rRNA markers supported the same MOTU delimitation and geographic segregation as those of COI, providing further evidence for the existence of seven deeply divergent lineages within the genus. The extent of genetic divergence between MOTUs observed in our study fits comfortably within the range reported for species of polychaetes, including Nereididae, thus providing a strong indication that they might constitute separate species. These results may therefore pave the way for integrative taxonomic studies, aiming to clarify the taxonomic status of the Laeonereis MOTUs herein reported. creator: Bruno R. Sampieri creator: Pedro E. Vieira creator: Marcos A. L. Teixeira creator: Victor C. Seixas creator: Paulo R. Pagliosa creator: Antonia Cecília Z. Amaral creator: Filipe O. Costa uri: https://doi.org/10.7717/peerj.11364 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Sampieri et al. title: Effectiveness of various bioreactors for thraustochytrid culture and production (Aurantiochytruim limacinum BUCHAXM 122) link: https://peerj.com/articles/11405 last-modified: 2021-05-27 description: This study aimed to develop bioreactors for cultivation of thraustochytrid, Aurantiochytrium limacinum BUCHAXM 122, that are low in cost and simple to operate. Obtaining maximum biomass and fatty acid production was a prerequisite. Three bioreactor designs were used: stirred tank bioreactor (STB), bubble bioreactor (BB) and internal loop airlift bioreactor (ILAB). The bioreactors were evaluated for their influence on oxygen mass transfer coefficient (kLa), using various spargers, mixing speed, and aeration rates. Biomass and DHA production from STB, BB, ILAB were then compared with an incubator shaker, using batch culture experiments. Results showed that a bundle of eight super-fine pore air stones was the best type of aeration sparger for all three bioreactors. Optimal culture conditions in STB were 600 rpm agitation speed and 2 vvm aeration rate, while 2 vvm and 1.5 vvm aeration provided highest biomass productivity in BB and ILAB, respectively. Antifoam agent was needed for all reactor types in order to reduce excessive foaming. Results indicated that with optimized conditions, these bioreactors are capable of thraustochytrid cultivation with a similar efficiency as cultivation using a rotary shaker. STB had the highest kLa and provided the highest biomass of 43.05 ± 0.35 g/L at 48 h. BB was simple in design, had low operating costs and was easy to build, but yielded the lowest biomass (27.50 ± 1.56 g/L). ILAB, on the other hand, had lower kLa than STB, but provided highest fatty acid productivity, of 35.36 ± 2.51% TFA. creator: Khanoksinee Sirirak creator: Sorawit Powtongsook creator: Sudarat Suanjit creator: Somtawin Jaritkhuan uri: https://doi.org/10.7717/peerj.11405 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Sirirak et al. title: First body of evidence suggesting a role of a tankyrase-binding motif (TBM) of vinculin (VCL) in epithelial cells link: https://peerj.com/articles/11442 last-modified: 2021-05-27 description: BackgroundAdherens junctions (AJ) are involved in cancer, infections and neurodegeneration. Still, their composition has not been completely disclosed. Poly(ADP-ribose) polymerases (PARPs) catalyze the synthesis of poly(ADP-ribose) (PAR) as a posttranslational modification. Four PARPs synthesize PAR, namely PARP-1/2 and Tankyrase-1/2 (TNKS). In the epithelial belt, AJ are accompanied by a PAR belt and a subcortical F-actin ring. F-actin depolymerization alters the AJ and PAR belts while PARP inhibitors prevent the assembly of the AJ belt and cortical actin. We wondered which PARP synthesizes the belt and which is the PARylation target protein. Vinculin (VCL) participates in the anchorage of F-actin to the AJ, regulating its functions, and colocalized with the PAR belt. TNKS has been formerly involved in the assembly of epithelial cell junctions.HypothesisTNKS poly(ADP-ribosylates) (PARylates) epithelial belt VCL, affecting its functions in AJ, including cell shape maintenance.Materials and MethodsTankyrase-binding motif (TBM) sequences in hVCL gene were identified and VCL sequences from various vertebrates, Drosophila melanogaster and Caenorhabditis elegans were aligned and compared. Plasma membrane-associated PAR was tested by immunocytofluorescence (ICF) and subcellular fractionation in Vero cells while TNKS role in this structure and cell junction assembly was evaluated using specific inhibitors. The identity of the PARylated proteins was tested by affinity precipitation with PAR-binding reagent followed by western blots. Finally, MCF-7 human breast cancer epithelial cells were subjected to transfection with Tol2-plasmids, carrying a dicistronic expression sequence including Gallus gallus wt VCL (Tol-2-GgVCL), or the same VCL gene with a point mutation in TBM-II (Tol2-GgVCL/*TBM) under the control of a β-actin promoter, plus green fluorescent protein following an internal ribosome entry site (IRES-GFP) to allow the identification of transfected cells without modifying the transfected protein of interest.Results and discussionIn this work, some of the hypothesis predictions have been tested. We have demonstrated that: (1) VCL TBMs were conserved in vertebrate evolution while absent in C. elegans; (2) TNKS inhibitors disrupted the PAR belt synthesis, while PAR and an endogenous TNKS pool were associated to the plasma membrane; (3) a VCL pool was covalently PARylated; (4) transfection of MCF-7 cells leading to overexpression of Gg-VCL/*TBM induced mesenchymal-like cell shape changes. This last point deserves further investigation, bypassing the limits of our transient transfection and overexpression system. In fact, a 5th testable prediction would be that a single point mutation in VCL TBM-II under endogenous expression control would induce an epithelial to mesenchymal transition (EMT). To check this, a CRISPR/Cas9 substitution approach followed by migration, invasion, gene expression and chemo-resistance assays should be performed. creator: Salomé Vilchez Larrea creator: Wanda Mariela Valsecchi creator: Silvia H. Fernández Villamil creator: Laura I. Lafon Hughes uri: https://doi.org/10.7717/peerj.11442 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Vilchez Larrea et al. title: Identification of key microRNAs and the underlying molecular mechanism in spinal cord ischemia-reperfusion injury in rats link: https://peerj.com/articles/11454 last-modified: 2021-05-27 description: Spinal cord ischemia-reperfusion injury (SCII) is a pathological process with severe complications such as paraplegia and paralysis. Aberrant miRNA expression is involved in the development of SCII. Differences in the experimenters, filtering conditions, control selection, and sequencing platform may lead to different miRNA expression results. This study systematically analyzes the available SCII miRNA expression data to explore the key differently expressed miRNAs (DEmiRNAs) and the underlying molecular mechanism in SCII. A systematic bioinformatics analysis was performed on 23 representative rat SCII miRNA datasets from PubMed. The target genes of key DEmiRNAs were predicted on miRDB. The DAVID and TFactS databases were utilized for functional enrichment and transcription factor binding analyses. In this study, 19 key DEmiRNAs involved in SCII were identified, 9 of which were upregulated (miR-144-3p, miR-3568, miR-204, miR-30c, miR-34c-3p, miR-155-3p, miR-200b, miR-463, and miR-760-5p) and 10 downregulated (miR-28-5p, miR-21-5p, miR-702-3p, miR-291a-3p, miR-199a-3p, miR-352, miR-743b-3p, miR-125b-2-3p, miR-129-1-3p, and miR-136). KEGG enrichment analysis on the target genes of the upregulated DEmiRNAs revealed that the involved pathways were mainly the cGMP-PKG and cAMP signaling pathways. KEGG enrichment analysis on the target genes of the downregulated DEmiRNAs revealed that the involved pathways were mainly the Chemokine and MAPK signaling pathways. GO enrichment analysis indicated that the target genes of the upregulated DEmiRNAs were markedly enriched in biological processes such as brain development and the positive regulation of transcription from RNA polymerase II promoter. Target genes of the downregulated DEmiRNAs were mainly enriched in biological processes such as intracellular signal transduction and negative regulation of cell proliferation. According to the transcription factor analysis, the four transcription factors, including SP1, GLI1, GLI2, and FOXO3, had important regulatory effects on the target genes of the key DEmiRNAs. Among the upregulated DEmiRNAs, miR-3568 was especially interesting. While SCII causes severe neurological deficits of lower extremities, the anti-miRNA oligonucleotides (AMOs) of miR-3568 improve neurological function. Cleaved caspase-3 and Bax was markedly upregulated in SCII comparing to the sham group, and miR-3568 AMO reduced the upregulation. Bcl-2 expression levels showed a opposite trend as cleaved caspase-3. The expression of GATA6, GATA4, and RBPJ decreased after SCII and miR-3568 AMO attenuated this upregulation. In conclusion, 19 significant DEmiRNAs in the pathogenesis of SCII were identified, and the underlying molecular mechanisms were validated. The DEmiRNAs could serve as potential intervention targets for SCII. Moreover, inhibition of miR-3568 preserved hind limb function after SCII by reducing apoptosis, possibly through regulating GATA6, GATA4, and RBPJ in SCII. creator: Fengshou Chen creator: Jie Han creator: Dan Wang uri: https://doi.org/10.7717/peerj.11454 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Chen et al. title: Identification of potential gene signatures associated with osteosarcoma by integrated bioinformatics analysis link: https://peerj.com/articles/11496 last-modified: 2021-05-27 description: Background Osteosarcoma (OS) is the most primary malignant bone cancer in children and adolescents with a high mortality rate. This work aims to screen novel potential gene signatures associated with OS by integrated microarray analysis of the Gene Expression Omnibus (GEO) database.Material and MethodsThe OS microarray datasets were searched and downloaded from GEO database to identify differentially expressed genes (DEGs) between OS and normal samples. Afterwards, the functional enrichment analysis, protein–protein interaction (PPI) network analysis and transcription factor (TF)-target gene regulatory network were applied to uncover the biological function of DEGs. Finally, two published OS datasets (GSE39262 and GSE126209) were obtained from GEO database for evaluating the expression level and diagnostic values of key genes.Results In total 1,059 DEGs (569 up-regulated DEGs and 490 down-regulated DEGs) between OS and normal samples were screened. Functional analysis showed that these DEGs were markedly enriched in 214 GO terms and 54 KEGG pathways such as pathways in cancer. Five genes (CAMP, METTL7A, TCN1, LTF and CXCL12) acted as hub genes in PPI network. Besides, METTL7A, CYP4F3, TCN1, LTF and NETO2 were key genes in TF-gene network. Moreover, Pax-6 regulated four key genes (TCN1, CYP4F3, NETO2 and CXCL12). The expression levels of four genes (METTL7A, TCN1, CXCL12 and NETO2) in GSE39262 set were consistent with our integration analysis. The expression levels of two genes (CXCL12 and NETO2) in GSE126209 set were consistent with our integration analysis. ROC analysis of GSE39262 set revealed that CYP4F3, CXCL12, METTL7A, TCN1 and NETO2 had good diagnostic values for OS patients. ROC analysis of GSE126209 set revealed that CXCL12, METTL7A, TCN1 and NETO2 had good diagnostic values for OS patients. creator: Yutao Jia creator: Yang Liu creator: Zhihua Han creator: Rong Tian uri: https://doi.org/10.7717/peerj.11496 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Jia et al. title: Bracon wasps for ecological pest control–a laboratory experiment link: https://peerj.com/articles/11540 last-modified: 2021-05-27 description: Biological control of pest insects by natural enemies may be an effective, cheap and environmentally friendly alternative to synthetic pesticides. The cosmopolitan parasitoid wasp species Bracon brevicornis Wesmael and B. hebetor Say (Hymenoptera: Braconidae) use lepidopteran species as hosts, including insect pests like Ephestia kuehniella or Ostrinia nubilalis. Here, we compare the reproductive success of both Bracon species on E. kuehniella in a laboratory experiment. We asked (1) how the reproductive success on a single host larva changes with temperature, (2) how it changes with temperature when more host larvae are present and (3) how temperature and availability of host larvae influence the efficacy of Bracon species as biological control agents. In general, differences between B. brevicornis and B. hebetor have been small. For rearing both Bracon species in the laboratory on one host larva, a temperature between 20–27 °C seems appropriate to obtain the highest number of offspring with a female-biased sex ratio. Rearing the braconid wasps on more than one host larva revealed a higher number of total offspring but less offspring per host larva on average. Again, highest numbers of offspring hatched at 27 °C and the sex ratio was independent from temperature. Although no parasitoids hatched at 12 °C and only few at 36 °C, host larvae were still paralyzed. The efficacy of B. brevicornis was higher than 80% at all numbers of host larvae presented at all temperatures while the efficacy of B. hebetor was less than 80% at 12 °C and 27 °C at low numbers of host larvae presented. In conclusion, practitioners can use either B. brevicornis or B. hebetor at low and high temperatures and at varying host densities to achieve high pest control efficacy. creator: Jessica Lettmann creator: Karsten Mody creator: Tore-Aliocha Kursch-Metz creator: Nico Blüthgen creator: Katja Wehner uri: https://doi.org/10.7717/peerj.11540 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Lettmann et al. title: The effect of a brown-rice diets on glycemic control and metabolic parameters in prediabetes and type 2 diabetes mellitus: a meta-analysis of randomized controlled trials and controlled clinical trials link: https://peerj.com/articles/11291 last-modified: 2021-05-26 description: BackgroundBrown rice is a whole-grain food that is often assumed to have a lower glycemic index compared to white rice. A few studies have objectively confirmed the effect of a brown-rice diet on glycemic control and metabolic parameters compared to a white-rice diet. The purpose of this study is to determine the effect of brown rice on improving glycemic control and metabolic parameters in prediabetes and type 2 diabetes. The researchers conducted a systematic review and meta-analysis of randomized controlled trials (RCTs) and controlled clinical trials.MethodsPRISMA guidelines were used as the basis of this systematic review. Relevant studies were identified by searching the following databases: Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE (PubMed), as well as Epistemonikos for randomized controlled trials (RCTs) and controlled clinical trials published not later than January 2021 involving adults with prediabetes and diabetes mellitus who were consuming brown rice compared to those consuming white rice. The primary outcomes measured were glycated hemoglobin (HbA1c) and fasting blood glucose (FBG) levels. The secondary outcomes were body weight, waist circumference, systolic and diastolic blood pressure levels, LDL and HDL-cholesterol levels. The mean differences (MDs) with 95% confidence intervals (CIs) between brown and white-rice-diet groups were calculated using a random-effects model.ResultsSeven trials involving 417 adults with prediabetes or type 2 diabetes were included in this study. Brown-rice diet did not improve the glycemic control because it had no effect on the HbA1c level (p = 0.15) and the FBG level (p = 0.95) compared to white-rice diet. Brown-rice diet reduced body weight (p < 0.00001; MD −2.2 kg; 95% CI [−3.13 to −1.26]; I2 = 0%). However, it had no effect on the waist circumference (p = 0.09), systolic blood pressure (p = 0.60) and diastolic blood pressure level (p = 0.40). HDL-cholesterol level is increased in brown-rice diet (p = 0.01; MD 0.10, 95% CI [0.02 to 0.17]; I2 = 44%) but it had no effect on the LDL-cholesterol level (p = 0.81).ConclusionsThe available evidence indicated that consuming brown rice in substitute for white rice does not affect glycemic control (HbA1c and FBG levels) in pre-diabetes and type 2 diabetes patients. Brown rice, however, may be used as an alternative for white rice in such patients because it was found to reduce body weight and increase the HDL-cholesterol level. The benefits of a brown-rice diet on glycemic control may not be detected in short-term studies. The obtained evidence in this meta-analysis ranged from low to moderate quality. Thus, more high-quality trials with a larger sample size and a longer follow-up duration are needed to further investigate the effects of a brown-rice diet on diabetes glycemic control with stronger evidence.PROSPERO registration number: CRD42019143266 creator: Anis Farhanah Abdul Rahim creator: Mohd Noor Norhayati creator: Aida Maziha Zainudin uri: https://doi.org/10.7717/peerj.11291 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Abdul Rahim et al. title: New insight into the divergent responses of plants to warming in the context of root endophytic bacterial and fungal communities link: https://peerj.com/articles/11340 last-modified: 2021-05-26 description: Plant adaptation under climate changes is critical to the maintenance of terrestrial ecosystem structure and function. Studying the response of the endophytic community to climate warming is a novel way to reveal the mechanism of host environmental adaptability because of the prominent role endophytes play in host nutrient acquisition and stress tolerance. However, host performance was generally neglected in previous relevant research, which limits our understanding of the relationships between the endophytic community and host responses to climate warming. The present study selected two plants with different responses to climate warming. Elymus nutans is more suitable for growing in warm environments at low altitude compared to Kobresia pygmaea. K. pygmaea and E. nutans were sampled along an altitude gradient in the natural grassland of Qinghai-Tibet Plateau, China. Root endophytic bacterial and fungal communities were analyzed using high throughput sequencing. The results revealed that hosts growing in more suitable habitats held higher endophytic fungal diversity. Elevation and host identity significantly affected the composition of the root endophytic bacterial and fungal community. 16S rRNA functional prediction demonstrated that hosts that adapted to lower temperatures recruited endophytic communities with higher abundance of genes related to cold resistance. Hosts that were more suitable for warmer and drier environments recruited endophytes with higher abundance of genes associated with nutrient absorption and oxidation resistance. We associated changes in the endophytic community with hosts adaptability to climate warming and suggested a synchronism of endophytic communities and hosts in environmental adaptation. creator: Xiaoting Wei creator: Fengyan Jiang creator: Bing Han creator: Hui Zhang creator: Ding Huang creator: Xinqing Shao uri: https://doi.org/10.7717/peerj.11340 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wei et al. title: Only two out of five articles by New Zealand researchers are free-to-access: a multiple API study of access, citations, cost of Article Processing Charges (APC), and the potential to increase the proportion of open access link: https://peerj.com/articles/11417 last-modified: 2021-05-26 description: We studied journal articles published by researchers at all eight New Zealand universities in 2017 to determine how many were freely accessible on the web. We wrote software code to harvest data from multiple sources, code that we now share to enable others to reproduce our work on their own sample set. In May 2019, we ran our code to determine which of the 2017 articles were open at that time and by what method; where those articles would have incurred an Article Processing Charge (APC) we calculated the cost if those charges had been paid. Where articles were not freely available we determined whether the policies of publishers in each case would have allowed deposit in a non-commercial repository (Green open access). We also examined citation rates for different types of access. We found that, of our 2017 sample set, about two out of every five articles were freely accessible without payment or subscription (41%). Where research was explicitly said to be funded by New Zealand’s major research funding agencies, the proportion was slightly higher at 45%. Where open articles would have incurred an APC we estimated an average cost per article of USD1,682 (for publications where all articles require an APC, that is, Gold open access) and USD2,558 (where APC payment is optional, Hybrid open access) at a total estimated cost of USD1.45m. Of the paid options, Gold is by far more common for New Zealand researchers (82% Gold, 18% Hybrid). In terms of citations, our analysis aligned with previous studies that suggest a correlation between publications being freely accessible and, on balance, slightly higher rates of citation. This is not seen across all types of open access, however, with Diamond OA achieving the lowest rates. Where articles were not freely accessible we found that a very large majority of them (88% or 3089 publications) could have been legally deposited in an institutional repository. Similarly, only in a very small number of cases had a version deposited in the repository of a New Zealand university made the difference between the publication being freely accessible or not (125 publications). Given that most New Zealand researchers support research being open, there is clearly a large gap between belief and practice in New Zealand’s research ecosystem. creator: Richard K.A. White creator: Anton Angelo creator: Deborah Fitchett creator: Moira Fraser creator: Luqman Hayes creator: Jessica Howie creator: Emma Richardson creator: Bruce White uri: https://doi.org/10.7717/peerj.11417 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 White et al. title: Key circular RNAs identified in male osteoporosis patients by whole transcriptome sequencing link: https://peerj.com/articles/11420 last-modified: 2021-05-26 description: BackgroundOsteoporosis (OP) is a systemic disease with bone loss and microstructural deterioration. Numerous noncoding RNAs (ncRNAs) have been proved to participate in various diseases, especially circular RNAs (circRNAs). However, the expression profile and mechanisms underlying circRNAs in male osteoporosis have not yet been explored.MethodsThe whole transcriptome expression profile and differences in mRNAs, circRNAs, and microRNAs (miRNAs) were investigated in peripheral blood samples of patients with osteoporosis and healthy controls consisting of males ≥ 60-years-old.ResultsA total of 398 circRNAs, 51 miRNAs, and 642 mRNAs were significantly and differentially expressed in osteoporosis compared to healthy controls. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the host genes of significantly differentially expressed circRNAs were mainly enriched in the regulation of cell cycle process: biological process (BP), organelle part cellular components (CC), protein binding molecular function (MF), Toll-like receptor signaling pathway, tumor necrosis factor (TNF) signaling pathway, and thyroid hormone signaling pathway. circRNA-miRNA-mRNA regulatory network was constructed using the differentially expressed RNAs. Moreover, key circRNAs (hsa_circ_0042409) in osteoporosis were discovered and validated by qPCR.ConclusionsThe key cicrRNAs plays a major role in the pathogenesis of osteoporosis and could be used as potential biomarkers or targets in the diagnosis and treatment of osteoporosis. creator: Haijin Zhang creator: Xue Song creator: Zongyan Teng creator: Sujun Cheng creator: Weigang Yu creator: Xiaoyi Yao creator: Zhiqiang Song creator: Yina Zhang uri: https://doi.org/10.7717/peerj.11420 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhang et al. title: Integrative species delimitation based on COI, ITS, and morphological evidence illustrates a unique evolutionary history of the genus Paracercion (Odonata: Coenagrionidae) link: https://peerj.com/articles/11459 last-modified: 2021-05-26 description: Paracercion are common ‘blue and black’ colored damselflies. We explore the species boundaries of Paracercion (Odonata: Coenagrionidae) using ABGD, bPTP, GMYC and Distance-based clustering. We finally got the molecular data of all nine species of Paracercion. P. hieroglyphicum and P. melanotum were combined into one putative species based on cytochrome c oxidase I (COI). However, they were separated into two putative species based on the nuclear segment including ITS1-5.8S-ITS2 (ITS). This suggests the introgression of mtDNA in Paracercion. Paracercion barbatum and Paracercion melanotum can be separated into two species based on COI, whereas they were combined into one putative species based on ITS, which suggests a hybridization event between them. The lower interspecific divergence (COI: 0.49%) between P. barbatum and Paracercion v-nigrum indicates a recent speciation event in Paracercion. Paracercion sieboldii and P. v-nigrum can be separated into two putative species based on COI, while they were frequently merged into the same putative species based on ITS. This can be explained by incomplete lineage sorting in nDNA. Besides, P. pendulum and P. malayanum were synonymized as junior synonyms of P. melanotum. P. luzonicum was confirmed not to belong to Paracercion. The possibility of introgression, hybridization, recent speciation and incomplete lineage sorting makes species delimitation, based on molecular data, difficult and complicates understanding of the evolutionary history of Paracercion. The discordance in COI and ITS also indicates the value of using markers from different sources in species delimitation studies. creator: Haiguang Zhang creator: Xin Ning creator: Xin Yu creator: Wen-Jun Bu uri: https://doi.org/10.7717/peerj.11459 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zhang et al. title: Autonomous Sensory Meridian Response self-reporters showed higher scores for cognitive reappraisal as an emotion regulation strategy link: https://peerj.com/articles/11474 last-modified: 2021-05-26 description: BackgroundAutonomous Sensory Meridian Response (ASMR) describes the experience of a pleasant tingling sensation along the back of the head, accompanied with a feeling of well-being and relaxation, in response to specific audio-visual stimuli, such as whispers, soft sounds, and personal attention. Previous works have assessed individual variations in personality traits associated with ASMR, but no research to date has explored differences in emotion regulation associated with ASMR. This omission occurred even when ASMR, a sensory-emotional experience, has been proposed to be located in a sound sensitivity spectrum as the opposite end of misophonia, a phenomenon associated with difficulties regulating emotions. The present work aimed to assess group differences between ASMR self-reporters and non-ASMR controls associated with emotion regulation strategies.MethodsWe used the validated Spanish version of the Emotion Regulation Questionnaire to assess individual differences in the use of cognitive reappraisal and expressive suppression.ResultsOur results showed that participants who experience ASMR had higher scores in the cognitive reappraisal subscale of the emotion regulation questionnaire than the non-ASMR group.ConclusionsIndividuals who experience ASMR reported higher use of cognitive reevaluation of emotionally arousing situations, suggesting more effectiveness in regulating emotions. Our finding further elucidates individual differences related to this experience, supporting that ASMR is a real psychophysiological phenomenon associated with other psychological constructs and has remarkable consequences in affective/emotional dimensions and general well-being. creator: Ricardo Morales creator: Daniela Ramírez-Benavides creator: Mario Villena-Gonzalez uri: https://doi.org/10.7717/peerj.11474 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Morales et al. title: Identification and analysis of Chrysanthemum nankingense NAC transcription factors and an expression analysis of OsNAC7 subfamily members link: https://peerj.com/articles/11505 last-modified: 2021-05-26 description: NAC (NAM, ATAF1-2, and CUC2) transcription factors (TFs) play a vital role in plant growth and development, as well as in plant response to biotic and abiotic stressors (Duan et al., 2019; Guerin et al., 2019). Chrysanthemum is a plant with strong stress resistance and adaptability; therefore, a systematic study of NAC TFs in chrysanthemum is of great significance for plant breeding. In this study, 153 putative NAC TFs were identified based on the Chrysanthemum nankingense genome. According to the NAC family in Arabidopsis and rice, a rootless phylogenetic tree was constructed, in which the 153 CnNAC TFs were divided into two groups and 19 subfamilies. Moreover, the expression levels of 12 CnNAC TFs belonging to the OsNAC7 subfamily were analyzed in C. nankingense under osmotic and salt stresses, and different tissues were tested during different growth periods. The results showed that these 12 OsNAC7 subfamily members were involved in the regulation of root and stem growth, as well as in the regulation of drought and salt stresses. Finally, we investigated the function of the CHR00069684 gene, and the results showed that CHR00069684 could confer improved salt and low temperature resistance, enhance ABA sensitivity, and lead to early flowering in tobacco. It was proved that members of the OsNAC7 subfamily have dual functions including the regulation of resistance and the mediation of plant growth and development. This study provides comprehensive information on analyzing the function of CnNAC TFs, and also reveals the important role of OsNAC7 subfamily genes in response to abiotic stress and the regulation of plant growth. These results provide new ideas for plant breeding to control stress resistance and growth simultaneously. creator: Hai Wang creator: Tong Li creator: Wei Li creator: Wang Wang creator: Huien Zhao uri: https://doi.org/10.7717/peerj.11505 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wang et al. title: Polysaccharides and polyphenol in dried Morinda citrifolia fruit tea after different processing conditions: Optimization analysis using response surface methodology link: https://peerj.com/articles/11507 last-modified: 2021-05-26 description: The increasing popularity of Morinda citrifolia has many medical and health benefits because of its rich polysaccharides (PSC) and polyphenols (PPN). It has become popular to brew the dry M. citrifolia fruit slice as tea in some regions of China. In this study, optimize the extraction parameters of M. citrifolia fruit tea polysaccharides and polyphenols using response surface methodology. The results indicated the highest PSC yield of 17% at 46 °C for 11 min and the ratio of water/M. citrifolia fruit powder was 78 mL/g. The optimum extraction of PPN was at 95 °C for 10 min and the ratio of water/M. citrifolia fruit powder 90 mL/g, with 8.93% yield. Using dry M. citrifolia fruit slices as a tea is reported for the first time. Based on the results, the maximum level of PSC can be obtained under condition by infusing about four dried M. citrifolia fruit slice with average thickness and size in warm boiled water for 11 min, taking a 300 mL cup (300 mL of water) for example. The maximum level of PPN can be obtained by adding three slices of dried M. citrifolia fruit slice to boiled water for 10 min. Considering the powder used in our study, the further pulverization of cutting into powder is more conducive to material precipitation. This study provides a scientific basis for obtaining PSC and PPN from dry M. citrifolia fruit slice tea by brewing. creator: Qingfen Wang creator: Fei Yang creator: Dandan Jia creator: Tian Wu uri: https://doi.org/10.7717/peerj.11507 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: The GRAS gene family in watermelons: identification, characterization and expression analysis of different tissues and root-knot nematode infestations link: https://peerj.com/articles/11526 last-modified: 2021-05-26 description: The family of GRAS plant-specific transcription factor plays diverse roles in numerous biological processes. Despite the identification and characterization of GRAS genes family in dozens of plant species, until now, GRAS members in watermelon (Citrullus lanatus) have not been investigated comprehensively. In this study, using bioinformatic analysis, we identified 37 GRAS genes in the watermelon genome (ClGRAS). These genes are classified into 10 distinct subfamilies based on previous research, and unevenly distributed on 11 chromosomes. Furthermore, a complete analysis was conducted to characterize conserved motifs and gene structures, which revealed the members within same subfamily that have analogous conserved gene structure and motif composition. Additionally, the expression pattern of ClGRAS genes was characterized in fruit flesh and rind tissues during watermelon fruit development and under red light (RL) as well as root knot nematode infestation. Finally, for verification of the availability of public transcriptome data, we also evaluated the expression levels of randomly selected four ClGRAS genes under RL and nematode infection by using qRT-PCR. The qRT-PCR results indicated that several ClGRAS genes were differentially expressed, implying their vital role in RL induction of watermelon resistance against root-knot nematodes. The results obtained in this study could be useful in improving the quality of watermelon. creator: Gongbo Lv creator: Xing Zheng creator: Yitian Duan creator: Yunyong Wen creator: Bin Zeng creator: Mingqiang Ai creator: Bin He uri: https://doi.org/10.7717/peerj.11526 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Lv et al. title: Taxonomic description and phylogenetic placement of two new species of Spalangiopelta (Hymenoptera: Pteromalidae: Ceinae) from Eocene Baltic amber link: https://peerj.com/articles/10939 last-modified: 2021-05-25 description: Spalangiopelta is a small genus of chalcid wasps that has received little attention despite the widespread distribution of its extant species. The fossil record of the genus is restricted to a single species from Miocene Dominican amber. We describe two new fossil species, Spalangiopelta darlingi sp. n. and Spalangiopelta semialba sp. n. from Baltic amber. The species can be placed within the extant genus Spalangiopelta based on the distinctly raised hind margin of the mesopleuron. 3D models reconstructed from µCT data were utilized to assist in the descriptions. Furthermore, we provide a key for the females of all currently known Spalangiopelta species. The phylogenetic placement of the fossils within the genus is analyzed using parsimony analysis based on morphological characters. Phylogenetic and functional relevance of two wing characters, admarginal setae and the hyaline break, are discussed. The newly described Baltic amber fossils significantly extend the minimum age of Spalangiopelta to the Upper Eocene. creator: Marina Moser creator: Roger A. Burks creator: Jonah M. Ulmer creator: John M. Heraty creator: Thomas van de Kamp creator: Lars Krogmann uri: https://doi.org/10.7717/peerj.10939 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Moser et al. title: Psychometric properties of the Attitudes towards Medical Communication Scale in nursing students link: https://peerj.com/articles/11034 last-modified: 2021-05-25 description: BackgroundAdequate communication skills in healthcare professionals are one of the key elements required for achieving high-quality healthcare. Thus, measurement instruments able to assess the dimensions related to these skills, including attitudes towards communication, are useful and convenient tools.ObjectivesTo (a) cross-culturally adapt and validate a scale to measure attitudes towards communication in a sample of nursing students in the Spanish environment; (b) describe the perceived attitudes of nursing degree students towards communication.MethodsWe conducted an instrumental study. First, we adapted the scale by applying a standardised linguistic validation procedure. After that, we determined its structural equivalence and evaluated its psychometric properties.ParticipantsA total of 255 students participated; their average age was 22.66 years (SD = 4.75) and 82% were female.ResultsThe internal consistency of the scale was adequate (0.75), and the data fit well with the model (CFI = 0.99; TLI = 0.99; RMSEA = .01 95% CI [.00–.05]). The overall instrument score poorly correlated with the self-efficacy in communication skills variable.ConclusionsThe attitudes towards communication scores for these nursing students were high. The Spanish version of the Attitudes Towards Health Communication scale had adequate psychometric properties and this tool could quickly and easily be applied to assess the attitudes of health profession students. creator: Silvia Escribano creator: Rocío Juliá-Sanchis creator: Sofía García-Sanjuán creator: Nereida Congost-Maestre creator: María José Cabañero-Martínez uri: https://doi.org/10.7717/peerj.11034 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Escribano et al. title: Evaluation of pro-apoptotic potential of taxifolin against liver cancer link: https://peerj.com/articles/11276 last-modified: 2021-05-25 description: Liver cancer is the second most common cause of cancer-induced deaths worldwide. Liver cirrhosis and cancer are a consequence of the abnormal angio-architecture formation of liver and formation of new blood vessels. This angiogenesis is driven by overexpression of hypoxia-inducible factor 1-alpha (Hif1-α) and vascular endothelial growth factor (VEGF). Apart from this, protein kinase B (Akt) is also impaired in liver cancer. Despite the advancement in conventional treatments, liver cancer remains largely incurable. Nowadays, the use of naturally occurring anticancer agents particularly flavonoids is subject to more attention due to their enhanced physicochemical properties. Therefore, this study underlines the use of a natural anticancer agent taxifolin in the treatment of liver cancer using hepatocellular carcinoma cell line HepG2 and Huh7. The aim of our study is to devise a natural and efficient solution for the disease prevalent in Pakistan. The study involved the assessment of binding of ligand taxifolin using molecular docking. The binding of taxifolin with the proteins (Hif1-α, VEGF and Akt) was calculated by docking using Vina and Chimera. Further evaluation was performed by cell viability assay (MTT 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) Assay), colony formation assay, cell migration assay, DNA ladder assay and flow cytometry. To see whether taxifolin directly affected expression levels, analysis of gene expression of Hif1-α, VEGF and Akt was performed using real-time polymerase chain reaction (qPCR) and western blotting. In silico docking experiments revealed that these proteins showed favorable docking scores with taxifolin. Treatment with taxifolin resulted in the inhibition of the liver cancer growth and migration, and induced apoptosis in HepG2 and Huh7 cell lines at an inhibitory concentration (IC50) value of 0.15 µM and 0.22 µM, respectively. The expression of HIF1-α, VEGF and Akt was significantly reduced in a dose- dependent manner. The inhibitory effect of taxifolin on hepatic cells suggested its chemopreventive and therapeutic potential. The studied compound taxifolin exhibited pronounced pro-apoptotic and hepatoprotective potential. Our study has confirmed the pro-apoptotic potential of taxifolin in liver cancer cell lines and will pave a way to the use of taxifolin as a chemotherapeutic agent after its further validation on the animal models and humans based epidemiological studies. creator: Sania Safdar Butt creator: Khushbukhat Khan creator: Yasmin Badshah creator: Mehak Rafiq creator: Maria Shabbir uri: https://doi.org/10.7717/peerj.11276 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Butt et al. title: The paeonol target gene autophagy-related 5 has a potential therapeutic value in psoriasis treatment link: https://peerj.com/articles/11278 last-modified: 2021-05-25 description: BackgroundPaeonol is a potent therapy for psoriasis. This study aimed to screen out paeonol-targeted genes in psoriasis and validate the potential of using paeonol for the management of psoriasis.MethodsMicroarray datasets were obtained from the Gene Expression Omnibus. The differentially expressed genes (DEGs) in the lesional skin samples and the overlapping genes between DEGs and paeonol- and psoriasis-related genes were defined as potential targets for psoriasis. After being treated with si-ATG5 and pc-ATG5, human HaCaT cells were treated with 100 ng/ml IL-22 and 10 ng/ml TNF-α with and without paeonol. Cell proliferation, apoptosis, and expression of interleukin (IL)-6, IL-1β, Beclin 1, ATG5, and p62 in HaCaT cells were determined using ESLIA, PCR, and Western blot analysis.ResultsA total of 779 DEGs were identified in the lesional skin samples compared with the non-lesional tissues. The autophagy-related 5 (ATG5) gene was the only gene that overlapped between the DEGs and genes related to paeonol and psoriasis. Cell proliferation, inflammatory cytokines (IL-6 and IL-1β), and ATG5 expression were increased in IL-22/TNF-α-stimulated HaCaT (model) cells compared with control. Paeonol treatment rescued all changes. si-ATG5 transfection increased inflammation and apoptosis in model cells compared with controls. pc-ATG5 prevented IL-22/TNF-α-induced changes in HaCaT cells. Also, si-ATG5 decreased p62 and Beclin 1 proteins, while pc-ATG5 increased them both.ConclusionsATG5-dependent autophagy plays a crucial role in psoriasis. The ATG5 gene might be a therapeutic target for the management of in vitro psoriasis. creator: Qian Zhang creator: Hongqiao Shi creator: Jiaan Zhang creator: Chenxue Jiang creator: Chunxiang Zhou uri: https://doi.org/10.7717/peerj.11278 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhang et al. title: Measuring pathway database coverage of the phosphoproteome link: https://peerj.com/articles/11298 last-modified: 2021-05-25 description: Protein phosphorylation is one of the best known post-translational mechanisms playing a key role in the regulation of cellular processes. Over 100,000 distinct phosphorylation sites have been discovered through constant improvement of mass spectrometry based phosphoproteomics in the last decade. However, data saturation is occurring and the bottleneck of assigning biologically relevant functionality to phosphosites needs to be addressed. There has been finite success in using data-driven approaches to reveal phosphosite functionality due to a range of limitations. The alternate, more suitable approach is making use of prior knowledge from literature-derived databases. Here, we analysed seven widely used databases to shed light on their suitability to provide functional insights into phosphoproteomics data. We first determined the global coverage of each database at both the protein and phosphosite level. We also determined how consistent each database was in its phosphorylation annotations compared to a global standard. Finally, we looked in detail at the coverage of each database over six experimental datasets. Our analysis highlights the relative strengths and weaknesses of each database, providing a guide in how each can be best used to identify biological mechanisms in phosphoproteomic data. creator: Hannah Huckstep creator: Liam G. Fearnley creator: Melissa J. Davis uri: https://doi.org/10.7717/peerj.11298 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Huckstep et al. title: partR2: partitioning R2 in generalized linear mixed models link: https://peerj.com/articles/11414 last-modified: 2021-05-25 description: The coefficient of determination R2 quantifies the amount of variance explained by regression coefficients in a linear model. It can be seen as the fixed-effects complement to the repeatability R (intra-class correlation) for the variance explained by random effects and thus as a tool for variance decomposition. The R2 of a model can be further partitioned into the variance explained by a particular predictor or a combination of predictors using semi-partial (part) R2 and structure coefficients, but this is rarely done due to a lack of software implementing these statistics. Here, we introduce partR2, an R package that quantifies part R2 for fixed effect predictors based on (generalized) linear mixed-effect model fits. The package iteratively removes predictors of interest from the model and monitors the change in the variance of the linear predictor. The difference to the full model gives a measure of the amount of variance explained uniquely by a particular predictor or a set of predictors. partR2 also estimates structure coefficients as the correlation between a predictor and fitted values, which provide an estimate of the total contribution of a fixed effect to the overall prediction, independent of other predictors. Structure coefficients can be converted to the total variance explained by a predictor, here called ‘inclusive’ R2, as the square of the structure coefficients times total R2. Furthermore, the package reports beta weights (standardized regression coefficients). Finally, partR2 implements parametric bootstrapping to quantify confidence intervals for each estimate. We illustrate the use of partR2 with real example datasets for Gaussian and binomial GLMMs and discuss interactions, which pose a specific challenge for partitioning the explained variance among predictors. creator: Martin A. Stoffel creator: Shinichi Nakagawa creator: Holger Schielzeth uri: https://doi.org/10.7717/peerj.11414 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Stoffel et al. title: Analysis of ceRNA networks and identification of potential drug targets for drug-resistant leukemia cell K562/ADR link: https://peerj.com/articles/11429 last-modified: 2021-05-25 description: BackgroundDrug resistance is the main obstacle in the treatment of leukemia. As a member of the competitive endogenous RNA (ceRNA) mechanism, underlying roles of lncRNA are rarely reported in drug-resistant leukemia cells.MethodsThe gene expression profiles of lncRNAs and mRNAs in doxorubicin-resistant K562/ADR and sensitive K562 cells were established by RNA sequencing (RNA-seq). Expression of differentially expressed lncRNAs (DElncRNAs) and DEmRNAs was validated by qRT-PCR. The potential biological functions of DElncRNAs targets were identified by GO and KEGG pathway enrichment analyses, and the lncRNA-miRNA-mRNA ceRNA network was further constructed. K562/ADR cells were transfected with CCDC26 and LINC01515 siRNAs to detect the mRNA levels of GLRX5 and DICER1, respectively. The cell survival rate after transfection was detected by CCK-8 assay.ResultsThe ceRNA network was composed of 409 lncRNA-miRNA pairs and 306 miRNA-mRNA pairs based on 67 DElncRNAs, 58 DEmiRNAs and 192 DEmRNAs. Knockdown of CCDC26 and LINC01515 increased the sensitivity of K562/ADR cells to doxorubicin and significantly reduced the half-maximal inhibitory concentration (IC50) of doxorubicin. Furthermore, knockdown of GLRX5 and DICER1 increased the sensitivity of K562/ADR cells to doxorubicin and significantly reduced the IC50 of doxorubicin.ConclusionsThe ceRNA regulatory networks may play important roles in drug resistance of leukemia cells. CCDC26/miR-140-5p/GLRX5 and LINC01515/miR-425-5p/DICER1 may be potential targets for drug resistance in K562/ADR cells. This study provides a promising strategy to overcome drug resistance and deepens the understanding of the ceRNA regulatory mechanism related to drug resistance in CML cells. creator: Zhaoping Liu creator: Yanyan Wang creator: Zhenru Xu creator: Shunling Yuan creator: