title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1046 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Cetaceans along the southeastern Brazilian coast: occurrence, distribution and niche inference at local scale link: https://peerj.com/articles/10000 last-modified: 2020-10-05 description: It is deemed important to understand cetacean occurrence and distribution to comprehend their ecological roles. The geographical occurrence of species’ niche can be used to better describe their potential distribution. The niche can be defined using environmental variables. Those variables are considered static and not affected by biological activities. The present study goal was to assess the occurrence and distribution of cetaceans along the southeastern Brazilian coast, as well as to define the fundamental and realized niche of each species and to investigate niche overlap at local scale. The environmental requirements for each species were also investigated throughout statistical tests. Sighting data were obtained through oceanographic surveys conducted between 2012 and 2015. The environmental variables available on MARSPEC and the software NicheA were used for the ecological niche modeling. A total of twelve cetacean species were identified and the potential distribution areas of the six commonest ones were defined. Even though the species presented different environmental preferences, most of them had partial overlap among niches and potential distribution areas. The environmental heterogeneity of the study area might support the co-occurrence of different species with different environmental requirements. creator: Giovanna Corrêa e Figueiredo creator: Karina Bohrer do Amaral creator: Marcos César de Oliveira Santos uri: https://doi.org/10.7717/peerj.10000 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Figueiredo et al. title: Are giant clams (Tridacna maxima) distractible? A multi-modal study link: https://peerj.com/articles/10050 last-modified: 2020-10-05 description: To properly assess risk, an animal must focus its attention on relevant external stimuli; however, attention can be reallocated when distracting stimuli are present. This reallocation of attention may interfere with an individual’s ability to effectively assess risk and may impede its response. Multiple stimuli presented together can have additive effects as distractors, and these include stimuli in different modalities. Although changes in noise and water flow are detectable by some bivalves, this has not been studied in the context of risk assessment or distraction. We experimentally exposed giant clams (Tridacna maxima) to changes in water particle movement through underwater sound (motorboat noise) and increased water flow to determine whether these stimuli, individually or together, modified risk assessment or caused distraction. We found that clams responded to sound, flow, and their combination by increasing frequency of mantle retractions (a potential anti-predator response) when exposed to a stimulus. Sound alone did not change risk assessment in either the latency to close or to reemerge following closure. However, when exposed to both stimuli simultaneously, clams increased their latency to close. We suggest that clams perceive sound and flow in an additive way, and are thus distracted. Interestingly, and uniquely, clams discriminate these multimodal stimuli through a single sensory modality. For sessile clams, anthropogenic noise is detectable, yet unavoidable, suggesting that they be especially vulnerable to marine noise pollution. creator: Ryan Doyle creator: Jonathan Kim creator: Angelika Pe creator: Daniel T. Blumstein uri: https://doi.org/10.7717/peerj.10050 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Doyle et al. title: Predictors of Gull-billed tern (Gelochelidon nilotica) nest survival in artificial coastal saltpans, Bohai Bay, China link: https://peerj.com/articles/10054 last-modified: 2020-10-05 description: BackgroundCoastal saltpans are a common supratidal human-modified wetland habitat found within many coastal landscape mosaics. Commercial salt production and aquaculture practices often result in the creation of