title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=989 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Prediction of state anxiety by machine learning applied to photoplethysmography data link: https://peerj.com/articles/10448 last-modified: 2021-01-15 description: BackgroundAs the human behavior is influenced by both cognition and emotion, affective computing plays a central role in human-machine interaction. Algorithms for emotions recognition are usually based on behavioral analysis or on physiological measurements (e.g., heart rate, blood pressure). Among these physiological signals, pulse wave propagation in the circulatory tree can be assessed through photoplethysmography (PPG), a non-invasive optical technique. Since pulse wave characteristics are influenced by the cardiovascular status, which is affected by the autonomic nervous activity and hence by the psychophysiological state, PPG might encode information about emotional conditions. The capability of a multivariate data-driven approach to estimate state anxiety (SA) of healthy participants from PPG features acquired on the brachial and radial artery was investigated.MethodsThe machine learning method was based on General Linear Model and supervised learning. PPG was measured employing a custom-made system and SA of the participants was assessed through the State-Trait Anxiety Inventory (STAI-Y) test.ResultsA leave-one-out cross-validation framework showed a good correlation between STAI-Y score and the SA predicted by the machine learning algorithm (r = 0.81; p = 1.87∙10−9). The preliminary results suggested that PPG can be a promising tool for emotions recognition, convenient for human-machine interaction applications. creator: David Perpetuini creator: Antonio Maria Chiarelli creator: Daniela Cardone creator: Chiara Filippini creator: Sergio Rinella creator: Simona Massimino creator: Francesco Bianco creator: Valentina Bucciarelli creator: Vincenzo Vinciguerra creator: Piero Fallica creator: Vincenzo Perciavalle creator: Sabina Gallina creator: Sabrina Conoci creator: Arcangelo Merla uri: https://doi.org/10.7717/peerj.10448 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Perpetuini et al. title: Municipal waste landfill as a source of polychlorinated biphenyls releases to the environment link: https://peerj.com/articles/10546 last-modified: 2021-01-15 description: This study aimed to investigate the impact of municipal waste landfill on polychlorinated biphenyls (PCBs) release to the environment concerning groundwater flow directions. The contents of polychlorinated biphenyls in soils, plants and water were analysed at various distances from the landfill. Thanks to low solubility PCBs in water groundwater flow direction, under the landfill, have an influence on PCBs concentration in groundwater. Strong PCBs’ sorption to organic matter caused that no affect groundwater flow directions on PCB content in soils and plants’ tissues was observed. The largest PCBs deposition zone was located 50 m from the contamination source (landfill). Tri-CB and tetra-CB homologues were capable of migration deep into the soil profile, which could be related to the geological material from which the soils under study were developed, as well as to the properties of the PCB homologues. creator: Marta Gabryszewska creator: Barbara Gworek uri: https://doi.org/10.7717/peerj.10546 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Gabryszewska and Gworek title: Vision of conspecifics decreases the effectiveness of ethanol on zebrafish behaviour link: https://peerj.com/articles/10566 last-modified: 2021-01-15 description: Aquatic organisms in pharmacology and toxicology research are often exposed to compounds in isolation prior to physiological or behavioural testing. Recent evidence suggests that the presence of conspecifics during a stressful event can modulate behavioural outcomes (called ‘social buffering’) when testing occurs within the same context. It is unknown, however, whether the social environment during exposure interacts with the efficacy of anxiety-altering substances when subsequently tested in the absence of conspecifics. In this study, zebrafish were individually exposed to habitat water or ethanol (1.0% vol/vol) while untreated conspecifics were visually present or absent during dosing. Using the novel object approach test, a validated test of boldness and anxiety-like behaviour, we observed significantly greater effects of ethanol in isolated fish, compared to fish with a view of conspecifics during dosing. These results were not explained by altered locomotion during exposure, which might otherwise increase drug uptake. This highlights the need to consider the social environment during exposure when conducting and interpreting behavioural research involving drug or toxicant exposure. creator: Rachel Dean creator: Nicole Hurst Radke creator: Nirudika Velupillai creator: Brian C. Franczak creator: Trevor J. Hamilton uri: https://doi.org/10.7717/peerj.10566 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Dean et al. title: Hyperglycemia in severe traumatic brain injury patients and its association with thirty-day mortality: a prospective observational cohort study in Uganda link: https://peerj.com/articles/10589 last-modified: 2021-01-15 description: BackgroundTraumatic brain injury (TBI) is a growing public health concern that can be complicated with an acute stress response. This response may be assessed by monitoring blood glucose levels but this is not