Yanglin Ou creator: Zeyu Luo creator: Feng Wen creator: Jing Liu creator: Ji Zhang uri: https://doi.org/10.7717/peerj.11429 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Liu et al. title: Cuffless blood pressure estimation based on haemodynamic principles: progress towards mobile healthcare link: https://peerj.com/articles/11479 last-modified: 2021-05-25 description: BackgroundAlthough cuff-sphygmomanometry is used worldwide in medical and healthcare fields, it is a fact that the use of an occlusive cuff to obtain blood pressure (BP) is troublesome and inconvenient. There have therefore been on-going efforts to devise methods that do not require the use of a cuff, almost all being based on the measurement of pulse wave velocity or pulse transit time, but so far few significant developments have been made, especially regarding measurement accuracy. We have previously reported a smartphone-based cuffless method using a linear multiple regression calibration model comprising of BP obtained with a cuff-sphygmomanometer as an objective variable and modified normalized pulse volume (mNPV: a measure of vasoconstrictive activity in a finger) and pulse rate (PR) as explanatory variables. This requires a number of subjects to construct a calibration model and thus is largely dependent on the accuracy due to the model. To address these drawbacks, we report here a new cuffless method to surpass considerably the results of our previous study as well as earlier works.MethodsWith this method we can estimate BP, with much higher accuracy, using mNPV and PR, both also obtained from a smartphone-derived photoplethysmogram. The subject firstly performs a cuff-based BP measurement in parallel with the acquisition of mNPV and PR from a smartphone. These parameters are set as initial values (BPc0, mNPV0 and PR0; initial calibration procedure). Then, the estimated BP (BPe) can be calculated from the relation: “BPe = (BPc0·PR·mNPV)/(PR0·mNPV0)”, which is derived from the so-called haemodynamic Ohm’s law. To validate this method, preliminary experiments using 13 volunteers were carried out to compare results from the new method with those from the cuff-sphygmomanometry, used as a reference.ResultsAltogether 299 paired data sets were analyzed: A good agreement was found between the cuff-based and the estimated BP values, with correlation coefficients of 0.968 for systolic BP (SBP), 0.934 for mean BP (MBP) and 0.844 for diastolic BP (DBP). Bland-Altman analyses for the BPe (SBPe, MBPe, DBPe) and the BPc (SBPc, MBPc, DBPc) values also supported these comparison results. Mean absolute differences between the BPe and the BPc values in total subjects were less than 5 mmHg. Fairly good tracking availability in terms of time series data of the BPc against the corresponding BPe values was also confirmed in each subject during the study periods (1–2 weeks for 12 subjects and about 4 months for one subject).DiscussionThe present study reported the successful development of the new cuffless BP estimation method, given as the status of a trial stage of investigation. This method could easily be used with various smartphones, smart watches, and finger-based devices, and it appears to have significant potential as a convenient substitute for conventional cuff-sphygmomanometers as well as for practical application to mobile healthcare. creator: Takehiro Yamakoshi creator: Peter Rolfe creator: Ken-ichi Yamakoshi uri: https://doi.org/10.7717/peerj.11479 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yamakoshi et al. title: Run for your life: can exercise be used to effectively target GLUT4 in diabetic cardiac disease? link: https://peerj.com/articles/11485 last-modified: 2021-05-25 description: The global incidence, associated mortality rates and economic burden of diabetes are now such that it is considered one of the most pressing worldwide public health challenges. Considerable research is now devoted to better understanding the mechanisms underlying the onset and progression of this disease, with an ultimate aim of improving the array of available preventive and therapeutic interventions. One area of particular unmet clinical need is the significantly elevated rate of cardiomyopathy in diabetic patients, which in part contributes to cardiovascular disease being the primary cause of premature death in this population. This review will first consider the role of metabolism and more specifically the insulin sensitive glucose transporter GLUT4 in diabetic cardiac disease, before addressing how we may use exercise to intervene in order to beneficially impact key functional clinical outcomes. creator: Peter R.T. Bowman creator: Godfrey L. Smith creator: Gwyn W. Gould uri: https://doi.org/10.7717/peerj.11485 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Bowman et al. title: Biotin-streptavidin-guided two-step pretargeting approach using PLGA for molecular ultrasound imaging and chemotherapy for ovarian cancer link: https://peerj.com/articles/11486 last-modified: 2021-05-25 description: BackgroundOvarian cancer seriously threatens the lives and health of women, and early diagnosis and treatment are still challenging. Pre-targeting is a promising strategy to improve the treatment efficacy of ovarian cancer and the results of ultrasound imaging.PurposeTo explore the effects of a pre-targeting strategy using streptavidin (SA) and paclitaxel (PTX)-loaded phase-shifting poly lactic-co-glycolic acid (PLGA) nanoparticles with perfluoro-n-pentane (PTX-PLGA-SA/PFPs) on the treatment and ultrasound imaging of ovarian cancer.MethodsPTX-PLGA/PFPs were prepared with a single emulsion (O/W) solvent evaporation method and SA was attached using carbodiimide. The encapsulation efficiency of PTX and the release characteristics were assessed with high performance liquid chromatography. The phase-change characteristics of the PTX-PLGA-SA/PFPs were investigated. The anti-carcinoembryonic antigen (CEA) antibody (Ab) was covalently attached to PTX-PLGA/PFPs via carbodiimide to create PTX-PLGA-Ab/PFPs. The targeting efficiency of the nanoparticles and the viability of ovarian cancer SKOV3 cells were evaluated in each group using a microscope, flow cytometry, and cell counting kit 8 assays.ResultsTHE PTX-PLGA-SA/PFPs were spheres with a size of 383.0 ± 75.59 nm. The encapsulation efficiency and loading capability of the nanoparticles for PTX were 71.56 ±  6.51% and 6.57 ± 0.61%, respectively. PTX was burst-released up to 70% in 2–3 d. When irradiated at 7.5 W for 3 min, the PTX-PLGA-SA/PFPs visibly enhanced the ultrasonography images (P < 0.05). At temperatures of 45°C and 60°C the nanoparticles phase-shifted into micro-bubbles and the sizes increased. The binding efficiencies of SA and Ab to the PTX-PLGA/PFPs were 97.16 ±  1.20% and 92.74 ± 5.75%, respectively. Pre-targeting resulted in a high binding efficacy and killing effect on SKOV3 cells (P < 0.05).ConclusionsThe two-step pre-targeting process can significantly enhance the targeting ability of PTX-loaded PLGA nanoparticles for ovarian cancer cells and substantially improve the therapeutic efficacy. This technique provides a new method for ultrasonic imaging and precise chemotherapy for ovarian cancer. creator: Hang Zhou creator: Jing Fu creator: Qihuan Fu creator: Yujie Feng creator: Ruixia Hong creator: Pan Li creator: Zhigang Wang creator: Xiaoling Huang creator: Fang Li uri: https://doi.org/10.7717/peerj.11486 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhou et al. title: Functional characterization of Lilium lancifolium cold-responsive Zinc Finger Homeodomain (ZFHD) gene in abscisic acid and osmotic stress tolerance link: https://peerj.com/articles/11508 last-modified: 2021-05-25 description: Background.We have previously performed an analysis of the cold-responsive transcriptome in the mature leaves of tiger lily (Lilium lancifolium) by gene co-expression network identification. The results has revealed that a ZFHD gene, notated as encoding zinc finger homeodomain protein, may play an essential regulating role in tiger lily response to cold stress.Methods.A further investigation of the ZFHD gene (termed as LlZFHD4) responding to osmotic stresses, including cold, salt, water stresses, and abscisic acid (ABA) was performed in this study. Based on the transcriptome sequences, the coding region and 5′ promoter region of LlZFHD4 were cloned from mature tiger lily leaves. Stress response analysis was performed under continuous 4 °C, NaCl, PEG, and ABA treatments. Functional characterization of LlZFHD4 was conducted in transgenic Arabidopsis, tobacco, and yeast.Results.LlZFHD4 encodes a nuclear-localized protein consisting of 180 amino acids. The N-terminal region of LlZFHD4 has transcriptional activation activity in yeast. The 4 °C, NaCl, PEG, and ABA treatments induced the expression of LlZFHD4. Several stress- or hormone-responsive cis-acting regulatory elements (T-Box, BoxI. and ARF) and binding sites of transcription factors (MYC, DRE and W-box) were found in the core promoter region (789 bp) of LlZFHD4. Also, the GUS gene driven by LlZFHD4 promoter was up-regulated by cold, NaCl, water stresses, and ABA in Arabidopsis. Overexpression of LlZFHD4 improved cold and drought tolerance in transgenic Arabidopsis; higher survival rate and better osmotic adjustment capacity were observed in LlZFHD4 transgenic plants compared to wild type (WT) plants under 4 °C and PEG conditions. However, LlZFHD4 transgenic plants were less tolerant to salinity and more hypersensitive to ABA compared to WT plants. The transcript levels of stress- and ABA-responsive genes were much more up-regulated in LlZFHD4 transgenic Arabidopsis than WT. These results indicate LlZFHD4 is involved in ABA signaling pathway and plays a crucial role in regulating the response of tiger lily to cold, salt and water stresses. creator: Yubing Yong creator: Yue Zhang creator: Yingmin Lyu uri: https://doi.org/10.7717/peerj.11508 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yong et al. title: Whole genome sequence analysis of multi drug resistant community associated methicillin resistant Staphylococcus aureus from food fish: detection of clonal lineage ST 28 and its antimicrobial resistance and virulence genes link: https://peerj.com/articles/11224 last-modified: 2021-05-24 description: Methicillin-resistant staphylococcus aureus (MRSA) sequence type 28 (ST 28) and spa type t021 is a CC30, prototype of ST-30, Community Associated-MRSA (CA-MRSA) (lukS-lukF +). It is a multi-drug resistant strain harbouring staphylococcal endotoxins, haemolysins, ureolysin, serine protease, and antimicrobial resistance genes. In this study, we report the draft genome sequence of this MRSA isolated from the most commonly used food fish, ribbon fish (Trichiurus lepturus). The total number of assembled paired-end high-quality reads was 7,731,542 with a total length of  2.8Mb of 2797 predicted genes. The unique ST28/ t021 CA- MRSA in fish is the first report from India, and in addition to antibiotic resistance is known to co-harbour virulence genes, haemolysins, aureolysins and endotoxins. Comprehensive comparative genomic analysis of CA-MRSA strain7 can help further understand their diversity, genetic structure, diversity and a high degree of virulence to aid in fisheries management. creator: Gopalan Krishnan Sivaraman creator: Visnuvinayagam Sivam creator: Balasubramanian Ganesh creator: Ravikrishnan Elangovan creator: Ardhra Vijayan creator: Mukteswar Prasad Mothadaka uri: https://doi.org/10.7717/peerj.11224 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sivaraman et al. title: Acute kidney disease in hospitalized acute kidney injury patients link: https://peerj.com/articles/11400 last-modified: 2021-05-24 description: BackgroundAcute kidney injury (AKI) and chronic kidney disease (CKD) have become worldwide public health problems, but little information is known about the epidemiology of acute kidney disease (AKD)—a state in between AKI and CKD. We aimed to explore the incidence and outcomes of hospitalized patients with AKD after AKI, and investigate the prognostic value of AKD in predicting 30-day and one-year adverse outcomes.MethodsA total of 2,556 hospitalized AKI patients were identified from three tertiary hospitals in China in 2015 and followed up for one year.AKD and AKD stage were defined according to the consensus report of the Acute Disease Quality Initiative 16 workgroup. Multivariable regression analyses adjusted for confounding variables were used to examine the association of AKD with adverse outcomes.ResultsAKD occurred in 45.4% (1161/2556) of all AKI patients, 14.5% (141/971) of AKI stage 1 patients, 44.6% (308/691) of AKI stage 2 patients and 79.6% (712/894) of AKI stage 3 patients. AKD stage 1 conferred a greater risk of Major Adverse Kidney Events within 30 days (MAKE30) (odds ratio [OR], 2.36; 95% confidence interval 95% CI [1.66–3.36]) than AKD stage 0 but the association only maintained in AKI stage 3 when patients were stratified by AKI stage. However, compared with AKD stage 0, AKD stage 2–3 was associated with higher risks of both MAKE30 and one-year chronic dialysis and mortality independent of the effects of AKI stage with OR being 31.35 (95% CI [23.42–41.98]) and 2.68 (95% CI [2.07–3.48]) respectively. The association between AKD stage and adverse outcomes in 30 days and one year was not significantly changed in critically ill and non-critically ill AKI patients. The results indicated that AKD is common among hospitalized AKI patients. AKD stage 2–3 provides additional information in predicting 30-day and one-year adverse outcomes over AKI stage. Enhanced follow-up of renal function of these patients may be warranted. creator: Ping Yan creator: Xiang-Jie Duan creator: Yu Liu creator: Xi Wu creator: Ning-Ya Zhang creator: Fang Yuan creator: Hao Tang creator: Qian Liu creator: Ying-Hao Deng creator: Hong-Shen Wang creator: Mei Wang creator: Shao-bin Duan uri: https://doi.org/10.7717/peerj.11400 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yan et al. title: Comparing the phosphorus use efficiency of pre-treated (organically) rock phosphate with soluble P fertilizers in maize under calcareous soils link: https://peerj.com/articles/11452 last-modified: 2021-05-24 description: In calcareous soils, phosphorus (P) availability to plant is impaired due to the formation of insoluble complexes with calcium and magnesium. Therefore, this study was executed to compare the P use efficiency (PUE) of four different P sources [rock phosphate (RP), acidulated rock phosphate (ARP), single super phosphate (SSP) and di ammonium phosphate (DAP)] alone or pre-treated with organic amendments (farm yard manure (FYM) enriched compost, simple compost and humic acid (HA)) along with control in maize crop under calcareous soils. All treatments irrespective of P sources received 90 kg P2O5 ha−1. Phosphorus application regardless of its sources and combination with organic amendments significantly improved maize growth, yield as well as P uptake and PUE. Rock phosphate when applied alone was recorded inferior but its performance significantly improved with compost or its pre-addition with FYM and HA, that further enhanced upon acidulation. Maize grain yield increased by 21, 22.2, 67.9 and 94% with RP, ARP, ARP enriched compost and ARP+ compost respectively, over control. Similarly, PUE of DAP improved from 31.7 to 43.1 and 39 with sample and enriched compost correspondingly. Post-harvest soil and grain P were at par for SSP, ARP and DAP alone or in conjugation with organic amendments when averaged across the amendments. These results suggested that pretreatment of P sources with organic amendments is an economical and more feasible approach to improve maize yield and PUE. Moreover, on-farm acidulation of RP may give at par results with SSP and DAP with cheaper rate and hence recommended for P management in maize in alkaline calcareous soils. creator: Maria Mussarat creator: Hazrat Ali creator: Dost Muhammad creator: Ishaq Ahmad Mian creator: Shadman Khan creator: Muhammad Adnan creator: Shah Fahad creator: Fazli Wahid creator: Khadim Dawar creator: Shamsher Ali creator: Afia Zia creator: Manzoor Ahmad creator: Sowm Khan creator: Wajid Ali Shah creator: Muhammad Romman creator: Rainaz Parvez creator: Manzer H. Siddiqui creator: Abid Khan creator: Depeng Wang creator: Xue Jiang uri: https://doi.org/10.7717/peerj.11452 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2021 Mussarat et al. title: The effects of genotypes and media composition on callogenesis, regeneration and cell suspension culture of chamomile (Matricaria chamomilla L.) link: https://peerj.com/articles/11464 last-modified: 2021-05-24 description: Background Chamomile is an important herb being used widely for medicinal purposes. Its multitherapeutic, cosmetic, and nutritional values have been established through years of traditional and scientific use and research. Increased use of medicinal plants necessitates rational use as well as sustainable production of such genetic resources. Plant in vitro micro-propagation poses unique opportunities for sustainable production of medicinal herbs, their regrowth and conservation. The present study aimed to investigate the effects of different explants, plant growth regulators (PGRs) combinations and media type on callogenesis, in vitro regeneration and cell suspension of six chamomile genotypes to enhance its sustainable production.MethodsThe shoot, lateral sprout, and leaf derived explants of six chamomile genotypes including Isfahan, Shiraz, Kazeron, Goral, Sharokashari and Presso were used for direct and indirect regeneration. For indirect regeneration various doses of NAA and kinetin were used to induce calli which were cultured on MS media containing PGRs for direct and indirect regeneration. Later, cell suspension was established and morphological characterization of CrO3 stained cells was carried out using microscopy.Results and DiscussionOur findings revealed that the highest callus percentage and callus volume were observed from lateral sprouts and shoots of genotype Isfahan on MS medium containing 1 mg/L NAA and 1 mg/L kinetin. The in vitro regeneration was found to be genotype dependent while 77% and 77.5% was the highest percentage for indirect and direct regeneration, respectively. Additionally, the maximum shoot number (two shoots/explant) and shoot length (2.22 cm) were also observed in Isfahan genotype. Cell suspension culture showed the highest fresh weight (18.59 g) and dry weight (1.707 g) with 0.75 g inoculum of the callus derived from lateral sprouts cultured on MS medium. Microscopy of CrO3 stained cells was carried on each 3rd day for 27 days that revealed larger and spongier cells in the early days as compared to final days when the cell number was greater but cell size was smaller.ConclusionThe callogenesis, organogenesis, and cell suspension culture of chamomile may be genotype dependent. Hence, optimization of media ingredients and culture conditions is of utmost importance for devising tissue culture based conservation strategy of any chamomile genotype and secondary metabolite production. creator: Aqeel Ahmad creator: Muhammad Tahir ul Qamar creator: Almeera Shoukat creator: Mehtab Muhammad Aslam creator: Mohsin Tariq creator: Mansor Hakiman creator: Faiz Ahmad Joyia uri: https://doi.org/10.7717/peerj.11464 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ahmad et al. title: ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses link: https://peerj.com/articles/11376 last-modified: 2021-05-21 description: Whole Genome Sequence (WGS) data from bacterial species is used for a variety of applications ranging from basic microbiological research, diagnostics, and epidemiological surveillance. The availability of WGS data from hundreds of thousands of individual isolates of individual microbial species poses a tremendous opportunity for discovery and hypothesis-generating research into ecology and evolution of these microorganisms. Flexibility, scalability, and user-friendliness of existing pipelines for population-scale inquiry, however, limit applications of systematic, population-scale approaches. Here, we present ProkEvo, an automated, scalable, reproducible, and open-source framework for bacterial population genomics analyses using WGS data. ProkEvo was specifically developed to achieve the following goals: (1) Automation and scaling of complex combinations of computational analyses for many thousands of bacterial genomes from inputs of raw Illumina paired-end sequence reads; (2) Use of workflow management systems (WMS) such as Pegasus WMS to ensure reproducibility, scalability, modularity, fault-tolerance, and robust file management throughout the process; (3) Use of high-performance and high-throughput computational platforms; (4) Generation of hierarchical-based population structure analysis based on combinations of multi-locus and Bayesian statistical approaches for classification for ecological and epidemiological inquiries; (5) Association of antimicrobial resistance (AMR) genes, putative virulence factors, and plasmids from curated databases with the hierarchically-related genotypic classifications; and (6) Production of pan-genome annotations and data compilation that can be utilized for downstream analysis such as identification of population-specific genomic signatures. The scalability of ProkEvo was measured with two datasets comprising significantly different numbers of input genomes (one with ~2,400 genomes, and the second with ~23,000 genomes). Depending on the dataset and the computational platform used, the running time of ProkEvo varied from ~3-26 days. ProkEvo can be used with virtually any bacterial species, and the Pegasus WMS uniquely facilitates addition or removal of programs from the workflow or modification of options within them. To demonstrate versatility of the ProkEvo platform, we performed a hierarchical-based population structure analyses from available genomes of three distinct pathogenic bacterial species as individual case studies. The specific case studies illustrate how hierarchical analyses of population structures, genotype frequencies, and distribution of specific gene functions can be integrated into an analysis. Collectively, our study shows that ProkEvo presents a practical viable option for scalable, automated analyses of bacterial populations with direct applications for basic microbiology research, clinical microbiological diagnostics, and epidemiological surveillance. creator: Natasha Pavlovikj creator: Joao Carlos Gomes-Neto creator: Jitender S. Deogun creator: Andrew K. Benson uri: https://doi.org/10.7717/peerj.11376 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Pavlovikj et al. title: Evaluating the cleavage efficacy of CRISPR-Cas9 sgRNAs targeting ineffective regions of Arabidopsis thaliana genome link: https://peerj.com/articles/11409 last-modified: 2021-05-21 description: The CRISPR-Cas9 system has recently evolved as a powerful mutagenic tool for targeted genome editing. The impeccable functioning of the system depends on the optimal design of single guide RNAs (sgRNAs) that mainly involves sgRNA specificity and on-target cleavage efficacy. Several research groups have designed algorithms and models, trained on mammalian genomes, for predicting sgRNAs cleavage efficacy. These models are also implemented in most plant sgRNA design tools due to the lack of on-target cleavage efficacy studies in plants. However, one of the major drawbacks is that almost all of these models are biased for considering only coding regions of the DNA while excluding ineffective regions, which are of immense importance in functional genomics studies especially for plants, thus making prediction less reliable. In the present study, we evaluate the on-target cleavage efficacy of experimentally validated sgRNAs designed against diverse ineffective regions of Arabidopsis thaliana genome using various statistical tests. We show that nucleotide preference in protospacer adjacent motif (PAM) proximal region, GC content in the PAM proximal seed region, intact RAR and 3rd stem loop structures, and free accessibility of nucleotides in seed and tracrRNA regions of sgRNAs are important determinants associated with their high on-target cleavage efficacy. Thus, our study describes the features important for plant sgRNAs high on-target cleavage efficacy against ineffective genomic regions previously shown to give rise to ineffective sgRNAs. Moreover, it suggests the need of developing an elaborative plant-specific sgRNA design model considering the entire genomic landscape including ineffective regions for enabling highly efficient genome editing without wasting time and experimental resources. creator: Afsheen Malik creator: Alvina Gul creator: Faiza Munir creator: Rabia Amir creator: Hadi Alipour creator: Mustafeez Mujtaba Babar creator: Syeda Marriam Bakhtiar creator: Rehan Zafar Paracha creator: Zoya Khalid creator: Muhammad Qasim Hayat uri: https://doi.org/10.7717/peerj.11409 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Malik et al. title: Spatiotemporal patterns and ecological consequences of a fragmented landscape created by damming link: https://peerj.com/articles/11416 last-modified: 2021-05-21 description: BackgroundDamming disrupts rivers and destroys neighboring terrestrial ecosystems through inundation, resulting in profound and long-lasting impacts on biodiversity and ecosystem processes far beyond the river system itself. Archipelagos formed by damming are often considered ideal systems for studying habitat fragmentation.MethodsHere we quantified the island attributes and landscape dynamics of the Thousand Island Lake (TIL) in China, which is one of the several long-term biodiversity/fragmentation research sites around the world. We also synthesized the major findings of relevant studies conducted in the region to further ecological understanding of damming and landscape fragmentation.ResultsOur results show that the vegetations on islands and the neighboring mainland were both recovering between 1985 and 2005 due to reforestation and natural succession, but the regeneration was partly interrupted after 2005 because of increasing human influences. While major changes in landscape composition occurred primarily in the lakefront areas and near-lakeshore islands, landscape patterns became structurally more complex and fragmented on both islands and mainland. About 80 studies from the TIL region show that the genetic, taxonomic, functional, and phylogenetic diversity on these islands were mainly influenced by island area at the patch scale, but fragmentation per se also affected species composition and related ecological processes at patch and landscape scales. In general, islands had lower species diversity but a steeper species-area relationship than the surrounding mainland. Fragmentation and edge effects substantially hindered ecological succession towards more densely vegetated forests on the islands. Environmental heterogeneity and filtering had a major impact on island biotic communities. We hypothesize that there are multiple mechanisms operating at different spatial scales that link landscape fragmentation and ecological dynamics in the TIL region, which beg for future studies. By focusing on an extensive spatiotemporal analysis of the island-mainland system and a synthesis of existing studies in the region, this study provides an important foundation and several promising directions for future studies. creator: Guang Hu creator: Maxwell Wilson creator: Bing-Bing Zhou creator: Chenwei Shang creator: Mingjian Yu creator: Jianguo Wu uri: https://doi.org/10.7717/peerj.11416 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Hu et al. title: Identification of KIF4A as a pan-cancer diagnostic and prognostic biomarker via bioinformatics analysis and validation in osteosarcoma cell lines link: https://peerj.com/articles/11455 last-modified: 2021-05-21 description: BackgroundCancer is a disease of abnormal cell proliferation caused by abnormal expression of cancer-related genes. However, it is still difficult to distinguish benign and malignant lesions in many cases. KIF4A has been reported to be associated with a variety of cancer lesions. We aimed to explore whether KIF4A could be used as a biomarker of pan-cancer diagnostic.MethodsWe identified twenty-eight cell cycle-related genes that were overexpressed in no less than ten types of cancer. We determined KIF4A mRNA and protein expression in osteosarcoma (OS) cells. Furthermore, to determine the effect of KIF4A in OS, we silenced KIF4A in OS cells and detected cell viability, colony formation, invasion, migration, apoptosis and cell cycle parameters.ResultsKIF4A exhibited upregulated expression in eleven types of cancer. Cell cycle-related genes are extensively overexpressed in various types of cancers. KIF4A overexpression can serve as a diagnostic and prognostic marker in various cancers. Silencing KIF4A inhibited the viability, colony formation, invasion and migration and induced apoptosis and cell cycle arrest of OS cells. Our findings revealed that high expression of KIF4A could serve as a diagnostic and prognostic marker in OS cancers.ConclusionKIF4A could serve as a pan-cancer diagnostic and prognostic marker. KIF4A could be used as a novel therapeutic target for OS. creator: Jiankang Pan creator: Xiaohua Lei creator: Xinzhan Mao uri: https://doi.org/10.7717/peerj.11455 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Pan et al. title: Destabilization of EpCAM dimer is associated with increased susceptibility towards cleavage by TACE link: https://peerj.com/articles/11484 last-modified: 2021-05-21 description: The cell-surface protein EpCAM is a carcinoma marker utilized in diagnostics and prognostics, and a promising therapeutic target. It is involved in nuclear signaling via regulated intramembrane proteolysis (RIP). Many aspects of this process are not fully understood, including the events at the molecular level leading to the exposure of cleavage sites, buried at the dimerization interface. To investigate the effect of dimer stability on cleavage susceptibility we prepared two mutants of human EpCAM ectodomain: a monomeric form, and a disulfide-stabilized dimeric form. We show that the disulfide-stabilized dimer is resistant to tumor necrosis factor-α-converting enzyme (TACE) cleavage, while the monomeric form is more susceptible than the predominantly dimeric wild type. This provides experimental evidence that the oligomeric state of EpCAM is a determinant in RIP and demonstrates the usefulness of the oligomeric state-specific mutants in investigations of EpCAM biological function. creator: Tomaž Žagar creator: Miha Pavšič creator: Aljaž Gaber uri: https://doi.org/10.7717/peerj.11484 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Žagar et al. title: The landscape of tumors-infiltrate immune cells in papillary thyroid carcinoma and its prognostic value link: https://peerj.com/articles/11494 last-modified: 2021-05-21 description: IntroductionThyroid cancer is a very common malignant tumor in the endocrine system, while the incidence of papillary thyroid carcinoma (PTC) throughout the world also shows a trend of increase year by year. In this study, we constructed two models: ICIscore and Riskscore. Combined with these two models, we can make more accurate and reasonable inferences about the prognosis of PTC patients.MethodsWe selected 481 PTC samples from TCGA and 147 PTC samples from GEO (49 samples in GSE33630, 65 samples in GSE35570 and 33 samples in GSE60542). We performed consistent clustering for them and divided them into three subgroups and screened differentially expressed genes from these three subgroups. Then we divided the differential genes into three subtypes. We also distinguished the up-regulated and down-regulated genes and calculated ICIscore for each PTC sample. ICIscore consists of two parts: (1) the PCAu was calculated from up-regulated genes. (2) the PCAd was calculated from down-regulated genes. The PCAu and PCAd of each sample were the first principal component of the relevant gene. What’s more, we divided the patients into two groups and constructed mRNA prognostic signatures. Additionally we also verified the independent prognostic value of the signature.ResultsThough ICIscore, we were able to observe the relationship between immune infiltration and prognosis. The result suggests that the activation of the immune system may have both positive and negative consequences. Though Riskscore, we could make more accurate predictions about the prognosis of patients with PTC. Meanwhile, we also generated and validated the ICIscore group and Riskscore group respectively.ConclusionAll the research results show that by combining the two models constructed, ICIscore and Riskscore, we can make a more accurate and reasonable inference about the prognosis of patients with clinical PTC patients. This suggests that we can provide more effective and reasonable treatment plan for clinical PTC patients. creator: Yanyi Huang creator: Tao Yi creator: Yushu Liu creator: Mengyun Yan creator: Xinli Peng creator: Yunxia Lv uri: https://doi.org/10.7717/peerj.11494 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Huang et al. title: ­Blue mussel (Mytilus spp.) cultivation in mesohaline eutrophied inner coastal waters: mitigation potential, threats and cost effectiveness link: https://peerj.com/articles/11247 last-modified: 2021-05-20 description: The EU-water framework directive (WFD) focuses on nutrient reductions to return coastal waters to the good ecological status. As of today, many coastal waters have reached a steady state of insufficient water quality due to continuous external nutrient inputs and internal loadings. This study focuses first on the current environmental status of mesohaline inner coastal waters to illustrate their needs of internal measures to reach demanded nutrient reductions and secondly, if mussel cultivation can be a suitable strategy to improve water quality. Therefore, nitrogen, phosphorus, chlorophyll a, and Secchi depth of nine mesohaline inner coastal waters in north east Germany were analyzed from 1990 to 2018. Two pilot mussel farms were used to evaluate their effectiveness as a mitigation measure and to estimate potential environmental risks, including the interactions with pathogenic vibrio bacteria. Further, estimated production and mitigation potential were used to assess economic profitability based on the sale of small sized mussels for animal feed and a compensation for nutrient mitigation. The compensation costs were derived from nutrient removal costs of a waste water treatment plant (WWTP). Results show that currently all nine water bodies do not reach the nutrient thresholds demanded by the WFD. However, coastal waters differ in nutrient pollution, indicating that some can reach the desired threshold values if internal measures are applied. The mitigation potential of mussel cultivation depends on the amount of biomass that is cultivated and harvested. However, since mussel growth is closely coupled to the salinity level, mussel cultivation in low saline environments leads to lower biomass production and inevitably to larger cultivation areas. If 50% of the case study area Greifswald Bay was covered with mussel farms the resulting nitrogen reduction would increase Secchi depth by 7.8 cm. However, high chlorophyll a values can hamper clearance rates (<20 mg m−3 = 0.43 l h−1 dry weight g−1) and therefore the mitigation potential. Also, the risk of mussel stock loss due to high summer water temperatures might affect the mitigation potential. The pilot farms had no significant effect on the total organic content of sediments beneath. However, increased values of Vibrio spp. in bio deposits within the pilot farm (1.43 106 ± 1.10 106CFU 100 ml−1 (reference site: 1.04 106 ± 1.45 106 CFU 100 ml−1) were measured with sediment traps. Hence, mussel farms might act as a sink for Vibrio spp. in systems with already high vibrio concentrations. However, more research is required to investigate the risks of Vibrio occurrence coupled to mussel farming. The economic model showed that mussel cultivation in environments below 12 PSU cannot be economic at current market prices for small size mussels and compensations based on nutrient removal cost of WWTPs. creator: Lukas Ritzenhofen creator: Anna-Lucia Buer creator: Greta Gyraite creator: Sven Dahlke creator: Annemarie Klemmstein creator: Gerald Schernewski uri: https://doi.org/10.7717/peerj.11247 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ritzenhofen et al. title: Osteology, relationships and functional morphology of Weigeltisaurus jaekeli (Diapsida, Weigeltisauridae) based on a complete skeleton from the Upper Permian Kupferschiefer of Germany link: https://peerj.com/articles/11413 last-modified: 2021-05-20 description: BackgroundWeigeltisauridae is a clade of small-bodied diapsids characterized by a horned cranial frill, slender trunk and limbs, and a patagium supported by elongated bony rods. Partial skeletons and fragments are definitively known only from upper Permian (Lopingian) rocks in England, Germany, Madagascar and Russia. Despite these discoveries, there have been few detailed descriptions of weigeltisaurid skeletons, and the homologies of many skeletal elements—especially the rods supporting the patagium—remain the subject of controversy.Materials & MethodsHere, we provide a detailed description of a nearly complete skeleton of Weigeltisaurus jaekeli from the upper Permian (Lopingian: Wuchiapingian) Kupferschiefer of Lower Saxony, Germany. Briefly addressed by past authors, the skeleton preserves a nearly complete skull, postcranial axial skeleton, appendicular skeleton, and patagial supports. Through comparisons with extant and fossil diapsids, we examine the hypotheses for the homologies of the patagial rods. To examine the phylogenetic position of Weigeltisauridae and characterize the morphology of the clade, we integrate the material and other weigeltisaurids into a parsimony-based phylogenetic analysis focused on Permo-Triassic non-saurian Diapsida and early Sauria (61 taxa, 339 characters).ResultsWe recognize a number of intriguing anatomical features in the weigeltisaurid skeleton described here, including hollow horns on the post-temporal arch, lanceolate teeth in the posterior portion of the maxilla, the absence of a bony arch connecting the postorbital and squamosal bones, elongate and slender phalanges that resemble those of extant arboreal squamates, and patagial rods that are positioned superficial to the lateral one third of the gastral basket. Our phylogenetic study recovers a monophyletic Weigeltisauridae including Coelurosauravus elivensis, Weigeltisaurus jaekeli, and Rautiania spp. The clade is recovered as the sister taxon to Drepanosauromorpha outside of Sauria (=Lepidosauria + Archosauria).ConclusionsOur anatomical observations and phylogenetic analysis show variety of plesiomorphic diapsid characters and apomorphies of Weigeltisauridae in the specimen described here. We corroborate the hypothesis that the patagial ossifications are dermal bones unrelated to the axial skeleton. The gliding apparatus of weigeltisaurids was constructed from dermal elements unknown in other known gliding diapsids. SMNK-PAL 2882 and other weigeltisaurid specimens highlight the high morphological disparity of Paleozoic diapsids already prior to their radiation in the early Mesozoic. creator: Adam C. Pritchard creator: Hans-Dieter Sues creator: Diane Scott creator: Robert R. Reisz uri: https://doi.org/10.7717/peerj.11413 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Pritchard et al. title: Accessory cusp expression at the enamel-dentine junction of hominin mandibular molars link: https://peerj.com/articles/11415 last-modified: 2021-05-20 description: Studies of hominin dental morphology frequently consider accessory cusps on the lower molars, in particular those on the distal margin of the tooth (C6 or distal accessory cusp) and the lingual margin of the tooth (C7 or lingual accessory cusp). They are often utilized in studies of hominin systematics, where their presence or absence is assessed at the outer enamel surface (OES). However, studies of the enamel-dentine junction (EDJ) suggest these traits may be more variable in development, morphology and position than previously thought. Building on these studies, we outline a scoring procedure for the EDJ expression of these accessory cusps that considers the relationship between these accessory cusps and the surrounding primary cusps. We apply this scoring system to a sample of Plio-Pleistocene hominin mandibular molars of Paranthropus robustus, Paranthropus boisei, Australopithecus afarensis, Australopithecus africanus, Homo sp., Homo habilis and Homo erectus from Africa and Asia (n = 132). We find that there are taxon-specific patterns in accessory cusp expression at the EDJ that are consistent with previous findings at the OES. For example, P. robustus M1s and M2s very often have a distal accessory cusp but no lingual accessory cusp, while H. habilis M1s and M2s show the opposite pattern. The EDJ also reveals a number of complicating factors; some apparent accessory cusps at the enamel surface are represented at the EDJ only by shouldering on the ridges associated with the main cusps, while other accessory cusps appear to have little or no EDJ expression at all. We also discuss the presence of double and triple accessory cusps, including the presence of a double lingual accessory cusp on the distal ridge of the metaconid in the type specimen of H. habilis (OH 7–M1) that is not clear at the OES due to occlusal wear. Overall, our observations, as well as our understanding of the developmental underpinnings of cusp patterning, suggest that we should be cautious in our comparisons of accessory cusps for taxonomic interpretations. creator: Thomas W. Davies creator: Zeresenay Alemseged creator: Agness Gidna creator: Jean-Jacques Hublin creator: William H. Kimbel creator: Ottmar Kullmer creator: Fred Spoor creator: Clément Zanolli creator: Matthew M. Skinner uri: https://doi.org/10.7717/peerj.11415 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2021 Davies et al. title: Older age and diclofenac are associated with increased risk of upper gastrointestinal bleeding in gout patients link: https://peerj.com/articles/11468 last-modified: 2021-05-20 description: BackgroundGouty arthritis is a disease of global burden in which defective metabolism of uric acid causes arthritis. Gouty arthritis or medications used for its treatment may lead to uric acid-associated complications such as upper gastrointestinal bleeding (UGIB) and renal impairment.MethodsIn this cross-sectional study with retrospective record review, 403 established gouty arthritis patients were recruited to determine the incidence of UGIB and associated factors among gout patients who were on regular nonsteroidal anti-inflammatory drugs (NSAIDs).ResultsThe mean age of the 403 gouty arthritis patients was 55.7 years old and the majority (n = 359/403; 89.1%) were male. The incidence of UGIB among gouty arthritis patients who were on NSAIDs was 7.2% (n = 29/403). Older age (p < 0.001), diclofenac medication (p = 0.003), pantoprazole medication (p = 0.003), end-stage renal failure (ESRF) (p = 0.007), smoking (p = 0.035), hypertension (p = 0.042) and creatinine (p = 0.045) were significant risk factors for UGIB among the gouty arthritis patients in univariable analysis. Older age (p = 0.001) and diclofenac medication (p < 0.001) remained significant risk factors for UGIB among the gouty arthritis patients in multivariable analysis.ConclusionsAge and diclofenac were significantly associated with UGIB among patients with gouty arthritis on regular NSAIDs, indicating that these factors increased the risks of developing UGIB in gout patients. Hence, these high-risk groups of gouty arthritis patients should be routinely monitored to avoid the potential onset of UGIB. Our data also suggest that diclofenac should be prescribed for the shortest duration possible to minimize the risk of developing UGIB in gout patients. creator: Wan Syamimee Wan Ghazali creator: Wan Mohd Khairul Bin Wan Zainudin creator: Nurul Khaiza Yahya creator: Asmahan Mohamed Ismail creator: Kah Keng Wong uri: https://doi.org/10.7717/peerj.11468 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wan Ghazali et al. title: Molecular epidemiology of vancomycin-resistant Enterococcus faecium clinical isolates in a tertiary care hospital in southern Thailand: a retrospective study link: https://peerj.com/articles/11478 last-modified: 2021-05-20 description: ObjectiveVancomycin-resistant enterococci are nosocomial pathogens that are responsible for commonly causing healthcare-associated infections, and they exhibit increased resistance to many antimicrobials, particularly to vancomycin. The epidemiological data available on vancomycin-resistant enterococci (VRE) in Thailand are inadequate.MethodsUsing enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR), this study investigated genes that encode antimicrobial resistance and genetic relatedness to further understand VRE prevalence. Ninety VRE isolates were collected between 2011 and 2019 from a tertiary care hospital in southern Thailand. Antimicrobial susceptibility was determined using the disk diffusion method and E-test methods. Multiplex PCR was performed to detect the van gene and virulence genes.ResultsThe study showed a high prevalence of diverse multidrug-resistant VRE strains. The prevalence of VRE infection was the highest in 2014 (28 isolates, 39.4%). VRE were mostly found in the urogenital tract (26 isolates, 28.9%), followed by the digestive tract (20%), body fluid, i.e., pancreatic cyst fluid, peritoneal dialysis fluid, Jackson–Pratt (JP) drain (20%), and blood specimens (10%). Patients in medical and surgical wards had 71.1% multi-drug-resistant and 28.9% extensively drug-resistant (XDR) VRE strains, respectively. The most prevalent antibiotic resistance was to ampicillin (74.4%). Susceptibility to gentamicin and meropenem were similar (7% and 10%, respectively). Four isolates (4.4%) were resistant to colistin. Only vanA was detected among the strains. The virulence gene test showed that the detection rates of enterococcal surface protein (esp) and hyaluronidase (hyl) genes were 91.1% and 5.6%, respectively. According to ERIC-PCR analysis, 51 of 90 strains had clonality, with a similarity rate of 95%.ConclusionsWe conclude that there is a need to implement infection control practices and active surveillance. Molecular techniques can effectively detect antibiotic-resistant genes, which would allow monitoring to control VRE infection in hospitals. creator: Phanvasri Saengsuwan creator: Kamonnut Singkhamanan creator: Siribhorn Madla creator: Natnicha Ingviya creator: Chonticha Romyasamit uri: https://doi.org/10.7717/peerj.11478 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Saengsuwan et al. title: Seminar-case learning model improves clinical teaching: a prospective randomized controlled trial link: https://peerj.com/articles/11487 last-modified: 2021-05-20 description: PurposeThe purpose of this research was to assess whether the efficacy of the seminar-case learning model is superior to the traditional lecture-based learning model in the gastroenterology curriculum for first-year graduate students.Materials & MethodsThis research was a prospective randomized controlled trial that enrolled 92 first-year postgraduate students with a rotation internship in the gastroenterology department. The students were randomly divided into 2 groups and then subjected to an identical version of the curriculum for 8 weeks. The experimental group (n = 50) used the seminar-case learning model, while the control group (n = 42) used the traditional lecture-based learning model. Examinations consisted of a theoretical test and a case analysis test, and anonymous questionnaires were used to assess teaching quality.ResultsAll participants completed the examinations and questionnaires. The average theoretical test score of the experimental group was no statistical significance with that of the control group (P = 0.17). The average case analysis test score of the experimental group was significantly higher than that of the