exposed coastal substrates that could provide suitable breeding habitat for waterbird populations; however, few studies have quantified waterbird breeding success in these artificial wetlands.MethodsHere we examine the nesting behavior of the Gull-billed tern (Gelochelidon nilotica) breeding in the Nanpu coastal saltpans of Bohai Bay, Yellow Sea, China over three consecutive nesting seasons (2017–2019) by using nest survival model in Program MARK.ResultsThe results revealed that nest survival of Gull-billed terns in coastal saltpans (0.697) was higher than previously published estimates from other regions, with an estimated daily survival rate (DSR) of 0.982 ± 0.001 (±95% CI). High nest survival was mainly attributed to low levels of human disturbances and low predation rates, while exposure to strong winds, flooding and silting were the main factors causing nest failure. Model-averaged estimates revealed that eggs laid in nests located on ‘habitat islands’ with feather or clam shell substrates were most likely to hatch. Initiation date, nest age, clutch size and quadratic effects of nearest-neighbor distance, nearest distance to road and nearest distance to water were all significant predictors of nest success, but the nest survival declined overall from 2017 to 2019 due to the degradation and loss of breeding habitat anthropogenically caused by rising water levels.DiscussionCoastal saltpans represent an alternative breeding habitat for the Gull-billed tern populations in Bohai Bay, but conservation management should prioritize flood prevention to improve the extent and quality of breeding habitat, concurrent with efforts to create further ‘habitat islands’ with suitable nesting substrate. creator: Fuxing Wu creator: Weipan Lei creator: Huw Lloyd creator: Zhengwang Zhang uri: https://doi.org/10.7717/peerj.10054 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wu et al. title: Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces link: https://peerj.com/articles/10071 last-modified: 2020-10-05 description: A Gram-positive, non-motile, rod-shaped facultative anaerobic bacterial strain SG502T was isolated from healthy human fecal samples in Brookings, SD, USA. The comparison of the 16S rRNA gene placed the strain within the family Erysipelotrichaceae. Within this family, Clostridium innocuum ATCC 14501T, Longicatena caecimuris strain PG-426-CC-2, Eubacterium dolichum DSM 3991T and E. tortuosum DSM 3987T(=ATCC 25548T) were its closest taxa with 95.28%, 94.17%, 93.25%, and 92.75% 16S rRNA sequence identities respectively. The strain SG502T placed itself close to C. innocuum in the 16S rRNA phylogeny. The members of genus Clostridium within family Erysipelotrichaceae was proposed to be reassigned to genus Erysipelatoclostridium to resolve the misclassification of genus Clostridium. Therefore, C. innocuum was also classified into this genus temporarily with the need to reclassify it in the future because of its difference in genomic properties. Similarly, genome sequencing of the strain and comparison with its 16S phylogenetic members and proposed members of the genus Erysipelatoclostridium, SG502T warranted a separate genus even though its 16S rRNA similarity was >95% when comapred to C. innocuum. The strain was 71.8% similar at ANI, 19.8% [17.4–22.2%] at dDDH and 69.65% similar at AAI to its closest neighbor C. innocuum. The genome size was nearly 2,683,792 bp with 32.88 mol% G+C content, which is about half the size of C. innocuum genome and the G+C content revealed 10 mol% difference. Phenotypically, the optimal growth temperature and pH for the strain SG502T were 37 °C and 7.0 respectively. Acetate was the major short-chain fatty acid product of the strain when grown in BHI-M medium. The major cellular fatty acids produced were C18:1ω9c, C18:0and C16:0. Thus, based on the polyphasic analysis, for the type strain SG502T (=DSM 107282T= CCOS 1889T), the name Dakotella fusiforme gen. nov., sp. nov., is proposed. creator: Sudeep Ghimire creator: Supapit Wongkuna creator: Joy Scaria uri: https://doi.org/10.7717/peerj.10071 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ghimire et al. title: Analysis of pedestrian activity