routine in remote settings. There is a paucity of data on the prevalence of hyperglycemia and variables associated with mortality after severe TBI in Uganda.ObjectiveWe aimed to determine the prevalence of hyperglycemia in patients with severe TBI and variables associated with 30-day mortality at Mulago National Referral Hospital in Uganda.MethodsWe consecutively enrolled a cohort 99 patients patients with severe TBI. Serum glucose levels were measured at admission and after 24 h. Other study variables included: mechanism of injury, CT findings, location and size of hematoma, and socio-demographics. The main outcome was mortality after 30 days of management and this was compared in patients with hyperglycemia more than 11.1 mmol/L to those without.ResultsMost patients (92.9%) were male aged 18–30 years (47%). Road Traffic Collisions were the most common cause of severe TBI (64.7%) followed by assault (17.1%) and falls (8.1%). Nearly one in six patients were admitted with hyperglycemia more than 11.1 mmol/L. The mortality rate in severe TBI patients with hyperglycemia was 68.8% (OR 1.47; 95% CI [0.236–9.153]; P = 0.063) against 43.7% in those without hyperglycemia. The presence of hypothermia (OR 10.17; 95% CI [1.574–65.669]; P = 0.015) and convulsions (OR 5.64; 95% CI [1.541–19.554]; P = 0.009) were significant predictors of mortality.ConclusionHypothermia and convulsions at admission were major predictors of mortality in severe TBI. Early hyperglycemia following severe TBI appears to occur with a tendency towards high mortality. These findings justify routine glucose monitoring and could form the basis for establishing a blood sugar control protocol for such patients in remote settings. creator: Paul Matovu creator: Musa Kirya creator: Moses Galukande creator: Joel Kiryabwire creator: John Mukisa creator: William Ocen creator: Michael Lowery Wilson creator: Anne Abio creator: Herman Lule uri: https://doi.org/10.7717/peerj.10589 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Matovu et al. title: Effectiveness of modifications to preadjusted appliance prescriptions based on racial dental characteristics assessed by the ABO Cast-Radiograph Evaluation: A propensity score matching study link: https://peerj.com/articles/10605 last-modified: 2021-01-15 description: BackgroundBecause racial discrepancies in dental characteristics are known to exist, designing preadjusted appliances according to racial normal occlusion data would be expected to improve treatment results. However, whether modifications based on racial characteristics can improve treatment outcomes in the clinic remains to be investigated.MethodsTo study the influence of prescription type on treatment outcomes, 91 patients treated with Chinese or Roth prescription appliances were selected as an initial sample. Two groups of patients were selected by propensity score matching (1:1) to limit the effects of confounding factors, including age, sex, case complexity, and extraction plan. Discrepancy Index and cervical vertebral maturation values were used to quantify case complexity and patient age, respectively. After matching, the final sample of 60 patients consisted of two groups of 30 patients each: group 1 had been treated with a Chinese prescription appliance and group 2 had been treated with a Roth prescription appliance. ABO casts and radiograph evaluation (CR-Eval) and lateral cephalograms were utilized to compare the treatment outcomes of the two groups.ResultsThe total ABO scores of groups 1 and 2 were 22.03 and 23.87, respectively. There were no significant differences between the two groups in total ABO score or in seven other sub-scores; however, there was a significant difference between the two groups in mandibular canine alignment score.ConclusionsThere are no significant differences in overall treatment outcomes between the Chinese and Roth prescription appliances. The Chinese prescription yielded better alignment results in the mandibular canine for Chinese patients. creator: Yanhao Chu creator: Lingling Zhang creator: Yatao Zhao creator: Fang Yi creator: Yanqin Lu uri: https://doi.org/10.7717/peerj.10605 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chu et al. title: Comparison of the effects of two laser photobiomodulation techniques on bio-physical properties of Zea mays L. seeds link: https://peerj.com/articles/10614 last-modified: 2021-01-15 description: BackgroundLaser applications in agriculture have recently gained much interest due to improved plant characteristics following laser treatment before the sowing of seeds. In this study, maize seeds were exposed to different levels of laser treatment prior to sowing to improve their field performance. The aim of this study is to evaluate the impact of pre-sowing laser photobiomodulation on the field emergence and growth of treated maize seeds.MethodsThe maize seeds were first photobiomodulated with two lasers: 1) a helium-neon (He–Ne) red laser (632.8 nm), and 2) a neodymium-doped yttrium aluminum garnet (Nd:YAG) green laser (532 nm). Following three replications of randomized complete block design (RCBD), four irradiation treatments were applied (45 s, 65 s, 85 s, and 105 s) at two power intensities (2 mW/cm2 and 4 mW/cm2).ResultsBased on the results, maize seeds pretreated with a green laser and 2 mW/cm2 power intensity for 105 s exhibited the highest rate of seed emergence (96%) compared to the untreated control seeds with a lower seed emergence rate (62.5%). Furthermore, maize seeds treated with