control group (P < 0.05). The indicators of the experimental group’s feedback were better than those of the control group, such that there were significantly higher learning interest and motivation, a better understanding of diseases and knowledge, improvements in clinical thinking and summary ability, and an active classroom atmosphere in the experimental group (P < 0.05). However, students in the experimental group felt more burdensome.ConclusionCompared to the traditional method, the seminar-case learning model showed a higher efficacy. The seminar-case learning model effectively improved students’ outcomes and satisfaction, which helped students narrow the gap between theoretical knowledge and clinical practical application. creator: Peiyuan Li creator: Bin Zeng creator: Xuanmin Chen creator: Zhifeng Liu creator: Jing Yang uri: https://doi.org/10.7717/peerj.11487 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: Efficacy of an improved method to screen semiochemicals of insect link: https://peerj.com/articles/11510 last-modified: 2021-05-20 description: BackgroundA combination of gas chromatography-electroantennographic detection (GC-EAD) and gas chromatography-mass spectrometry (GC-MS) is typically used to screen active compounds that play a role in the regulation of insect behavior. This method uses two kinds of gas chromatography (GC) equipment and needs to compare compounds between the two chromatograms, and it is tedious and costly. To improve detection efficiency, as well as reduce costs and the rate of missed detection, we designed a system connecting gas chromatography (GC), electroantennography (EAG), and mass spectrometry (MS), with MS used instead of the flame ionization detector (FID) as the GC-EAD detector. To verify the feasibility of the improved method, we compare two methods—GC-EAG-MS and GC-EAD—through a series of experiments. Some researchers made similar improvements, but these were not compared with GC-EAD, and their method needed to be improved in the synchronization and split ratio. Our method has been optimized and improved in these aspects.MethodsHelicoverpa armigera was the test organism; the improved method and conventional method were used to detect known and unknown compounds, as well as screen out active compounds that could generate responses in H. armigera antennae.ResultsScreening known single compounds using the two methods, the active compound benzaldehyde was detected in all seven concentrations of solution. By using the two methods, the five same active compounds of Helicoverpa armigera were detected in high concentration solution of the mixed compounds (100 mg L−1, 50 mg L−1); the four same active compounds were detected at 20 mg L−1 concentration; two identical same compounds were detected in low concentration solution (concentrations of 10 mg L−1 and below). By using the two methods, six identical active compounds of Helicoverpa armigera were detected in unknown compounds.ConclusionThe improved method was consistent with the conventional method in terms of accuracy and sensitivity. However, compared with the traditional methods, Gas chromatography-electroantennographic-mass spectrometry (GC-EAG-MS) saved the cost of GC and FID equipment, thereby greatly lowering the experimental cost. In the experiment, GC-EAG-MS combined the two experimental operations of screening active substances by GC-EAD and identifying active substances by GC-MS into one, which not only reduced the experimental steps, but also avoided the false positive caused by the comparison of the two chromatograms, and it greatly reduced the difficulty level of the overall experimental analysis. GC-EAG-MS is more convenient, efficient, economical, and practical, and could confidently replace traditional methods. With further optimization, it could be widely applied in the study of plant and insect chemical ecology. creator: Chongyang Li creator: Jianmin Cao creator: Xiufang Wang creator: Pengjun Xu creator: Xinwei Wang creator: Guangwei Ren uri: https://doi.org/10.7717/peerj.11510 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: High fructose exposure modifies the amount of adipocyte-secreted microRNAs into extracellular vesicles in supernatants and plasma link: https://peerj.com/articles/11305 last-modified: 2021-05-19 description: BackgroundHigh fructose exposure induces metabolic and endocrine responses in adipose tissue. Recent evidence suggests that microRNAs in extracellular vesicles are endocrine signals secreted by adipocytes. Fructose exposure on the secretion of microRNA by tissues and cells is poorly studied. Thus, the aim of this study was to evaluate the effect of fructose exposure on the secretion of selected microRNAs in extracellular vesicles from 3T3-L1 cells and plasma from Wistar rats.Methods3T3-L1 cells were exposed to 550 µM of fructose or standard media for four days, microRNAs levels were determined in extracellular vesicles of supernatants and cells by RT-qPCR. Wistar rats were exposed to either 20% fructose drink or tap water for eight weeks, microRNAs levels were determined in extracellular vesicles of plasma and adipose tissue by RT-qPCR.ResultsThis study showed that fructose exposure increased the total number of extracellular vesicles released by 3T3-L1 cells (p = 0.0001). The levels of miR-143-5p were increased in extracellular vesicles of 3T3-L1 cells exposed to fructose (p = 0.0286), whereas miR-223-3p levels were reduced (p = 0.0286). Moreover, in plasma-derived extracellular vesicles, miR-143-5p was higher in fructose-fed rats (p = 0.001), whereas miR-223-3p (p = 0.022), miR-342-3p (p = 0.0011), miR-140-5p (p = 0.0129) and miR-146b-5p (p = 0.0245) were lower.ConclusionFructose exposure modifies the levels of microRNAs in extracellular vesicles in vitro and in vivo. In particular, fructose exposure increases miR-143-5p, while decreases miR-223-3p and miR-342-3p. creator: Adrián Hernández-Díazcouder creator: Javier González-Ramírez creator: Abraham Giacoman-Martínez creator: Guillermo Cardoso-Saldaña creator: Eduardo Martínez-Martínez creator: Horacio Osorio-Alonso creator: Ricardo Márquez-Velasco creator: José L. Sánchez-Gloria creator: Yaneli Juárez-Vicuña creator: Guillermo Gonzaga creator: Laura Gabriela Sánchez-Lozada creator: Julio César Almanza-Pérez creator: Fausto Sánchez-Muñoz uri: https://doi.org/10.7717/peerj.11305 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hernández-Díazcouder et al. title: Changes in anti-nutrient, phytochemical, and micronutrient contents of different processed rubber (Hevea brasiliensis) seed meals link: https://peerj.com/articles/11327 last-modified: 2021-05-19 description: Rubber (Hevea brasiliensis) is a perennial plant crop grown in many parts of Africa, South East Asia, and South America, especially within the hot and humid climatic regions. Rubber seed, either as feed or food, is a useful raw material to produce edible oil and protein. Despite the huge quantity of rubber seeds produced in Nigeria and its potential as a protein source, rubber seeds still appear neglected and under-utilised as feed/food given its perception as inedible and toxic due to the high concentration of cyanogenic glycoside. Therefore, the quest for effective processing technique(s) that would enhance its food use application is very fitting. This current study was directed to determine the changes in anti-nutrient, phytochemical, and micronutrient contents of different processed rubber seed meals. Specifically, the rubber seeds underwent processing, which employed boiling and the combined action of boiling and fermentation methods that brought about three seed meal flour groups, i.e., raw (RRSM), boiled (BRSM), and fermented (FRSM) seed meals. These were subsequently analysed for anti-nutrient/phytochemical (oxalate, phytate, tannin, phenols, saponin, hydrogen cyanide (HCN), alkaloids, flavonoids, and trypsin inhibitors), and micronutrient (which involved minerals (magnesium, phosphorus, calcium, iron, zinc, potassium, sodium, manganese, lead, and selenium) and vitamin (vitamin B1, B2, B3, C, E, and beta carotene)) contents. The results showed that the processing methods used to achieve the RRSM, BRSM, and FRSM, reduced the anti-nutrients (phytate, tannin, and oxalate) below the acceptable limits, and the HCN below the toxic levels. Importantly, the processing methods herein have not yet succeeded in removing HCN in the (processed) rubber seed meals, but can be seen to be heading toward the right direction. The FRSM obtained significantly lower (p < 0.05) anti-nutrient/phytochemical, but significantly higher (p < 0.05) mineral contents, compared with the other groups (RRSM and BRSM), except for flavonoids that obtained a 30% increase over the BRSM. Some mineral and vitamin contents could be lost in the BRSM compared to the others (RRSM and FRSM) in this study. Additionally, the FRSM obtained higher vitamin contents, after those of RRSM. Overall, the combined action of boiling and fermentation should be recommended for the proper utilisation of rubber seed as food/feed. creator: Chidinma M. Agbai creator: Ijeoma A. Olawuni creator: Chigozie E. Ofoedu creator: Chidi J. Ibeabuchi creator: Charles Odilichukwu R. Okpala creator: Ivan Shorstkii creator: Małgorzata Korzeniowska uri: https://doi.org/10.7717/peerj.11327 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Agbai et al. title: Local-scale impact of wind energy farms on rare, endemic, and threatened plant species link: https://peerj.com/articles/11390 last-modified: 2021-05-19 description: BackgroundWind energy farms have become a popular solution to produce green energy worldwide. Their development within protected areas has increased dramatically in the past decade, and the effects on the rare, endemic and threatened plant species (i.e., protected plant species), essential for habitat conservation and management, are little known. Only a few studies directly quantify the impacts of wind energy farms on them. Our study analyzes the impact of wind energy farms on rare, endemic, and threatened plant species in steppic habitats and their recovery potential over a ten-year period on a wind energy farm within the Dealurile Agighiolului Natura 2000 site (Dobrogea Region, SE Romania).MethodsWe surveyed the rare, endemic, and threatened plant species within a radius of approximately 50 m around each of the 17 wind towers during the wind farm operational phase. We selected 34 plots to allow the investigation of two types of areas: (1) a disturbed area overlapping the technological platform, where the vegetation was removed before construction, and (2) an adjacent undisturbed area. To understand the effects of the wind energy farm on the rare, endemic, and threatened plant species diversity and the differences between the disturbed and undisturbed areas, we calculated under both conditions: (1) plant species richness; (2) sample-size-based rarefaction and extrapolation with Hill numbers parameterized by species richness; (3) non-metric multidimensional scaling of Jaccard dissimilarity index; (4) functional diversity; (5) beta-diversity (including replacement and nestedness of species).ResultsAs a result of the disturbances caused by the wind energy farm’s development, we identified a sharp contrast between the diversity of rare, endemic, and threatened plants inhabiting disturbed and undisturbed areas near the wind towers. Our research showed that less than 40% of the total inventoried rare, endemic, and threatened species colonized the disturbed sites. Species turnover within undisturbed plots was higher than disturbed plots, implying that the plant community’s heterogeneity was high. However, a higher richness in rare, endemic, and threatened plant species was found in the plots around the wind towers in grasslands of primary type. Sample-size-based rarefaction and extrapolation with Hill numbers by observed species richness indicated an accurate estimation of species richness in disturbed habitats, demonstrating that recovery after wind energy farm construction was incomplete after ten years of low-intensity plant restoration and conservation activities. Thus, we consider that operating activities must be reconfigured to allow the complete recovery of the communities with rare, endemic, and threatened plant species. creator: Mihaela Urziceanu creator: Paulina Anastasiu creator: Laurentiu Rozylowicz creator: Tatiana Eugenia Sesan uri: https://doi.org/10.7717/peerj.11390 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Urziceanu et al. title: SPMLMI: predicting lncRNA–miRNA interactions in humans using a structural perturbation method link: https://peerj.com/articles/11426 last-modified: 2021-05-19 description: Long non-coding RNA (lncRNA)–microRNA (miRNA) interactions are quickly emerging as important mechanisms underlying the functions of non-coding RNAs. Accordingly, predicting lncRNA–miRNA interactions provides an important basis for understanding the mechanisms of action of ncRNAs. However, the accuracy of the established prediction methods is still limited. In this study, we used structural consistency to measure the predictability of interactive links based on a bilayer network by integrating information for known lncRNA–miRNA interactions, an lncRNA similarity network, and an miRNA similarity network. In particular, by using the structural perturbation method, we proposed a framework called SPMLMI to predict potential lncRNA–miRNA interactions based on the bilayer network. We found that the structural consistency of the bilayer network was higher than that of any single network, supporting the utility of bilayer network construction for the prediction of lncRNA–miRNA interactions. Applying SPMLMI to three real datasets, we obtained areas under the curves of 0.9512 ± 0.0034, 0.8767 ± 0.0033, and 0.8653 ± 0.0021 based on 5-fold cross-validation, suggesting good model performance. In addition, the generalizability of SPMLMI was better than that of the previously established methods. Case studies of two lncRNAs (i.e., SNHG14 and MALAT1) further demonstrated the feasibility and effectiveness of the method. Therefore, SPMLMI is a feasible approach to identify novel lncRNA–miRNA interactions underlying complex biological processes. creator: Mingmin Xu creator: Yuanyuan Chen creator: Wei Lu creator: Lingpeng Kong creator: Jingya Fang creator: Zutan Li creator: Liangyun Zhang creator: Cong Pian uri: https://doi.org/10.7717/peerj.11426 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Xu et al. title: MicroRNA panel in serum reveals novel diagnostic biomarkers for prostate cancer link: https://peerj.com/articles/11441 last-modified: 2021-05-19 description: PurposeMicroRNAs (miRNAs), which could be stably preserved and detected in serum or plasma, could act as biomarkers in cancer diagnosis. Prostate cancer is the second cancer in males for incidence. This study aimed to establish a miRNA panel in peripheral serum which could act as a non-invasive biomarker helping diagnosing PC.MethodsA total of 86 PC patients and 86 normal control serum samples were analyzed through a four-stage experimental process using quantitative real-time polymerase chain reaction. Logistic regression method was used to construct a diagnostic model based on the differentially expressed miRNAs in serum. Receiver operating characteristic curves were constructed to evaluate the diagnostic accuracy. We also compared the 3-miRNA panel with previously reported biomarkers and verified in four public datasets. In addition, the expression characteristics of the identified miRNAs were further explored in tissue and serum exosomes samples.ResultsWe identified a 3-miRNA signature including up-regulated miR-146a-5p, miR-24-3p and miR-93-5p for PC detection. Areas under the receiver operating characteristic curve of the 3-miRNA panel for the training, testing and external validation phase were 0.819, 0.831 and 0.814, respectively. The identified signature has a very stable diagnostic performance in the large cohorts of four public datasets. Compared with previously identified miRNA biomarkers, the 3-miRNA signature in this study has superior performance in diagnosing PC. What’s more, the expression level of miR-93-5p was also elevated in exosomes from PC samples. However, in PC tissues, none of the three miRNAs showed significantly dysregulated expression.ConclusionsWe established a three-miRNA panel (miR-146a-5p, miR-24-3p and miR-93-5p) in peripheral serum which could act as a non-invasive biomarker helping diagnosing PC. creator: Shiyu Zhang creator: Cheng Liu creator: Xuan Zou creator: Xiangnan Geng creator: Xin Zhou creator: XingChen Fan creator: Danxia Zhu creator: Huo Zhang creator: Wei Zhu uri: https://doi.org/10.7717/peerj.11441 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhang et al. title: K-mer-based machine learning method to classify LTR-retrotransposons in plant genomes link: https://peerj.com/articles/11456 last-modified: 2021-05-19 description: Every day more plant genomes are available in public databases and additional massive sequencing projects (i.e., that aim to sequence thousands of individuals) are formulated and released. Nevertheless, there are not enough automatic tools to analyze this large amount of genomic information. LTR retrotransposons are the most frequent repetitive sequences in plant genomes; however, their detection and classification are commonly performed using semi-automatic and time-consuming programs. Despite the availability of several bioinformatic tools that follow different approaches to detect and classify them, none of these tools can individually obtain accurate results. Here, we used Machine Learning algorithms based on k-mer counts to classify LTR retrotransposons from other genomic sequences and into lineages/families with an F1-Score of 95%, contributing to develop a free-alignment and automatic method to analyze these sequences. creator: Simon Orozco-Arias creator: Mariana S. Candamil-Cortés creator: Paula A. Jaimes creator: Johan S. Piña creator: Reinel Tabares-Soto creator: Romain Guyot creator: Gustavo Isaza uri: https://doi.org/10.7717/peerj.11456 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Orozco-Arias et al. title: miRcorrNet: machine learning-based integration of miRNA and mRNA expression profiles, combined with feature grouping and ranking link: https://peerj.com/articles/11458 last-modified: 2021-05-19 description: A better understanding of disease development and progression mechanisms at the molecular level is critical both for the diagnosis of a disease and for the development of therapeutic approaches. The advancements in high throughput technologies allowed to generate mRNA and microRNA (miRNA) expression profiles; and the integrative analysis of these profiles allowed to uncover the functional effects of RNA expression in complex diseases, such as cancer. Several researches attempt to integrate miRNA and mRNA expression profiles using statistical methods such as Pearson correlation, and then combine it with enrichment analysis. In this study, we developed a novel tool called miRcorrNet, which performs machine learning-based integration to analyze miRNA and mRNA gene expression profiles. miRcorrNet groups mRNAs based on their correlation to miRNA expression levels and hence it generates groups of target genes associated with each miRNA. Then, these groups are subject to a rank function for classification. We have evaluated our tool using miRNA and mRNA expression profiling data downloaded from The Cancer Genome Atlas (TCGA), and performed comparative evaluation with existing tools. In our experiments we show that miRcorrNet performs as good as other tools in terms of accuracy (reaching more than 95% AUC value). Additionally, miRcorrNet includes ranking steps to separate two classes, namely case and control, which is not available in other tools. We have also evaluated the performance of miRcorrNet using a completely independent dataset. Moreover, we conducted a comprehensive literature search to explore the biological functions of the identified miRNAs. We have validated our significantly identified miRNA groups against known databases, which yielded about 90% accuracy. Our results suggest that miRcorrNet is able to accurately prioritize pan-cancer regulating high-confidence miRNAs. miRcorrNet tool and all other supplementary files are available at https://github.com/malikyousef/miRcorrNet. creator: Malik Yousef creator: Gokhan Goy creator: Ramkrishna Mitra creator: Christine M. Eischen creator: Amhar Jabeer creator: Burcu Bakir-Gungor uri: https://doi.org/10.7717/peerj.11458 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yousef et al. title: Chemical synthesis of peptidoglycan mimetic–disaccharide-tetrapeptide conjugate and its hydrolysis by bacteriophage T5, RB43 and RB49 L-alanyl-D-glutamate peptidases link: https://peerj.com/articles/11480 last-modified: 2021-05-19 description: BackgroundEndolysins of a number of bacteriophages, including coliphages T5, RB43, and RB49, target the peptidoglycans of the bacterial cell wall. The backbone of these bacterial peptidoglycans consist of alternating N-acetylglucosamine and N-acetylmuramic acid residues that is further “reinforced” by the peptide subunits. Because of the mesh-like structure and insolubility of peptidoglycans, the processes of the peptidoglycan binding and hydrolysis by enzymes cannot be studied by spectral methods. To overcome these issues we synthesized and analyzed here one of the simplest water soluble peptidoglycan mimetics.MethodsA compound has been synthesized that mimics the peptidoglycan fragment of the bacterial cell wall, N-acetylglucosaminyl-β(1-4)-N-acetylmuramoyl-l-alanyl-γ-d-glutamyl-l-alanyl-d-alanine. NMR was used to study the degradation of this peptidoglycan mimetic by lytic l-alanoyl-d-glutamate peptidases of colibacteriophages T5, RB43, and RB49 (EndoT5, EndoRB43, and EndoRB49, respectively).ResultsThe resulting glycopeptide mimetic was shown to interact with the studied enzymes. Its hydrolysis occurred through the bond between l-Ala and d-Glu. This artificial substrate mimetic was hydrolyzed by enzymes at different rates, which decreased outside the pH optimum. The EndoT5 demonstrated the lowest hydrolysis rate, whereas the EndoRB49-driven hydrolysis was the fastest one, and EndoRB43 displayed an intermediate potency. These observations are consistent with the hypothesis that EndoRB49 is characterized by the lowest selectivity, and hence the potentially broader spectrum of the peptidoglycan types subjected to hydrolysis, which was put forward in the previous study. We also show that to hydrolyze this glycopeptide mimetic, enzymes approach the glycopeptide near the methyl groups of all three alanines. creator: Viatcheslav Azev creator: Alexey Chulin creator: Maxim Molchanov creator: Dmitry Prokhorov creator: Galina Mikoulinskaia creator: Vladimir N. Uversky creator: Viktor Kutyshenko uri: https://doi.org/10.7717/peerj.11480 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Azev et al. title: Liver proteome alterations in psychologically distressed rats and a nootropic drug link: https://peerj.com/articles/11483 last-modified: 2021-05-19 description: BackgroundChronic psychological distress is considered today a pandemic due to the modern lifestyle and has been associated with various neurodegenerative, autoimmune, or systemic inflammation-related diseases. Stress is closely related to liver disease exacerbation through the high activity of the endocrine and autonomic nervous systems, and the connection between the development of these pathologies and the physiological effects induced by oxidative stress is not yet completely understood. The use of nootropics, as the cognitive enhancer and antioxidant piracetam, is attractive to repair the oxidative damage. A proteomic approach provides the possibility to obtain an in-depth comprehension of the affected cellular processes and the possible consequences for the body. Therefore, we considered to describe the effect of distress and piracetam on the liver proteome.MethodsWe used a murine model of psychological stress by predatory odor as a distress paradigm. Female Sprague-Dawley rats were distributed into four experimental groups (n = 6 − 7/group) and were exposed or not to the stressor for five days and treated or not with piracetam (600 mg/kg) for six days. We evaluated the liver proteome by one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (1D-SDS-PAGE) followed by liquid chromatography-tandem mass spectrometry (GeLC-MS/MS). Besides, we analyzed the activity of liver antioxidant enzymes, the biochemical parameters in plasma and rat behavior.ResultsOur results showed that distress altered a wide range of proteins involved in amino acids metabolism, glucose, and fatty acid mobilization and degradation on the way to produce energy, protein folding, trafficking and degradation, redox metabolism, and its implications in the development of the non-alcoholic fatty liver disease (NAFLD). Piracetam reverted the changes in metabolism caused by distress exposure, and, under physiological conditions, it increased catabolism rate directed towards energy production. These results confirm the possible relationship between chronic psychological stress and the progression of NAFLD, as well as we newly evidenced the controversial beneficial effects of piracetam. Finally, we propose new distress biomarkers in the liver as the protein DJ-1 (PARK7), glutathione peroxidase 1 (GPX), peroxiredoxin-5 (PRDX5), glutaredoxin 5 (GLRX5), and thioredoxin reductase 1 (TXNDR1), and in plasma as biochemical parameters related to kidney function such as urea and blood urea nitrogen (BUN) levels. creator: Raquel González-Fernández creator: Mariana Grigoruţă creator: Sarahi Chávez-Martínez creator: Eliel Ruiz-May creator: José Miguel Elizalde-Contreras creator: José Valero-Galván creator: Alejandro Martínez-Martínez uri: https://doi.org/10.7717/peerj.11483 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 González-Fernández et al. title: Description of three new species of Geometridae (Lepidoptera) using species delimitation in an integrative taxonomy approach for a cryptic species complex link: https://peerj.com/articles/11304 last-modified: 2021-05-18 description: The genus Eois Hübner (Geometridae: Larentiinae) comprises 254 valid species, 217 of which were described from the Neotropics and 31 of those having their type locality in Brazil. Since this species rich genus has never been revised, and may potentially include many cryptic undescribed species, Eois embodies a problematic taxonomic scenario. The actual diversity of Eois is greatly underestimated and the Brazilian fauna is poorly known, both because of inadequate sampling and because of the potential existence of cryptic species "hidden" within some nominal taxa. In this study we investigated the diversity within a cryptic species complexes associated to the E. pallidicosta and E. odatis clades. We describe three new species Eois oya Moraes & Montebello sp. nov., Eois ewa Moraes & Stanton sp. nov., and Eois oxum Moraes & Freitas sp. nov., in an integrative taxonomy approach, using morphology, host plant use and species delimitation tools. creator: Simeão S. Moraes creator: Ygor Montebello creator: Mariana A. Stanton creator: Lydia Fumiko Yamaguchi creator: Massuo J. Kato creator: André V.L. Freitas uri: https://doi.org/10.7717/peerj.11304 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Moraes et al. title: Native to designed: microbial α-amylases for industrial applications link: https://peerj.com/articles/11315 last-modified: 2021-05-18 description: Backgroundα-amylases catalyze the endo-hydrolysis of α-1,4-D-glycosidic bonds in starch into smaller moieties. While industrial processes are usually performed at harsh conditions, α-amylases from mainly the bacteria, fungi and yeasts are preferred for their stabilities (thermal, pH and oxidative) and specificities (substrate and product). Microbial α-amylases can be purified and characterized for industrial applications. While exploring novel enzymes with these properties in the nature is time-costly, the advancements in protein engineering techniques including rational design, directed evolution and others have privileged their modifications to exhibit industrially ideal traits. However, the commentary on the strategies and preferably mutated residues are lacking, hindering the design of new mutants especially for enhanced substrate specificity and oxidative stability. Thus, our review ensures wider accessibility of the previously reported experimental findings to facilitate the future engineering work.Survey methodology and objectivesA traditional review approach was taken to focus on the engineering of microbial α-amylases to enhance industrially favoured characteristics. The action mechanisms of α- and β-amylases were compared to avoid any bias in the research background. This review aimed to discuss the advances in modifying microbial α-amylases via protein engineering to achieve longer half-life in high temperature, improved resistance (acidic, alkaline and oxidative) and enhanced specificities (substrate and product). Captivating results were discussed in depth, including the extended half-life at 100 °C, pH 3.5 and 10, 1.8 M hydrogen peroxide as well as enhanced substrate (65.3%) and product (42.4%) specificities. These shed light to the future microbial α-amylase engineering in achieving paramount biochemical traits ameliorations to apt in the industries.ConclusionsMicrobial α-amylases can be tailored for specific industrial applications through protein engineering (rational design and directed evolution). While the critical mutation points are dependent on respective enzymes, formation of disulfide bridge between cysteine residues after mutations is crucial for elevated thermostability. Amino acids conversion to basic residues was reported for enhanced acidic resistance while hydrophobic interaction resulted from mutated hydrophobic residues in carbohydrate-binding module or surface-binding sites is pivotal for improved substrate specificity. Substitution of oxidation-prone methionine residues with non-polar residues increases the enzyme oxidative stability. Hence, this review provides conceptual advances for the future microbial α-amylases designs to exhibit industrially significant characteristics. However, more attention is needed to enhance substrate specificity and oxidative stability since they are least reported. creator: Si Jie Lim creator: Siti Nurbaya Oslan uri: https://doi.org/10.7717/peerj.11315 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Lim and Oslan title: High glucose treatment promotes extracellular matrix proteome remodeling in Müller glial cells link: https://peerj.com/articles/11316 last-modified: 2021-05-18 description: BackgroundThe underlying pathomechanisms in diabetic retinopathy (DR) remain incompletely understood. The aim of this study was to add to the current knowledge about the particular role of retinal Müller glial cells (RMG) in the initial processes of DR.MethodsApplying a quantitative proteomic workflow, we investigated changes of primary porcine RMG under short term high glucose treatment as well as glycolysis inhibition treatment.ResultsWe revealed significant changes in RMG proteome primarily in proteins building the extracellular matrix (ECM) indicating fundamental remodeling processes of ECM as novel rapid response to high glucose treatment. Among others, Osteopontin (SPP1) as well as its interacting integrins were significantly downregulated and organotypic retinal explant culture confirmed the selective loss of SPP1 in RMG upon treatment. Since SPP1 in the retina has been described neuroprotective for photoreceptors and functions against experimentally induced cell swelling, it’s rapid loss under diabetic conditions may point to a direct involvement of RMG to the early neurodegenerative processes driving DR. Data are available via ProteomeXchange with identifier PXD015879. creator: Sandra Sagmeister creator: Juliane Merl-Pham creator: Agnese Petrera creator: Cornelia A. Deeg creator: Stefanie M. Hauck uri: https://doi.org/10.7717/peerj.11316 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sagmeister et al. title: Co-application of mineral and organic fertilizers under deficit irrigation improves the fruit quality of the Wonderful pomegranate link: https://peerj.com/articles/11328 last-modified: 2021-05-18 description: BackgroundThe aim of this study was to determine the individual and interactive effects of various irrigation regimes and fertilizer treatments on the quality of the Wonderful pomegranate cultivar.MethodsTwo field experiments were conducted over two consecutive growing seasons (2018 and 2019) to determine the individual and interactive effects of various organic and mineral fertilizer treatments on the fruit quality of the Wonderful pomegranate under various irrigation conditions. A split-plot experimental design was used, in which the main plots included three levels of irrigation (100%, 80%, and 60% of evapotranspiration) while the subplots included five fertilizer treatments with different co-application ratios of mineral and organic fertilizers.ResultsAll tested physicochemical properties of the fruit were significantly affected by the irrigation treatment, with irrigation at 80% of evapotranspiration representing the best strategy for reducing water use and improving fruit quality. Moreover, the co-application of mineral and organic fertilizers had a significant effect on fruit quality, with 75% mineral + 25% organic fertilizer improving all of the physical and chemical properties of the fruit in both experimental seasons. Irrigation and the co-application of mineral and organic fertilizers also had a significant interaction effect on the physicochemical attributes of fruit, which further increased fruit quality.ConclusionsThe co-application of organic and mineral fertilizers produced better quality pomegranate fruit than mineral fertilizer alone under deficit irrigation conditions. This technique could therefore be applied to improve the fruiting of horticultural trees in arid growing regions. creator: Khalid F. Almutairi creator: Mahmoud Abdel-Sattar creator: Ahmed M. Mahdy creator: Mohamed A. El-Mahrouky uri: https://doi.org/10.7717/peerj.11328 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Almutairi et al. title: The effects of the depth of fertilization on losses of nitrogen and phosphorus and soil fertility in the red paddy soil of China link: https://peerj.com/articles/11347 last-modified: 2021-05-18 description: Nitrogen (N) and phosphorus (P) losses from agroecosystems are dominant nonpoint pollution. To minimize the losses of N and P, the optimal depth of fertilization was explored using a soil column study with the red paddy soil as the research objects. The losses of N and P were measured under five depths of fertilization (0, 5, 7.5, 10, and 12.5 cm) as well as no fertilization. The results showed that ammonia volatilization was significantly decreased with increasing fertilization depth within 0–10 cm, and there was no significant difference among the 10 cm, 12.5 cm, and no-fertilization treatments. Comparing with surface fertilization (0 cm), N and P losses by runoff could be reduced by 30.7–67.1% and 96.9–98.7% respectively by fertilization at 5–12.5 cm. In addition, deep fertilization (5–12.5 cm) did not increase N and P losses by leaching at the depth of 40 cm. Total N and P contents in the tillage layer of soil were increased by 5.1 to 22.8% and by −1.0 to 7.5%, respectively. Fertilization at 10cm depth has the potential to minimal environmental impact in the red paddy soil of south China, at this depth, NH3 volatilization was reduced by 95.1%, and N and P losses by runoff were reduced by 62.0% and 98.4%, respectively, compared with surface fertilization. creator: Kun Hou creator: Ying Huang creator: Xiangmin Rong creator: Jianwei Peng creator: Chang Tian creator: Yongliang Han uri: https://doi.org/10.7717/peerj.11347 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hou et al. title: Hospital-based case control study and animal study on the relationship between nonylphenol exposure and depression link: https://peerj.com/articles/11384 last-modified: 2021-05-18 description: ObjectivesThe aim of this work is to explore the association between chronic exposure to nonylphenol (NP), a representative environmental endocrine disruptor (EED), and the risk of depression and its potential mechanism.MethodsA hospital-based case control study was conducted from August to December 2018. Forty-one patients with confirmed depression and 47 healthy volunteers were recruited. In vitro, 20 rats were randomly divided into the control group (corn oil) and NP exposure group (n = 10 per group), which were gavaged at a dose of 4 mg/kg w/day for 180 days.ResultsThe depressed patient group had higher Zung Self-Rating Depression Scale (SDS) (P < 0.001) and Self-Rating Anxiety Scale (SAS) (P < 0.001) scores than the healthy group. The serum NP level (P = 0.009) in the depressed group was higher than that in the healthy group, and the BDNF level (P = 0.001) was lower. The serum levels of monoamine neurotransmitters dopamine (DA) (P = 0.070), epinephrine (E) (P = 0.001), and noradrenaline (NE) (P = 0.000) were lower than those in the healthy group. In the sucrose preference test, the sucrose preference time for the exposure group of rats was lower than that of the control group (P < 0.001). In the forced swim test, a longer resting time was measured for the exposure group of rats as compared to the control group (P < 0.05). The level of NP (P < 0.001) in the brain tissue of the NP exposure group was higher than that in the control group, and the serum level of brain-derived neurotrophic factor (BDNF) (P = 0.004) was lower. Histopathological examination of the brain biopsies illustrated that the neuronal cells and nuclei in the hippocampus of the exposed group exhibited slight shrinkage.ConclusionChronic exposure to NP at environmental doses will result in the accumulation of NP in the brain and blood, and induction of depression, which might be associated with the alterations in the expression levels of BDNF and monoamine neurotransmitters. creator: Ya Luo creator: Weihong Xu creator: Wei Ou creator: Ting Wang creator: Changwei Yang creator: Songying Xie creator: Jie Yu creator: Jie Xu uri: https://doi.org/10.7717/peerj.11384 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Luo et al. title: Prediction and injury risk based on movement patterns and flexibility in a 6-month prospective study among physically active adults link: https://peerj.com/articles/11399 last-modified: 2021-05-18 description: BackgroundPhysical activity has many health benefits but also carries a risk of injury. Some universal factors are connected with an increased risk regardless of the type of sport. Identifying these factors may help predict injuries and aid in their prevention.AimThe aim of this study is to determine the level of injury risk and the accuracy of injury prediction during a prospective 6-month period based on the quality of movement patterns and level of flexibility among average physically active young adults.Material and MethodsA group of 123 young, physically active adults were recruited for this study. The International Physical Activity Questionnaire (IPAQ) was used to determine their level of physical activity. The author’s own Injury History Questionnaire (IHQ) was used to retrospectively collect injury data from the 12 months before the study and prospectively collect data during the six month observation period. The Functional Movement Screen (FMS) test was conducted to assess the movement patterns quality and a sit-and-reach test was conducted to measure lower back and hamstrings flexibility.ResultsLow-quaility movement patterns (14≥ FMS) increased the injury risk level sevenfold. A level of flexibility reduced by one cm increased the risk of injury by 6%. Previous injuries also increased the risk of injury reccurence 6.4 times. Predicting injury occurrence based on the quality of movement patterns allows for an accuracy of 73%, whereas flexibility allows for a 41% accuracy. The simultaneous use of these two factors did not improve injury prediction accuracy.ConclusionThe risk of an injury increases with low-quality movement patterns, a low level of flexibility, and previous injuries. Preventative strategies should include shaping high-quality movement patterns, the right level of flexibility, and the full healing of injuries before resuming activities. The quality of movement patterns is an accurate predictor of injury risk, but lower back and hamstrings flexibility is not a reliable predictor of injury. creator: Dawid Koźlenia creator: Jarosław Domaradzki uri: https://doi.org/10.7717/peerj.11399 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Koźlenia and Domaradzki title: Field and laboratory metabolism and thermoregulation in rhinoceros auklets link: https://peerj.com/articles/11460 last-modified: 2021-05-18 description: Seabirds spend most of their lives at sea, except when visiting their breeding sites. Since the thermal conductivity of water is 25 times higher than that of air, seabirds resting on water lose heat and expend a considerable amount of energy for thermoregulation. For example, rhinoceros auklet (Cerorhinca monocerata), a medium-sized (480–620 g) alcid, spends most of its time floating on the sea. In order to estimate the cost of this behavior in terms of their daily energy expenditure (DEE), we studied rhinoceros auklets breeding on Teuri Island, Hokkaido Japan. We measured their resting metabolic rate (RMR) in air and on water by respirometry, and estimated their DEE by the doubly labeled water method. While RMR on water did not vary significantly between 10 °C and 15 °C, it was significantly higher at 5 °C. Air temperature (5.0–20.0 °C) had no effect on RMR. The DEE of free-ranging auklets averaged 1,005.5 kJ day−1 (±130.2, n = 3). Our results indicate that RMRs are elevated for auklets resting on water, particularly below their lower critical temperature (LCT), compared with in air. Accordingly, spending time above their LCT on water at any time of year will provide enhanced benefits, particularly to seabirds such as rhinoceros auklets which rest a considerable amount of time on water. creator: Aika Umeyama creator: Yasuaki Niizuma creator: Masaki Shirai uri: https://doi.org/10.7717/peerj.11460 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Umeyama et al. title: Microsatellite instability and Epstein-Barr virus combined with PD-L1 could serve as a potential strategy for predicting the prognosis and efficacy of postoperative chemotherapy in gastric cancer link: https://peerj.com/articles/11481 last-modified: 2021-05-18 description: BackgroundMicrosatellite instability (MSI) and Epstein-Barr virus (EBV)-positive molecular subtypes exhibit complex immune responses in gastric cancer (GC), and PD-L1 has emerged as a prognostic biomarker associated with the cancer immune microenvironment. This study aimed to determine the prognostic value of molecular subtypes and whether the addition of PD-L1 would accurately predict the prognosis and guide postoperative chemotherapy for GC patients.MethodsWe performed molecular subtyping of tissue microarray slides from 226 GC patients who were treated with radical gastrectomy. The MSI status and PD-L1 expression were evaluated through immunohistochemistry (IHC) and EBV status through situ hybridization. Multiplex polymerase chain reaction (PCR) was also performed on 50 cases to validate the accuracy of IHC in defining MSI status. Differences in overall survival (OS) were assessed using the Kaplan-Meier method, log-rank test and Cox proportional hazards regression model.ResultsAmong the 226 GC patients, 52 (23.2%) patients were classified as the MSI subtype, 11 (4.9%) were EBV+ subtype, and 161 (71.9%) were MSS (Microsatellite stable) /EBV− subtype according to TCGA analysis. Two patients were both positive for MSI and EBV infection. EBV+ cases showed higher PD-L1 positivity than MSI cases and MSS/EBV− cases (81.8% vs. 50.0% vs. 35.4%, P = 0.003). Compared with the non-MSS/EBV− (MSI or EBV+ cases) subgroup, GC patients with MSS/EBV− were associated with the worst outcomes (HR = 1.610, 95% CI [1.046–2.479], P = 0.031). MSS/EBV− GCs alone could benefit from postoperative chemotherapy (HR = 0.452, 95% CI [0.299–0.682], P < 0.001), and PD-L1-positive expression could also predict a better prognosis (HR = 0.612, 95% CI [0.389–0.962], P = 0.033) in this subgroup. Considering both chemotherapy efficacy and PD-L1 expression in the MSS/EBV− subgroup, chemotherapy could improve the prognosis for PD-L1-negative MSS/EBV− GCs (HR = 0.357, 95% CI [0.217–0.587], P < 0.001) but not PD-L1-positive MSS/EBV− GCs.ConclusionsMolecular subtyping combined with PD-L1 expression could serve as a potential strategy to better predict prognosis and guide postoperative chemotherapy of GC patients. creator: Na Yang creator: Yanhua Wu creator: Meishan Jin creator: Zhifang Jia creator: Yueqi Wang creator: Donghui Cao creator: Lili Qin creator: Xueying Wang creator: Min Zheng creator: Xueyuan Cao creator: Jing Jiang uri: https://doi.org/10.7717/peerj.11481 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yang et al. title: An integrative monograph of Carex section Schoenoxiphium (Cyperaceae) link: https://peerj.com/articles/11336 last-modified: 2021-05-17 description: Carex section Schoenoxiphium (Cariceae, Cyperaceae) is endemic to the Afrotropical biogeographic region and is mainly distributed in southern and eastern Africa, with its center of diversity in eastern South Africa. The taxon was formerly recognized as a distinct genus and has a long history of taxonomic controversy. It has also an important morphological and molecular background in particular dealing with the complexity of its inflorescence and the phylogenetic relationships of its species. We here present a fully updated and integrative monograph of Carex section Schoenoxiphium based on morphological, molecular and cytogenetic data. A total of 1,017 herbarium specimens were examined and the majority of the species were studied in the field. Previous molecular phylogenies based on Sanger-sequencing of four nuclear and plastid DNA regions and RAD-seq were expanded. For the first time, chromosome numbers were obtained, with cytogenetic counts on 44 populations from 15 species and one hybrid. Our taxonomic treatment recognizes 21 species, one of them herein newly described (C. gordon-grayae). Our results agree with previous molecular works that have found five main lineages in Schoenoxiphium. We provide detailed morphological descriptions, distribution maps and analytical drawings of all accepted species in section Schoenoxiphium, an identification key, and a thorough nomenclatural survey including 19 new typifications and one nomen novum. creator: Modesto Luceño creator: Tamara Villaverde creator: José Ignacio Márquez-Corro creator: Rogelio Sánchez-Villegas creator: Enrique Maguilla creator: Marcial Escudero creator: Pedro Jiménez-Mejías creator: Manuel Sánchez-Villegas creator: Monica Miguez creator: Carmen Benítez-Benítez creator: A. Muthama Muasya creator: Santiago Martín-Bravo uri: https://doi.org/10.7717/peerj.11336 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Luceño et al. title: Trp-574-Leu mutation in wild mustard (Sinapis arvensis L.) as a result of als inhibiting herbicide applications link: https://peerj.com/articles/11385 last-modified: 2021-05-17 description: Wheat is one of the most important crops grown all around the world. Weeds cause significant yield loss and damage to wheat and their control is generally based on herbicide application. Regular use leads to herbicide resistance in weeds. This study aims to reveal molecular detection of Sinapis arvensis resistance mutation against ALS inhibiting herbicides. For this purpose, survey studies have been carried out in wheat growing areas in Amasya, Çorum, Tokat, and Yozgat provinces and wild mustard seeds have been collected from 310 different fields. According to bioassay tests with tribenuron-methyl, 13 of these populations, have not been affected by the registered dose of herbicide. When survived populations were subjected