before and during COVID-19 lockdown, using webcam time-lapse from Cracow and machine learning link: https://peerj.com/articles/10132 last-modified: 2020-10-05 description: At the turn of February and March 2020, COVID-19 pandemic reached Europe. Many countries, including Poland imposed lockdown as a method of securing social distance between potentially infected. Stay-at-home orders and movement control within public space not only affected the touristm industry, but also the everyday life of the inhabitants. The hourly time-lapse from four HD webcams in Cracow (Poland) are used in this study to estimate how pedestrian activity changed during COVID-19 lockdown. The collected data covers the period from 9 June 2016 to 19 April 2020 and comes from various urban zones. One zone is tourist, one is residential and two are mixed. In the first stage of the analysis, a state-of-the-art machine learning algorithm (YOLOv3) is used to detect people. Additionally, a non-standard application of the YOLO method is proposed, oriented to the images from HD webcams. This approach (YOLOtiled) is less prone to pedestrian detection errors with the only drawback being the longer computation time. Splitting the HD image into smaller tiles increases the number of detected pedestrians by over 50%. In the second stage, the analysis of pedestrian activity before and during the COVID-19 lockdown is conducted for hourly, daily and weekly averages. Depending on the type of urban zone, the number of pedestrians decreased from 33% in residential zones to 85% in tourist zones located in the Old Town. The presented method allows for more efficient detection and counting of pedestrians from HD time-lapse webcam images compared to SSD, YOLOv3 and Faster R-CNN. The result of the research is a published database with the detected number of pedestrians from the four-year observation period for four locations in Cracow. creator: Robert Szczepanek uri: https://doi.org/10.7717/peerj.10132 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Szczepanek title: Effects of early life stage exposure of largemouth bass to atrazine or a model estrogen (17α-ethinylestradiol) link: https://peerj.com/articles/9614 last-modified: 2020-10-02 description: Endocrine disrupting contaminants are of continuing concern for potentially contributing to reproductive dysfunction in largemouth and smallmouth bass in the Chesapeake Bay watershed (CBW) and elsewhere. Exposures to atrazine (ATR) have been hypothesized to have estrogenic effects on vertebrate endocrine systems. The incidence of intersex in male smallmouth bass from some regions of CBW has been correlated with ATR concentrations in water. Fish early life stages may be particularly vulnerable to ATR exposure in agricultural areas, as a spring influx of pesticides coincides with spawning and early development. Our objectives were to investigate the effects of early life stage exposure to ATR or the model estrogen 17α-ethinylestradiol (EE2) on sexual differentiation and gene expression in gonad tissue. We exposed newly hatched largemouth bass (LMB, Micropterus salmoides) from 7 to 80 days post-spawn to nominal concentrations of 1, 10, or 100 µg ATR/L or 1 or 10 ng EE2/L and monitored histological development and transcriptomic changes in gonad tissue. We observed a nearly 100% female sex ratio in LMB exposed to EE2 at 10 ng/L, presumably due to sex reversal of males. Many gonad genes were differentially expressed between sexes. Multidimensional scaling revealed clustering by gene expression of the 1 ng EE2/L and 100 µg ATR/L-treated male fish. Some pathways responsive to EE2 exposure were not sex-specific. We observed differential expression in male gonad in LMB exposed to EE2 at 1 ng/L of several genes involved in reproductive development and function, including star, cyp11a2, ddx4 (previously vasa), wnt5b, cyp1a and samhd1. Expression of star, cyp11a2 and cyp1a in males was also responsive to ATR exposure. Overall, our results confirm that early development is a sensitive window for estrogenic endocrine disruption in LMB and are consistent with the hypothesis that ATR exposure induces some estrogenic responses in the developing