to dose-effect study and herbicides were applied at 26-fold, the highest and lowest resistance coefficients were determined as 7.2 (A-007) and 1.02 (T-034) respectively. In addition, B domain region from ALS gene was amplified and analyzed in molecular studies to determine point mutation in wild mustard against ALS herbicides. The PCR products were sequenced and target-site mutation to Leucine was observed at Trp-574 amino acide. In the study, point mutation in Trp-574 amino acide and Trp-574 Leu mutation in Sinapis arvensis have been detected for the first time in Turkey. creator: Bahadir Sin creator: İzzet Kadıoglu uri: https://doi.org/10.7717/peerj.11385 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sin et al. title: Group B Streptococcus and the vaginal microbiome among pregnant women: a systematic review link: https://peerj.com/articles/11437 last-modified: 2021-05-17 description: BackgroundVaginal microbiome studies frequently report diversity metrics and communities of microbiomes associated with reproductive health outcomes. Reports of Streptococcus agalactiae (also known as Group B Streptococcus or GBS), the leading cause of neonatal infectious morbidity and mortality, are notably lacking from the studies of the vaginal microbiome, despite being a known contributor to preterm birth and other complications. Therefore, the purpose of this systematic review was to explore the frequency of GBS reporting in vaginal microbiome literature pertaining to pregnancy and to examine methodological bias that contributes to differences in species and genus-level microbiome reporting. Lack of identification of GBS via sequencing-based approaches due to methodologic or reporting bias may result incomplete understanding of bacterial composition during pregnancy and subsequent birth outcomes.MethodologyA systematic review was conducted following the PRISMA guideline. Three databases (PubMed, CINAHL, and Web of Science) were used to identify papers for review based on the search terms “vaginal microbiome”, “pregnancy”, and “16S rRNA sequencing”. Articles were evaluated for methods of DNA extraction and sequencing, 16S region, taxonomy classification database, number of participants or vaginal specimens, and pregnancy trimester.ResultsForty-five research articles reported employing a metagenomic approach or 16S approach for vaginal microbiome analysis during pregnancy that explicitly reported taxonomic composition and were included in this review. Less than 30% of articles reported the presence of GBS (N = 13). No significant differences in methodology were identified between articles that reported versus did not report GBS. However, there was large variability across research methods used for vaginal microbiome analysis and species-level bacterial community reporting.ConclusionConsiderable differences in study design and data formatting methods may contribute to underrepresentation of GBS, and other known pathogens, in existing vaginal microbiome literature. Previous studies have identified considerable variation in methodology across vaginal microbiome studies. This study adds to this body of work because in addition to laboratory or statistical methods, how results and data are shared (e.g., only analyzing genus level data or 20 most abundant microbes), may hinder reproducibility and limit our understanding of the influence of less abundant microbes. Sharing detailed methods, analysis code, and raw data may improve reproducibility and ability to more accurately compare microbial communities across studies. creator: Sungju Lim creator: Shilpa Rajagopal creator: Ye Ryn Jeong creator: Dumebi Nzegwu creator: Michelle L. Wright uri: https://doi.org/10.7717/peerj.11437 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Lim et al. title: Machine learning in dental, oral and craniofacial imaging: a review of recent progress link: https://peerj.com/articles/11451 last-modified: 2021-05-17 description: Artificial intelligence has been emerging as an increasingly important aspect of our daily lives and is widely applied in medical science. One major application of artificial intelligence in medical science is medical imaging. As a major component of artificial intelligence, many machine learning models are applied in medical diagnosis and treatment with the advancement of technology and medical imaging facilities. The popularity of convolutional neural network in dental, oral and craniofacial imaging is heightening, as it has been continually applied to a broader spectrum of scientific studies. Our manuscript reviews the fundamental principles and rationales behind machine learning, and summarizes its research progress and its recent applications specifically in dental, oral and craniofacial imaging. It also reviews the problems that remain to be resolved and evaluates the prospect of the future development of this field of scientific study. creator: Ruiyang Ren creator: Haozhe Luo creator: Chongying Su creator: Yang Yao creator: Wen Liao uri: https://doi.org/10.7717/peerj.11451 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ren et al. title: The impact of COVID-19 pandemic on the level of depression among health care workers: cross-sectional study link: https://peerj.com/articles/11469 last-modified: 2021-05-17 description: BackgroundThe outbreak of the novel Corona Virus Infectious Disease 2019 (COVID-19) has spread rapidly to many countries leading to thousands of deaths globally. The burden of this pandemic has affected the physical and mental health of the frontline health care workers (HCWs) who are exposed to high risk of infection and psychological stressors.AimsThe aim is to measure the level of depression among healthcare workers in Saudi Arabia during COVID-19 pandemic to establish interventional strategies.MethodA descriptive cross-sectional study was used to conduct the current study. The data of this study was recruited between 15 June and 15 July 2020 from healthcare providers who work in both public and private healthcare sectors in Riyadh and Eastern province in Saudi Arabia utilizing a self-administered questionnaire. The study was approved by the Institutional Review Board at Dr. Sulaiman Al Habib Medical Group (IRB Log No. RC20.06.88-2). Data were collected by using The Zung Self-Rating Depression Scale SDS. A total of 900 healthcare providers working in the healthcare setting during COVID-19 pandemic were invited to participate in the study. A total of 650 healthcare providers participated in the study by completing and submitting the survey.ResultsAlmost 30% suffered from depression which can be divided into three categories; mild depression (26.2%), moderate/major (2.5%) and severe/extreme (0.8%). The finding shows that the level of depression among respondents at the age range of 31–40 years old was significantly higher than the level of depression among respondents with the age above 50 years old. Non-Saudi healthcare workers experienced more depression than Saudi workers. It also shows how nurses suffered from depression compared to their physician colleagues. Those who did not suffer from sleeping disorder perceived more depression as compared to those who are having sleeping disorder.ConclusionIt is recommended that health care facilities should implement strategies to reduce the prevalence of mental health problems among healthcare providers and eventually it will improve their performance in provision of safe and high-quality care for patients. creator: Abbas Al Mutair creator: Alya Al Mutairi creator: Zainab Ambani creator: Abbas Shamsan creator: Sana AlMahmoud creator: Saad Alhumaid uri: https://doi.org/10.7717/peerj.11469 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Al Mutair et al. title: Longer leisure walking time is associated with positive self-rated health among adults and older adults: a Brazilian nationwide study link: https://peerj.com/articles/11471 last-modified: 2021-05-17 description: BackgroundTo verify the association between weekly leisure walking time and positive self-rated health in the Brazilian adult and elderly population.MethodsThis cross-sectional study used information collected in 2019 across all regions of Brazil. This study included 25,785 people aged ≥ 18 years (mean = 51.6; standard deviation = 18.0) from all capitals of the Brazilian states who reported practicing walking as physical activity during leisure time. Self-rated health was the dependent variable (positive or negative). The leisure walking time/week was the main exposure and it was categorized in “150 minutes/week”, “150–299 minutes/week” and “≥ 300 minutes/week”. We used binary logistic regression to estimate odds ratio (OR) and 95% confidence intervals (95% CI) that was adjusted for relevant covariates.ResultsWe found that individuals who reported leisure walking for a period from 150 to 299 minutes/week and those who reported walking for a period ≥ 300 minutes/week were respectively 28% (OR = 1.28. 95% CI [1.10–1.48]) and 52% (OR = 1.52. 95% CI [1.27–1.82]) more likely of perceiving their health positively compared to those who reported walking for a period < 150 minutes/week. Individuals who reported leisure walking time <150 minutes/week had 72.3% (95% CI [70.4–74.1]) probability of perceiving their health positively. Individuals who reported leisure walking time from 150 to 299 minutes/week had 76.6% (95% CI [75.0 –78.3) probability of perceiving their health positively. On the other hand, individuals who reported leisure walking time ≥ 300 minutes/week had 79.2% probability (95% CI [77.1–81.4]) of perceiving their health positively.ConclusionLonger leisure walking time was associated with positive self-rated health among adults and older adults in Brazil. creator: Diego Augusto Santos Silva uri: https://doi.org/10.7717/peerj.11471 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Silva title: Multi-scale analysis of the characteristics of the changing landscape of the typical mountainous region of Southwest China over the past 40 years link: https://peerj.com/articles/10923 last-modified: 2021-05-14 description: ContextYunnan Province is an important ecological security barrier in China. This study investigated the temporal and spatial changes to landscape ecology and is of great significance for guiding landscape protection and future socio-economic development.ObjectivesTo analyze the temporal and spatial changes of the landscape patterns at the county, river basin, and provincial levels, and clarify and describe the temporal and spatial differentiation characteristics of the landscape patterns in Yunnan Province.MethodsBased on landscape ecology, GIS spatial analysis, and spatio-temporal change analysis, nine landscape pattern indices, and spatial autocorrelation for different years, were calculated.ResultsThe landscape of Yunnan Province has evolved as a whole toward isolation. The indices of separation and fragmentation changed significantly from 2010 to 2015. From 2015 to 2018 the rate of fragmentation decreased. Fragmentation in the Nu Jiang and Irrawaddy River basins was less than in other basins. The landscape patterns of the Jinsha and Pearl River basins were relatively fragmented due to human activity, socioeconomic development, and utilization. The differences between the Lancang and Red River Basins were relatively small and at an intermediate level.ConclusionsSpatial autocorrelation analysis indicated that there are three areas with typical clusters, namely the Hengduan Mountains where the degree of fragmentation of the landscape was low, while landscape connectivity and aggregation were high. The subtropical region of Southern Yunnan displayed high landscape heterogeneity, a complex shape index, and high connectivity and sprawl. Central Yunnan exhibited a fragmented landscape with poor connectivity and aggregation. These three regions correspond with “the three screens and two belts” in the Main Functional Planning Area of Yunnan Province. creator: Fang Liu creator: Wanbin Wang creator: Jinliang Wang creator: Xingzi Zhang creator: Jing Ren creator: Yuexiong Liu uri: https://doi.org/10.7717/peerj.10923 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liu et al. title: Consequences of herbal mixture supplementation on milk performance, ruminal fermentation, and bacterial diversity in water buffaloes link: https://peerj.com/articles/11241 last-modified: 2021-05-14 description: This study was aimed to evaluate the potential of a herbal mixture (HM) to improve production performance, rumen fermentation, and milk fatty acid profile in water buffaloes. Sixteen Murrah buffaloes (in four groups) were fed for 10 weeks with the same basal diet supplemented with 0 (control); 20 (HM20), 30 (HM30), and 40 (HM40) g/buffalo per day. The herbal mixture contained an equal quantity of black pepper (fruit), ginger (tubers), cinnamon (bark), peppermint (leaves), ajwain (seeds) and garlic (bulbs). After two weeks of adaptation, daily milk yield, and weekly milk composition were recorded. On the last day of the experiment, rumen contents were collected to determine rumen fermentation parameters and bacterial diversity through 16S rRNA sequencing. Results revealed no effect of treatment on dry matter intake (DMI), rumen fermentation parameters, and daily milk yield. However, milk fat (%) showed a tendency to increase (p = 0.07) in HM20 as compared with the control group. A significant increase in mono and polyunsaturated fatty acids (C14:1, C16:1, C18:2n6 and C18:3) whereas a decrease in saturated fatty acids (C18:0) in milk was observed in HM20 as compared with the control group. No significant change in bacterial diversity parameters (alpha and beta diversity) was observed in response to the treatment. Despite the substantial variation observed in the relative abundance of bacteria among treatment groups, no significant effect of treatment was observed when compared with the control group. Correlation analysis revealed several positive and negative correlations of rumen bacteria with rumen volatile fatty acids (VFA) and milk yield traits. Bacterial genera including Succinivibrionaceae, Butyrivibrio, Pseudobutyrivibrio, and Lachnospiraceae showed a positive correlation with VFA and milk yield traits. Overall, we observed 52 positive and 10 negative correlations of rumen bacteria with milk fatty acid contents. Our study revealed the potential of the herbal mixture at a lower supplemental level (20 g/day) to increase milk fat (%) and unsaturated fatty acid content in buffalo. creator: Faizul Hassan creator: Zhenhua Tang creator: Hossam M. Ebeid creator: Mengwei Li creator: Kaiping Peng creator: Xin Liang creator: Chengjian Yang uri: https://doi.org/10.7717/peerj.11241 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hassan et al. title: The multi metal-resistant bacterium Cupriavidus metallidurans CH34 affects growth and metal mobilization in Arabidopsis thaliana plants exposed to copper link: https://peerj.com/articles/11373 last-modified: 2021-05-14 description: Copper (Cu) is important for plant growth, but high concentrations can lead to detrimental effects such as primary root length inhibition, vegetative tissue chlorosis, and even plant death. The interaction between plant-soil microbiota and roots can potentially affect metal mobility and availability, and, therefore, overall plant metal concentration. Cupriavidus metallidurans CH34 is a multi metal-resistant bacterial model that alters metal mobility and bioavailability through ion pumping, metal complexation, and reduction processes. The interactions between strain CH34 and plants may affect the growth, metal uptake, and translocation of Arabidopsis thaliana plants that are exposed to or not exposed to Cu. In this study, we looked also at the specific gene expression changes in C. metallidurans when co-cultured with Cu-exposed A. thaliana. We found that A. thaliana’s rosette area, primary and secondary root growth, and dry weight were affected by strain CH34, and that beneficial or detrimental effects depended on Cu concentration. An increase in some plant growth parameters was observed at copper concentrations lower than 50 µM and significant detrimental effects were found at concentrations higher than 50 µM Cu. We also observed up to a 90% increase and 60% decrease in metal accumulation and mobilization in inoculated A. thaliana. In turn, copper-stressed A. thaliana altered C. metallidurans colonization, and cop genes that encoded copper resistance in strain CH34 were induced by the combination of A. thaliana and Cu. These results reveal the complexity of the plant-bacteria-metal triad and will contribute to our understanding of their applications in plant growth promotion, protection, and phytoremediation strategies. creator: Claudia Clavero-León creator: Daniela Ruiz creator: Javier Cillero creator: Julieta Orlando creator: Bernardo González uri: https://doi.org/10.7717/peerj.11373 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Clavero-León et al. title: DZNep, an inhibitor of the histone methyltransferase EZH2, suppresses hepatic fibrosis through regulating miR-199a-5p/SOCS7 pathway link: https://peerj.com/articles/11374 last-modified: 2021-05-14 description: BackgroundHepatic fibrosis is a common response to chronic liver injury. Recently, the role of DZNep (a histone methyltransferase EZH2 inhibitor) in repressing pulmonary and renal fibrosis was verified. However, the potential effect of DZNep on hepatic fibrosis has not been elucidated.MethodsThe hepatic fibrosis model was established in rats treated with CCl4 and in hepatic stellate cells (HSCs) treated with TGF-β1. The liver tissues were stained with H&E and Masson’s trichrome. The expression of EZH2, SOCS7, collagen I, αSMA mRNA and miR-199-5p was assessed using qPCR, immunohistochemical or western blot analysis. A dual-luciferase reporter assay was carried out to validate the regulatory relationship of miR-199a-5p with SOCS7.ResultsThe EZH2 level was increased in CCl4-treated rats and in TGF-β1-treated HSCs, whereas DZNep treatment significantly inhibited EZH2 expression. DZNep repressed hepatic fibrosis in vivo and in vitro, as evidenced by the decrease of hepatic fibrosis markers (α-SMA and Collagen I). Moreover, miR-199a-5p expression was repressed by DZNep in TGF-β1-activated HSCs. Notably, downregulation of miR-199a-5p decreased TGF-β1-induced expression of fibrosis markers. SOCS7 was identified as a direct target of miR-199a-5p. The expression of SOCS7 was decreased in TGF-β1-activated HSCs, but DZNep treatment restore d SOCS7 expression. More importantly, SOCS7 knockdown decreased the effect of DZNep on collagen I and α SMA expression in TGF-β1-activated HSCs.ConclusionsDZNep suppresses hepatic fibrosis through regulating miR-199a-5p/SOCS7 axis, suggesting that DZNep may represent a novel treatment for fibrosis. creator: Rongrong Ding creator: Jianming Zheng creator: Ning Li creator: Qi Cheng creator: Mengqi Zhu creator: Yanbing Wang creator: Xinlan Zhou creator: Zhanqing Zhang creator: Guangfeng Shi uri: https://doi.org/10.7717/peerj.11374 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ding et al. title: Oxidative stress induces cell death partially by decreasing both mRNA and protein levels of nicotinamide phosphoribosyltransferase in differentiated PC12 cells link: https://peerj.com/articles/11401 last-modified: 2021-05-14 description: Background.Multiple studies have indicated crucial roles of NAD+ deficiency in several neurological diseases and aging. It is critical to discover the mechanisms underlying the NAD+ deficiency. A decreased level of Nicotinamide phosphoribosyltransferase (Nampt)—an important enzyme in the salvage pathway of NAD+ synthesis—has been found under certain pathological conditions, while the mechanisms underlying the Nampt decrease are unclear. The purpose of this study is to test the hypothesis that oxidative stress can produce decreased Nampt, and to investigate the biological effects of Nampt on NAD+ synthesis and cell survival under both basal and oxidative stress conditions.Methods.We used differentiated PC12 cells as a cellular model to investigate the effects of oxidative stress on the levels of Nampt. Multiple assays, including flow cytometry-based cell death assays and NAD+ assays were conducted.Results.First, oxidative stress can decrease the levels of Nampt mRNA and Nampt protein; second, Nampt plays significant roles in NAD+ synthesis under both basal conditions and oxidative stress conditions; third, Nampt plays critical roles in cell survival under both basal conditions and oxidative stress conditions; and fourth, oxidative stress produced decreased NAD+ levels and cell survival partially by decreasing Nampt. Collectively, our study has indicated that oxidative stress is a pathological factor leading to decreased Nampt, which plays important roles in oxidative stress-produced decreases in NAD+ levels and cell survival. Our findings have indicated major roles of Nampt in maintaining NAD+ levels and cell survival under both basal and oxidative stress conditions. creator: Cuiyan Zhou creator: Weihai Ying uri: https://doi.org/10.7717/peerj.11401 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zhou and Ying title: The relationship between PLOD1 expression level and glioma prognosis investigated using public databases link: https://peerj.com/articles/11422 last-modified: 2021-05-14 description: BackgroundGlioma is the most common type of intracranial tumor with high malignancy and poor prognosis despite the use of various aggressive treatments. Targeted therapy and immunotherapy are not effective and new biomarkers need to be explored. Some Procollagen-lysine 2-oxyglutarate 5-dioxygenase (PLOD) family members have been found to be involved in the metastasis and progression of tumors. Both PLOD2 and PLOD3 had been reported to be highly expressed in gliomas, while the prognostic value of PLOD1 remains to be further illustrated, so we want to investigate the PLOD1 expression in glioma and its clinical implication.MethodsWe collected gene expression and corresponding clinical data of glioma from the Chinese Glioma Genome Atlas (CGGA) database, The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. First, we analyzed the expression and mutation of PLOD1 in gliomas and its relationship with clinicopathologic characteristics. Then, we conducted survival analysis, prognostic analysis and nomogram construction of the PLOD1 gene. Finally, we conducted gene ontology (GO) enrichment analysis and gene set enrichment analysis (GSEA) to explore possible mechanisms and gene co-expression analysis was also be performed.ResultsThe results showed that the expression level of PLOD1 was higher in gliomas than normal tissues, and high expression of PLOD1 was related to poor survival which can serve as an oncogenic factor and an independent prognostic indicator for glioma patients. Both the GO and GSEA analysis showed high expression of PLOD1 were enriched in Extracellular matrix (ECM) related pathways, the co-expression analysis revealed that PLOD1 was positively related to HSPG2, COL6A2, COL4A2, FN1, COL1A1, COL4A1, CD44, COL3A1, COL1A2 and SPP1, and high expression of these genes were also correlated to poor prognosis of glioma.ConclusionsThe results showed that high expression of PLOD1 leads to poor prognosis, and PLOD1 is an independent prognostic factor and a novel biomarker for the treatment of glioma. Furthermore, targeting PLOD1 is most likely a potential therapeutic strategy for glioma patients. creator: Lei Tian creator: Huandi Zhou creator: Guohui Wang creator: Wen yan Wang creator: Yuehong Li creator: Xiaoying Xue uri: https://doi.org/10.7717/peerj.11422 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Tian et al. title: DNA barcoding of Austrian snow scorpionflies (Mecoptera, Boreidae) reveals potential cryptic diversity in Boreus westwoodi link: https://peerj.com/articles/11424 last-modified: 2021-05-14 description: BackgroundSnow scorpionflies (genus Boreus) belong to a family of Mecoptera, Boreidae, that has been vastly neglected by entomological researchers due to their shift in seasonality to the winter months. Their activity during this time is regarded as a strategy for predator avoidance and regular sightings on snow fields suggest that this also facilitates dispersal. However, many aspects about snow scorpionflies, especially systematics, taxonomy, distribution of species, phylogenetics and phylogeography have remained fairly unexplored until today. In this study, we fill some of these gaps by generating a reference DNA barcode database for Austrian snow scorpionflies in the frame of the Austrian Barcode of Life initiative and by characterising morphological diversity in the study region.MethodsInitial species assignment of all 67 specimens was based on male morphological characters previously reported to differ between Boreus species and, for females, the shape of the ovipositor. DNA barcoding of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene was carried out for all 67 samples and served as a basis for BIN assignment, genetic distance calculations, as well as alternative species delimitation analyses (ABGD, GMYC, bGMYC, bPTP) and a statistical parsimony network to infer phylogenetic relationships among individual samples/sampling sites.ResultsMorphological investigations suggested the presence of both Boreus hyemalis and Boreus westwoodi in Austria. DNA barcoding also separated the two species, but resulted in several divergent clades, the paraphyly of B. westwoodi in Austria, and high levels of phylogeographic structure on a small geographic scale. Even though the different molecular species delimitation methods disagreed on the exact number of species, they unequivocally suggested the presence of more than the traditionally recognized two Boreus species in Austria, thus indicating potential cryptic species within the genus Boreus in general and especially in B. westwoodi. creator: Lukas Zangl creator: Elisabeth Glatzhofer creator: Raphael Schmid creator: Susanne Randolf creator: Stephan Koblmüller uri: https://doi.org/10.7717/peerj.11424 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zangl et al. title: Identification of diagnostic genes and vital microRNAs involved in rheumatoid arthritis: based on data mining and experimental verification link: https://peerj.com/articles/11427 last-modified: 2021-05-14 description: BackgroundThe pathogenesis of rheumatoid arthritis (RA) is complex. This study aimed to identify diagnostic biomarkers and transcriptional regulators that underlie RA based on bioinformatics analysis and experimental verification.Material and MethodsWe applied weighted gene co-expression network analysis (WGCNA) to analyze dataset GSE55457 and obtained the key module most relevant to the RA phenotype. We then conducted gene function annotation, gene set enrichment analysis (GSEA) and immunocytes quantitative analysis (CIBERSORT). Moreover, the intersection of differentially expressed genes (DEGs) and genes within the key module were entered into the STRING database to construct an interaction network and to mine hub genes. We predicted microRNA (miRNA) using a web-based tool (miRDB). Finally, hub genes and vital miRNAs were validated with independent GEO datasets, RT-qPCR and Western blot.ResultsA total of 367 DEGs were characterized by differential expression analysis. The WGCNA method divided genes into 14 modules, and we focused on the turquoise module containing 845 genes. Gene function annotation and GSEA suggested that immune response and inflammatory signaling pathways are the molecular mechanisms behind RA. Nine hub genes were screened from the network and seven vital regulators were obtained using miRNA prediction. CIBERSORT analysis identified five cell types enriched in RA samples, which were closely related to the expression of hub genes. Through ROC curve and RT-qPCR validation, we confirmed five genes that were specific for RA, including CCL25, CXCL9, CXCL10, CXCL11, and CXCL13. Moreover, we selected a representative gene (CXCL10) for Western blot validation. Vital miRNAs verification showed that only the differences in has-miR-573 and has-miR-34a were statistically significant.ConclusionOur study reveals diagnostic genes and vital microRNAs highly related to RA, which could help improve our understanding of the molecular mechanisms underlying the disorder and provide theoretical support for the future exploration of innovative therapeutic approaches. creator: Conglin Ren creator: Mingshuang Li creator: Yang Zheng creator: Fengqing Wu creator: Weibin Du creator: Renfu Quan uri: https://doi.org/10.7717/peerj.11427 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ren et al. title: EGFR mutation status yield from bronchoalveolar lavage in patients with primary pulmonary adenocarcinoma compared to a venous blood sample and tissue biopsy link: https://peerj.com/articles/11448 last-modified: 2021-05-14 description: BackgroundIn recent years, there has been a revolution in the genomic profiling and molecular typing of lung cancer. A key oncogene is the epidermal growth factor receptor (EGFR). The gold standard for determining EGFR mutation status is tissue biopsy, where a histological specimen is taken by a bronchoscopic or surgical method (transbronchial biopsy, forceps biopsy, etc.). However, in clinical practice the tissue sample is often insufficient for morphological and molecular analysis. Bronchoalveolar lavage is a validated diagnostic method for pathogenic infections in the lower respiratory tract, yet its diagnostic value for oncogenic mutation testing in lung cancer has not been extensively investigated. This study aims to compare the prevalence of EGFR mutation status in bronchoalveolar lavage and peripheral blood referring to the gold standard - tissue biopsy in patients with primary lung adenocarcinoma.MethodsTwenty-six patients with adenocarcinoma were examined for EGFR mutation from tissue biopsy, peripheral blood sample and bronchoalveolar lavage.ResultsThirteen patients had wild type EGFR and the other 13 had EGFR mutation. EGFR mutation from a peripheral blood sample was identified in 38.5% (5/13) of patients, whereas EGFR mutation obtained from bronchoalveolar lavage (BAL) was identified in 92.3% (12/13). This study demonstrates that a liquid biopsy sample for EGFR status from BAL has a higher sensitivity compared to a venous blood sample. creator: Nikolay Yanev creator: Evgeni Mekov creator: Dinko Valev creator: Georgi Yankov creator: Vladimir Milanov creator: Stoyan Bichev creator: Natalia Gabrovska creator: Dimitar Kostadinov uri: https://doi.org/10.7717/peerj.11448 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yanev et al. title: Seasonal variation of 25-Hydroxyvitamin D and indices of carbohydrate and lipid metabolism in postmenopausal women link: https://peerj.com/articles/11341 last-modified: 2021-05-13 description: BackgroundSome studies indicate vitamin D’s significant contribution to metabolic processess. Therefore, the purpose of this study was to evaluate the level of carbohydrate and lipid metabolism indices in relation to seasonal changes in 25-hydroxyvitamin D (25(OH)D) concentration in postmenopausal women.MethodsSixteen postmenopausal women meeting health criteria and not using vitamin D supplementation were included in the study. Seasonal variation of somatic features and the serum concentration of 25(OH)D, glucose, insulin, parathormon, sclerostin and lipid profile were determined on two terms (autumn-winter).ResultsComparative analysis of the variables between the study terms revealed a marked decrease in the concentration of 25(OH)D (p ≤ 0.0001), insulin (p < 0.05), insulin resistance index (HOMA-IR), (p < 0.05). The significant positive correlations of changes (Δ) between autumn and winter in 25(OH)D with body mass (p < 0.05), and fat mass (p ≤ 0.01), measured in the first study term, in the group of women with normal body mass index (BMI), and negative correlation with fat mass (p < 0.05) in women with a BMI value above the reference values, were found. The relationship analysis showed that in women with normal BMI, the decrease in 25(OH)D concentrations was greater when the body fat percentage was higher, whereas in women with a BMI value above the reference values, the higher the fat percentage, the smaller was the decrease in 25(OH)D concentration.ConclusionsSeasonal changes in 25(OH)D concentration did not significantly affect the concentration of carbohydrate and lipid metabolism indices. The magnitude of decline in 25(OH)D levels depends on the fat mass. We suppose that environmental or lifestyle-related factors, e.g., nutritional behaviours, may have had more influence on metabolic indices than changes in 25(OH)D. creator: Anna Huta-Osiecka creator: Krystian Wochna creator: Zbigniew Kasprzak creator: Alicja Nowak uri: https://doi.org/10.7717/peerj.11341 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Huta-Osiecka et al. title: Exploring the behavioral reactions to a mirror in the nocturnal grey mouse lemur: sex differences in avoidance link: https://peerj.com/articles/11393 last-modified: 2021-05-13 description: Most mirror-image stimulation studies (MIS) have been conducted on social and diurnal animals in order to explore self-recognition, social responses, and personality traits. Small, nocturnal mammals are difficult to study in the wild and are under-represented in experimental behavioral studies. In this pilot study, we explored the behavioral reaction of a small nocturnal solitary forager—the grey mouse lemur (Microcebus murinus)—an emergent animal model in captivity. We assessed whether MIS can be used to detect a repeatable behavioral reaction, whether individuals will present a similar reaction toward a conspecific and the mirror, and whether males and females respond similarly. We tested 12 individuals (six males and six females) twice in three different contexts: with a mirror, with a live conspecific, and with a white board as a neutral control. We detected significant repeatability for the activity component of the behavioral reaction. There was a significant effect of the context and the interaction between presentation context and sex for avoidance during the first session for males but not for females. Males avoided the mirror more than they avoided a live conspecific. This pilot study opens a discussion on the behavioral differences between males and females regarding social interactions and reproduction in the nocturnal solitary species, and suggests that males are more sensitive to context of stimulation than females. creator: Pauline B. Zablocki-Thomas creator: Grégoire Boulinguez-Ambroise creator: Camille Pacou creator: Justine Mézier creator: Anthony Herrel creator: Fabienne Aujard creator: Emmanuelle Pouydebat uri: https://doi.org/10.7717/peerj.11393 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zablocki-Thomas et al. title: Identification of Vitamin D-related gene signature to predict colorectal cancer prognosis link: https://peerj.com/articles/11430 last-modified: 2021-05-13 description: Colorectal cancer (CRC) is one of the most common malignant carcinomas worldwide with poor prognosis, imposing an increasingly heavy burden on patients. Previous experiments and epidemiological studies have shown that vitamin D and vitamin D-related genes play a vital role in CRC. Therefore, we aimed to construct a vitamin D-related gene signature to predict prognosis in CRC. The CRC data from The Cancer Genome Atlas (TCGA) was performed as the training set. A total of 173 vitamin D-related genes in the TCGA CRC dataset were screened, and 17 genes associated with CRC prognosis were identified from them. Then, a vitamin D-related gene signature consisting of those 17 genes was established by univariate and multivariate Cox analyses. Moreover, four external datasets (GSE17536, GSE103479, GSE39582, and GSE17537) were used as testing set to validate the stability of this signature. The high-risk group presented a significantly poorer overall survival than low-risk group in both of training set and testing sets. Besides, the areas under the curve (AUCs) for signature on OS in training set at 1, 3, and 5 years were 0.710, 0.708, 0.710 respectively. The AUCs of the ROC curve in GSE17536 for 1, 3, and 5 years were 0.649, 0.654, and 0.694. These results indicated the vitamin D-related gene signature model could effectively predict the survival status of CRC patients. This vitamin D-related gene signature was also correlated with TNM stage in CRC clinical parameters, and the higher risk score from this model was companied with higher clinical stage. Furthermore, the high accuracy of this prognostic signature was validated and confirmed by nomogram model. In conclusion, we have proposed a novel vitamin D-related gene model to predict the prognosis of CRC, which will help provide new therapeutic targets and act as potential prognostic biomarkers for CRC. creator: Luping Bu creator: Fengxing Huang creator: Mengting Li creator: Yanan Peng creator: Haizhou Wang creator: Meng Zhang creator: Liqun Peng creator: Lan Liu creator: Qiu Zhao uri: https://doi.org/10.7717/peerj.11430 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Bu et al. title: Identification of the biological function of miR-9 in spinal cord ischemia-reperfusion injury in rats link: https://peerj.com/articles/11440 last-modified: 2021-05-13 description: Spinal cord ischemia–reperfusion injury (SCII) is still a serious problem, and the mechanism is not fully elaborated. In the rat SCII model, qRT-PCR was applied to explore the altered expression of miR-9 (miR-9a-5p) after SCII. The biological function of miR-9 and its potential target genes based on bioinformatics analysis and experiment validation in SCII were explored next. Before the surgical procedure of SCII, miR-9 mimic and inhibitor were intrathecally infused. miR-9 mimic improved neurological function. In addition, miR-9 mimic reduced blood-spinal cord barrier (BSCB) disruption, inhibited apoptosis and decreased the expression of IL-6 and IL-1β after SCII. Gene Ontology (GO) analysis demonstrated that the potential target genes of miR-9 were notably enriched in several biological processes, such as “central nervous system development”, “regulation of growth” and “response to cytokine”. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the potential target genes of miR-9 were significantly enriched in several signaling pathways, including “Notch signaling pathway”, “MAPK signaling pathway”, “Focal adhesion” and “Prolactin signaling pathway”. We further found that the protein expression of MAP2K3 and Notch2 were upregulated after SCII while miR-9 mimic reduced the increase of MAP2K3 and Notch2 protein. miR-9 mimic or MAP2K3 inhibitor reduced the release of IL-6 and IL-1β. miR-9 mimic or si-Notch2 reduced the increase of cleaved-caspase3. Moreover, MAP2K3 inhibitor and si-Notch2 reversed the effects of miR-9 inhibitor. In conclusion, overexpression of miR-9 improves neurological outcomes after SCII and might inhibit BSCB disruption, neuroinflammation, and apoptosis through MAP2K3-, or Notch2-mediated signaling pathway in SCII. creator: Fengshou Chen creator: Jie Han creator: Xiaoqian Li creator: Zaili Zhang creator: Dan Wang uri: https://doi.org/10.7717/peerj.11440 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Chen et al. title: Cannabinoids from inflorescences fractions of Trema orientalis (L.) Blume (Cannabaceae) against human pathogenic bacteria link: https://peerj.com/articles/11446 last-modified: 2021-05-13 description: BackgroundCannabinoids; tetrahydrocannabinol (THC), cannabidiol (CBD) and cannabinol (CBN), might show antibacterial activity. Trema orientalis is a species in the Cannabaceae that is closely related to Cannabis through plastome phylogenetic evidence. This species is widely distributed throughout tropical Asia and is used as traditional medicine, particularly for the treatment of infectious diseases. However, no studies on the antibacterial activity of cannabinoid-containing inflorescences extracts are available. Thus, the aim of this study was to determine cannabinoid content and antibacterial activity of inflorescences fractions from T. orientalis native to Thailand.MethodsWe hypothesized that inflorescences from T. orientalis might display cannabinoids similar to Cannabis because of their close taxonomic relationship. We extracted the mature inflorescences and infructescence of T. orientalis in three disparate populations from different Thailand floristic regions. Extractions were subsequently partitioned into hydrophilic and lipophilic fractions using distilled water and chloroform. The lipophilic extracts were further fractionated by the column chromatography with gradient elution and analyzed by gas chromatography-mass spectrometry (GC-MS). Characterized cannabinoids were used in bioassays with multidrug-resistance bacteria.ResultsLipophilic extracts and fractions of inflorescences from all Thailand floristic regions consistently displayed cannabinoids (THC, CBD and CBN) in various quantities. These extracts exhibited inhibitory activity for Staphylococcus aureus, Pseudomonas aeruginosa, and Acinetobacter baumannii strains with minimum inhibitory concentration values varying from 31.25 to 125 µg/mL.ConclusionOur study is the first to report cannabinoid detection in extracts from inflorescences of T. orientalis, a species in the Cannabaceae. These extracts and their fractions containing cannabinoids showed pronounced antibacterial activity. The use of analytic methods also demonstrated reproducible cannabinoid extraction. creator: Tiwtawat Napiroon creator: Keerati Tanruean creator: Pisit Poolprasert creator: Markus Bacher creator: Henrik Balslev creator: Manop Poopath creator: Wichai Santimaleeworagun uri: https://doi.org/10.7717/peerj.11446 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Napiroon et al. title: In silico characterization and homology modeling of cytosolic APX gene predicts novel glycine residue modulating waterlogging stress response in pigeon pea link: https://peerj.com/articles/10888 last-modified: 2021-05-12 description: Ascorbate peroxidase (APX) is a member of the family of heme-containing peroxidases having a similar structure with Cytochrome c peroxidase (CCP) that effectively scavenge cytosolic and chloroplastic hydrogen peroxide (H2O2) under various stresses. In this study, computational characterization and homology analysis of APX protein from waterlogging tolerant (ICPL 84023) and sensitive (ICP 7035) pigeon pea genotypes were carried out resulting in 100% homology with Glycine max in case of former and 99% in later genotypes respectively with 97.39% alignment coverage among each other. The model structure was further refined by various tools like PROCHECK, ProSA, and Verify3D. The planned model of the APX enzyme was then tested to dock with H2O2along with molecular dynamics (MD) simulation analysis. The docked complex of ICPL 84023 showed the best G-score (23.39 kcal/mol) in comparison to ICP 7035 (16.74 kcal/mol) depicting the higher production of APX for scavenging reactive oxygen species (ROS) production making this genotype more tolerant. The important binding residues in the ICPL 84023-H2O2complex (SER1, THR4, GLU23, and GLY13) have shown less fluctuation than the ICP 7035-H2O2 complex (SER1, THR4, and GLU23). Overall, our results showed that amino acid residue glycine in ICPL 84023 APX gene has a high binding affinity with H2O2 which could be a key factor associated with waterlogging stress tolerance in pigeon pea. creator: Anshika Tyagi creator: Sandhya Sharma creator: Harsha Srivastava creator: Nagendra Kumar Singh creator: Kishor Gaikwad uri: https://doi.org/10.7717/peerj.10888 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Tyagi et al. title: Differentially expressed genes, lncRNAs, and competing endogenous RNAs in Kawasaki disease link: https://peerj.com/articles/11169 last-modified: 2021-05-12 description: BackgroundKawasaki disease (KD) is an acute and febrile systemic vasculitis of unknown etiology. This study aimed to identify the competing endogenous RNA (ceRNA) networks of lncRNAs, miRNAs, and genes in KD and explore the molecular mechanisms underlying KD.MethodsGSE68004 and GSE73464 datasets were downloaded from the Gene Expression Omnibus. Differentially expressed lncRNAs (DElncRNAs) and genes (DEGs) in KD were identified using the criteria of p < 0.05 and | log2 (fold change) | ≥ 1. MicroRNAs (miRNAs) related to KD were searched from databases. The lncRNA-miRNA-mRNA networks involving the DElncRNAs and DEGs were constructed.ResultsA total of 769 common upregulated, 406 common downregulated DEGs, and six DElncRNAs were identified in the KD samples. The lncRNA-miRNA-mRNA network consisted of four miRNAs, three lncRNAs (including the upregulated PSORS1C3, LINC00999, and the downregulated SNHG5) and four DEGs (including the downregulated GATA3 and the upregulated SOD2, MAPK14, and PPARG). Validation in the GSE18606 dataset showed that intravenous immunoglobulin treatment significantly alleviated the deregulated profiles of the above RNAs in KD patients. Three ceRNA networks of LINC00999-hsa-miR-6780-SOD2, PSORS1C3-hsa-miR-216a-PPARG/MAPK14, and SNHG5-hsa-miR-132/hsa-miR-92-GATA3 were identified. Four genes were associated with functional categories, such as inflammatory response and vascular endothelial cell.ConclusionsThe ceRNA networks involve genes, such as SOD2, MAPK14, and PPARG, and lncRNAs, including PSORS1C3, LINC00999, and SNHG5, which might play a key role in the pathogenesis and development of KD by regulating inflammation. creator: Changsheng Guo creator: Yuanqing Hua creator: Zuanhao Qian uri: https://doi.org/10.7717/peerj.11169 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Guo et al. title: Effect of extreme temperature changes on phenolic, flavonoid contents and antioxidant activity of tomato seedlings (Solanum lycopersicum L.) link: https://peerj.com/articles/11193 last-modified: 2021-05-12 description: BackgroundClimatic changes are the most important abiotic factor affecting plant growth, crop quality and nutritional value. Plants exposed to thermal stress respond by accumulation of secondary metabolites/molecules (SMs). Tomato (Solanum lycopersicum) is a cosmopolitan crop, eaten by most of the world’s people because it is highly nutritious plant. It is cultivated in more than 16 thousand hectares in Saudi Arabia and thus is influenced by extreme climatic changes.ObjectiveIn the current study, the phytochemical effect of thermal stress was investigated in seedlings of S. lycopersicum. Such information will be very helpful in developing more tolerant tomato cultivars in a climate change scenario.MethodsSeedlings of S. lycopersicum were subjected to heat shock; HS1 and HS2 (45 and 50 °C) and cold shock; CS (4 °C) in comparison to control; Con (25 °C). Phenolic compounds, flavonoids, total phenolic content (TPC), total flavonoid content (TFC) and antioxidant activity were estimated under the four temperature treatments.ResultsUsing 23 standards (17 phenolic and six flavonoids), HPLC resulted in the estimation of 16, 20, 15 and 18 compounds for Con, CS, HS1 and HS2, respectively. Differences in the amounts of total phenolics, and total flavonoids were strongly correlated to thermal stress. CS plants exhibited the highest number of signals and the highest absolute quantities of total phenolics, flavonoids and sum of both. The major peaks of phenolics were (Chlorogenic acid, Resvertol), (Vanillic acid, Benzoic acid, Quinol), (Vanillic acid, Benzoic acid) and (Vanillic acid, Benzoic acid) for Con, CS, HS1 and HS2, respectively. The major peaks of flavonoids were (Quercetin, Myricetin), (Quercetin, Rutin), (Quercetin, Rutin, Catechin) and (Quercetin) for Con, CS, HS1 and HS2, respectively. CS plants contain the highest amounts of Benzoic acid (8010.37 mg/kg FW) and Quercetin (2319.48 mg/kg FW). The highest TPC (131 mg GAE/100 g FW) and TFC (61 mg QE/100 g FW) were determined in the case of CS plants. In terms of IC50s, the CS plants showed the highest antioxidant activities (lowest values) in both of DPPH (467.73 µM TE/100 g FW) and ABTS (8.97 µM TE/100 g FW) assays.ConclusionsOur findings supported that the complexity and quantity of phenolics and flavonoids in tomato’s extract are strongly related to thermal stress. Additionally, the CS plants demonstrated more desirable phytochemical profile over the other treatments. CS plants exhibited higher number, absolute amounts of SMs, higher TPC and TFC than those of Con, HS1 and HS2 plants. Additionally, CS plants showed higher antioxidant activity than that of both HS1 and HS2 plants. Such results are very useful in justifying mechanism of tolerance in tomato plant to thermal stress in the context of climate change. Additional research has turned on to reveal molecular response of tomato to such thermal stress. creator: Haifa A.S. Alhaithloul creator: Fatma H. Galal creator: AlaaEddeen M. Seufi uri: https://doi.org/10.7717/peerj.11193 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Alhaithloul et al. title: Response of Escherichia coli minimal ter operon to UVC and auto-aggregation: pilot study link: https://peerj.com/articles/11197 last-modified: 2021-05-12 description: AimThe study of minimal ter operon as a determinant of tellurium resistance (TeR) is important for the purpose of confirming the relationship of these genes to the pathogenicity of microorganisms. The ter operon is widespread among bacterial species and pathogens, implicated also in phage inhibition, oxidative stress and colicin resistance. So far, there is no experimental evidence for the role of the Escherichia coli (E. coli) minimal ter operon in ultraviolet C (UVC) resistance, biofilm formation and auto-aggregation. To identify connection with UVC resistance of the minimal ter operon, matched pairs of Ter-positive and -negative E. coli cells were stressed and differences in survival and whole genome sequence analysis were performed. This study was aimed also to identify differences in phenotype of cells induced by environmental stress.MethodsIn the current study, a minimal ter operon(terBCDEΔF) originating from the uropathogenic strain E. coli KL53 was used. Clonogenic assay was the method of choice to determine cell reproductive death after treatment with UVC irradiation at certain time intervals. Bacterial suspensions were irradiated with 254 nm UVC-light (germicidal lamp in biological safety cabinet) in vitro. UVC irradiance output was 2.5 mW/cm2 (calculated at the UVC device aperture) and plate-lamp distance of 60 cm. DNA damage analysis was performed using shotgun sequencing on Illumina MiSeq platform. Biofilm formation was measured by a crystal violet retention assay. Auto-aggregation assay was performed according to the Ghane, Babaeekhou & Ketabi (2020).ResultsA large fraction of Ter-positive E. coli cells survived treatment with 120-s UVC light (300 mJ/cm2) compared to matched Ter-negative cells; ∼5-fold higher resistance of Ter-positive cells to UVC dose (p = 0.0007). Moreover, UVC surviving Ter-positive cells showed smaller mutation rate as Ter-negative cells. The study demonstrated that a 1200-s exposure to UVC (3,000 mJ/cm2) was sufficient for 100% inhibition of growth for all the Ter-positive and -negative E. coli cells. The Ter-positive strain exhibited of 26% higher auto-aggregation activities and was able to inhibit biofilm formation over than Ter- negative strain (**** P < 0.0001).ConclusionOur study shows that Ter-positive cells display lower sensitivity to UVC radiation, corresponding to a presence in minimal ter operon. In addition, our study suggests that also auto-aggregation ability is related to minimal ter operon. The role of the minimal ter operon (terBCDEΔF) in resistance behavior of E. coli under environmental stress is evident. creator: Lenka Jánošíková creator: Lenka Pálková creator: Dušan Šalát creator: Andrej Klepanec creator: Katarina Soltys uri: https://doi.org/10.7717/peerj.11197 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Jánošíková et al. title: Brain-derived neurotrophic factor increases cell number of neural progenitor cells derived from human induced pluripotent stem cells link: https://peerj.com/articles/11388 last-modified: 2021-05-12 description: BackgroundSeveral pieces of evidence from in vitro studies showed that brain-derived neurotrophic factor (BDNF) promotes proliferation and differentiation of neural stem/progenitor cells (NSCs) into neurons. Moreover, the JAK2 pathway was proposed to be associated with mouse NSC proliferation. BDNF could activate the STAT-3 pathway and induce proliferation in mouse NSCs. However, its effects on proliferation are not fully understood and JAK/STAT pathway was proposed to play a role in this activity.MethodsIn the present study, the effects of BDNF on cell proliferation and neurite outgrowth of Alzheimer’s disease (AD) induced pluripotent stem cells (iPSCs)-derived human neural progenitor cells (hNPCs) were examined. Moreover, a specific signal transduction pathway important in cell proliferation was investigated using a JAK2 inhibitor (AG490) to clarify the role of that pathway.ResultsThe proliferative effect of BDNF was remarkably observed as an increase in Ki-67 positive cells. The cell number of hNPCs was significantly increased after BDNF treatment represented by cellular metabolic activity of the cells measured by MTT assay. This noticeable effect was statistically shown at 20 ng/ml of BDNF treatment. BDNF, however, did not promote neurite outgrowth but increased neuronal cell number. It was found that AG490 suppressed hNPCs proliferation. However, this inhibitor partially decreased BDNF-induced hNPCs proliferation. These results demonstrated the potential role of BDNF for the amelioration of AD through the increase of AD-derived hNPCs number. creator: Panetha Pansri creator: Phetcharat Phanthong creator: Nopparat Suthprasertporn creator: Yindee Kitiyanant creator: Alisa Tubsuwan creator: Andras Dinnyes creator: Julianna Kobolak creator: Narisorn Kitiyanant uri: https://doi.org/10.7717/peerj.11388 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2021 Pansri et al. title: Genome-wide identification of the Tubby-Like Protein (TLPs) family in medicinal model plant Salvia miltiorrhiza link: https://peerj.com/articles/11403 last-modified: 2021-05-12 description: Tubby-Like Proteins (TLPs) are important transcription factors with many functions and are found in both animals and plants. In plants, TLPs are thought to be involved in the abiotic stress response. To reveal the potential function of TLPs in the medicinal model plant Salvia miltiorrhiza, we identified 12 S. miltiorrhiza TLPs (SmTLPs) and conducted a comprehensive analysis. We examined SmTLP gene structure, protein structure, phylogenetics, and expression analysis. Our results show that all SmTLPs, except SmTLP11, have a complete typical Tub domain. Promoter analysis revealed that most SmTLPs are involved in hormone and abiotic stress responses. Expression analysis revealed that the 12 SmTLPs could be divided into three categories: those specifically expressed in roots, those specifically expressed in stems, and those specifically expressed in leaves. Additional studies have shown that SmTLP10 may play an important role in the plant cold resistance, while SmTLP12 may be involved in the S. miltiorrhiza ABA metabolic pathway. Our study represents the first comprehensive investigation of TLPs in S. miltiorrhiza. These data may provide useful clues for future studies and may support the hypotheses regarding the role of TLPs in plant abiotic stress process. All in all, we may provide a reference for improving S. miltiorrhiza quality using genetic engineering technology. creator: Kai Wang creator: Yating Cheng creator: Li Yi creator: Hailang He creator: Shaofeng Zhan creator: Peng Yang uri: https://doi.org/10.7717/peerj.11403 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Comparative transcriptome profiling of a resistant vs susceptible bread wheat (Triticum aestivum L.) cultivar in response to water deficit and cold stress link: https://peerj.com/articles/11428 last-modified: 2021-05-12 description: Bread wheat (Triticum aestivum L.) is one of the most important agricultural plants wearing abiotic stresses, such as water deficit and cold, that cause its productivity reduction. Since resistance to abiotic factors is a multigenic trait, therefore modern genome-wide approaches can help to involve various genetic material in breeding. One technique is full transcriptome analysis that reveals groups of stress response genes serving marker-assisted selection markers. Comparing transcriptome profiles of the same genetic material under several stresses is essential and makes the whole picture. Here, we addressed this by studying the transcriptomic response to water deficit and cold stress for two evolutionarily distant bread wheat varieties: stress-resistant cv. Saratovskaya 29 (S29) and stress-sensitive cv. Yanetzkis Probat (YP). For the first time, transcriptomes for these cultivars grown under abiotic stress conditions were obtained using Illumina based MACE technology. We identified groups of genes involved in response to cold and water deficiency stresses, including responses to each stress factor and both factors simultaneously that may be candidates for resistance genes. We discovered a core group of genes that have a similar pattern of stress-induced expression changes. The particular expression pattern was revealed not only for the studied varieties but also for the published transcriptomic data on cv. Jing 411 and cv. Fielder. Comparative transcriptome profiling of cv. S29 and cv. YP in response to water deficit and cold stress confirmed the hypothesis that stress-induced expression change is unequal within a homeologous gene group. As a rule, at least one changed significantly while the others had a relatively lower expression. Also, we found several SNPs distributed throughout the genomes of cv. S29 and cv. YP and distinguished the studied varieties from each other and the reference cv. Chinese Spring. Our results provide new data for genomics-assisted breeding of stress-tolerant wheat cultivars. creator: Dmitrii K. Konstantinov creator: Ulyana S. Zubairova creator: Anton A. Ermakov creator: Alexey V. Doroshkov uri: https://doi.org/10.7717/peerj.11428 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Konstantinov et al. title: Psychometric properties of the Swedish version of the satisfaction with life scale in a sample of individuals with mental illness link: https://peerj.com/articles/11432 last-modified: 2021-05-12 description: BackgroundHealth assessment among individuals with mental health problems often involves measures of ill-being (e.g., anxiety, depression). Health is, however, defined as a state of physical, mental and social well-being and not merely the absence of disease (WHO, 1948, 2001). Hence, in order to address mental illness during the 21st century, we need to develop methods for the prevention, identification and treatment of mental illness; but also, for the promotion, identification, and maintenance of well-being. In this context, over three decades of subjective well-being research have resulted in the development of measures of positive aspects of human life, such as the Satisfaction with Life Scale (Diener et al., 1985). Our aim was to investigate the psychometric properties of the Satisfaction with Life Scale in a Swedish population of individuals with mental illness using both Classical Test Theory (CTT) and Item Response Theory (IRT).MethodA total of 264 participants (age mean = 43.46, SD = 13.31) diagnosed with different types of mental illness answered to the Swedish version of the Satisfaction with Life Scale (five items, 7-point scale: 1 = strongly disagree, 7 = strongly agree).ResultsWe found positive and significant relationships between the five items of the scale (r ranging from 0.37 to 0.75), good reliability (Cronbach’s alpha = 0.86), and that the one-factor solution had best goodness of fit (loadings between 0.52–0.88, p < 0.001). Additionally, there were no significant differences in comparative fit indexes regarding gender and occupation status. All items had high discrimination values (between 1.95–3.81), but item 5 (“If I could live my life over, I would change almost nothing”); which had a moderate discrimination value (1.17) and the highest estimated difficulty on response 7 (3.06). Moreover, item 2 (“The conditions of my life are excellent”) had less discrimination and redundant difficulty with both item 1 (“In most ways my life is close to my ideal”; 2.03) on response 7 and with item 3 (“I am satisfied with my life”; –1.21) on response 1. The five items together provided good information, with especial good reliability and small standard error within −1.00 up to about 2.00 and the highest amount of test information at 0.00 of the level of life satisfaction within this population.ConclusionsConsistent with previous research, the scale had good reliability and provided good information across most of the latent trait range. In addition, within this population, sociodemographic factors such as gender and occupation status do not influence how individuals respond to the items in the scale. However, the items couldn’t measure extreme levels of low/high life satisfaction. We suggest replication of these findings, the test of additional items, and the modification of items 2 and 5 in order to use the scale among individuals with mental illness. creator: Danilo Garcia creator: Ali Al Nima creator: Maryam Kazemitabar creator: Clara Amato creator: Franco Lucchese creator: Marko Mihailovic creator: Nobuhiko Kijima uri: https://doi.org/10.7717/peerj.11432 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Garcia et al. title: Analysis of multi-omics differences in left-side and right-side colon cancer link: https://peerj.com/articles/11433 last-modified: 2021-05-12 description: BackgroundColon cancer is one of the most common tumors in the digestive tract. Studies of left-side colon cancer (LCC) and right-side colon cancer (RCC) show that these two subtypes have different prognoses, outcomes, and clinical responses to chemotherapy. Therefore, a better understanding of the importance of the clinical classifications of the anatomic subtypes of colon cancer is needed.MethodsWe collected colon cancer patients’ transcriptome data, clinical information, and somatic mutation data from the Cancer Genome Atlas (TCGA) database portal. The transcriptome data were taken from 390 colon cancer patients (172 LCC samples and 218 RCC samples); the somatic mutation data included 142 LCC samples and 187 RCC samples. We compared the expression and prognostic differences of LCC and RCC by conducting a multi-omics analysis of each using the clinical characteristics, immune microenvironment, transcriptomic differences, and mutation differences. The prognostic signatures was validated using the internal testing set, complete set, and external testing set (GSE39582). We also verified the independent prognostic value of the signature.ResultsThe results of our clinical characteristic analysis showed that RCC had a significantly worse prognosis than LCC. The analysis of the immune microenvironment showed that immune infiltration was more common in RCC than LCC. The results of differential gene analysis showed that there were 360 differentially expressed genes, with 142 upregulated genes in LCC and 218 upregulated genes in RCC. The mutation frequency of RCC was generally higher than that of LCC. BRAF and KRAS gene mutations were the dominant genes mutations in RCC, and they had a strong mutual exclusion with APC, while APC gene mutation was the dominant gene mutation in LCC. This suggests that the molecular mechanisms of RCC and LCC differed. The 4-mRNA and 6-mRNA in the prognostic signatures of LCC and RCC, respectively, were highly predictive and may be used as independent prognostic factors.ConclusionThe clinical classification of the anatomic subtypes of colon cancer is of great significance for early diagnosis and prognostic risk assessment. Our study provides directions for individualized treatment of left and right colon cancer. creator: Yanyi Huang creator: Jinzhong Duanmu creator: Yushu Liu creator: Mengyun Yan creator: Taiyuan Li creator: Qunguang Jiang uri: https://doi.org/10.7717/peerj.11433 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Huang et al. title: O-GlcNAcylation is a key regulator of multiple cellular metabolic pathways link: https://peerj.com/articles/11443 last-modified: 2021-05-12 description: O-GlcNAcylation modifies proteins in serine or threonine residues in the nucleus, cytoplasm, and mitochondria. It regulates a variety of cellular biological processes and abnormal O-GlcNAcylation is associated with diabetes, cancer, cardiovascular disease, and neurodegenerative diseases. Recent evidence has suggested that O-GlcNAcylation acts as a nutrient sensor and signal integrator to regulate metabolic signaling, and that dysregulation of its metabolism may be an important indicator of pathogenesis in disease. Here, we review the literature focusing on O-GlcNAcylation regulation in major metabolic processes, such as glucose metabolism, mitochondrial oxidation, lipid metabolism, and amino acid metabolism. We discuss its role in physiological processes, such as cellular nutrient sensing and homeostasis maintenance. O-GlcNAcylation acts as a key regulator in multiple metabolic processes and pathways. Our review will provide a better understanding of how O-GlcNAcylation coordinates metabolism and integrates molecular networks. creator: Hongshuo Zhang creator: Zhen Li creator: Yufei Wang creator: Ying Kong uri: https://doi.org/10.7717/peerj.11443 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zhang et al. title: First days at sea: depicting migration patterns of juvenile seabirds in highly impacted seascapes link: https://peerj.com/articles/11054 last-modified: 2021-05-11 description: Increasing human activities have detrimental consequences on marine ecosystems and their impact can have cumulative effects. Within marine ecosystems, seabirds respond to ecosystem variability and face multiple human pressures, especially threatened species. In long-lived species, juveniles and immatures could represent up to 50% of the total population, but their migratory movements remain largely unknown. Here, we depict the migratory patterns of juvenile Balearic shearwaters Puffinus mauretanicus, the most threatened European seabird, using miniaturised satellite transmitters. At the end of the 2012 breeding season, five tagged juveniles left the breeding colonies of Eivissa Island (western Mediterranean) the first week of July. They moved westwards to reach the Atlantic Ocean between 3 and 13 days afterwards. Juveniles showed a two-phase migratory pattern: they first travelled slower close to the breeding colonies, and then moved towards their wintering areas in the Atlantic Ocean by rapid directional movements. Environmental cues (e.g.,marine productivity, water mass distribution, frontal systems) might have a prominent role in driving the migratory patterns of juvenile Balearic shearwaters, moving from warm and poor marine areas in the Mediterranean Sea to cooler and rich non-breeding grounds in the Atlantic Ocean. Based on observational findings, we observed certain spatial overlap of juvenile Balearic shearwaters with areas of high human impact, but the relationship between flying travel speed and both fishing effort and cumulative human impacts were not statistically significant. These results suggest that more research is needed to assess whether the movement patterns of migrating juveniles are affected by human activities. Therefore, understanding the at-sea spatial ecology of juveniles should be a priority for research and conservation due to the importance of this population component in long-lived species, as well as assessing their vulnerability to multiple anthropogenic pressures. creator: Maite Louzao creator: Karine Delord creator: David García creator: Isabel Afán creator: José Manuel Arcos creator: Henri Weimerskirch uri: https://doi.org/10.7717/peerj.11054 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Louzao et al. title: Variation in the sacroiliac joint in Felidae link: https://peerj.com/articles/11116 last-modified: 2021-05-11 description: Felidae species show a great diversity in their diet, foraging and hunting strategies, from small to large prey. Whether they belong to solitary or group hunters, the behavior of cats to subdue resisting small or large prey presents crucial differences. It is assumed that pack hunting reduces the per capita risk of each individual. We hypothesize that the sacroiliac articulation plays a key role in stabilizing the predator while subduing and killing prey. Using CT-scan from 59 felid coxal bones, we calculated the angle between both iliac articular surfaces. Correlation of this inter-iliac angle with body size was calculated and ecological stressors were evaluated on inter-iliac angle. Body size significantly influences inter-iliac angle with small cats having a wider angle than big cats. Arboreal species have a significantly larger angle compared to cursorial felids with the smallest value, and to scansorial and terrestrial species with intermediate angles. Felids hunting large prey have a smaller angle than felids hunting small and mixed prey. Within the Panthera lineage, pack hunters (lions) have a larger angle than all other species using solitary hunting strategy. According to the inter-iliac angle, two main groups of felids are determined: (i) predators with an angle of around 40° include small cats (i.e., Felis silvestris, Leopardus wiedii, Leptailurus serval, Lynx Canadensis, L. rufus; median = 43.45°), the only pack-hunting species (i.e., Panthera leo; median = 37.90°), and arboreal cats (i.e., L. wiedii, Neofelis nebulosa; median = 49.05°), (ii) predators with an angle of around 30° include solitary-hunting big cats (i.e., Acinonyx jubatus, P. onca, P. pardus, P. tigris, P. uncia; median = 31.80°). We suggest different pressures of selection to interpret these results. The tightening of the iliac wings around the sacrum probably enhances big cats’ ability for high speed and large prey control. In contrast, pack hunting in lions reduced the selective pressure for large prey. creator: Jean-Pierre Pallandre creator: Franck Lavenne creator: Eric Pellé creator: Grégory Breton creator: Mélina Ribaud creator: Vincent Bels uri: https://doi.org/10.7717/peerj.11116 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Pallandre et al. title: Different visual manipulations have similar effects on quasi-static and dynamic balance responses of young and older people link: https://peerj.com/articles/11221 last-modified: 2021-05-11 description: BackgroundStudies demonstrated that the older adults can be more susceptible to balance instability after acute visual manipulation. There are different manipulation approaches used to investigate the importance of visual inputs on balance, e.g., eyes closed and blackout glasses. However, there is evidence that eyes open versus eyes closed results in a different organization of human brain functional networks. It is, however, unclear how different visual manipulations affect balance, and whether such effects differ between young and elderly persons. Therefore, this study aimed to determine whether different visual manipulation approaches affect quasi-static and dynamic balance responses differently, and to investigate whether balance responses of young and older adults are affected differently by these various visual conditions.MethodsThirty-six healthy participants (20 young and 16 older adults) performed balance tests (quasi-static and unexpected perturbations) under four visual conditions: Eyes Open, Eyes Closed, Blackout Glasses, and Dark Room. Center of pressure (CoP) and muscle activation (EMG) were quantified.ResultsAs expected, visual deprivation resulted in larger CoP excursions and higher muscle activations during balance tests for all participants. Surprisingly, the visual manipulation approach did not influence balance control in either group. Furthermore, quasi-static and dynamic balance control did not differ between young or older adults. The visual system plays an important role in balance control, however, similarly for both young and older adults. Different visual deprivation approaches did not influence balance results, meaning our results are comparable between participants of different ages. Further studies should investigate whether a critical illumination level may elicit different postural responses between young and older adults. creator: Daniel Schmidt creator: Felipe P. Carpes creator: Thomas L. Milani creator: Andresa M.C. Germano uri: https://doi.org/10.7717/peerj.11221 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Schmidt et al. title: Experimental indications of gardeners’ anecdotes that snails interfere with invasive slugs link: https://peerj.com/articles/11309 last-modified: 2021-05-11 description: The invasive Spanish slug (Arion vulgaris) is an important pest species in agriculture and horticulture in Europe. In the last decades it has spread across the continent where it outcompetes native slug and snail species, thus posing a threat for biodiversity. A popular anecdote suggests to promote Roman snails (Helix pomatia) in gardens because they are able to control A. vulgaris. We examined a potential interrelationship between these two species using a mesocosm experiment with lettuce plants. 13C-15N stable isotope labelling of lettuce allowed us to investigate interactions between Helix and Arion on weight gain/loss and herbivory. Additionally, we wanted to know whether different watering regimes (daily vs. every 3rd day watering of weekly amount) and earthworms alter these interactions. Egg predation of Helix on Arion eggs was further tested in a food-choice experiment. Arion showed a five times higher herbivory per body mass than Helix in a single-species setting. However, in mesocosms containing both species percentage of herbivory per body mass was significantly lower than in Arion-only mesocosms, especially when watered every three days. Overall isotope uptake via eaten lettuce was unaffected by the presence of the other species. Only very little predation (three out of 200 eggs) of Helix on Arion eggs was observed. Our results provide no evidence for a clear dismissal or confirmation of the popular gardener’s anecdote that Helix snails have a negative effect on Arion abundance or herbivory. creator: Daniel Dörler creator: Verena Dorn creator: Theresia Widhalm creator: Micha Horacek creator: Florian Heigl creator: Pia Euteneuer creator: Friedrich Leisch creator: Thomas Frank creator: Johann G. Zaller uri: https://doi.org/10.7717/peerj.11309 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Dörler et al. title: Limb myology and muscle architecture of the Indian rhinoceros Rhinoceros unicornis and the white rhinoceros Ceratotherium simum (Mammalia: Rhinocerotidae) link: https://peerj.com/articles/11314 last-modified: 2021-05-11 description: Land mammals support and move their body using their musculoskeletal system. Their musculature usually presents varying adaptations with body mass or mode of locomotion. Rhinocerotidae is an interesting clade in this regard, as they are heavy animals potentially reaching three tons but are still capable of adopting a galloping gait. However, their musculature has been poorly studied. Here we report the dissection of both forelimb and hindlimb of one neonate and one adult each for two species of rhinoceroses, the Indian rhinoceros (Rhinoceros unicornis) and the white rhinoceros (Ceratotherium simum). We show that their muscular organisation is similar to that of their relatives, equids and tapirs, and that few evolutionary convergences with other heavy mammals (e.g. elephants and hippopotamuses) are present. Nevertheless, they show clear adaptations to their large body mass, such as more distal insertions for the protractor and adductor muscles of the limbs, giving them longer lever arms. The quantitative architecture of rhino muscles is again reminiscent of that of horses and tapirs, although contrary to horses, the forelimb is much stronger than the hindlimb, which is likely due to its great role in body mass support. Muscles involved mainly in counteracting gravity (e.g. serratus ventralis thoracis, infraspinatus, gastrocnemius, flexores digitorum) are usually highly pennate with short fascicles facilitating strong joint extension. Muscles involved in propulsion (e.g. gluteal muscles, gluteobiceps, quadriceps femoris) seem to represent a compromise between a high maximal isometric force and long fascicles, allowing a reasonably fast and wide working range. Neonates present higher normalized maximal isometric force than the adults for almost every muscle, except sometimes for the extensor and propulsor muscles, which presumably acquire their great force-generating capacity during the growth of the animal. Our study clarifies the way the muscles of animals of cursorial ancestry can adapt to support a greater body mass and calls for further investigations in other clades of large body mass. creator: Cyril Etienne creator: Alexandra Houssaye creator: John R. Hutchinson uri: https://doi.org/10.7717/peerj.11314 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Etienne et al. title: Identification of robust diagnostic and prognostic gene signatures in different grades of gliomas: a retrospective study link: https://peerj.com/articles/11350 last-modified: 2021-05-11 description: BackgroundGliomas are the most common primary tumors of the central nervous system. The complexity and heterogeneity of the tumor makes it difficult to obtain good biomarkers for drug development. In this study, through The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA), we analyze the common diagnostic and prognostic moleculer markers in Caucasian and Asian populations, which can be used as drug targets in the future.MethodsThe RNA-seq data from Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) were analyzed to identify signatures. Based on the signatures, the prognosis index (PI) of every patient was constructed to predict the prognostic risk. Also, gene ontology (GO) functional enrichment analysis and KEGG analysis were conducted to investigate the biological functions of these mRNAs. Glioma patients’ data in the CGGA database were introduced to validate the effectiveness of the signatures among Chinese populations. Excluding the previously reported prognostic markers of gliomas from this study, the expression of HSPA5 and MTPN were examined by qRT-PCR and immunohistochemical assay.ResultsIn total, 20 mRNAs were finally selected to build PI for patients from TCGA, including 16 high-risk genes and four low-risk genes. For Chinese patients, the log-rank test p values of PI were both less than 0.0001 in two independent datasets. And the AUCs were 0.831 and 0.907 for 3 years of two datasets, respectively. Moreover, among these 20 mRNAs, 10 and 15 mRNAs also had a significant predictive effect via univariate COX analysis in CGGA_693 and CGGA_325, respectively. qRT-PCR and Immunohistochemistry assay indicated that HSPA5 and MTPN over-expressed in Glioma samples compared to normal samples.ConclusionThe 20-gene signature can forecast the risk of Glioma in TCGA effectively, moreover it can also predict the risks of Chinese patients through validation in the CGGA database. HSPA5 and MTPN are possible biomarkers of gliomas suitable for all populations to improve the prognosis of these patients. creator: Jieting Liu creator: Hongrui Zhang creator: Jingyun Zhang creator: Zhitong Bing creator: Yingbin Wang creator: Qiao Li creator: Kehu Yang uri: https://doi.org/10.7717/peerj.11350 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liu et al. title: Artificial light source selection in seaweed production: growth of seaweed and biosynthesis of photosynthetic pigments and soluble protein link: https://peerj.com/articles/11351 last-modified: 2021-05-11 description: Seaweed growth is often limited by light. Artificial light supply has been well studied in terrestrial agriculture, however, much less is known about its effect in seaweed aquaculture. In this study, the effects of four artificial light sources (white, red, green, and blue LEDs light) on a brown alga Sargassum fusiforme and a green alga Ulva pertusa were investigated. Seaweed growth, accumulation of photosynthetic pigments (chlorophyll a and carotenoid), and soluble protein were evaluated. White LED light was the optimal supplementary light when cultivating Ulva pertusa and Sargassum fusiforme, because it promoted seaweed growth while maintaining protein production. Meanwhile, red LED was unfavored in the cultivation of S. fusiforme, as it affected the seaweed growth and has a lower residual energy ratio underneath the water. LEDs would be a promising supplementary light source for seaweed cultivation. creator: Shitao Huang creator: Ke Li creator: Yaoru Pan creator: Yan Yu creator: Thomas Wernberg creator: Thibaut de Bettignies creator: Jiaping Wu creator: Chaosheng Zhou creator: Zhixing Huang creator: Xi Xiao uri: https://doi.org/10.7717/peerj.11351 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Huang et al. title: Durnonovariaodus maiseyi gen. et sp. nov., a new hybodontiform shark-like chondrichthyan from the Upper Jurassic Kimmeridge Clay Formation of England link: https://peerj.com/articles/11362 last-modified: 2021-05-11 description: A partial skeleton of a hybodontiform shark-like chondrichthyan from the Upper Jurassic Kimmeridge Clay Formation of Dorset, England, is described and designated as a new genus and species, Durnonovariaodus maiseyi gen. et sp. nov. The holotype and only known specimen, which is represented by disarticulated splanchnocranial elements with associated teeth, a single dorsal fin spine, the pelvic girdle, as well as unidentifiable cartilage fragments, plus countless dermal denticles, exhibits a puzzling combination of dental and skeletal features, providing important new insights into the morphological and ecological diversity of hybodontiforms. Durnonovariaodus gen. nov. displays a unique set of dental characters, showing close morphological resemblance to Secarodus from the Middle Jurassic of England, which was erected for distinctive, strongly labio-lingually compressed multicuspid cutting teeth originally described as Hybodus polyprion. Skeletally, Durnonovariaodus gen. nov. resembles Hybodus and Egertonodus in having a palatoquadrate with a palatobasal process and an ethmoidal articular surface, combined with the possession of dorsal fin spines ornamented with costae. Therefore, and given the absence of any conclusive phylogenetic framework, Durnonovariaodus maiseyi gen. et sp. nov. is here tentatively referred to Hybodontidae until more complete material becomes available in order to enable a more reliable suprageneric identification. The holotype of Durnonovariaodus maiseyi gen. et sp. nov. contains two separate pelvic half-girdles, a feature previously considered as evolutionarily primitive among hybodontiforms. However, unfused pelvic half-girdles also occur in the supposedly closely related species Hybodus hauffianus and may in fact have been more widely distributed among hybodontiforms than previously thought, thus rendering the phylogenetic utility of separated pelvic half-girdles for inferring hybodontiform interrelationships difficult and unresolved. creator: Sebastian Stumpf creator: Steve Etches creator: Charlie J. Underwood creator: Jürgen Kriwet uri: https://doi.org/10.7717/peerj.11362 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Stumpf et al. title: Morphological variability and genetic diversity in Carex buxbaumii and Carex hartmaniorum (Cyperaceae) populations link: https://peerj.com/articles/11372 last-modified: 2021-05-11 description: BackgroundCarex buxbaumii and C. hartmaniorum are sister species of the clade Papilliferae within the monophyletic section Racemosae. An unambiguous identification of these species is relatively difficult due to the interspecific continuum of some morphological characters as well as the intraspecific variability. The study was aimed at determining the range of variability, both morphological and genetic, within and between these two closely related and similar species.MethodsThe sedges were collected during botanical expeditions to Armenia, Estonia, the Netherlands, and Poland. The morphological separation of the two species and their populations was tested using the Discriminant Function Analysis (DFA). The genetic variability of the 19 Carex populations was assessed in the presence of eight Inter Simple Sequence Repeat (ISSR) primers.ResultsResults of the study indicate a considerable genetic affinity between the two sedge species (mean Si = 0.619). However, the populations of C. hartmaniorum are, morphologically and genetically, more homogenous than the populations of C. buxbaumii. Compared to C. hartmaniorum, C. buxbaumii usually has wider leaf blades, a shorter inflorescence, a lower number of spikes which are shorter, but wider, and longer bracts and utricles. The AMOVA showed a larger variation between the populations of C. buxbaumii, representing 25.65% of the total variation in the taxon. Two populations of C. buxbaumii (from Poland and Estonia) are separated from the remaining populations, both genetically and morphologically; their individuals show shorter utricles and glumes, compared to the typical specimens of C. buxbaumii, and correspond with the morphology of putative infraspecific taxa described by Cajander (var. brevisquamosa and var. confusa).ConclusionsThe taxonomic status of the putative infraspecific taxa within C. buxbaumii requires further studies throughout the distribution range of C. buxbaumii, addressing habitats, morphology and genetics (including a chromosome count or a combination of different genetic methods), particularly as the variability in C. buxbaumii may be associated with the species’ polyploid origin. creator: Helena Więcław creator: Magdalena Szenejko creator: Thea Kull creator: Zofia Sotek creator: Ewa Rębacz-Maron creator: Jacob Koopman uri: https://doi.org/10.7717/peerj.11372 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Więcław et al. title: Prokaryotic communities from a lava tube cave in La Palma Island (Spain) are involved in the biogeochemical cycle of major elements link: https://peerj.com/articles/11386 last-modified: 2021-05-11 description: Lava caves differ from karstic caves in their genesis and mineral composition. Subsurface microbiology of lava tube caves in Canary Islands, a volcanic archipelago in the Atlantic Ocean, is largely unknown. We have focused the investigation in a representative lava tube cave, Fuente de la Canaria Cave, in La Palma Island, Spain, which presents different types of speleothems and colored microbial mats. Four samples collected in this cave were studied using DNA next-generation sequencing and field emission scanning electron microscopy for bacterial identification, functional profiling, and morphological characterization. The data showed an almost exclusive dominance of Bacteria over Archaea. The distribution in phyla revealed a majority abundance of Proteobacteria (37–89%), followed by Actinobacteria, Acidobacteria and Candidatus Rokubacteria. These four phyla comprised a total relative abundance of 72–96%. The main ecological functions in the microbial communities were chemoheterotrophy, methanotrophy, sulfur and nitrogen metabolisms, and CO2 fixation; although other ecological functions were outlined. Genome annotations of the especially representative taxon Ga0077536 (about 71% of abundance in moonmilk) predicted the presence of genes involved in CO2 fixation, formaldehyde consumption, sulfur and nitrogen metabolisms, and microbially-induced carbonate precipitation. The detection of several putative lineages associated with C, N, S, Fe and Mn indicates that Fuente de la Canaria Cave basalts are colonized by metabolically diverse prokaryotic communities involved in the biogeochemical cycling of major elements. creator: Jose Luis Gonzalez-Pimentel creator: Tamara Martin-Pozas creator: Valme Jurado creator: Ana Zelia Miller creator: Ana Teresa Caldeira creator: Octavio Fernandez-Lorenzo creator: Sergio Sanchez-Moral creator: Cesareo Saiz-Jimenez uri: https://doi.org/10.7717/peerj.11386 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Gonzalez-Pimentel et al. title: Mapping open knowledge institutions: an exploratory analysis of Australian universities link: https://peerj.com/articles/11391 last-modified: 2021-05-11 description: While the movement for open research has gained momentum in recent years, there remain concerns about the broader commitment to openness in knowledge production and dissemination. Increasingly, universities are under pressure to transform themselves to engage with the wider community and to be more inclusive. Open knowledge institutions (OKIs) provide a framework that encourages universities to act with the principles of openness at their centre; not only should universities embrace digital open access (OA), but also lead actions in cultivating diversity, equity, transparency and positive changes in society. This leads to questions of whether we can evaluate the progress of OKIs and what are potential indicators for OKIs. As an exploratory study, this article reports on the collection and analysis of a list of potential OKI indicators. Data for these indicators are gathered for 43 Australian universities. The indicators provide high-dimensional and complex signals about university performances. They show evidence of large disparities in characteristics such as Indigenous employment and gender equity, and a preference for repository-mediated OA across Australian universities. We demonstrate use of the OKI evaluation framework to categorise these indicators into three platforms of diversity, communication and coordination. The analysis provides new insights into the Australian open knowledge landscape and ways of mapping different paths of OKIs. creator: Chun-Kai (Karl) Huang creator: Katie Wilson creator: Cameron Neylon creator: Alkim Ozaygen creator: Lucy Montgomery creator: Richard Hosking uri: https://doi.org/10.7717/peerj.11391 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Huang et al. title: Shiftwork, functional bowel symptoms, and the microbiome link: https://peerj.com/articles/11406 last-modified: 2021-05-11 description: BackgroundThere are about 15 million Americans working full-time on evening, night, or rotating shifts. Between 48% and 81.9% of those working rotating or night shifts report abdominal pain, constipation, diarrhea and other symptoms of functional bowel disorders. The basis for this high prevalence of functional bowel disorders, including irritable bowel syndrome (IBS), among shift workers is unknown. Animal studies, however, suggest that circadian disruption, similar to that in shift workers, may contribute to the development of GI complaints among shift workers by altering the composition and normal diurnal rhythmicity of the resident intestinal microbes. Therefore, the present study was designed to determine if there were differences in (1) composition and diversity of the microbiome of night shift workers compared to day shift workers; and (2) the composition and diversity of the microbiome among shift workers experiencing functional bowel symptoms compared to shift workers who did not experience functional bowel symptoms.MethodsFifty-one full time staff nurses who worked either 12-hour day or night shifts completed demographic information, and the Rome III IBS module. They also collected two samples of gut microbiota before the beginning and at the end of their last work shift on day 14, using validated field-tested methods consistent with the Human Microbiome Project. After DNA extraction, 16S rRNA sequencing and assignment to the genus level was completed, samples were then compared to determine if there were (1) differences in the diversity and profile of the microbiome by shift type; (2) if there were differences in the microbiome by time of day for collection; and (3) whether there were differences in the diversity and profile of the microbiome of nurses with IBS and those without IBS.ResultsThere were no differences in alpha or beta diversity of gut microbiota when specimens from day and night shift nurses were compared. There were however marginal differences in beta diversity when specimens collected at the beginning and end of the shifts were compared, with seven OTUs being differentially abundant when collected from day shift workers in the evening. There were also three OTUs to be differentially abundant in participants reporting IBS symptoms. creator: Ann E. Rogers creator: Yi-Juan Hu creator: Ye Yue creator: Emily F. Wissel creator: Robert A. Petit III creator: Simone Jarrett creator: Jennifer Christie creator: Timothy D. Read uri: https://doi.org/10.7717/peerj.11406 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Rogers et al. title: GBP2 as a potential prognostic biomarker in pancreatic adenocarcinoma link: https://peerj.com/articles/11423 last-modified: 2021-05-11 description: BackgroundPancreatic adenocarcinoma (PAAD) is a disease with atypical symptoms, an unfavorable response to therapy, and a poor outcome. Abnormal guanylate-binding proteins (GBPs) play an important role in the host’s defense against viral infection and may be related to carcinogenesis. In this study, we sought to determine the relationship between GBP2 expression and phenotype in patients with PAAD and explored the possible underlying biological mechanism.MethodWe analyzed the expression of GBP2 in PAAD tissues using a multiple gene expression database and a cohort of 42 PAAD patients. We evaluated GBP2’s prognostic value using Kaplan–Meier analysis and the Cox regression model. GO and KEGG enrichment analysis, co-expression analysis, and GSEA were performed to illustrate the possible underlying biological mechanism. CIBERSORT and the relative expression of immune checkpoints were used to estimate the relationship between GBP2 expression and tumor immunology.ResultGBP2 was remarkably overexpressed in PAAD tissue. The overexpression of GBP2 was correlated with an advanced T stage and poor overall survival (OS) and GBP2 expression was an independent risk factor for OS in PAAD patients. Functional analysis demonstrated that positively co-expressed genes of GBP2 were closely associated with pathways in cancer and the NOD-like receptor signaling pathway. Most of the characteristic immune checkpoints, including PDCD1, PDCDL1, CTLA4, CD80, TIGIT, LAG3, IDO2, and VISTA, were significantly expressed in the high-GBP2 expression group compared with the low-GBP2 expression group.ConclusionGBP2 acted as a potential prognostic biomarker and was associated with immune infiltration and the expression of immune checkpoints in PAAD. creator: Bo Liu creator: Rongfei Huang creator: Tingting Fu creator: Ping He creator: Chengyou Du creator: Wei Zhou creator: Ke Xu creator: Tao Ren uri: https://doi.org/10.7717/peerj.11423 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liu et al. title: Eating habits, lifestyle behaviors and stress during the COVID-19 pandemic quarantine among Peruvian adults link: https://peerj.com/articles/11431 last-modified: 2021-05-11 description: Background and aimsThe coronavirus disease 2019 (COVID‐19) outbreak has led to an unprecedented public health crisis. In Peru, although the quarantine is no longer mandatory, it was during the first months of 2020. To date, no studies have assessed the impact of the COVID-19 on the eating patterns and lifestyle context in the country. We aimed to describe the eating habits, lifestyle behaviors and stress during the COVID-19 pandemic quarantine among Peruvian adults.MethodsWe conducted a cross-sectional study. We used an online survey to collect information regarding eating habits, self-perceived stress and sedentary lifestyle among adults over 18 years of age residing in Lima-Peru and who complied with strict home quarantine. We presented our data according to the weight variation of the participants.ResultsA total of 686 were finally included in the study. The 82.9% were female, the median BMI was 25.97 kg/m2 (IQR: 23.37–29.41) and 68.2% reported a significant variation in their weight (38.9% increased and 29.3% lost weight). All bad habits were significantly associated