gonad. However, ATR-specific and EE2-specific responses were also observed. creator: Jessica K. Leet creator: Catherine A. Richter creator: Robert S. Cornman creator: Jason P. Berninger creator: Ramji K. Bhandari creator: Diane K. Nicks creator: James L. Zajicek creator: Vicki S. Blazer creator: Donald E. Tillitt uri: https://doi.org/10.7717/peerj.9614 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Acarbose-metformin is more effective in glycemic variability control than repaglinide-metformin in T2DM patients inadequately controlled with metformin: a retrospective cohort study link: https://peerj.com/articles/9905 last-modified: 2020-10-02 description: BackgroundAcarbose and repaglinide are widely used either by themselves or in combination with other medications. However, their efficacy in diabetes control has not been compared when used in combination with metformin.MethodsThe present study aimed to compare their effects on glycemic variability (GV) control when taken with metformin for type 2 diabetes mellitus (T2DM) inadequately controlled with metformin alone. In this retrospective cohort study, T2DM patients who were treated with either acarbose-metformin or repaglinide-metformin combination were recruited. Either acarbose 100 mg or repaglinide 2 mg triple daily was taken for the subsequent 12 weeks in combination with metformin. Demographic data, biochemical data and 7-point glycemic self-monitoring conducted with capillary blood (SMBG) data were reviewed after one week and 12 weeks. The primary outcome including glucose control and changes in GV as well as other factors affecting GV and the incidence of hypoglycemia were also analyzed.ResultsOf the 305 T2DM patients enrolled, data from 273 subjects, 136 in the acarbose-metformin group (M+A) and 137 in the repaglinide-metformin group (M+R) were analyzed. Both regimens improved glycemic control at 12 weeks post commencement of new medications. GV, expressed as the mean amplitude of plasma glycemic excursions (MAGE, 5.0 ± 2.6 vs. 2.8 ± 1.6 mmol/L, p < 0.001 in M+A; 5.1 ± 2.5 vs. 2.9 ± 1.3 mmol/L, p < 0.001 in M+R), standard deviation of blood glucose (SDBG, 3.6 ± 1.3 vs. 2.0 ± 0.9 mmol/L, p < 0.001 in M+A; 3.7 ± 1.3 vs. 2.4 ± 1.3 p < 0.001 in M+R), coefficient of variation of blood glucose (CVBG, (0.30 ± 0.09 vs. 0.21 ± 0.1, p < 0.001 in M+A; 0.31 ± 0.09 vs. 0.24 ± 0.12, p < 0.001 in M+R), postprandial amplitude of glycemic excursions (PPGE, 5.2 ± 2.6 vs. 2.8 ± 1.6 mmol/L, p < 0.001 in M+A; 5.3 ± 2.5 vs. 2.9 ± 1.3 mmol/L, p < 0.001 in M+R) or largest amplitude of glycemic excursions (LAGE, 9.8 ± 3.6 vs. 5.4 ± 2.4 mmol/L, p < 0.001 in M+A; 10.1 ± 3.4 vs. 6.3 ± 3.2 mmol/L, p < 0.001 in M+R) decreased significantly after the addition of acarbose or repaglinide (p < 0.05 respectively). Compared with repaglinide-metformin, acarbose-metformin was more effective in GV control at 12 weeks post commencement of new medications (p < 0.05). This study indicates that both acarbose-metformin and repaglinide-metformin combinations could effectively reduce GV and the acarbose-metformin combination seems to be more effective than the repaglinide-metformin combination. However, this conclusion should be confirmed by future large-scaled and more comprehensive studies due to the limitations of the present study. creator: Guoli Du creator: Wanrun Xie creator: Yinxia Su creator: Yao Ma creator: Xiaoming Gao creator: Sheng Jiang creator: Huazheng Liang uri: https://doi.org/10.7717/peerj.9905 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Du et al. title: A novel dual MEK/PDK1 inhibitor 9za retards the cell cycle at G0/G1 phase and induces mitochondrial apoptosis in non-small cell lung cancer cells link: https://peerj.com/articles/9981 last-modified: 2020-10-02 description: BackgroundA novel dual MEK/PDK1 inhibitor named 9za has been synthesized by our research team. Preliminary study showed that 9za possessed potent cytotoxicity and proapoptosis in non-small cell lung cancer (NSCLC) cells. Nevertheless, the precise underlying mechanism is vague.MethodsIn this work, we adopted the MTT assay, the Cell Cycle Detection Kit, and the JC-1 staining assay to detect the cell viability, the