with weight gain, except for prolonged fasting. Additionally, a sitting time longer than usual (p = 0.001), being in front of a screen for more than five hours in the last week (p = 0.002), and most of the stressful scenarios were significantly associated with weight gain.ConclusionAlmost four out of ten participants gained weight during the quarantine. This was associated with unhealthy eating habits, physical inactivity, and stressful scenarios. creator: Hellen S. Agurto creator: Ana L. Alcantara-Diaz creator: Eduardo Espinet-Coll creator: Carlos J. Toro-Huamanchumo uri: https://doi.org/10.7717/peerj.11431 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Agurto et al. title: Mahalanobis distances for ecological niche modelling and outlier detection: implications of sample size, error, and bias for selecting and parameterising a multivariate location and scatter method link: https://peerj.com/articles/11436 last-modified: 2021-05-11 description: The Mahalanobis distance is a statistical technique that has been used in statistics and data science for data classification and outlier detection, and in ecology to quantify species-environment relationships in habitat and ecological niche models. Mahalanobis distances are based on the location and scatter of a multivariate normal distribution, and can measure how distant any point in space is from the centre of this kind of distribution. Three different methods for calculating the multivariate location and scatter are commonly used: the sample mean and variance-covariance, the minimum covariance determinant, and the minimum volume ellipsoid. The minimum covariance determinant and minimum volume ellipsoid were developed to be robust to outliers by minimising the multivariate location and scatter for a subset of the full sample, with the proportion of the full sample forming the subset being controlled by a user-defined parameter. This outlier robustness means the minimum covariance determinant and the minimum volume ellipsoid are highly relevant for ecological niche analyses, which are usually based on natural history observations that are likely to contain errors. However, natural history observations will also contain extreme bias, to which the minimum covariance determinant and the minimum volume ellipsoid will also be sensitive. To provide guidance for selecting and parameterising a multivariate location and scatter method, a series of virtual ecological niche modelling experiments were conducted to demonstrate the performance of each multivariate location and scatter method under different levels of sample size, errors, and bias. The results show that there is no optimal modelling approach, and that choices need to be made based on the individual data and question. The sample mean and variance-covariance method will perform best on very small sample sizes if the data are free of error and bias. At larger sample sizes the minimum covariance determinant and minimum volume ellipsoid methods perform as well or better, but only if they are appropriately parameterised. Modellers who are more concerned about the prevalence of errors should retain a smaller proportion of the full data set, while modellers more concerned about the prevalence of bias should retain a larger proportion of the full data set. I conclude that Mahalanobis distances are a useful niche modelling technique, but only for questions relating to the fundamental niche of a species where the assumption of multivariate normality is reasonable. Users of the minimum covariance determinant and minimum volume ellipsoid methods must also clearly report their parameterisations so that the results can be interpreted correctly. creator: Thomas R. Etherington uri: https://doi.org/10.7717/peerj.11436 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Etherington title: Alterations in mechanical muscle characteristics and postural control induced by tennis match-play in young players link: https://peerj.com/articles/11445 last-modified: 2021-05-11 description: BackgroundCentral and peripheric fatigue indicators are among the main reasons for performance decline following competition. Because of the impact of these factors on performance, how these variables are affected by match-play could be of interest, especially in young tennis players.ObjectiveThis study aimed to investigate alterations induced by a simulated tennis match on postural control and muscle characteristics in young tennis players.MethodSeventeen male junior players took part in pre- and post-competition testing sessions performing postural control (displacement, speed and surface area of center of pressures) and muscle characteristics measurements (tone, stiffness, time to relaxation and elasticity). Between trials, participants played an 80-min simulated tennis match.ResultsNo significant differences were observed in any of the tested variables. Moderate-to-large effect sizes (ES) for decreased stiffness and tone and greater time to relaxation were found between pre- and post-conditions in the right rectus abdominis (−9.8%, −4.4% and 7.8%; ES = 0.8, 0.54 and −0.85). Also, a decrease in tone was found in the right vastus medialis (−7.1%; ES = 0.56), while surface area of the center of pressures with eyes open showed trends towards increasing in post-match measurements (55.9%; ES = 0.56).ConclusionAn 80-min simulated tennis match seems insufficient to elicit significant changes in postural control and mechanical muscle characteristics. Results suggest that physiological responses triggered by match-play were closer to those seen after a moderate activity than those present following a strenuous task. creator: Joshua Colomar creator: Francisco Corbi creator: Ernest Baiget uri: https://doi.org/10.7717/peerj.11445 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Colomar et al. title: Patient characteristics and cardiac surgical outcomes at a tertiary care hospital in Kenya, 2008–2017: a retrospective study link: https://peerj.com/articles/11191 last-modified: 2021-05-10 description: BackgroundCardiac surgeries are high risk procedures that require specialized care and access to these procedures is often limited in resource-poor countries. Although fatalities for surgical patients across Africa are twice that of the global rate, cardiac surgical mortality continent-wide is only slightly higher than all-surgical mortality. Understanding demographic and health characteristics of patients and the associations of these characteristics with morbidity and mortality events is important in guiding care decisions. Therefore, the objectives of this study were to: (a) describe the characteristics of cardiac surgical patients; (b) identify the associations between these characteristics and morbidity and mortality events following cardiac surgery.MethodsPatient characteristics and post-surgical complications were abstracted for all cardiac surgical patients treated at a tertiary care hospital in Kenya from 2008 to 2017. Descriptive analyses of demographic factors, co-morbidities, peri-operative conditions, and post-surgical complications were conducted for adult and pediatric patients. Cochran-Armitage trend test was used to assess temporal trends in risk of death. Multivariable ordinary logistic and Firth logistic models were used to investigate predictors of surgical outcomes.ResultsThe study included a total of 181 patients (150 adult and 31 pediatric patients). Most (91.3%) adult patients had acquired conditions while 45.2% of the pediatric patients had congenital defects. Adult patients tended to have co-morbid conditions including hypertension (16.7%), diabetes mellitus (7.3%), and nephropathy (6.7%). Most patients (76.0% adults and 96.8% pediatric patients) underwent ≤ 2 surgical procedures during their hospital stay. Seventy percent of adult and 54.8% of the pediatric patients experienced at least one post-surgical complication including mediastinal hemorrhage, acute kidney injury and death. Patient characteristics played the greatest roles in predicting post-surgical complications. For adult patients, significant predictors of acute kidney injury included atrial fibrillation (OR = 18.25; p = .001), mitral valve replacement (OR = 0.14; p = .019), and use of cardiopulmonary bypass (OR = 0.06; p = .002). Significant predictors of 30-day mortality were age (OR = 1.05; p = .015) and atrial fibrillation (OR = 4.12, p = .018). Although the number of surgeries increased over the decade-long study period, there were no significant (p = .467) temporal trends in the risk of death.ConclusionsAwareness of demographic and peri-surgical factors that are predictors of complications is useful in guiding clinical decisions to reduce morbidity and mortality. Identification of co-morbidities as the most useful predictors of post-surgical complications suggests that patient characteristics may be a larger contributor to the incidence of complications than surgical practices. creator: Tamara Chavez-Lindell creator: Bob Kikwe creator: Anthony Gikonyo creator: Agricola Odoi uri: https://doi.org/10.7717/peerj.11191 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chavez-Lindell et al. title: The postcranial skeleton of Cerrejonisuchus improcerus (Crocodyliformes: Dyrosauridae) and the unusual anatomy of dyrosaurids link: https://peerj.com/articles/11222 last-modified: 2021-05-10 description: Dyrosauridae is a clade of neosuchian crocodyliforms that diversified in terrestrial and aquatic environments across the Cretaceous-Paleogene transition. The postcranial anatomy of dyrosaurids has long been overlooked, obscuring both their disparity and their locomotive adaptations. Here we thoroughly describe of the postcranial remains of an unusually small dyrosaurid, Cerrejonisuchus improcerus, from the middle-late Paleocene Cerrejón Formation of Colombia, and we provide a wealth of new data concerning the postcranial anatomy of the key dyrosaurids: Congosaurus bequaerti and Hyposaurus rogersii. We identify a series of postcranial autapomorphies in Cerrejonisuchus improcerus (an elliptic-shaped odontoid laterally wide, a ulna possessing a double concavity, a fibula bearing a widely flattened proximal end, a pubis showing a large non-triangular distal surface) as well as functionally-important traits such as a relatively long ulna (85% of the humerus’ length), short forelimb (83% of hindlimb’s length), or thoracic vertebra bearing comparatively large lateral process (with widened parapophysis and diapophysis) along with strongly arched thoracic ribs allowing a more sturdy and cylindrical rib cage. These indicate a more terrestrial lifestyle for Cerrejonisuchus compared to the derived members of the clade. We also built a dataset of 187 traits on 27 taxa, that extensively samples the cranial and postcranial architectures of exemplar crocodyliforms. We analyze these data in via Principal Coordinate Analysis (PCoA) to visualize the postcranial morphospace occupation of Dyrosauridae, Thalattosuchia, and Crocodylia. Our data reveal the existence of a distinctive postcranial anatomy for Dyrosauridae that is markedly distinct from that of crocodylians. As a result, modern crocodylians are probably not good functional analog for extinct crocodyliformes. Postcranial data should also be more widely used in phylogenetic and disparity analyses of Crocodyliformes. creator: Isaure Scavezzoni creator: Valentin Fischer uri: https://doi.org/10.7717/peerj.11222 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Scavezzoni and Fischer title: Body composition and bone mineral density in athletes with a physical impairment link: https://peerj.com/articles/11296 last-modified: 2021-05-10 description: BackgroundThe impact of the type and the severity of disability on whole-body and regional body composition (BC), and bone mineral density (BMD) must be considered for dietary advice in athletes with a physical impairment (PI). This study aimed to investigate the impact of the type and the severity of disability on BC, the pattern of distribution of fat mass at the regional level, and BMD in athletes with a PI.MethodsForty-two male athletes with spinal cord injury (SCI, n = 24; age = 40.04 ± 9.95 years, Body Mass Index [BMI] = 23.07 ± 4.01 kg/m2) or unilateral lower limb amputation (AMP, n = 18; age = 34.39 ± 9.19 years, BMI = 22.81 ± 2.63 kg/m2) underwent a Dual-Energy X-Ray Absorptiometry scan. Each athlete with a PI was matched by age with an able-bodied athlete (AB, n = 42; age = 37.81 ± 10.31 years, BMI = 23.94 ± 1.8 kg/m2).ResultsOne-Way Analysis of Variance showed significant differences between the SCI, AMP and AB groups for percentage fat mass (%FM) (P < 0.001, eta squared = 0.440). Post-hoc analysis with Bonferroni’s correction showed that athletes with SCI had significantly higher %FM vs. the AMP and AB groups (25.45 ± 5.99%, 21.45 ± 4.21% and 16.69 ± 2.56%, respectively; P = 0.008 vs. AMP and P < 0.001 vs. AB). The %FM was also significantly higher in the AMP vs. the AB group (P < 0.001). Whole-body BMD was negatively affected in SCI athletes, with about half of them showing osteopenia or osteoporosis. In fact, the mean BMD and T-score values in the SCI group (1.07 ± 0.09 g/cm2 and −1.25 ± 0.85, respectively) were significantly lower in comparison with the AB group (P = 0.001 for both) as well as the AMP group (P = 0.008 for both). The type of disability affected BC and BMD in the trunk, android, gynoid and leg regions in SCI athletes and the impaired leg only in AMP athletes.ConclusionsIn conclusion, the type of disability and, partly, the severity of PI impact on BC and BMD in athletes with a PI. Nutritionists, sports medicine doctors, clinicians, coaches and physical conditioners should consider athletes with SCI or AMP separately. Athletes with a PI would benefit from specific nutrition and training programs taking into account the type of their disability. creator: Valentina Cavedon creator: Marco Sandri creator: Ilaria Peluso creator: Carlo Zancanaro creator: Chiara Milanese uri: https://doi.org/10.7717/peerj.11296 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Cavedon et al. title: A review of sourdough starters: ecology, practices, and sensory quality with applications for baking and recommendations for future research link: https://peerj.com/articles/11389 last-modified: 2021-05-10 description: The practice of sourdough bread-making is an ancient science that involves the development, maintenance, and use of a diverse and complex starter culture. The sourdough starter culture comes in many different forms and is used in bread-making at both artisanal and commercial scales, in countries all over the world. While there is ample scientific research related to sourdough, there is no standardized approach to using sourdough starters in science or the bread industry; and there are few recommendations on future directions for sourdough research. Our review highlights what is currently known about the microbial ecosystem of sourdough (including microbial succession within the starter culture), methods of maintaining sourdough (analogous to land management) on the path to bread production, and factors that influence the sensory qualities of the final baked product. We present new hypotheses for the successful management of sourdough starters and propose future directions for sourdough research and application to better support and engage the sourdough baking community. creator: Martha D. Calvert creator: Anne A. Madden creator: Lauren M. Nichols creator: Nick M. Haddad creator: Jacob Lahne creator: Robert R. Dunn creator: Erin A. McKenney uri: https://doi.org/10.7717/peerj.11389 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Calvert et al. title: Media exposure predicts acute stress and probable acute stress disorder during the early COVID-19 outbreak in China link: https://peerj.com/articles/11407 last-modified: 2021-05-10 description: BackgroundThe COVID-19 has led to unprecedented psychological stress on the general public. However, the associations between media exposure to COVID-19 and acute stress responses have not been explored during the early COVID-19 outbreak in China.MethodsAn online survey was conducted to investigate the relationships between media exposure to COVID-19 and acute stress responses, and to recognize associated predictors of acute stress responses on a sample of 1,450 Chinese citizens from February 3 to February 10, 2020. Media exposure questionnaire related to COVID-19 was developed to assess media exposure time, media exposure forms and media exposure content. The Stanford Acute Stress Reaction Questionnaire (SASRQ) was used to measure acute stress responses, including continuous acute stress symptom scores and the risk of probable acute stress disorder (ASD). A series of regression analyses were conducted.ResultsLonger media exposure time and social media use were associated with higher acute stress and probable ASD. Viewing the situation of infected patients was associated with higher acute stress, whereas viewing the latest news about pandemic data was associated with lower odds of probable ASD. Being females, living in Hubei Province, someone close to them diagnosed with COVID-19, history of mental illness, recent adverse life events and previous collective trauma exposure were risk factors for acute stress responses.ConclusionsThese findings confirmed the associations between indirect media exposure to pandemic events and acute stress responses. The governments should be aware of the negative impacts of disaster-related media exposure and implement appropriate interventions to promote psychological well-being following pandemic events. creator: Yu Luo creator: Xiangcai He creator: Shaofeng Wang creator: Jinjin Li creator: Yu Zhang uri: https://doi.org/10.7717/peerj.11407 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Luo et al. title: Biogeography of the Southern Ocean: environmental factors driving mesoplankton distribution South of Africa link: https://peerj.com/articles/11411 last-modified: 2021-05-10 description: Spatial distribution of zooplankton communities depends on numerous factors, especially temperature and salinity conditions (hydrological factor), sampled depth, chlorophyll concentration, and diel cycle. We analyzed and compared the impact of these factors on mesoplankton abundance, biodiversity, quantitative structure based on proportion of taxa and qualitative structure based on presence/absence of taxa in the Southern Ocean. Samples (43 stations, three vertical strata sampled at each station, 163 taxa identified) were collected with a Juday net along the SR02 transect in December 2009. Mesoplankton abundance in discrete vertical layers ranged from 0.2 to 13,743.6 ind. m−3, i.e., five orders of magnitude, maximal and minimal values were recorded in the upper mixed and in the deepest layer, respectively. Within the combined 300-m layer, abundances ranged from 16.0 to 1,455.0 ind. m−3, i.e., two orders of magnitude suggesting that integral samples provide little information about actual variations of mesoplankton abundances. A set of analyses showed that depth was the major driver of mesoplankton distribution (abundance, biodiversity, quantitative structure), hydrological factors influenced two of them (quantitative and qualitative structure), chlorophyll concentration strongly affected only quantitative structure, and diel cycle had an insignificant effect on mesoplankton distribution. Using our current knowledge of the fine structure of the Antarctic Circumpolar Current, we compared effects of four hydrological fronts, i.e., boundaries between different water-masses with distinct environmental characteristics, and eight dynamic jets (narrow yet very intense currents) on mesoplankton distribution. Subtropical, Polar, and Subantarctic Fronts drove quantitative and qualitative structure of mesoplankton assemblages (decreasing in order of influence), while the Southern Boundary affected only qualitative structure. Effects of dynamic jets were insignificant. We suggest that mesoplankton composition is driven by hydrological parameters and further maintained through compartmentalization by fronts. Impact of local eddies and meanders on biodiversity, abundance, qualitative and quantitative structure of mesoplankton is comparable to that of hydrological fronts. Qualitative structure of mesoplankton assemblages mirrors hydrological structure of the Southern Ocean better than quantitative structure and may be recommended for biogeographic analyses of the Southern Ocean. Comparisons with previous reports from the same area retrieved no significant changes in mesoplankton distribution during the period 1992–2009. creator: Alexander Vereshchaka creator: Eteri Musaeva creator: Anastasiia Lunina uri: https://doi.org/10.7717/peerj.11411 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Vereshchaka et al. title: Nostolepis scale remains (stem Chondrichthyes) from the Lower Devonian of Qujing, Yunnan, China link: https://peerj.com/articles/11093 last-modified: 2021-05-07 description: Based initially on microfossils, Nostolepis is one of the first known ‘acanthodians’, which constitute a paraphyletic assemblage of plesiomorphic members of the total group Chondrichthyes. Its wide distribution has potential implications for stratigraphic comparisons worldwide. Six species of Nostolepis have been reported in China, including one species from the Xitun Formation (Lochkovian, Lower Devonian) of Qujing, eastern Yunnan. Acid preparation of rock samples from the Xitun Formation has yielded abundant acanthodian remains. Based on both morphological and histological examinations, here we identify five species of Nostolepis, including two new species. N. qujingensis sp. nov. is characterized by thin scales devoid of the neck anteriorly and the dentine tubules rarely present in the anterior part of the crown. N. digitus sp. nov. is characterized by parallel ridges on anterior and lateral margins of the crown, and the neck constricted and ornamented with pore openings. We extend the duration of N. striata in China from the Pridoli of Silurian (Yulungssu Formation) to the Lower Devonian in Qujing and report the first occurrences of N. amplifica and N. consueta in this region. This study increases the diversity of the Lower Devonian Xitun Fauna and provides a better understanding of the paleogeographic distribution of Nostolepis. creator: Qiang Li creator: Xindong Cui creator: Plamen Stanislavov Andreev creator: Wenjin Zhao creator: Jianhua Wang creator: Lijian Peng creator: Min Zhu uri: https://doi.org/10.7717/peerj.11093 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: Type of organic fertilizer rather than organic amendment per se increases abundance of soil biota link: https://peerj.com/articles/11204 last-modified: 2021-05-07 description: Addition of organic amendments is a commonly used practice to offset potential loss of soil organic matter from agricultural soils. The aim of the present study was to examine how long-term addition of organic matter affects the abundance of different soil biota across trophic levels and the role that the quality of the organic amendments plays. Here we used a 17-year-old fertilization experiment to investigate soil biota responses to four different organic fertilizers, compared with two mineral nitrogen fertilizers and no fertilization, where the organic fertilizers had similar carbon content but varied in their carbon to nitrogen ratios. We collected soil samples and measured a wide range of organisms belonging to different functional groups and trophic levels of the soil food web. Long-term addition of organic and mineral fertilizers had beneficial effects on the abundances of most soil organisms compared with unfertilized soil, but the responses differed between soil biota. The organic fertilizers generally enhanced bacteria and earthworms. Fungi and nematodes responded positively to certain mineral and organic fertilizers, indicating that multiple factors influenced by the fertilization may affect these heterogeneous groups. Springtails and mites were less affected by fertilization than the other groups, as they were present at relatively high abundances even in the unfertilized treatment. However, soil pH had a great influence on springtail abundance. In summary, the specific fertilizer was more important in determining the numerical and compositional responses of soil biota than whether it was mineral or organic. Overall, biennial organic amendments emerge as insufficient, by themselves, to promote soil organisms in the long run, and would need to be added annually or combined with other practices affecting soil quality, such as no or reduced tillage and other crop rotations, to have a beneficial effect. creator: Maria Viketoft creator: Laura G.A. Riggi creator: Riccardo Bommarco creator: Sara Hallin creator: Astrid R. Taylor uri: https://doi.org/10.7717/peerj.11204 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Viketoft et al. title: The regulation of immune checkpoints by the hypoxic tumor microenvironment link: https://peerj.com/articles/11306 last-modified: 2021-05-07 description: The tumor microenvironment (TME) influences the occurrence and progression of tumors, and hypoxia is an important characteristic of the TME. The expression of programmed death 1 (PD1)/programmed death-ligand 1 (PDL1), cytotoxic T-lymphocyte-associated antigen 4 (CTLA4), and other immune checkpoints in hypoxic malignant tumors is often significantly increased, and is associated with poor prognosis. The application of immune checkpoint inhibitors (ICIs) for treating lung cancer, urothelial carcinoma, and gynecological tumors has achieved encouraging efficacy; however, the rate of efficacy of ICI single-drug treatment is only about 20%. In the present review, we discuss the possible mechanisms by which the hypoxic TME regulates immune checkpoints. By activating hypoxia-inducible factor-1α (HIF-1α), regulating the adenosine (Ado)-A2aR pathway, regulating the glycolytic pathway, and driving epithelial-mesenchymal transition (EMT) and other biological pathways, hypoxia regulates the expression levels of CTLA4, PD1, PDL1, CD47, lymphocyte activation gene 3 (LAG3), T-cell immunoglobulin and mucin domain 3 (TIM3), and other immune checkpoints, which interfere with the immune effector cell anti-tumor response and provide convenient conditions for tumors to escape immune surveillance. The combination of HIF-1α inhibitors, Ado-inhibiting tumor immune microenvironment regulatory drugs, and other drugs with ICIs has good efficacy in both preclinical studies and phase I-II clinical studies. Exploring the effects of TME hypoxia on the expression of immune checkpoints and the function of infiltrating immune cells has greatly clarified the relationship between the hypoxic TME and immune escape, which is of great significance for the development of new drugs and the search for predictive markers of the efficacy of immunotherapy for treating malignant tumors. In the future, combination therapy with hypoxia pathway inhibitors and ICIs may be an effective anti-tumor treatment strategy. creator: Min Hu creator: Yongfu Li creator: Yuting Lu creator: Miao Wang creator: Yingrui Li creator: Chaoying Wang creator: Qin Li creator: Hong Zhao uri: https://doi.org/10.7717/peerj.11306 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hu et al. title: DNA methylome and transcriptome analysis established a model of four differentially methylated positions (DMPs) as a diagnostic marker in esophageal adenocarcinoma early detection link: https://peerj.com/articles/11355 last-modified: 2021-05-07 description: BackgroundEsophageal carcinogenesis involves in alterations of DNA methylation and gene transcription. This study profiled genomic DNA methylome vs. gene expression using transcriptome data on esophageal adenocarcinoma (EAC) tissues from the online databases in order to identify methylation biomarkers in EAC early diagnosis.Materials and MethodsThe DNA methylome and transcriptome data were downloaded from the UCSC Xena, Gene Expression Omnibus (GEO), and The Cancer Genome Atlas (TCGA) databases and then bioinformatically analyzed for the differentially methylated positions (DMPs) vs. gene expression between EAC and normal tissues. The highly methylated DMPs vs. reduced gene expression in EAC were selected and then stratified with those of the corresponding normal blood samples and other common human cancers to construct an EAC-specific diagnostic model. The usefulness of this model was further verified in other three GEO datasets of EAC tissues.ResultA total of 841 DMPs were associated with expression of 320 genes, some of which were aberrantly methylated in EAC tissues. Further analysis showed that four (cg07589773, cg10474350, cg13011388 and cg15208375 mapped to gene IKZF1, HOXA7, EFS and TSHZ3, respectively) of these 841 DMPs could form and establish a diagnostic model after stratified them with the corresponding normal blood samples and other common human cancers. The data were further validated in other three GEO datasets on EAC tissues in early EAC diagnosis.ConclusionThis study revealed a diagnostic model of four genes methylation to diagnose EAC early. Further study will confirm the usefulness of this model in a prospective EAC cases. creator: Weilin Peng creator: Guangxu Tu creator: Zhenyu Zhao creator: Boxue He creator: Qidong Cai creator: Pengfei Zhang creator: Xiong Peng creator: Shuai Shi creator: Xiang Wang uri: https://doi.org/10.7717/peerj.11355 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Peng et al. title: Transgenerational effects on development following microplastic exposure in Drosophila melanogaster link: https://peerj.com/articles/11369 last-modified: 2021-05-07 description: BackgroundPlastic pollution affects all ecosystems, and detrimental effects to animals have been reported in a growing number of studies. However, there is a paucity of evidence for effects on terrestrial animals in comparison to those in the marine realm.MethodsWe used the fly Drosophila melanogaster to study the effects that exposure to plastics may have on life history traits and immune response. We reared flies in four conditions: In media containing 1% virgin polyethylene, with no chemical additives; in media supplemented with 1% or 4% polyvinyl chloride, known to have a high content of added chemicals; and control flies in non-supplemented media. Plastic particle size ranged from 23–500 µm. We studied fly survival to viral infection, the length of the larval and pupal stage, sex ratios, fertility and the size of the resultant adult flies. We then performed crossings of F1 flies in non-supplemented media and looked at the life history traits of the F2.ResultsFlies treated with plastics in the food media showed changes in fertility and sex ratio, but showed no differences in developmental times, adult size or the capacity to fight infections in comparison with controls. However, the offspring of treated flies reared in non-supplemented food had shorter life cycles, and those coming from both polyvinyl chloride treatments were smaller than those offspring of controls. creator: Eva Jimenez-Guri creator: Katherine E. Roberts creator: Francisca C. García creator: Maximiliano Tourmente creator: Ben Longdon creator: Brendan J. Godley uri: https://doi.org/10.7717/peerj.11369 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Jimenez-Guri et al. title: The impact of COVID-19 pandemic on nitrogen dioxide levels in Nigeria link: https://peerj.com/articles/11387 last-modified: 2021-05-07 description: The Coronavirus disease (COVID-19) has been transmitted worldwide over a very short time after it originated in China in December 2019. In an attempt to control its spread and reduce its health impacts, several countries including those in the African continent imposed restrictive measures that was termed “lockdown”. The outcomes of this lockdown have been reported to be beneficial to air quality worldwide. The main objective of this study is to assess the impact of lockdown due to COVID-19 on nitrogen dioxide (NO2) levels over six major cities in Nigeria. Maps extracted from satellite (Sentinel-5P) were used to indicate the significant reduction in the level of NO2 in the selected cities in Nigeria during two time-intervals, pre-lockdown (December, 2019) and during lockdown (April, 2020). The results show a significant reduction in NO2 levels during the lockdown period compared with its levels during the pre-lockdown period in 2019. The reduction in NO2 concentration levels during lockdown is likely due to less traffic, social distancing and restrictions on business and human activities. There could be an element of uncertainty in the results due to seasonality, as the comparison is done with a different season. However, the magnitude of change due to lockdown is probably much higher than the seasonal variability. Although COVID-19 has negatively impacted the health and economic status of all regions worldwide, it has benefited some aspects of air quality in most countries including Nigeria. This indicates that anthropogenic activities may be managed to reduce air pollution and positively impact the health of human beings. creator: Johnson Adedeji Olusola creator: Adebola Adekunle Shote creator: Abdellah Ouigmane creator: Rima J. Isaifan uri: https://doi.org/10.7717/peerj.11387 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Olusola et al. title: Effects of education methods on self-efficacy of smoking cessation counseling among medical students link: https://peerj.com/articles/11408 last-modified: 2021-05-07 description: BackgroundMedical students need to receive training in providing smoking cessation counseling to provide effective smoking cessation interventions to smokers when they become doctors. This study examined the smoking cessation education curricula and factors affecting counseling self-efficacy (CSE) in smoking cessation treatment among medical students.MethodsIn a multicenter cross-sectional study, we obtained demographic information, personal history of tobacco use and intention to quit smoking, exposure to secondhand smoke in the school premises during the past week, the experience of learning about tobacco in each medical school, tobacco-related medical knowledge, and self-efficacy in smoking cessation counseling on medical students of four Korean medical schools.ResultsAmong 1,416 medical students eligible, 313 (22.1%) students completed a self-administered questionnaire. Only 20.3% of the students reported positive CSE on smoking cessation. The factors affecting positive CSE were scores of ≥ 60 on tobacco-related medical knowledge, smoking experience, and blended learning (p = 0.014, 0.005, and 0.015, respectively).ConclusionThis study shows that high scores in tobacco-related medical knowledge and blended learning are correlated with positive CSE for smoking cessation counseling. creator: Ara Cho creator: Jeonggyu Lee creator: YunJin Kim creator: Byung Mann Cho creator: Sang Yeoup Lee creator: Eunhee Kong creator: Minjeong Kim creator: Jinseung Kim creator: Dong Sik Jung creator: Seongho Han uri: https://doi.org/10.7717/peerj.11408 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Cho et al. title: Competing endogenous RNA network identifies mRNA biomarkers for overall survival of lung adenocarcinoma: two novel on-line precision medicine predictive tools link: https://peerj.com/articles/11412 last-modified: 2021-05-07 description: BackgroundIndividual mortality risk predicted curve at the individual level can provide valuable information for directing individual treatment decision. The present study attempted to explore potential post-transcriptional biological regulatory mechanism related with overall survival of lung adenocarcinoma (LUAD) patients through competitive endogenous RNA (ceRNA) network and develop two precision medicine predictive tools for predicting the individual mortality risk curves for overall survival of LUAD patients.MethodsMultivariable Cox regression analyses were performed to explore the potential prognostic indicators, which were used to construct a prognostic model for overall survival of LUAD patients. Time-dependent receiver operating characteristic (ROC) curves were used to assess the predictive performance of prognostic model.ResultsThere were 494 LUAD patients in model cohort and 233 LUAD patients in validation cohort. Differentially expressed mRNAs, miRNAs, and lncRNAs were identified between LUAD tissues and normal tissues. A ceRNA regulatory network was constructed on previous differentially expressed mRNAs, miRNAs, and lncRNAs. Fourteen mRNA biomarkers were identified as independent risk factors by multivariate Cox regression and used to develop a prognostic model for overall survival of LUAD patients. The C-indexes of prognostic model in model group were 0.786 (95% CI [0.744–0.828]), 0.736 (95% CI [0.694–0.778]) and 0.766 (95% CI [0.724–0.808]) for one year, two year and three year overall survival respectively. Two precision medicine predicted tools were developed for predicting individual mortality risk curves for LUAD patients.ConclusionThe current study explored potential post-transcriptional biological regulatory mechanism and prognostic biomarkers for overall survival of LUAD patients. Two on-line precision medicine predictive tools were helpful to predict the individual mortality risk predicted curves for overall survival of LUAD patients. Smart Cancer Survival Predictive System could be used at https://zhangzhiqiao2.shinyapps.io/Smart_cancer_predictive_system_9_LUAD_E1002/. creator: Jinsong Lin creator: Shubiao Lu creator: Zhijian Jiang creator: Chongjing Hu creator: Zhiqiao Zhang uri: https://doi.org/10.7717/peerj.11412 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2021 Lin et al. title: Cranial anatomy of Besanosaurus leptorhynchus Dal Sasso & Pinna, 1996 (Reptilia: Ichthyosauria) from the Middle Triassic Besano Formation of Monte San Giorgio, Italy/Switzerland: taxonomic and palaeobiological implications link: https://peerj.com/articles/11179 last-modified: 2021-05-06 description: Besanosaurus leptorhynchus Dal Sasso & Pinna, 1996 was described on the basis of a single fossil excavated near Besano (Italy) nearly three decades ago. Here, we re-examine its cranial osteology and assign five additional specimens to B. leptorhynchus, four of which were so far undescribed. All of the referred specimens were collected from the Middle Triassic outcrops of the Monte San Giorgio area (Italy/Switzerland) and are housed in various museum collections in Europe. The revised diagnosis of the taxon includes the following combination of cranial characters: extreme longirostry; an elongate frontal not participating in the supratemporal fenestra; a prominent ‘triangular process’ of the quadrate; a caudoventral exposure of the postorbital on the skull roof; a prominent coronoid (preglenoid) process of the surangular; tiny conical teeth with coarsely-striated crown surfaces and deeply-grooved roots; mesial maxillary teeth set in sockets; distal maxillary teeth set in a short groove. All these characters are shared with the holotype of Mikadocephalus gracilirostris Maisch & Matzke, 1997, which we consider as a junior synonym of B. leptorhynchus. An updated phylogenetic analysis, which includes revised scores for B. leptorhynchus and several other shastasaurids, recovers B. leptorhynchus as a basal merriamosaurian, but it is unclear if Shastasauridae form a clade, or represent a paraphyletic group. The inferred body length of the examined specimens ranges from 1 m to about 8 m. The extreme longirostry suggests that B. leptorhynchus primarily fed on small and elusive prey, feeding lower in the food web than an apex predator: a novel ecological specialisation never reported before the Anisian in a large diapsid. This specialization might have triggered an increase of body size and helped to maintain low competition among the diverse ichthyosaur fauna of the Besano Formation. creator: Gabriele Bindellini creator: Andrzej S. Wolniewicz creator: Feiko Miedema creator: Torsten M. Scheyer creator: Cristiano Dal Sasso uri: https://doi.org/10.7717/peerj.11179 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Bindellini et al. title: Function, structure and quality of striated muscles in the lower extremities in patients with late onset Pompe Disease—an MRI study link: https://peerj.com/articles/10928 last-modified: 2021-05-06 description: BackgroundPompe Disease (PD) is a rare inherited metabolic myopathy, caused by lysosomal-α-glucosidase (GAA) deficiency, which leads to glycogen accumulation within the lysosomes, resulting in cellular and tissue damage. Due to the emergence of a disease modifying treatment with recombinant GAA there has been a large increase in studies of late onset Pompe Disease (LOPD) during the last decade.MethodsThe present study evaluates muscle quality in 10 patients with LOPD receiving treatment with enzyme replacement therapy and in 10 age and gender matched healthy controls applying T1-weighted Dixon MR imaging and isokinetic dynamometry. Muscle quality was determined by muscle strength in relation to muscle size (contractile cross-sectional area, CSA) and to muscle quality (fat fraction). A follow-up evaluation of the patients was performed after 8–12 months. Patient evaluations also included: six-minute walking test (6MWT), forced vital capacity, manual muscle testing and SF-36 questionnaire.ResultsFat fraction of knee flexors (0.15 vs 0.07, p < 0.05) and hip muscles (0.11 vs 0.07, p < 0.05) were higher in patients than controls. In patients, contractile CSA correlated with muscle strength (knee flexors: r = 0.86, knee extensors: r = 0.88, hip extensors: r = 0.83, p < 0.05). No correlation was found between fat fraction and muscle strength. The fat fraction of thigh muscles did not correlate with scores from the clinical tests nor did it correlate with the 6MWT. During follow-up, the contractile CSA of the knee extensors increased by 2%. No other statistically significant change was observed. Quantitative MRI reflects muscle function in patients with LOPD, but larger long-term studies are needed to evaluate its utility in detecting changes over time. creator: Michael Vaeggemose creator: Rosa Andersen Mencagli creator: Julie Schjødtz Hansen creator: Bianca Dräger creator: Steffen Ringgaard creator: John Vissing creator: Henning Andersen uri: https://doi.org/10.7717/peerj.10928 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Vaeggemose et al. title: Concurrent anemia and stunting among schoolchildren in Wonago district in southern Ethiopia: a cross-sectional multilevel analysis link: https://peerj.com/articles/11158 last-modified: 2021-05-06 description: BackgroundEven if many schoolchildren in Ethiopia are anemic and stunted, few have studied the co-existence of anemia and stunting among schoolchildren in Ethiopia. In addition, multilevel analysis to explore the variation in prevalence of concurrent anemia and stunting (CAS) across schools and classes is rarely applied. Thus, we aimed to assess the prevalence and risk factors of CAS at the individual, household, and school level among schoolchildren in southern Ethiopia.MethodsWe recruited 864 students aged 7–14 years from the Wonago district in southern Ethiopia using a three-stage random sampling, assigning four schools to level one, 24 classes to level two. We then randomly selected 36 children from each class, and recorded their weight, height, haemoglobin, intestinal helminthic infections, hygienic practices, dietary practices, household food insecurity, and socio-demographic information. A multivariate, multilevel logistic regression model was applied to detect potential risk factors for CAS.ResultsThe prevalence of CAS was 10.5% (85/810) among schoolchildren, which increased with age in years (adjusted odds ratio [aOR] 1.39 [95% confidence interval 1.13, 1.71, P = 0.002]) and among children who always did not wash their hands with soap after use of latrine (aOR 4.30 [1.21, 15.3, P = 0.02]). Children who walked barefoot (aOR 10.4 [2.77, 39.1, P = 0.001]), were infected with Trichuris trichiura (aOR 1.74 [1.05, 2.88, P = 0.03]), or had head lice infestation (aOR 1.71 [1.01, 2.92, P = 0.04]) had higher CAS prevalence. Prevalence rates of CAS were low in those using treated drinking water (aOR 0.32 [95% CI 0.11, 0.97, P = 0.04]). Most of the risk factors for CAS were identified at the individual level. The clustering effect measured by the intra-cluster correlation coefficient was 6.8% at school level and 19% at class.ConclusionCAS prevalence is a moderate public health problem among schoolchildren in southern Ethiopia and varies across classes and schools. After controlling for clustering effects at the school and class levels, we found an association between CAS and increasing age, not always washing hands with soap after using latrine, walking barefoot, and T. trichiura infection. Using treated water for drinking was found to have a protective effect against CAS. Thus, educating children on personal hygiene and provision of safe drinking water could reduce the CAS burden in schoolchildren in rural areas of southern Ethiopia. creator: Hiwot Hailu Amare creator: Bernt Lindtjorn uri: https://doi.org/10.7717/peerj.11158 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Amare and Lindtjorn title: First complete mitogenomes of Diamesinae, Orthocladiinae, Prodiamesinae, Tanypodinae (Diptera: Chironomidae) and their implication in phylogenetics link: https://peerj.com/articles/11294 last-modified: 2021-05-06 description: BackgroundThe mitochondrial genome (mitogenome) has been extensively used for phylogenetic and evolutionary analysis in Diptera, but the study of mitogenome is still scarce in the family Chironomidae.MethodsHere, the first complete mitochondrial genomes of four Chironomid species representing Diamesinae, Orthocladiinae, Prodiamesinae and Tanypodinae are presented. Coupled with published mitogenomes of two, a comparative mitochondrial genomic analysis between six subfamilies of Chironomidae was carried out.ResultsMitogenomes of Chironomidae are conserved in structure, each contains 37 typical genes and a control region, and all genes arrange the same gene order as the ancestral insect mitogenome. Nucleotide composition is highly biased, the control region displayed the highest A + T content. All protein coding genes are under purifying selection, and the ATP8 evolves at the fastest rate. In addition, the phylogenetic analysis covering six subfamilies within Chironomidae was conducted. The monophyly of Chironomidae is strongly supported. However, the topology of six subfamilies based on mitogenomes in this study is inconsistent with previous morphological and molecular studies. This may be due to the high mutation rate of the mitochondrial genetic markers within Chironomidae. Our results indicate that mitogenomes showed poor signals in phylogenetic reconstructions at the subfamily level of Chironomidae. creator: Chen-Guang Zheng creator: Xiu-Xiu Zhu creator: Li-Ping Yan creator: Yuan Yao creator: Wen-Jun Bu creator: Xin-Hua Wang creator: Xiao-Long Lin uri: https://doi.org/10.7717/peerj.11294 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zheng et al. title: Seagrass structural and elemental indicators reveal high nutrient availability within a tropical lagoon in Panama link: https://peerj.com/articles/11308 last-modified: 2021-05-06 description: Seagrass meadows are valued coastal habitats that provide ecological and economic benefits around the world. Despite their importance, many meadows are in decline, driven by a variety of anthropogenic impacts. While these declines have been well documented in some regions, other locations (particularly within the tropics) lack long-term monitoring programs needed to resolve seagrass trends over time. Effective and spatially-expansive monitoring within under-represented regions is critical to provide an accurate perspective on seagrass status and trends. We present a comprehensive dataset on seagrass coverage and composition across 24 sites in Bahía Almirante, a lagoon along the Caribbean coast of Panama. Using a single survey, we focus on capturing spatial variation in seagrass physical and elemental characteristics and provide data on key seagrass bio-indicators, such as leaf morphology (length and