cell cycle distribution and the mitochondrial membrane potential (MMP), respectively. Cell apoptosis was measured by the morphology observation under a light microscope, Annexin V-FITC/propidium iodide (PI) apoptosis detection and the colorimetric TUNEL assay. Western blot was used to monitor the cell cycle-, apoptosis-related proteins and relevant proteins involved in the signaling pathways.ResultsThe MTT assay demonstrated that 9za sharply decreased the viability of NSCLC cells. Cell cycle analysis revealed that low concentrations of 9za arrested the cell cycle at the G0/G1 phase , which was further confirmed by the decreased levels of Cyclin D1, cyclin-dependent kinase 4 (CDK4) and cyclin-dependent kinase 6 (CDK6). Additionally, morphological observations, Annexin V-FITC/propidium iodide (PI) apoptosis analysis and TUNEL assays indicated that high concentrations of 9za induced cell apoptosis. Furthermore, the JC-1 staining assay revealed that the mitochondrial membrane potential was downregulated following 9za exposure. Western blot also showed that 9za markedly decreased the expression levels of total Bcl-2, Cytochrome C in the mitochondria and BCL2 associated X (BAX) in the cytoplasm. However, the levels of BAX in the mitochondria, Cytochrome C in the cytoplasm, active caspase-9, active caspase-3 and cleaved–PARP showed the opposite changes. Moreover, the dose-dependent decreased phosphorylation levels of PDK1, protein kinase B (Akt), MEK and extracellular signal regulated kinase 1/2 (ERK1/2) after 9za treatment verified that 9za was indeed a dual MEK/PDK1 inhibitor, as we expected. Compared with a single MEK inhibitor PD0325901 or a single PDK1 inhibitor BX517, the dual MEK/PDK1 inhibitor 9za could strengthen the cytotoxic and proapoptotic effect, indicating that the double blocking of the MEK and PDK1 signaling pathways plays stronger cell growth inhibition and apoptosis induction roles than the single blocking of the MEK or PDK1 signaling pathway in NSCLC cells. Our work elucidated the molecular mechanisms for 9za as a novel drug candidate against NSCLC. creator: Rangru Liu creator: Zutao Yu creator: Zhuo Chen creator: Danqi Liu creator: Fengying Huang creator: Qianbin Li creator: Gaoyun Hu creator: Xinan Yi creator: Xi Li creator: Honghao Zhou creator: Zhaoqian Liu uri: https://doi.org/10.7717/peerj.9981 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: The effect of long-term volleyball training on the level of somatic parameters of female volleyball players in various age categories link: https://peerj.com/articles/9992 last-modified: 2020-10-02 description: Volleyball is an exceedingly popular physical activity in the adolescent population, especially with females. The study objective was to assess the effect of volleyball training and natural ontogenetic development on the somatic parameters of adolescent girls. The study was implemented in a group of 130 female volleyball players (aged 12.3 ± 0.5 – 18.1 ± 0.6 years) along with 283 females from the general population (aged 12.3 ± 0.5 – 18.2 ± 0.5 years). The measured parameters included: body height (cm), body mass (kg), body fat (kg, %), visceral fat (cm2), body water (l), fat free mass (kg) and skeletal muscle mass (kg, %). Starting at the age of 13, the volleyball players had significantly lower body fat ratio and visceral fat values than those in the general population (p < 0.001 in body fat % and p < 0.01 in visceral fat). In volleyball players, the mean body fat (%) values were 17.7 ± 6.6 in 12-year-old players, 16.7 ± 4.9 in 13-year-old players, 18.5 ± 3.9 in 16-year-old players, and 19.3 ± 3.1 in 18-year-old players. In the general population, the mean body fat (%) values were 19.6 ± 6.3 in 12-year-old girls, 21.7 ± 6.4 in 13-year-old girls, 23.4 ± 6.1 in 16-year-old girls, and 25.8 ± 7.0 in 18-year-old girls. The visceral fat (cm2) mean values were 36.4 ± 19.3 in 12-year-old players, 39.2 ± 16.3 in 13-year-old players, 45.7 ± 14.7 in 16-year-old players, and 47.2 ± 12.4 in 18-year-old players. In the general population, the mean visceral fat (cm2) values were 41.4 ± 21.1 in 12-year-old girls, 48.4 ± 21.5 in 13-year-old girls, 58.0 ± 24.7 in 