width), elemental content (% nitrogen and phosphorus) and stable isotopic signatures (δ13C and δ15N). We further explore relationships between these variables and water depth (proxy for light availability) and proximity to shore (proxy for terrestrial inputs). The seagrass assemblage was mostly monospecific (dominated by Thalassia testudinum) and restricted to shallow water (<3 m). Above-ground biomass varied widely, averaging 71.7 g dry mass m−2, yet ranging from 24.8 to 139.6 g dry mass m−2. Leaf nitrogen content averaged 2.2%, ranging from 1.76 to 2.57%, while phosphorus content averaged 0.19% and ranged from 0.15 to 0.23%. These values were high compared to other published reports for T. testudinum, indicating elevated nutrient availability within the lagoon. Seagrass stable isotopic characteristics varied slightly and were comparable with other published values. Leaf carbon signatures (δ13C) ranged from −11.74 to −6.70‰ and were positively correlated to shoreline proximity, suggesting a contribution of terrestrial carbon to seagrass biomass. Leaf nitrogen signatures (δ15N) ranged from −1.75 to 3.15‰ and showed no correlation with shoreline proximity, suggesting that N sources within the bay were not dominated by localized point-source discharge of treated sewage. Correlations between other seagrass bio-indicators and environmental metrics were mixed: seagrass cover declined with depth, while biomass was negatively correlated with N, indicating that light and nutrient availability may jointly regulate seagrass cover and biomass. Our work documents the response of seagrass in Bahía Almirante to light and nutrient availability and highlights the eutrophic status of this bay. Using the broad spatial coverage of our survey as a baseline, we suggest the future implementation of a continuous and spatially expansive seagrass monitoring program within this region to assess the health of these important systems subject to global and local stressors. creator: Julie Gaubert-Boussarie creator: Andrew H. Altieri creator: J. Emmett Duffy creator: Justin E. Campbell uri: https://doi.org/10.7717/peerj.11308 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Gaubert-Boussarie et al. title: Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines link: https://peerj.com/articles/11344 last-modified: 2021-05-06 description: Animals, plants, and algae rely on symbiotic microorganisms for their development and functioning. Genome sequencing and genomic analyses of these microorganisms provide opportunities to construct metabolic networks and to analyze the metabolism of the symbiotic communities they constitute. Genome-scale metabolic network reconstructions rest on information gained from genome annotation. As there are multiple annotation pipelines available, the question arises to what extent differences in annotation pipelines impact outcomes of these analyses. Here, we compare five commonly used pipelines (Prokka, MaGe, IMG, DFAST, RAST) from predicted annotation features (coding sequences, Enzyme Commission numbers, hypothetical proteins) to the metabolic network-based analysis of symbiotic communities (biochemical reactions, producible compounds, and selection of minimal complementary bacterial communities). While Prokka and IMG produced the most extensive networks, RAST and DFAST networks produced the fewest false positives and the most connected networks with the fewest dead-end metabolites. Our results underline differences between the outputs of the tested pipelines at all examined levels, with small differences in the draft metabolic networks resulting in the selection of different microbial consortia to expand the metabolic capabilities of the algal host. However, the consortia generated yielded similar predicted producible compounds and could therefore be considered functionally interchangeable. This contrast between selected communities and community functions depending on the annotation pipeline needs to be taken into consideration when interpreting the results of metabolic complementarity analyses. In the future, experimental validation of bioinformatic predictions will likely be crucial to both evaluate and refine the pipelines and needs to be coupled with increased efforts to expand and improve annotations in reference databases. creator: Elham Karimi creator: Enora Geslain creator: Arnaud Belcour creator: Clémence Frioux creator: Méziane Aïte creator: Anne Siegel creator: Erwan Corre creator: Simon M. Dittami uri: https://doi.org/10.7717/peerj.11344 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Karimi et al. title: Genome-wide identification, classification and expression profile analysis of the HSF gene family in Hypericum perforatum link: https://peerj.com/articles/11345 last-modified: 2021-05-06 description: Heat shock transcription factors (HSFs) are critical regulators of plant responses to various abiotic and biotic stresses, including high temperature stress. HSFs are involved in regulating the expression of heat shock proteins (HSPs) by binding with heat stress elements (HSEs) to defend against high-temperature stress. The H. perforatum genome was recently fully sequenced; this provides a valuable resource for genetic and functional analysis. In this study, 23 putative HpHSF genes were identified and divided into three groups (A, B, and C) based on phylogeny and structural features. Gene structure and conserved motif analyses were performed on HpHSFs members; the DNA-binding domain (DBD), hydrophobic heptad repeat (HR-A/B), and exon-intron boundaries exhibited specific phylogenetic relationships. In addition, the presence of various cis-acting elements in the promoter regions of HpHSFs underscored their regulatory function in abiotic stress responses. RT-qPCR analyses showed that most HpHSF genes were expressed in response to heat conditions, suggesting that HpHSFs play potential roles in the heat stress resistance pathway. Our findings are advantageous for the analysis and research of the function of HpHSFs in high temperature stress tolerance in H. perforatum. creator: Li Zhou creator: Xiaoding Yu creator: Donghao Wang creator: Lin Li creator: Wen Zhou creator: Qian Zhang creator: Xinrui Wang creator: Sumin Ye creator: Zhezhi Wang uri: https://doi.org/10.7717/peerj.11345 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhou et al. title: BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains link: https://peerj.com/articles/11396 last-modified: 2021-05-06 description: Bacteriophages are broadly classified into two distinct lifestyles: temperate and virulent. Temperate phages are capable of a latent phase of infection within a host cell (lysogenic cycle), whereas virulent phages directly replicate and lyse host cells upon infection (lytic cycle). Accurate lifestyle identification is critical for determining the role of individual phage species within ecosystems and their effect on host evolution. Here, we present BACPHLIP, a BACterioPHage LIfestyle Predictor. BACPHLIP detects the presence of a set of conserved protein domains within an input genome and uses this data to predict lifestyle via a Random Forest classifier that was trained on a dataset of 634 phage genomes. On an independent test set of 423 phages, BACPHLIP has an accuracy of 98% greatly exceeding that of the previously existing tools (79%). BACPHLIP is freely available on GitHub (https://github.com/adamhockenberry/bacphlip) and the code used to build and test the classifier is provided in a separate repository (https://github.com/adamhockenberry/bacphlip-model-dev) for users wishing to interrogate and re-train the underlying classification model. creator: Adam J. Hockenberry creator: Claus O. Wilke uri: https://doi.org/10.7717/peerj.11396 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hockenberry and Wilke title: Construction of an immune-related signature with prognostic value for colon cancer link: https://peerj.com/articles/10812 last-modified: 2021-05-05 description: BackgroundColon cancer is the third most common malignant tumor in the world. Although immunotherapy has been used in cancer treatment, there is still no first-line immunotherapy method for colon cancer. Therefore, it is essential to search for potential immunotherapy targets and molecular biomarkers for early diagnosis and prognosis.MethodsIn this study, we downloaded transcriptome data from The Cancer Genome Atlas (TCGA) and immune-related genes from the ImmPort database. Then we filtered genes with prognostic value and constructed an immune-related signature. Patients were classified into low- and high-risk groups, and we exerted a series of analysis between the signature and clinical phenotypes. Additionally, we used protein-protein interaction networks, gene set enrichment analysis (GSEA) and single-sample gene-set enrichment analysis (ssGSEA) to explore the underlying mechanism of this signature. Furthermore, the accuracy of this signature was verified, using two data sets from Gene Expression Omnibus (GEO).ResultsWe selected 12 immune-related genes to construct the immune-related signature. Low-risk group had a higher level of immunity compared to high-risk group. The expression level of HLA genes and checkpoint-related genes were statistically different in low- and high-risk groups. This signature showed its prognostic value in TCGA cohort and 2 GEO data sets. The signature also had strong correlation with TNM classification, stage, survival state and lymphatic invasion. The mechanism of the signature may be related to several transcription factors and CD8+ T cell in the tumor microenvironment.ConclusionIn conclusion, this immune-related signature is of great prognosis value for colon cancer and its biofunction might be correlated with HLA genes, checkpoint-related genes and high-infiltrating T cells in tumor tissues. creator: Yunxia Lv creator: Xinyi Wang creator: Yu Ren creator: Xiaorui Fu creator: Taiyuan Li creator: Qunguang Jiang uri: https://doi.org/10.7717/peerj.10812 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Lv et al. title: Comparison of ultrafiltration and iron chloride flocculation in the preparation of aquatic viromes from contrasting sample types link: https://peerj.com/articles/11111 last-modified: 2021-05-05 description: Viral metagenomes (viromes) are a valuable untargeted tool for studying viral diversity and the central roles viruses play in host disease, ecology, and evolution. Establishing effective methods to concentrate and purify viral genomes prior to sequencing is essential for high quality viromes. Using virus spike-and-recovery experiments, we stepwise compared two common approaches for virus concentration, ultrafiltration and iron chloride flocculation, across diverse matrices: wastewater influent, wastewater secondary effluent, river water, and seawater. Viral DNA was purified by removing cellular DNA via chloroform cell lysis, filtration, and enzymatic degradation of extra-viral DNA. We found that viral genomes were concentrated 1-2 orders of magnitude more with ultrafiltration than iron chloride flocculation for all matrices and resulted in higher quality DNA suitable for amplification-free and long-read sequencing. Given its widespread use and utility as an inexpensive field method for virome sampling, we nonetheless sought to optimize iron flocculation. We found viruses were best concentrated in seawater with five-fold higher iron concentrations than the standard used, inhibition of DNase activity reduced purification effectiveness, and five-fold more iron was needed to flocculate viruses from freshwater than seawater—critical knowledge for those seeking to apply this broadly used method to freshwater virome samples. Overall, our results demonstrated that ultrafiltration and purification performed better than iron chloride flocculation and purification in the tested matrices. Given that the method performance depended on the solids content and salinity of the samples, we suggest spike-and-recovery experiments be applied when concentrating and purifying sample types that diverge from those tested here. creator: Kathryn Langenfeld creator: Kaitlyn Chin creator: Ariel Roy creator: Krista Wigginton creator: Melissa B. Duhaime uri: https://doi.org/10.7717/peerj.11111 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Langenfeld et al. title: Genome-wide identification and characterization of NAC genes in Brassica juncea var. tumida link: https://peerj.com/articles/11212 last-modified: 2021-05-05 description: BackgroundNAC (NAM, ATAF1/2, and CUC2) transcription factors play an important role in plant growth and development. However, in tumorous stem mustard (Brassica juncea var. tumida), one of the economically important crops cultivated in southwest China and some southeast Asian countries, reports on the identification of NAC family genes are lacking. In this study, we conducted a genome-wide investigation of the NAC family genes in B. juncea var. tumida, based on its recently published genome sequence data.MethodsThe NAC genes were identified in B. juncea var. tumida using the bioinformatics approach on the whole genome level. Additionally, the expression of BjuNAC genes was analyzed under high- and low-temperature stresses by quantitative real-time PCR (qRT-PCR).ResultsA total of 300 BjuNAC genes were identified, of which 278 were mapped to specific chromosomes. Phylogenetic analysis of B. juncea var. tumida, Brassica rapa, Brassica nigra, rice and Arabidopsis thaliana NAC proteins revealed that all NAC genes were divided into 18 subgroups. Furthermore, gene structure analysis showed that most of the NAC genes contained two or three exons. Conserved motif analysis revealed that BjuNAC genes contain a conserved NAM domain. Additionally, qRT-PCR data indicated that thirteen BjuNAC genes with a varying degree of up-regulation during high-temperature stress. Conversely, four BjuNAC genes (BjuNAC006, BjuNAC083, BjuNAC170 and BjuNAC223) were up-regulated and two BjuNAC genes (BjuNAC074 and BjuNAC295) down-regulated under low temperature, respectively. Together, the results of this study provide a strong foundation for future investigation of the biological function of NAC genes in B. juncea var. tumida. creator: Longxing Jiang creator: Quan Sun creator: Yu Wang creator: Pingan Chang creator: Haohuan Kong creator: Changshu Luo creator: Xiaohong He uri: https://doi.org/10.7717/peerj.11212 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Jiang et al. title: Identification of P2RY13 as an immune-related prognostic biomarker in lung adenocarcinoma: A public database-based retrospective study link: https://peerj.com/articles/11319 last-modified: 2021-05-05 description: BackgroundLung adenocarcinoma (LUAD) is the leading histological subtype of non-small cell lung cancer (NSCLC).MethodsIn the present study, the gene matrixes of LUAD were downloaded from The Cancer Genome Atlas to infer immune and stromal scores with the ‘Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression data’ (ESTIMATE) algorithm and identified immune-related differentially expressed genes (DEGs) between the high- and low-stromal/immune score groups. Next, all DEGs were subjected to univariate Cox regression and survival analyses to screen out prognostic biomarkers in the tumor microenvironment (TME), and were validated in the Gene Expression Omnibus database. Single-sample gene set enrichment analysis (ssGSEA) was performed to assess the level of tumor-infiltrating immune cells (TIICs) and immune functions, and GSEA was used to identified pathways altered by prognostic biomarkers.ResultsSurvival analysis showed that LUAD in the high-immune and stromal score group had a better clinical prognosis. A total of 303 immune-related DEGs were detected. Univariate Cox regression and survival analyses revealed that P2Y purinoceptor 13 (P2RY13) was a favorable factor for the prognosis of LUAD. ssGSEA and Spearman correlation analysis demonstrated that P2RY13 was highly correlated with various TIICs and immune functions. Several immune-associated pathways were enriched between the high- and low-expression P2RY13 groups.ConclusionP2RY13 may be a potential prognostic indicator and is highly associated with the TME in LUAD. However, further experimental studies are required to validate the present findings. creator: Jiang Lin creator: Chunlei Wu creator: Dehua Ma creator: Quanteng Hu uri: https://doi.org/10.7717/peerj.11319 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Lin et al. title: Variance of vegetation coverage and its sensitivity to climatic factors in the Irtysh River basin link: https://peerj.com/articles/11334 last-modified: 2021-05-05 description: BackgroundClimate change is an important factor driving vegetation changes in arid areas. Identifying the sensitivity of vegetation to climate variability is crucial for developing sustainable ecosystem management strategies. The Irtysh River is located in the westerly partition of China, and its vegetation cover is more sensitive to climate change. However, previous studies rarely studied the changes in the vegetation coverage of the Irtysh River and its sensitivity to climate factors from a spatiotemporal perspective.MethodsWe adopted a vegetation sensitivity index based on remote sensing datasets of high temporal resolution to study the sensitivity of vegetation to climatic factors in the Irtysh River basin, then reveal the driving mechanism of vegetation cover change.ResultsThe results show that 88.09% of vegetated pixels show an increasing trend in vegetation coverage, and the sensitivity of vegetation to climate change presents spatial heterogeneity. Sensitivity of vegetation increases with the increase of coverage. Temperate steppe in the northern mountain and herbaceous swamp and broadleaf forest in the river valley, where the normalized difference vegetation index is the highest, show the strongest sensitivity, while the desert steppe in the northern plain, where the NDVI is the lowest, shows the strongest memory effect (or the strongest resilience). Relatively, the northern part of this area is more affected by a combination of precipitation and temperature, while the southern plains dominated by desert steppe are more sensitive to precipitation. The central river valley dominated by herbaceous swamp is more sensitive to temperature-vegetation dryness index. This study underscores that the sensitivity of vegetation cover to climate change is spatially differentiated at the regional scale. creator: Feifei Han creator: Junjie Yan creator: Hong-bo Ling uri: https://doi.org/10.7717/peerj.11334 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Han et al. title: Temporal and spatial dynamics of gastrointestinal parasite infection in Père David’s deer link: https://peerj.com/articles/11335 last-modified: 2021-05-05 description: BackgroundThe Père David’s deer (Elaphurus davidianus) population was established from only a small number of individuals. Their genetic diversity is therefore relatively low and transmissible (parasitic) diseases affecting them merit further attention. Parasitic infections can affect the health, survival, and population development of the host. However, few reports have been published on the gastrointestinal parasites of Père David’s deer. The aims of this study were: (1) to identify the intestinal parasites groups in Père David’s deer; (2) to determine their prevalence and burden and clarify the effects of different seasons and regions on various indicators of Père David’s deer intestinal parasites; (3) to evaluate the effects of the Père David’s deer reproductive period on these parasites; (4) to reveal the regularity of the parasites in space and time.MethodsIn total, 1,345 Père David’s deer faecal samples from four regions during four seasons were tested using the flotation (saturated sodium nitrate solution) to identify parasites of different genus or group, and the McMaster technique to count the number of eggs or oocysts.ResultsFour groups of gastrointestinal parasites were found, of which strongyles were dominant; their prevalence and burden were significantly higher than other groups. Significant temporal and spatial effects on gastrointestinal parasitic infection were found. Parasite diversity, prevalence, parasite burden, and aggregation were the highest in summer. Among the four regions, parasite diversity, prevalence, and burden were the highest in the Dongting Lake area. In addition, parasite diversity and burden during the reproductive period of Père David’s deer was significantly higher than during the post-reproductive period.ConclusionsThe summer season and the reproductive period of Père David’s deer had great potential for parasite transmission, and there is a high risk of parasite outbreaks in the Dongting Lake area. creator: Shanghua Xu creator: Shumiao Zhang creator: Xiaolong Hu creator: Baofeng Zhang creator: Shuang Yang creator: Xin Hu creator: Shuqiang Liu creator: Defu Hu creator: Jiade Bai uri: https://doi.org/10.7717/peerj.11335 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Xu et al. title: Histopathological analysis of zebrafish after introduction of non-biodegradable polyelectrolyte microcapsules into the circulatory system link: https://peerj.com/articles/11337 last-modified: 2021-05-05 description: Polyelectrolyte microcapsules are among the most promising carriers of various sensing substances for their application inside the bloodstream of vertebrates. The long-term effects of biodegradable microcapsules in mammals are relatively well studied, but this is not the case for non-biodegradable microcapsules, which may be even more generally applicable for physiological measurements. In the current study, we introduced non-biodegradable polyelectrolyte microcapsules coated with polyethylene glycol (PMs-PEG) into the circulatory system of zebrafish to assess their long-term effects on fish internal organs with histopathologic analysis. Implantation of PMs-PEG was not associated with the formation of microclots or thrombi in thin capillaries; thus, the applied microcapsules had a low aggregation capacity. The progression of the immune response to the implant depended on the time and the abundance of microparticles in the tissues. We showed that inflammation originated from recognition and internalization of PMs-PEG by phagocytes. These microcapsule-filled immune cells have been found to migrate through the intestinal wall into the lumen, demonstrating a possible mechanism for partial microparticle elimination from fish. The observed tissue immune response to PMs-PEG was local, without a systemic effect on the fish morphology. The most pronounced chronic severe inflammatory reaction was observed near the injection site in renal parenchyma and within the abdominal cavity since PMs-PEG were administered with kidney injection. Blood clots and granulomatosis were noted at the injection site but were not found in the kidneys outside the injection site. Single microcapsules brought by blood into distal organs did not have a noticeable effect on the surrounding tissues. The severity of noted pathologies of the gills was insufficient to affect respiration. No statistically significant alterations in hepatic morphology were revealed after PMs-PEG introduction into fish body. Overall, our data demonstrate that despite they are immunogenic, non-biodegradable PMs-PEG have low potential to cause systemic effects if applied in the minimal amount necessary for detection of fluorescent signal from the microcapsules. creator: Ekaterina Borvinskaya creator: Anton Gurkov creator: Ekaterina Shchapova creator: Andrei Mutin creator: Maxim Timofeyev uri: https://doi.org/10.7717/peerj.11337 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Borvinskaya et al. title: ToRQuEMaDA: tool for retrieving queried Eubacteria, metadata and dereplicating assemblies link: https://peerj.com/articles/11348 last-modified: 2021-05-05 description: TQMD is a tool for high-performance computing clusters which downloads, stores and produces lists of dereplicated prokaryotic genomes. It has been developed to counter the ever-growing number of prokaryotic genomes and their uneven taxonomic distribution. It is based on word-based alignment-free methods (k-mers), an iterative single-linkage approach and a divide-and-conquer strategy to remain both efficient and scalable. We studied the performance of TQMD by verifying the influence of its parameters and heuristics on the clustering outcome. We further compared TQMD to two other dereplication tools (dRep and Assembly-Dereplicator). Our results showed that TQMD is primarily optimized to dereplicate at higher taxonomic levels (phylum/class), as opposed to the other dereplication tools, but also works at lower taxonomic levels (species/strain) like the other dereplication tools. TQMD is available from source and as a Singularity container at [https://bitbucket.org/phylogeno/tqmd ]. creator: Raphaël R. Léonard creator: Marie Leleu creator: Mick Van Vlierberghe creator: Luc Cornet creator: Frédéric Kerff creator: Denis Baurain uri: https://doi.org/10.7717/peerj.11348 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Léonard et al. title: TCF7L2 rs7903146 polymorphism association with diabetes and obesity in an elderly cohort from Brazil link: https://peerj.com/articles/11349 last-modified: 2021-05-05 description: BackgroundType 2 diabetes mellitus (T2DM) and obesity are complex pandemic diseases in the 21st century. Worldwide, the T allele rs7903146 in the TCF7L2 gene is recognized as a strong GWAS signal associated with T2DM. However, the association between the C allele and obesity is still poorly explored and needs to be replicated in other populations. Thus, the primary objectives of this study were to evaluate the TCF7L2 rs7903146 association with T2DM according to BMI status and to determine if this variant is related to obesity and BMI variation in a cohort of elderly Brazilians.MethodsA total of 1,023 participants from an elderly census-based cohort called SABE (Saúde, Bem Estar e Envelhecimento—Health, Well-Being and Aging) were stratified by BMI status and type 2 diabetes presence. The TCF7L2 genotypes were filtered from the Online Archive of Brazilian Mutations (ABraOM—Online Archive of Brazilian Mutations) database, a web-based public database with sequencing data of samples of the SABE’s participants. Logistic regression models and interaction analyses were performed. The BMI variation (∆BMI) was calculated from anthropometric data collected in up to two time-points with a ten-year-assessment interval.ResultsThe association between the rs7903146 T allele and T2DM was inversely proportional to the BMI status, with an increased risk in the normal weight group (OR 3.36; 95% CI [1.46–7.74]; P = 0.004). We confirmed the T allele association with risk for T2DM after adjusting for possible confound ing variables (OR 2.35; 95% CI [1.28–4.32]; P = 0.006). Interaction analysis showed that the increased risk for T2DM conferred by the T allele is modified by BMI (Pinteraction = 0.008), age (Pinteraction = 0.005) and gender (Pinteraction = 0.026). A T allele protective effect against obesity was observed (OR 0.71; 95% CI [0.54–0.94]; P = 0.016). The C allele increased obesity risk (OR 1.40; 95% CI [1.06–1.84]; P = 0.017) and the CC genotype showed a borderline association with abdominal obesity risk (OR 1.28; 95% CI [1.06–1.67]; P = 0.045). The CC genotype increased the obesity risk factor after adjusting for possible confounding variables (OR 1.41; 95% CI [1.06–1.86]; P = 0.017). An increase of the TT genotype in the second tertile of ∆BMI values was observed in participants without type 2 diabetes (OR 5.13; 95% CI [1.40–18.93]; P = 0.009) in the recessive genetic model.ConclusionWe confirmed that the rs7903146 is both associated with T2DM and obesity. The TCF7L2 rs7903146 T allele increased T2DM risk in the normal weight group and interacted with sex, age and BMI, while the C allele increased obesity risk. The TT genotype was associated with a lesser extent of BMI variation over the SABE study’s 10-year period. creator: Lais Bride creator: Michel Naslavsky creator: Guilherme Lopes Yamamoto creator: Marilia Scliar creator: Lucia HS Pimassoni creator: Paola Sossai Aguiar creator: Flavia de Paula creator: Jaqueline Wang creator: Yeda Duarte creator: Maria Rita Passos-Bueno creator: Mayana Zatz creator: Flávia Imbroisi Valle Errera uri: https://doi.org/10.7717/peerj.11349 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Bride et al. title: Non-specific low back pain: cross-sectional study of 11,423 children and youth and the association with the perception of heaviness in carrying of schoolbags link: https://peerj.com/articles/11220 last-modified: 2021-05-04 description: BackgroundCarrying a schoolbag is a daily activity for most children and adolescents.The perception of a schoolbag’s weight depends upon the individual and is a relevant theme in schoolchildren. Describing the association between the perception of heaviness in carrying a schoolbag and NLBP can facilitate the planning of preventive programs, quite different from those based on specific weight limits for schoolbags in children and youth.ObjectiveTo determine the prevalence of non-specific low back pain (NLBP) and to analyse the association between the perception of heaviness in carrying of schoolbags and NLBP in Polish children and youth aged 10–19.MethodsThis study included 11,423 children and youth (6,252 girls and 5,171 boys) from Poland. An original questionnaire was used to assess NLBP prevalence.ResultsAmong 11,423 of the respondents, 41.5% of the respondents admitted that they had experienced NLBP in the period of the last 12 months. The percentage of individuals reporting NLBP increased with age of participants, p < 0.001. Girls reported NLBP more often than boys (p < 0.001). Students with NLBP declared that their school backpack was heavy more often than students without LBP. Students who thought that their backpacks weighed too much manifested a 1.44 (95% Cl [1.33–1.55]) times higher probability to experience NLBP.ConclusionIn the examined group of schoolchildren a frequent occurrence of NLBP (41.5%) was noted. Its occurrence was related to female sex and age. Students who thought that their backpacks weighed too much manifested higher probability to develop NLBP. creator: Agnieszka Kędra creator: Magdalena Plandowska creator: Przemysław Kędra creator: Dariusz Czaprowski uri: https://doi.org/10.7717/peerj.11220 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kędra et al. title: Braincase anatomy of the Paleocene crocodyliform Rhabdognathus revealed through high resolution computed tomography link: https://peerj.com/articles/11253 last-modified: 2021-05-04 description: Dyrosaurids were highly specialized, largely marine, relatives of living crocodylians, and one of the few archosaur lineages to survive the K-Pg extinction. Dyrosaurids lived during the Cretaceous to the Eocene and represent a unique combination of morphology and ecology not seen in living crocodylians. Little is known about their endocranial anatomy, leaving many questions about their neurosensory adaptations unaddressed. Recently, µCT (micro-computed tomography) scans were made of a well-preserved skull of Rhabdognathus, a Paleocene dyrosaurid from Mali. This marks the first time the braincase and neurosensory features of a dyrosaurid have been examined using CT. We focus our attention to three specific internal structures: the cranial endocast; the inner ear; and the paratympanic sinuses. The cranial endocast of Rhabdognathus revealed novel features including a unique conformation of its paratympanic system, a prominent dorsal venous system that communicates with the external skull table, extremely enlarged tympanic vestibules that meet at the midline of the endocranium, a prominent spherical cerebrum, and elongate olfactory tracts accounting for half the total endocast length. The bizarre laterally facing lateral Eustachian foramen of dyrosaurids is now understood to be a complex fossa including both a ventrally directed lateral Eustachian foramen and a laterally directed foramen for the basioccipital diverticulum. A novel median pterygopharyngeal canal was discovered connecting the pharynx to the adductor chamber. These revelations require a reinterpretation of the associated external foramina visible on the posterior of the skull in dyrosaurids and potentially their close relatives the pholidosaurids. The olfactory tract terminates in an enlarged olfactory region possessing complex bony projections—a unique morphology perhaps serving to increase surface area for olfaction. The inner ear of Rhabdognathus exhibits characteristics seen in both Pelagosaurus and Gavialis. The vestibule is spherical, as in Gavialis, but is significantly expanded. The semicircular canals are enlarged but pyramidal in shape as in the thalattosuchian Pelagosaurus. The proportion of the cochlear length to total endosseous labyrinth height is roughly 0.5 in Rhabdognathus implying that the hearing capabilities resemble that of thalattosuchians. A suite of expanded sense organs (e.g., bony olfactory lamina; hypertrophied vestibule of the inner ear), and the clear expansion of the cerebrum to a more symmetrical and spherical shape suggest that dyrosaurids possess neuroanatomical modifications facilitating an agile predatory near-shore ecology. creator: Arthur Erb creator: Alan H. Turner uri: https://doi.org/10.7717/peerj.11253 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Erb and Turner title: Evaluation of cellulose degrading bacteria isolated from the gut-system of cotton bollworm, Helicoverpa armigera and their potential values in biomass conversion link: https://peerj.com/articles/11254 last-modified: 2021-05-04 description: BackgroundCotton bollworm, Helicoverpa armigera is a widely distributed, devastating pest of over 200 crop plants that mainly consist of some cellulosic materials. Despite its economic importance as a pest, little is known about the diversity and community structure of gut symbiotic bacteria potentially functioned in cellulose digestion in different gut-sections of H. armigera. In view of this lacuna, we attempted to evaluate and characterize cellulose-degrading bacteria (CDB) from foregut, midgut, and hindgut -regions of H. armigera by using a culture-dependent approach.MethodologyThe symbiotic bacteria were isolated from different gut-systems of H. armigera by enrichment techniques using Carboxymethyl cellulose sodium salt (CMC) as carbon source. The isolated bacteria were purified and subsequently screened for cellulose-degradation by plate-based method to display the zones of CMC clearance around the colonies. The identification and phylogeny of the gut-bacteria were reconstructed by using 16S rRNA gene sequencing. Different enzymes such as endoglucanase, exoglucanase, β-glucosidase, and xylanase were assayed to determine the cellulolytic repertoire of the isolated bacteria.ResultsThe enrichment of CDB and subsequent plate based screening methods resulted in isolation of 71 bacteria among which 54% of the bacteria were obtained from foregut. Among the isolated bacteria, 25 isolates showed discernible cellulose-degradation potential on CMC-agar plates. The phylogenetic analysis based on 16S rRNA gene amplification and sequencing affiliated these cellulolytic bacteria to two major phyla viz., Firmicutes and Proteobacteria. The members of the genus Klebsiella accounted for 39.43% of the total isolated bacteria while 31% of the Bacillus strains were enriched from hindgut region. The principal component analysis (PCA) further suggested that the members of Bacillus and Klebsiella together dominated the foregut and hindgut regions as they accounted for 68% of the total CDB. The four potential isolates selected on the basis of plate-based activities were further evaluated for their lignocellulases production by using various agricultural wastes as substrates. The PCA of the enzyme activities demonstrated that potential isolates majorly secreted endoglucanase and xylanase enzymes. Among the agro-wastes, multivariate analysis validated wheat husk (WH) and sugarcane bagasse (SCB) as most favorable substrates for xylanase and endoglucanase productions respectively. The overall findings suggest that H. armigera harbors diverse bacterial communities in different gut-sections that could assist the host in digestion processes, which may potentially serve as a valuable reservoir of some unique symbionts applied for biomass conversion in biofuel industry. creator: Mudasir A. Dar creator: Afrin F. Shaikh creator: Kiran D. Pawar creator: Rongrong Xie creator: Jianzhong Sun creator: Sabariswaran Kandasamy creator: Radhakrishna S. Pandit uri: https://doi.org/10.7717/peerj.11254 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Dar et al. title: Taphonomy and taxonomy of a juvenile lambeosaurine (Ornithischia: Hadrosauridae) bonebed from the late Campanian Wapiti Formation of northwestern Alberta, Canada link: https://peerj.com/articles/11290 last-modified: 2021-05-04 description: Hadrosaurid (duck-billed) dinosaur bonebeds are exceedingly prevalent in upper Cretaceous (Campanian–Maastrichtian) strata from the Midwest of North America (especially Alberta, Canada, and Montana, U.S.A) but are less frequently documented from more northern regions. The Wapiti Formation (Campanian–Maastrichtian) of northwestern Alberta is a largely untapped resource of terrestrial palaeontological information missing from southern Alberta due to the deposition of the marine Bearpaw Formation. In 2018, the Boreal Alberta Dinosaur Project rediscovered the Spring Creek Bonebed, which had been lost since 2002, along the northern bank of the Wapiti River, southwest of Grande Prairie. Earlier excavations and observations of the Spring Creek Bonebed suggested that the site yielded young hadrosaurines. Continued work in 2018 and 2019 recovered ~300 specimens that included a minimum of eight individuals, based on the number of right humeri. The morphology of several recovered cranial elements unequivocally supports lambeosaurine affinities, making the Spring Creek sample the first documented occurrence of lambeosaurines in the Wapiti Formation. The overall size range and histology of the bones found at the site indicate that these animals were uniformly late juveniles, suggesting that age segregation was a life history strategy among hadrosaurids. Given the considerable size attained by the Spring Creek lambeosaurines, they were probably segregated from the breeding population during nesting or caring for young, rather than due to different diet and locomotory requirements. Dynamic aspects of life history, such as age segregation, may well have contributed to the highly diverse and cosmopolitan nature of Late Cretaceous hadrosaurids. creator: Brayden Holland creator: Phil R. Bell creator: Federico Fanti creator: Samantha M. Hamilton creator: Derek W. Larson creator: Robin Sissons creator: Corwin Sullivan creator: Matthew J. Vavrek creator: Yanyin Wang creator: Nicolás E. Campione uri: https://doi.org/10.7717/peerj.11290 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Holland et al. title: The chemical composition of free-range and conventionally-farmed eggs available to Canadians in rural Nova Scotia link: https://peerj.com/articles/11357 last-modified: 2021-05-04 description: In rural Nova Scotia (NS), many small family farms raise free-range hens that consume a varied diet that is different from that of conventionally-farmed hens in caged housing systems. However, it is not known how this varied diet impacts the quality of these eggs. The objective of the present study was to compare the chemical composition of free-range eggs obtained from a small family farm in rural NS to that of conventionally-farmed eggs purchased from a local grocery store. The values obtained from the present study were also compared to published values in the Canadian Nutrient File (CNF) and the U.S. Department of Agriculture FoodData Central database. The egg components and the amino acid compositions were evaluated, and protein concentrations were determined using the Kjeldahl method whereas the fatty acid profiles of the egg yolks were determined using gas chromatography. No difference (P = 0.3) in protein content was observed in free-range eggs (10.6 ± 1.1%) compared to conventionally-farmed eggs (9.7 ± 0.6%). Similar values were also observed for the physical properties of the two types of eggs measured except for the weights of the egg shells. Conversely, the amino acid cysteine, was in higher amounts (P = 0.05) 0.26 g/100 g in the CNF compared to the measured values of ~0.16 g/100 g. Notably, the polyunsaturated linoleic acid (C18:2n-6) was higher (P = 0.001) in the free-range eggs (45.6%) compared to (40.8%) the conventionally-farmed eggs. The cholesterol content of egg yolks was lower in free-range eggs (253.4 ± 0.01 mg/extra-large yolk or 14 mg cholesterol/g of yolk) vs. for conventionally-farmed eggs (263 ± 0.7 mg/extra-large yolk or 15.4 mg cholesterol/g of yolk), respectively. In terms of protein nutrition, free-range eggs may be a suitable alternative to conventionally-farmed eggs, moreover, the lower cholesterol content may be a favourable attribute for Canadian consumers who wish to purchase local free-range eggs. creator: Marcia M. English uri: https://doi.org/10.7717/peerj.11357 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 English title: Effects of extraction methods on protein properties obtained from paddy rice and germinated paddy rice link: https://peerj.com/articles/11365 last-modified: 2021-05-04 description: Rice protein has attracted considerable attention recently due to its physiological effects. This study extracted the proteins from paddy rice (PR) and germinated paddy rice (GPR) using three methods i.e., alkaline, sodium dodecyl sulfate (SDS) reagent and enzymatic extractions. The extracted proteins or protein fractions were assessed for their properties using various techniques. Data were analyzed by 2′3 factorial design experiment. It was found that germination and extraction methods significantly affected the concentration of protein fractions when analyzed by Bradford assay. Average protein fraction concentration of the GPR was lower than that of PR. SDS-PAGE patterns of protein fractions obtained from PR and GPR using any extraction method displayed similar protein profiles. Three major protein bands at about 13 kDa (prolamin), 22–23 kDa (basic glutelin) and 37–39 kDa (acidic glutelin) with small amount of 57 kDa proglutelin were observed. For amino acid profile, germination increased the content of most amino acids, resulting in the higher content of amino acids in GPR, excepted for some amino acids. When processed with in vitro digestion, protein fractions from GPR exhibited a higher level of digestibility than those from PR as evidenced by the less intensity of the protein bands obtained from SDS-PAGE. Alkaline and SDS reagent extractions provided more digestible protein fractions than enzymatic extraction. Extraction methods also influenced phase transition of protein fractions as investigated by a DSC. Alkaline extraction resulted in protein fractions with higher phase transition temperature than the other methods. For antioxidant capacity, extraction methods as well as germination significantly affected antioxidant capacity of the protein fractions. Enzymatic extraction provided protein fractions with the best antioxidant capacity. creator: Wirot Likittrakulwong creator: Pisit Poolprasert creator: Khongsak Srikaeo uri: https://doi.org/10.7717/peerj.11365 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Likittrakulwong et al. title: The Sugar Transporter family in wheat (Triticum aestivum. L): genome-wide identification, classification, and expression profiling during stress in seedlings link: https://peerj.com/articles/11371 last-modified: 2021-05-04 description: The sugar transporter protein (STP) plays a crucial role in regulating plant growth and stress tolerance. We performed genome-wide identification and expression analysis of the STP gene family to investigate the STPSs’ potential roles in the growth of wheat seedlings under stress. Here, a total of 81 TaSTP genes containing the Sugar_tr conserved motif were identified within the wheat genome. Bioinformatic studies including phylogenetic tree, chromosome position, and tandem repeat were performed to analyze the identified genes. The 81 TaSTP genes can be classified into five main groups according to their structural and phylogenetic features, with several subgroups, which were located separately on chromosomes A, B, and D. Moreover, six gene clusters were formed with more than three genes each. The results of three comparative syntenic maps of wheat associated with three representative species suggested that STP genes have strong relationships in monocots. qRT-PCR analysis confirmed that most TaSTP genes displayed different expression profiles after seedlings were subjected to six days of different stress (10% PEG6000, 150 mM NaCl, and their combination, respectively), suggesting that these genes may be involved in regulating plant growth and stress tolerance. In conclusion, 81 TaSTP genes were identified and their expressions changed under stress, indicating TaSTP’s potential roles in wheat growth monosaccharide distribution is regulated. creator: Hongzhan Liu creator: Chaoqiong Li creator: Lin Qiao creator: Lizong Hu creator: Xueqin Wang creator: Junsheng Wang creator: Xianle Ruan creator: Guangyu Yang creator: Guihong Yin creator: Chunping Wang creator: Zhongke Sun creator: Keshi Ma creator: Lili Li uri: https://doi.org/10.7717/peerj.11371 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liu et al. title: Mining TCGA database for gene expression in ovarian serous cystadenocarcinoma microenvironment link: https://peerj.com/articles/11375 last-modified: 2021-05-04 description: BackgroundOvarian cancer is one of the leading causes of female deaths worldwide. Ovarian serous cystadenocarcinoma occupies about 90% of it. Effective and accurate biomarkers for diagnosis, outcome prediction and personalized treatment are needed urgentlyMethodsGene expression profile for OSC patients was obtained from the TCGA database. The ESTIMATE algorithm was used to calculate immune scores and stromal scores of expression data of ovarian serous cystadenocarcinoma samples. Survival results between high and low groups of immune and stromal score were compared and differentially expressed genes (DEGs) were screened out by limma package. The Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and the protein-protein interaction (PPI) network analysis were performed with the g:Profiler database, the Cytoscape and Search Tool for the Retrieval of Interacting Genes (STRING-DB). Survival results between high and low immune and stromal score groups were compared. Kaplan-Meier plots based on TCGA follow up information were generated to evaluate patients’ overall survival.ResultsEighty-six upregulated DEGs and one downregulated DEG were identified. Three modules, which included 49 nodes were chosen as important networks. Seven DEGs (VSIG4, TGFBI, DCN, F13A1, ALOX5AP, GPX3, SFRP4) were considered to be correlated with poor overall survival.ConclusionSeven DEGs (VSIG4, TGFBI, DCN, F13A1, ALOX5AP, GPX3, SFRP4) were correlated with poor overall survival in our study. This new set of genes can become strong predictor of survival, individually or combined. Further investigation of these genes is needed to validate the conclusion to provide novel understanding of tumor microenvironment with ovarian serous cystadenocarcinoma prognosis and treatment. creator: Youzheng Xu creator: Yixin Xu creator: Chun Wang creator: Baoguo Xia creator: Qingling Mu creator: Shaohong Luan creator: Jun Fan uri: https://doi.org/10.7717/peerj.11375 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Xu et al. title: Comprehensive analysis based on DNA methylation and RNA-seq reveals hypermethylation of the up-regulated WT1 gene with potential mechanisms in PAM50 subtypes of breast cancer link: https://peerj.com/articles/11377 last-modified: 2021-05-04 description: BackgroundBreast cancer (BC), one of the most widespread cancers worldwide, caused the deaths of more than 600,000 women in 2018, accounting for about 15% of all cancer-associated deaths in women that year. In this study, we aimed to discover potential prognostic biomarkers and explore their molecular mechanisms in different BC subtypes using DNA methylation and RNA-seq.MethodsWe downloaded the DNA methylation datasets and the RNA expression profiles of primary tissues of the four BC molecular subtypes (luminal A, luminal B, basal-like, and HER2-enriched), as well as the survival information from The Cancer Genome Atlas (TCGA). The highly expressed and hypermethylated genes across all the four subtypes were screened. We examined the methylation sites and the downstream co-expressed genes of the selected genes and validated their prognostic value using a different dataset (GSE20685). For selected transcription factors, the downstream genes were predicted based on the Gene Transcription Regulation Database (GTRD). The tumor microenvironment was also evaluated based on the TCGA dataset.ResultsWe found that Wilms tumor gene 1 (WT1), a transcription factor, was highly expressed and hypermethylated in all the four BC subtypes. All the WT1 methylation sites exhibited hypermethylation. The methylation levels of the TSS200 and 1stExon regions were negatively correlated with WT1 expression in two BC subtypes, while that of the gene body region was positively associated with WT1 expression in three BC subtypes. Patients with low WT1 expression had better overall survival (OS). Five genes including COL11A1, GFAP, FGF5, CD300LG, and IGFL2 were predicted as the downstream genes of WT1. Those five genes were dysregulated in the four BC subtypes. Patients with a favorable 6-gene signature (low expression of WT1 and its five predicted downstream genes) exhibited better OS than that with an unfavorable 6-gene signature. We also found a correlation between WT1 and tamoxifen using STITCH. Higher infiltration rates of CD8 T cells, plasma cells, and monocytes were found in the lower quartile WT1 group and the favorable 6-gene signature group. In conclusion, we demonstrated that WT1 is hypermethylated and up-regulated in the four BC molecular subtypes and a 6-gene signature may predict BC prognosis. creator: Chongyang Ren creator: Xiaojiang Tang creator: Haitao Lan uri: https://doi.org/10.7717/peerj.11377 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ren et al. title: Bootstrap methods can help evaluate monitoring program performance to inform restoration as part of an adaptive management program link: https://peerj.com/articles/11378 last-modified: 2021-05-04 description: The objective of many fish and wildlife restoration programs is to utilize management actions to change the state of a system. Because restoration programs are often expensive, iteratively assessing whether the restoration is having the desired outcome is a critical aspect of learning how to inform ongoing and sampling designs to evaluate proposed restoration programs. We provide an example of how we are using data resampling as part of an adaptive restoration process to test the effectiveness of a restoration action and associated monitoring program to restore the degraded Lone Cabbage oyster reef in Suwannee Sound, Florida in the northeast Gulf of Mexico. We use a resampling framework through simulations to inform the progress of the restoration efforts by examining the direction and magnitude of the differences in live oyster counts between restored and unrestored (wild) reefs over time. In addition, we evaluated the effort (number of sites sampled) needed to determine the effect of restoration to understand how many surveys should be conducted in subsequent sampling seasons. These efforts allow us to provide timely insight into the effectiveness of both our monitoring efforts and restoration strategy which is of critical importance not only to the restoration of Lone Cabbage Reef but to larger restoration efforts within the Gulf of Mexico as part of the consolidated Deepwater Horizon settlements and funded restoration efforts. creator: Jennifer F. Moore creator: William E. Pine III uri: https://doi.org/10.7717/peerj.11378 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Moore and Pine III title: The autistic-like behaviors development during weaning and sexual maturation in VPA-induced autistic-like rats is accompanied by gut microbiota dysbiosis link: https://peerj.com/articles/11103 last-modified: 2021-05-03 description: Researches on gut microbiota in autism have mostly focused on children, but the dynamic changes of gut microbiota from weaning to adulthood were still not clear because of the difficulty of diagnosing autism. In this study, autistic-like rats indued by valproate (VPA) were tracked from weaning (end of breastfeeding; four weeks old) to sexual maturation (food; eight weeks old). Autistic-like rats were found to show obvious developmental disorders. During weaning, autistic-like rats only exhibited obvious repetitive stereotyped behaviors, but the autistic-like behaviors were fully apparent upon sexual maturation. Significant differences were observed between the gut microbiota of autistic-like and healthy rats across both age groups. The correlation analysis results revealed that the correlation between behaviors and some microbiota, especially Helicobacter, did not vary with age or diet. The total amount of short-chain fatty acids (SCFAs) decreased, butyric acid metabolism decreased, and propionic acid metabolism increased in the feces of autistic-like rats. The correlation between autistic-like behaviors and the butyric acid and propionic acid levels did not vary with diet or age. Inositol phosphate metabolism, amino acid metabolism, and lipopolysaccharide biosynthesis were significantly associated with autistic-like behaviors. Our results showed that although the microbiota and SCFAs related to autism were affected by age and diet, some remained consistent irrespective of age and diet, and they could be considered two of the factors related to autistic-like behaviors development. creator: Qingmin Kong creator: Peijun Tian creator: Jianxin Zhao creator: Hao Zhang creator: Gang Wang creator: Wei Chen uri: https://doi.org/10.7717/peerj.11103 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kong et al. title: A new phylogenetic hypothesis of Tanystropheidae (Diapsida, Archosauromorpha) and other “protorosaurs”, and its implications for the early evolution of stem archosaurs link: https://peerj.com/articles/11143 last-modified: 2021-05-03 description: The historical clade “Protorosauria” represents an important group of archosauromorph reptiles that had a wide geographic distribution between the Late Permian and Late Triassic. “Protorosaurs” are characterized by their long necks, which are epitomized in the genus Tanystropheus and in Dinocephalosaurus orientalis. Recent phylogenetic analyses have indicated that “Protorosauria” is a polyphyletic clade, but the exact relationships of the various “protorosaur” taxa within the archosauromorph lineage is currently uncertain. Several taxa, although represented by relatively complete material, have previously not been assessed phylogenetically. We present a new phylogenetic hypothesis that comprises a wide range of archosauromorphs, including the most exhaustive sample of “protorosaurs” to date and several “protorosaur” taxa from the eastern Tethys margin that have not been included in any previous analysis. The polyphyly of “Protorosauria” is confirmed and therefore we suggest the usage of this term should be abandoned. Tanystropheidae is recovered as a monophyletic group and the Chinese taxa Dinocephalosaurus orientalis and Pectodens zhenyuensis form a new archosauromorph clade, Dinocephalosauridae, which is closely related to Tanystropheidae. The well-known crocopod and former “protorosaur” Prolacerta broomi is considerably less closely related to Archosauriformes than was previously considered. creator: Stephan N.F. Spiekman creator: Nicholas C. Fraser creator: Torsten M. Scheyer uri: https://doi.org/10.7717/peerj.11143 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Spiekman et al. title: Predictors of work-related musculoskeletal symptoms in shoulders among nursing assistants working in nursing homes link: https://peerj.com/articles/11152 last-modified: 2021-05-03 description: Nursing assistants (NAs) working in nursing homes (NHs) are at higher risk for work-related musculoskeletal symptoms (WRMSs) than their counterparts working in other health care settings. Worldwide, NAs have ranked shoulders in the top three body parts at risk of WRMSs. However, factors associated with their shoulder WRMSs are currently unknown. The aim of this study was to identify these associated risk factors among NAs working in NHs. 440 NAs from 47 nursing homes (with 60–90% response rate from each nursing home), recruited by convenience sampling, participated in this cross-sectional study in 2014–2015. A validated and reliable questionnaire was used for data collection. Information on demographic, job content questionnaire (JCQ), perceived physical exertion (PE), workstyle, ergonomic and manual handling knowledge and other work-related factors was collected using a self-administered questionnaire. 53% of the participants reported experiencing with WRMSs in their shoulders. Nine associated factors of shoulder WRMSs were identified using bivariate analysis. With the adjustment of age and gender using multivariable logistic regression, body mass index (OR = .931, 95% CI [.874–.991]), job title of health workers (OR = 2.72, 95% CI [1.18–6.25]) and workstyle-working through pain (OR = 1.06, 95% CI [1.01–1.11]) remained as predictors. Effort should be directed at integrating “workstyle intervention” into lifestyle physical activity training for NAs. creator: Kin Cheung creator: Ka Yan Ma creator: Hin Hei Cheung creator: Chun Ho Lee creator: In Mink Mavis Chan creator: Sin Ting Cheung creator: Wing Yee Chung creator: Sun Sun Yeung creator: Wing Chi Lo uri: https://doi.org/10.7717/peerj.11152 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Cheung et al. title: Intact tactile anisotropy despite altered hand perception in complex regional pain syndrome: rethinking the role of the primary sensory cortex in tactile and perceptual dysfunction link: https://peerj.com/articles/11156 last-modified: 2021-05-03 description: Complex Regional Pain Syndrome (CRPS) is characterised by pain, autonomic, sensory and motor abnormalities. It is associated with changes in the primary somatosensory cortex (S1 representation), reductions in tactile sensitivity (tested by two-point discrimination), and alterations in perceived hand size or shape (hand perception). The frequent co-occurrence of these three phenomena has led to the assumption that S1 changes underlie tactile sensitivity and perceptual disturbances. However, studies underpinning such a presumed relationship use tactile sensitivity paradigms that involve the processing of both non-spatial and spatial cues. Here, we used a task that evaluates anisotropy (i.e., orientation-dependency; a feature of peripheral and S1 representation) to interrogate spatial processing of tactile input in CRPS and its relation to hand perception. People with upper limb CRPS (n = 14) and controls with (n = 15) or without pain (n = 19) judged tactile distances between stimuli-pairs applied across and along the back of either hand to provide measures of tactile anisotropy. Hand perception was evaluated using a visual scaling task and questionnaires. Data were analysed with generalised estimating equations. Contrary to our hypotheses, tactile anisotropy was bilaterally preserved in CRPS, and the magnitude of anisotropic perception bias was comparable between groups. Hand perception was distorted in CRPS but not related to the magnitude of anisotropy or bias. Our results suggest against impairments in spatial processing of tactile input, and by implication S1 representation, as the cause of distorted hand perception in CRPS. Further work is warranted to elucidate the mechanisms of somatosensory dysfunction and distorted hand perception in CRPS. creator: Annika Reinersmann creator: Ian W. Skinner creator: Thomas Lücke creator: Nicola Massy-Westropp creator: Henrik Rudolf creator: G. Lorimer Moseley creator: Tasha R. Stanton uri: https://doi.org/10.7717/peerj.11156 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Reinersmann et al. title: Coverage and quality of DNA barcode references for Central and Northern European Odonata link: https://peerj.com/articles/11192 last-modified: 2021-05-03 description: BackgroundDragonflies and damselflies (Odonata) are important components in biomonitoring due to their amphibiotic lifecycle and specific habitat requirements. They are charismatic and popular insects, but can be challenging to identify despite large size and often distinct coloration, especially the immature stages. DNA-based assessment tools rely on validated DNA barcode reference libraries evaluated in a supraregional context to minimize taxonomic incongruence and identification mismatches.MethodsThis study reports on findings from the analysis of the most comprehensive DNA barcode dataset for Central European Odonata to date, with 103 out of 145 recorded European species included and publicly deposited in the Barcode of Life Data System (BOLD). The complete dataset includes 697 specimens (548 adults, 108 larvae) from 274 localities in 16 countries with a geographic emphasis on Central Europe. We used BOLD to generate sequence divergence metrics and to examine the taxonomic composition of the DNA barcode clusters within the dataset and in comparison with all data on BOLD.ResultsOver 88% of the species included can be readily identified using their DNA barcodes and the reference dataset provided. Considering the complete European dataset, unambiguous identification is hampered in 12 species due to weak mitochondrial differentiation and partial haplotype sharing. However, considering the known species distributions only two groups of five species possibly co-occur, leading to an unambiguous identification of more than 95% of the analysed Odonata via DNA barcoding in real applications. The cases of small interspecific genetic distances and the observed deep intraspecific variation in Cordulia aenea (Linnaeus, 1758) are discussed in detail and the corresponding taxa in the public reference database are highlighted. They should be considered in future applications of DNA barcoding and metabarcoding and represent interesting evolutionary biological questions, which call for in depth analyses of the involved taxa throughout their distribution ranges. creator: Matthias Geiger creator: Stephan Koblmüller creator: Giacomo Assandri creator: Andreas Chovanec creator: Torbjørn Ekrem creator: Iris Fischer creator: Andrea Galimberti creator: Michał Grabowski creator: Elisabeth Haring creator: Axel Hausmann creator: Lars Hendrich creator: Stefan Koch creator: Tomasz Mamos creator: Udo Rothe creator: Björn Rulik creator: Tomasz Rewicz creator: Marcia Sittenthaler creator: Elisabeth Stur creator: Grzegorz Tończyk creator: Lukas Zangl creator: Jerome Moriniere uri: https://doi.org/10.7717/peerj.11192 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Geiger et al. title: Self-compassion, ego-resiliency, coping with stress and the quality of life of parents of children with autism spectrum disorder link: https://peerj.com/articles/11198 last-modified: 2021-05-03 description: BackgroundThe literature shows a fairly coherent picture of the types of difficulties parents face. Adaptive both coping styles and resources, such as self-compassion and ego-resiliency, indicated as important predictors of the quality of life among parents of children with autism spectrum disorder. The aim of the study was to determine the links between self-compassion and ego-resiliency, coping with stress and quality of life among parents of children with autism spectrum disorder in a Polish sample (N = 76).MethodsA cross-sectional study was conducted. The CISS, Self-Compassion Scale-Short, Ego-Resiliency Scale, and Quality of Life Questionnaire were used.ResultsRegression analysis was carried out to address the research question. It was confirmed that both resources studied exhibited negative relations with emotion-oriented coping, while ego-resiliency was also positively correlated with task- and avoidance-oriented strategies. The hierarchical multiple regression conducted in three steps indicated that ego-resiliency (18%) and emotion-oriented (14%) were the strongest predictors of quality of life among parents of children with ASD.ConclusionsThe obtained results proved that ego-resiliency and a task-oriented coping strategy were important indicators of the quality of life of parents of children with ASD. creator: Anna Pyszkowska creator: Kamila Wrona uri: https://doi.org/10.7717/peerj.11198 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Pyszkowska and Wrona title: Lactobacillus reuteri TSR332 and Lactobacillus fermentum TSF331 stabilize serum uric acid levels and prevent hyperuricemia in rats link: https://peerj.com/articles/11209 last-modified: 2021-05-03 description: BackgroundUric acid (UA) is the end product of purine metabolism in the liver and is excreted by the kidneys. When purine metabolism is impaired, the serum UA level will be elevated (hyperuricemia) and eventually lead to gout. During evolution, humans and some primates have lost the gene encoding uricase, which is vital in UA metabolism. With the advances of human society, the prevalence of hyperuricemia has dramatically increased because of the refined food culture. Hyperuricemia can be controlled by drugs, such as allopurinol and probenecid. However, these drugs have no preventive effect and are associated with unpleasant side effects. An increasing number of probiotic strains, which are able to regulate host metabolism and prevent chronic diseases without harmful side effects, have been characterized. The identification of probiotic strains, which are able to exert beneficial effects on UA metabolism, will provide an alternative healthcare strategy for patients with hyperuricemia, especially for those who are allergic to anti-hyperuricemia drugs.MethodsTo elicit hyperuricemia, rats in the symptom control group (HP) were injected with potassium oxonate and fed a high-purine diet. Rats in the probiotic groups received the high-purine diet, oxonate injection, and supplements of probiotic strains TSR332, TSF331, or La322. Rats in the blank control group (C) received a standard diet (AIN-93G) and oxonate injection.ResultsPurine-utilizing strains of probiotics were screened using high-pressure liquid chromatography (HPLC) in vitro, and the lowering effect on serum UA levels was analyzed in hyperuricemia rats in vivo. We found that Lactobacillus reuteri strain TSR332 and Lactobacillus fermentum strain TSF331 displayed significantly strong assimilation of inosine (90%; p = 0.00003 and 59%; p = 0.00545, respectively) and guanosine (78%; p = 0.00012 and 51%; p = 0.00062, respectively) within 30 min in vitro. Further animal studies revealed that serum UA levels were significantly reduced by 60% (p = 0.00169) and 30% (p = 0.00912), respectively, in hyperuricemic rats treated with TSR332 and TSF331 for 8 days. Remarkably, TSR332 ameliorated the occurrence of hyperuricemia, and no evident side effects were observed. Overall, our study indicates that TSR332 and TSF331 are potential functional probiotic strains for controlling the development of hyperuricemia. creator: Yi-Wei Kuo creator: Shih-Hung Hsieh creator: Jui-Fen Chen creator: Cheng-Ruei Liu creator: Ching-Wei Chen creator: Yu-Fen Huang creator: Hsieh-Hsun Ho uri: https://doi.org/10.7717/peerj.11209 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kuo et al. title: Molecular evidence for cross boundary spread of Salmonella spp. in meat sold at retail markets in the middle Mekong basin area link: https://peerj.com/articles/11255 last-modified: 2021-05-03 description: BackgroundThe surrounding areas of the middle Mekong basin, particularly along the border between Thailand and Lao People’s Democratic Republic (Lao PDR), are high-risk areas for many livestock-associated foodborne illnesses, especially salmonellosis. This study aimed to determine the prevalence and characteristics of Salmonella spp. contamination in pork, beef and chicken meats sold at retail markets in the Thailand-Laos border area surrounding the Thai-Lao Friendship Bridge I from January to May 2019. We focused on the prevalent serotypes, antimicrobial susceptibility profiles and the multilocus sequence type (MLST) genotypes of the collected Salmonella strains.ResultsFrom a total of 370 meat samples collected, 63% were positive for Salmonella, with the prevalence of 73%, 60% and 56% from pork, beef and chicken meat samples, respectively. Of all the positive samples, 53 serotypes were identified. Of these, Salmonella enterica serovar London accounted for the majority (27%), followed by serovars Corvallis (14%), and Rissen (6%). Resistance against tetracycline was found at the highest frequency (50%), followed by ampicillin (35%) and sulfamethoxazole-trimethoprim (28%). MLST revealed no evidence of shared genetic relatedness of Salmonella at retail sites among Thailand-Laos border zone. However, a diverse range of Salmonella genotypes were spread over the area. Besides, the persistence of the residential pathogen and sharing of the supply route within-country can be inferred.ConclusionsGiven the high levels of contamination of retail meats, regular disinfecting of all working areas and quality control checking at pre-retail stage must be applied to reduce the transmission of Salmonella and other foodborne pathogens to consumers. The findings of this study will make a significant contribution to the current understanding of Salmonella epidemiology to enhance food security in the region. creator: Dethaloun Meunsene creator: Thanaporn Eiamsam-ang creator: Prapas Patchanee creator: Ben Pascoe creator: Phacharaporn Tadee creator: Pakpoom Tadee uri: https://doi.org/10.7717/peerj.11255 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Meunsene et al. title: Prediction of DNA binding proteins using local features and long-term dependencies with primary sequences based on deep learning link: https://peerj.com/articles/11262 last-modified: 2021-05-03 description: DNA-binding proteins (DBPs) play pivotal roles in many biological functions such as alternative splicing, RNA editing, and methylation. Many traditional machine learning (ML) methods and deep learning (DL) methods have been proposed to predict DBPs. However, these methods either rely on manual feature extraction or fail to capture long-term dependencies in the DNA sequence. In this paper, we propose a method, called PDBP-Fusion, to identify DBPs based on the fusion of local features and long-term dependencies only from primary sequences. We utilize convolutional neural network (CNN) to learn local features and use bi-directional long-short term memory network (Bi-LSTM) to capture critical long-term dependencies in context. Besides, we perform feature extraction, model training, and model prediction simultaneously. The PDBP-Fusion approach can predict DBPs with 86.45% sensitivity, 79.13% specificity, 82.81% accuracy, and 0.661 MCC on the PDB14189 benchmark dataset. The MCC of our proposed methods has been increased by at least 9.1% compared to other advanced prediction models. Moreover, the PDBP-Fusion also gets superior performance and model robustness on the PDB2272 independent dataset. It demonstrates that the PDBP-Fusion can be used to predict DBPs from sequences accurately and effectively; the online server is at http://119.45.144.26:8080/PDBP-Fusion/. creator: Guobin Li creator: Xiuquan Du creator: Xinlu Li creator: Le Zou creator: Guanhong Zhang creator: Zhize Wu uri: https://doi.org/10.7717/peerj.11262 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: Assessing kinesthetic proprioceptive function of the upper limb: a novel dynamic movement reproduction task using a robotic arm link: https://peerj.com/articles/11301 last-modified: 2021-05-03 description: BackgroundProprioception refers to the perception of motion and position of the body or body segments in space. A wide range of proprioceptive tests exists, although tests dynamically evaluating sensorimotor integration during upper limb movement are scarce. We introduce a novel task to evaluate kinesthetic proprioceptive function during complex upper limb movements using a robotic device. We aimed to evaluate the test–retest reliability of this newly developed Dynamic Movement Reproduction (DMR) task. Furthermore, we assessed reliability of the commonly used Joint Reposition (JR) task of the elbow, evaluated the association between both tasks, and explored the influence of visual information (viewing arm movement or not) on performance during both tasks.MethodsDuring the DMR task, participants actively reproduced movement patterns while holding a handle attached to the robotic arm, with the device encoding actual position throughout movement. In the JR task, participants actively reproduced forearm positions; with the final arm position evaluated using an angle measurement tool. The difference between target movement pattern/position and reproduced movement pattern/position served as measures of accuracy. In study 1 (N = 23), pain-free participants performed both tasks at two test sessions, 24-h apart, both with and without visual information available (i.e., vision occluded using a blindfold). In study 2 (N = 64), an independent sample of pain-free participants performed the same tasks in a single session to replicate findings regarding the association between both tasks and the influence of visual information.ResultsThe DMR task accuracy showed good-to-excellent test–retest reliability, while JR task reliability was poor: measurements did not remain sufficiently stable over testing days. The DMR and JR tasks were only weakly associated. Adding visual information (i.e., watching arm movement) had different performance effects on the tasks: it increased JR accuracy but decreased DMR accuracy, though only when the DMR task started with visual information available (i.e., an order effect).DiscussionThe DMR task’s highly standardized protocol (i.e., largely automated), precise measurement and involvement of the entire upper limb kinetic chain (i.e., shoulder, elbow and wrist joints) make it a promising tool. Moreover, the poor association between the JR and DMR tasks indicates that they likely capture unique aspects of proprioceptive function. While the former mainly captures position sense, the latter appears to capture sensorimotor integration processes underlying kinesthesia, largely independent of position sense. Finally, our results show that the integration of visual and proprioceptive information is not straightforward: additional visual information of arm movement does not necessarily make active movement reproduction more accurate, on the contrary, when movement is complex, vision appears to make it worse. creator: Kristof Vandael creator: Tasha R. Stanton creator: Ann Meulders uri: https://doi.org/10.7717/peerj.11301 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Vandael et al. title: Association of sleep duration and sleep quality with hypertension in oil workers in Xinjiang link: https://peerj.com/articles/11318 last-modified: 2021-05-03 description: ObjectiveThe aim of this study is to explore sleep status and hypertension among oil workers in Xinjiang, China. It may provide new ideas and basis for the precise prevention and treatment of hypertension in occupational population.MethodsSleep status and hypertension were investigated in 3,040 workers by a multi-stage cluster sampling method in six oil field bases in Karamay City, Xinjiang. The Pittsburgh Sleep Quality Index was used to evaluate the sleep status of workers. Logistic regression was used to analyze the relationship between sleep duration and sleep quality, and hypertension. Stratified analysis was also performed.ResultsOur results show: 1. Insufficient sleep duration (OR = 1.51, 95% CI [1.19–1.90]) and poor sleep quality (OR = 1.78, 95% CI [1.33–2.38] were positively associated with hypertension. 2. Stratified analysis indicated insufficient sleep duration was associated with increased risk of hypertension in females (OR = 1.54, 95% CI [1.16–2.04]) than males (OR = 1.49, 95% CI [1.00–2.23]), and the risk of hypertension in the group <30 years old (OR = 9.03, 95% CI [2.32–35.15]) was higher than that in the group of 30–45 years old (OR = 1.59, 95% CI [1.14–2.20]). However, in the group > 45 years old, sleeping > 8 h was associated with increased risk of hypertension (OR = 3.36, 95% CI [1.42–7.91]). Oil workers doing shift work had a higher risk of hypertension (OR = 1.55, 95% CI [1.16–2.07]) to no shift work (OR = 1.48, 95% CI [1.02–2.15]). The risk of hypertension in the group with < 10 years of service (OR = 4.08, 95% CI [1.92–8.83]) was higher than that in the group with length of service of 10–20 years (OR = 2.79, 95% CI [1.59–4.86]). Poor sleep quality was associated with risk for hypertension in females (OR = 1.78, 95% CI [1.26–2.49]), those doing shift work (OR = 1.70, 95% CI [1.17–2.47]), those with length of service of > 20 years (OR = 1.64, 95% CI [1.18–2.27]). The risk of hypertension in the group 30–45 years old is higher than that in the group > 45 years old (OR30–45 years old = 1.71, 95% CI [1.10–2.66]; OR > 45 years old = 1.60, 95% CI [1.09–2.34]). ConclusionInsufficient sleep duration and poor sleep quality are the potential factors affecting hypertension in Xinjiang oil workers. creator: Fen Yang creator: Yuanyue Zhang creator: Ruiying Qiu creator: Ning Tao uri: https://doi.org/10.7717/peerj.11318 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yang et al. title: Outcomes of critically ill end-stage kidney disease patients who underwent major surgery link: https://peerj.com/articles/11324 last-modified: 2021-05-03 description: PurposeEnd-stage kidney disease (ESKD) is a major worldwide health problem. Patients with ESKD are thought to have a significant risk for development of complications following an operation. However, the study of ESKD and its outcomes following major operations remains rare, particularly in critical illness. Therefore, this study aimed to demonstrate how the outcomes of ESKD patients were affected when they underwent a major operation and were admitted to the intensive care unit (ICU), compared with non-ESKD patients.MethodsA retrospective matched case cohort study was conducted in 122 critically ill surgical patients who underwent a major operation and were admitted to the ICU, during 2013 and 2016. Sixty-one ESKD patients who required long-term dialysis were enrolled and compared with 61 matched non-ESKD patients. The matching criteria were the same age interval (±5 years), gender, and type of operation. The ICU mortality was compared to the primary outcome of the study.ResultsPatients’ baseline characteristics between ESKD and non-ESKD were similar to a priori matching criteria and other demographics, except for pre-existing diabetes mellitus and hypertension, which were found significantly more in ESKD (p = 0.03 and 0.04, respectively). For operations, ESKD showed a higher grade of the American Society of Anesthesiologist (ASA) physical status (p < 0.001), but there were no differences for emergency surgery (p = 0.71) and duration of operation (p = 0.34). At ICU admission, the severity of illness measured by the Sequential Organ Failure Assessment (SOFA) score was greater in ESKD (8.9 ± 2.6 vs 5.6 ± 2.5; p < 0.001). However, after eliminating renal domain, SOFA non-renal score was equivalent (5.7 ± 2.2 vs 5.2 ± 2.3, p = 0.16). The ICU mortality was significantly higher in critically-ill surgical patients with ESKD than non-ESKD (23% vs 5%, p=0.007), along with hospital mortality rates (34% vs 10%, p = 0.002). The multivariable logistic regression analyses adjusted for age and SOFA non-renal score demonstrated that ESKD had a significant association with ICU and hospital mortality (adjOR = 5.59; 95%CI [1.49–20.88], p = 0.01 and adjOR = 4.55; 95%CI[1.67–12.44], p = 0.003, respectively).ConclusionPatients who underwent a major operation and needed intensive care admission with pre-existing ESKD requiring long-term dialysis were associated with greater mortality than patients without ESKD. More careful assessment before, during, and after major surgical procedures should be performed in this group of patients to improve post-operative outcomes. creator: Peerawitch Petchmak creator: Yuthapong Wongmahisorn creator: Konlawij Trongtrakul uri: https://doi.org/10.7717/peerj.11324 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Petchmak et al. title: Genetic diversity and population structure analysis in a large collection of white clover (Trifolium repens L.) germplasm worldwide link: https://peerj.com/articles/11325 last-modified: 2021-05-03 description: White clover is an important temperate legume forage with high nutrition. In the present study, 448 worldwide accessions were evaluated for the genetic variation and polymorphisms using 22 simple sequence repeat (SSR) markers. All the markers were highly informative, a total of 341 scored bands were amplified, out of which 337 (98.83%) were polymorphic. The PIC values ranged from 0.89 to 0.97 with an average of 0.95. For the AMOVA analysis, 98% of the variance was due to differences within the population and the remaining 2% was due to differences among populations. The white clover accessions were divided into different groups or subgroups based on PCoA, UPGMA, and STRUCTURE analyses. The existence of genetic differentiation between the originally natural and introduced areas according to the PCoA analysis of the global white clover accessions. There was a weak correlation between genetic relationships and geographic distribution according to UPGMA and STRUCTURE analyses. The results of the present study will provide the foundation for future breeding programs, genetic improvement, core germplasm collection establishment for white clover. creator: Feifei Wu creator: Sainan Ma creator: Jie Zhou creator: Chongyang Han creator: Ruchang Hu creator: Xinying Yang creator: Gang Nie creator: Xinquan Zhang uri: https://doi.org/10.7717/peerj.11325 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wu et al. title: Local patterns of arbuscular mycorrhizal fungal diversity and community structure in a natural Toona ciliata var. pubescens forest in South Central China link: https://peerj.com/articles/11331 last-modified: 2021-05-03 description: Toona ciliata var. pubescens (Toona in Meliaceae) (Tc) is listed as an endangered species, and there are natural regeneration obstacles due to its long-term excessive exploitation and utilization. Arbuscular mycorrhizal fungi (AMF) can produce beneficial effects for plant growth and natural regeneration. However, the characteristics of the AMF community in natural Tc forests are poorly understood. The Illumina PE250 high-throughput sequencing method was used to study the characteristics of the AMF community in the rhizosphere soil and roots associated with three dominant tree species (Tc; Padus buergeriana, Pb; and Maesa japonica, Mj) in a natural Tc forest in Guanshan National Natural Reserve, South Central China. The results found that Glomeraceae was the most abundant AMF family in the rhizosphere soil and roots. Moreover, the relative abundance of Archaeosporaceae in rhizosphere soil was significantly larger than that in the roots; in contrast, the relative abundance of Glomeraceae in rhizosphere soil was significantly lower than that in the roots (p < 0.05). Regarding different tree species, the relative abundances of Acaulosporaceae and Geosiphonaceae were larger in Mj and Tc than in Pb. AMF operational taxonomic units (OTUs) were 1.30-, 1.43-, and 1.71-fold higher in the Tc, Pb, and Mj rhizosphere soil, respectively, than in the corresponding roots. Nevertheless, higher AMF community richness was found in the roots compared to that in the rhizosphere soil based on the Chao index. This finding indicated that AMF of a relatively high aggregation degree were in roots, and more AMF groups with relatively low abundance occurred in the rhizosphere soil, which correspondingly lowered the calculated richness index of the AMF community. A redundancy analysis showed that different soil chemical properties impacted variations in the AMF community characteristics differently. This study has great significance for the interpretation of AMF diversity survey and the application design of AMF in vegetation restoration. creator: Jianfeng Pan creator: Qiong Wang creator: Xiaoyan Guo creator: Xueru Jiang creator: Qiangqiang Cheng creator: Li Fu creator: Wei Liu creator: Lu Zhang uri: https://doi.org/10.7717/peerj.11331 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Pan et al. title: re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files link: https://peerj.com/articles/11333 last-modified: 2021-05-03 description: BackgroundHigh-throughput sequencing platforms generate a massive amount of high-dimensional genomic datasets that are available for analysis. Modern and user-friendly bioinformatics tools for analysis and interpretation of genomics data becomes essential during the analysis of sequencing data. Different standard data types and file formats have been developed to store and analyze sequence and genomics data. Variant Call Format (VCF) is the most widespread genomics file type and standard format containing genomic information and variants of sequenced samples.ResultsExisting tools for processing VCF files don’t usually have an intuitive graphical interface, but instead have just a command-line interface that may be challenging to use for the broader biomedical community interested in genomics data analysis. re-Searcher solves this problem by pre-processing VCF files by chunks to not load RAM of computer. The tool can be used as standalone user-friendly multiplatform GUI application as well as web application (https://nla-lbsb.nu.edu.kz). The software including source code as well as tested VCF files and additional information are publicly available on the GitHub repository (https://github.com/LabBandSB/re-Searcher). creator: Daniyar Karabayev creator: Askhat Molkenov creator: Kaiyrgali Yerulanuly creator: Ilyas Kabimoldayev creator: Asset Daniyarov creator: Aigul Sharip creator: Ainur Ashenova creator: Zhaxybay Zhumadilov creator: Ulykbek Kairov uri: https://doi.org/10.7717/peerj.11333 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2021 Karabayev et al. title: Centromere protein N may be a novel malignant prognostic biomarker for hepatocellular carcinoma link: https://peerj.com/articles/11342 last-modified: 2021-05-03 description: BackgroundHepatocellular carcinoma (HCC) is one of the deadliest tumors. The majority of HCC is detected in the late stage, and the clinical results for HCC patients are poor. There is an urgent need to discover early diagnostic biomarkers and potential therapeutic targets for HCC.MethodsThe GSE87630 and GSE112790 datasets from the Gene Expression Omnibus (GEO) database were downloaded to analyze the differentially expressed genes (DEGs) between HCC and normal tissues. R packages were used for Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses of the DEGs. A Search Tool for Retrieval of Interacting Genes (STRING) database was used to develop a protein-protein interaction (PPI) network, and also cytoHubba, Molecular Complex Detection (MCODE), EMBL-EBI, CCLE, Gene Expression Profiling Interactive Analysis (GEPIA), and Oncomine analyses were performed to identify hub genes. Gene expression was verified with a third GEO dataset, GSE25097. The Cancer Genome Atlas (TCGA) database was used to explore the correlations between the hub genes and clinical indexes of HCC patients. The functions of the hub genes were enriched by gene set enrichment analysis (GSEA), and the biological significance of the hub genes was explored by real-time polymerase chain reaction (qRT-PCR), western blot, immunofluorescence, CCK-8, colony formation, Transwell and flow cytometry assays with loss-of-function experiments in vitro.ResultsCentromere protein N (CENPN) was screened as a hub gene affecting HCC tumorigenesis. Evaluation by Cox regression showed that a high level of CENPN expression was an independent danger variable for poor prognosis of HCC. GSEA showed that high CENPN expression was linked to the following pathways: liver cancer subclass proliferation, cell cycle, p53 signaling pathway, Rb1 pathway, positive regulation of cell cycle G1/S phase transition, and DNA damage response signal transduction by p53 class moderators. Further cell experiments showed that knocking down CENPN expression decreased the proliferation and colony-forming abilities of HepG2 and Huh7 cells as well as Ki67 expression in these cell lines. The cell cycle was arrested in G1 phase, which is consistent with previous experiments on CENPN downregulation., but neither migration nor invasion were significantly affected. Western blot results revealed that the expression of p53, p27, p21, CDK4, cyclin D1, CDK2, cyclin E, pRb, E2F1 and c-myc decreased after CENPN knockdown, but there was no significant change in total Rb levels. In addition, CENPN-knockdown cells subjected to irradiation showed significantly enhanced of γ-H2AX expression and reduced colony formation.ConclusionCENPN functions as an oncogene in HCC and may be a therapeutic target and promising prognostic marker for HCC. creator: Qingqing Wang creator: Xiaoyan Yu creator: Zhewen Zheng creator: Fengxia Chen creator: Ningning Yang creator: Yunfeng Zhou uri: https://doi.org/10.7717/peerj.11342 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Serum metabolomic profiling reveals an increase in homocitrulline in Chinese patients with nonalcoholic fatty liver disease: a retrospective study link: https://peerj.com/articles/11346 last-modified: 2021-05-03 description: BackgroundsNonalcoholic fatty liver disease (NAFLD) has multiple causes, is triggered by individual genetic susceptibility, environmental factors, and metabolic disturbances, and may be triggered by acquired metabolic stress. The metabolic profiles of NAFLD show significant ethnic differences, and the metabolic characteristics of NAFLD in Chinese individuals are unclear. Our study aimed to identify the metabolites and pathways associated with NAFLD in a Chinese cohort.MethodsOne hundred participants, including 50 NAFLD patients and 50 healthy controls, were enrolled in this retrospective observational study at Jinling Hospital in Nanjing; serum samples were collected from the patients and healthy subjects. The metabolome was determined in all samples by liquid chromatography-hybrid quadrupole time-of-flight mass spectrometry (LC-Q/TOF-MS). Univariate and multivariate statistical analyses were used to compare the metabolic profiles between the two groups.ResultsThe comparison indicated that the levels of 89 metabolites were different between the two groups. The glycerophospholipid family of metabolites was the most abundant family of metabolites that demonstrated significant differences. L-acetylcarnitine, L-homocitrulline, and glutamic acid were the top three metabolites ranked by VIP score and had favorable effective functions for diagnosis. Moreover, pathway enrichment analysis suggested 14 potentially different metabolic pathways between NAFLD patients and healthy controls based on their impact value. Biological modules involved in the lipid and carbohydrate metabolism had the highest relevance to the conditions of NAFLD. Glycerophospholipid metabolism had the strongest associations with the conditions of NAFLD.ConclusionsOur data suggest that the serum metabolic profiles of NAFLD patients and healthy controls are different. L-Homocitrulline was remarkably increased in NAFLD patients. creator: Yarong Yang creator: Zexin Huang creator: Zhao Yang creator: Ying Qi creator: Hui Shi creator: Yifei Zhou creator: Fangyu Wang creator: Miaofang Yang uri: https://doi.org/10.7717/peerj.11346 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yang et al. title: Sphenofontis velserae gen. et sp. nov., a new rhynchocephalian from the Late Jurassic of Brunn (Solnhofen Archipelago, southern Germany) link: https://peerj.com/articles/11363 last-modified: 2021-05-03 description: The Solnhofen Archipelago is well known for its fossil vertebrates of Late Jurassic age, among which figure numerous rhynchocephalian specimens, representing at least six and up to nine genera. A new taxon, named Sphenofontis velserae gen. et sp. nov., increases rhynchocephalian diversity in the Solnhofen Archipelago and is herein described based on a single, well-preserved specimen originating from the Late Kimmeridgian of the Brunn quarry, near Regensburg. The exquisite preservation of the holotype allowed a detailed description of the animal, revealing a skeletal morphology that includes both plesiomorphic and derived features within rhynchocephalians. Sphenofontis is herein referred to Neosphenodontia and tentatively to sphenodontine sphenodontids. It notably differs from all other rhynchocephalians known from the Jurassic of Europe, showing instead closer resemblance with the Middle Jurassic Cynosphenodon from Mexico and especially the extant Sphenodon. This is evidence for a wide distribution of taxa related to the extant tuatara early in the Mesozoic, and also for the presence of less-specialized rhynchocephalians coexisting with more derived forms during the earliest time in the history of the Solnhofen Archipelago. creator: Andrea Villa creator: Roel Montie creator: Martin Röper creator: Monika Rothgaenger creator: Oliver W.M. Rauhut uri: https://doi.org/10.7717/peerj.11363 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Villa et al. title: Ecosystem services show variable responses to future climate conditions in the Colombian páramos link: https://peerj.com/articles/11370 last-modified: 2021-05-03 description: BackgroundThe páramos, the high-elevation ecosystems of the northern Andes, are well-known for their high species richness and provide a variety of ecosystem services to local subsistence-based communities and regional urbanizations. Climate change is expected to negatively affect the provision of these services, but the level of this impact is still unclear. Here we assess future climate change impact on the ecosystem services provided by the critically important páramos of the department of Boyacá in Colombia, of which over 25% of its territory is páramo.MethodsWe first performed an extensive literature review to identify useful species of Boyacá, and selected 103 key plant species that, based on their uses, support the provision of ecosystem services in the páramos. We collated occurrence information for each key species and using a Mahalanobis distance approach we applied climate niche modelling for current and future conditions.ResultsWe show an overall tendency of reduction in area for all ecosystem services under future climate conditions (mostly a loss of 10% but reaching up to a loss of 40%), but we observe also increases, and responses differ in intensity loss. Services such as Food for animals, Material and Medicinal, show a high range of changes that includes both positive and negative outcomes, while for Food for humans the responses are mostly substantially negative. Responses are less extreme than those projected for individual species but are often complex because a given ecosystem service is provided by several species. As the level of functional or ecological redundancy between species is not yet known, there is an urgency to expand our knowledge on páramos ecosystem services for more species. Our results are crucial for decision-makers, social and conservation organizations to support sustainable strategies to monitor and mitigate the potential consequences of climate change for human livelihoods in mountainous settings. creator: Mauricio Diazgranados creator: Carolina Tovar creator: Thomas R. Etherington creator: Paula A. Rodríguez-Zorro creator: Carolina Castellanos-Castro creator: Manuel Galvis Rueda creator: Suzette G.A. Flantua uri: https://doi.org/10.7717/peerj.11370 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Diazgranados et al.