16-year-old girls, and 69.1 ± 43.7 in 18-year-old girls. In volleyball players, lower body fat ratio corresponded with a higher skeletal muscle mass ratio. The differences found in skeletal muscle mass ratio were also significant starting at the age of 13 (p < 0.001). The mean skeletal muscle mass (%) values were 44.1 ± 3.4 in 12-year-old volleyball players, 45.4 ± 2.5 in 13-year-old players, 45.0 ± 2.2 in 16-year-old players, and 44.7 ± 1.8 in 18-year-old players. In the general population, the mean skeletal muscle mass (%) values were 42.8 ± 3.2 in 12-year-old girls, 42. ± 4.1 in 13-year-old girls, 41.9 ± 3.3 in 16-year-old girls, and 40.6 ± 3.7 in 18-year-old girls. Differences in body composition between the individual age groups were similar between the volleyball players and girls in the general population. The results indicate that regular volleyball training influences the body composition of young females however the development of body composition parameters is subject to their ontogenetic development. creator: Petr Kutáč creator: David Zahradnik creator: Miroslav Krajcigr creator: Václav Bunc uri: https://doi.org/10.7717/peerj.9992 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kutáč et al. title: Differentially expressed genes related to oxidoreductase activity and glutathione metabolism underlying the adaptation of Phragmites australis from the salt marsh in the Yellow River Delta, China link: https://peerj.com/articles/10024 last-modified: 2020-10-02 description: The common reed (Phragmites australis) is a dominant species in the coastal wetlands of the Chinese Yellow River Delta, where it tolerates a wide range of salinity. Recent environmental changes have led to the increase of soil salinity in this region, which has degraded much of the local vegetation. Clones of common reeds from the tidal marsh may have adapted to local high salinity habitat through selection on genes and metabolic pathways conferring salt tolerance. This study aims to reveal molecular mechanisms underlying salt tolerance in the tidal reed by comparing them to the salt-sensitive freshwater reed under salt stress. We employed comparative transcriptomics to reveal the differentially expressed genes (DEGs) between these two types of common reeds under different salinity conditions. The results showed that only three co-expressed genes were up-regulated and one co-expressed gene was down-regulated between the two reed types. On the other hand, 1,371 DEGs were exclusively up-regulated and 285 DEGs were exclusively down-regulated in the tidal reed compared to the control, while 115 DEGs were exclusively up-regulated and 118 DEGs were exclusively down-regulated in the freshwater reed compared to the control. From the pattern of enrichment of transcripts involved in salinity response, the tidal reed was more active and efficient in scavenging reactive oxygen species (ROS) than the freshwater reed, with the tidal reed showing significantly higher gene expression in oxidoreductase activity. Furthermore, when the reeds were exposed to salt stress, transcripts encoding glutathione metabolism were up-regulated in the tidal reed but not in the freshwater reed. DEGs related to encoding glutathione reductase (GR), glucose-6-phosphate 1-dehydrogenase (G6PDH), 6-phosphogluconate dehydrogenase (6PD), glutathione S-transferase (GST) and L-ascorbate peroxidase (LAP) were revealed as especially highly differentially regulated and therefore represented candidate genes that could be cloned into plants to improve salt tolerance. Overall, more genes were up-regulated in the tidal reed than in the freshwater reed from the Yellow River Delta when under salt stress. The tidal reed efficiently resisted salt stress by up-regulating genes encoding for oxidoreductase activity and glutathione metabolism. We suggest that this type of common reed could be extremely useful in the ecological restoration of degraded, high salinity coastal wetlands in priority. creator: Liwen Zhang creator: Lin Chen creator: Feng Lu creator: Ziting Liu creator: Siqun Lan creator: Guangxuan Han uri: https://doi.org/10.7717/peerj.10024 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al.