a red laser for 45 s showed an increased vigor index compared to the other treatment options and the control (P < 0.01). The treatment groups also showed statistically significant differences in seedling growth characteristics compared to the control group p < 0.01. The green laser produced a significant enhancement of about 24.20 cm in seedling length, 8.2 leaves/plant, and 3.4 cm in stem diameter compared to the untreated seeds. Moreover, the green laser treatment showed 57.4 days to anthesis, which was earlier than the untreated seeds (61.4 days). The results showed that the protein, oil, and starch contents of the seeds irradiated with the green laser were 17.54%, 6.18%, and 73.32%, respectively, compared to the seeds irradiated by the red laser with 16.51%, 6.33%, and 71.05%, respectively.ConclusionsThe photo biomodulation of maize seeds using a green laser light can improve the field emergence, seedling growth, and seed quality of the treated seed compared to the red laser treatment. creator: Mohammed Hasan creator: Marlia M. Hanafiah creator: Intsar H.H. Alhilfy creator: Ziad Aeyad Taha uri: https://doi.org/10.7717/peerj.10614 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hasan et al. title: Gene signatures with predictive and prognostic survival values in human osteosarcoma link: https://peerj.com/articles/10633 last-modified: 2021-01-15 description: Osteosarcoma is a common malignancy seen mainly in children and adolescents. The disease is characterized by poor overall prognosis and lower survival due to a lack of predictive markers. Many gene signatures with diagnostic, prognostic, and predictive values were evaluated to achieve better clinical outcomes. Two public data series, GSE21257 and UCSC Xena, were used to identify the minimum number of robust genes needed for a predictive signature to guide prognosis of patients with osteosarcoma. The lasso regression algorithm was used to analyze sequencing data from TCGA-TARGET, and methods such as Cox regression analysis, risk factor scoring, receiving operating curve, KMplot prognosis analysis, and nomogram were used to characterize the prognostic predictive power of the identified genes. Their utility was assessed using the GEO osteosarcoma dataset. Finally, the functional enrichment analysis of the identified genes was performed. A total of twenty-gene signatures were found to have a good prognostic value for predicting patient survival. Gene ontology analysis showed that the key genes related to osteosarcoma were categorized as peptide–antigen binding, clathrin-coated endocytic vesicle membrane, peptide binding, and MHC class II protein complex. The osteosarcoma related genes in these modules were significantly enriched in the processes of antigen processing and presentation, phagocytosis, cell adhesion molecules, Staphylococcus aureus infection. Twenty gene signatures were identified related to osteosarcoma, which would be helpful for predicting prognosis of patients with OS. Further, these signatures can be used to determine the subtypes of osteosarcoma. creator: Zhongpeng Qiu creator: Xinhui Du creator: Kai Chen creator: Yi Dai creator: Sibo Wang creator: Jun Xiao creator: Gang Li uri: https://doi.org/10.7717/peerj.10633 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Qiu et al. title: High expression of MAPK-14 promoting the death of chondrocytes is an important signal of osteoarthritis process link: https://peerj.com/articles/10656 last-modified: 2021-01-15 description: BackgroundOsteoarthritis (OA) is one of the most common degenerative diseases worldwide. Many researchers are studying the pathogenesis of OA, however, it is still unclear.MethodsScreening and validation of OA relevant hub genes are an important part of exploring their potential molecular mechanism. Therefore, this study aims to explore and verify the mechanisms of hub genes in the OA by bioinformatics, qPCR, fluorescence and propidium iodide staining.ResultsMicroarray datasets GSE43923, GSE55457 and GSE12021 were collected in the Gene Expression Omnibus (GEO), including 45 samples, which divided into 23 osteoarthritis knee joint samples and 22 samples of normal knee joint. Thereafter, 265 differentiallyexpressedgenes (DEGs) were identified in all, which divided into 199 upregulated genes and 66 downregulated genes. The hub genes MAPK-14, PTPRC, PTPN12 were upregulated, while B9D1 was downregulated. In order to further confirm the expression of screening differential genes in human chondrocytes, the human chondrocytes were extracted from a joint replacement surgery and stained with toluidine blue for identification. Compared with normal chondrocytes, OA chondrocytes had high expression of COL I protein and low expression of COL II protein. The expression levels of MAPK-14, PTPRC and PTPN12 in OA chondrocytes were significantly higher than the expression levels of B9D1 in normal chondrocytes. Moreover, the inflammatory necrosis of OA chondrocytes was increased compared with the normal chondrocytes by propidium iodide staining.ConclusionsThe high expression of MAPK-14 works as a promoter of chondrocytes death and an important signal of the osteoarthritis process. creator: Zhiqin Deng creator: Xiaotian Hu creator: Murad Alahdal creator: Jianquan Liu creator: Zhe Zhao creator: Xiaoqiang Chen creator: Junxiong Xie creator: Li Duan creator: Daping Wang creator: Wencui Li uri: https://doi.org/10.7717/peerj.10656 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Deng et al. title: Clusters of sub-Saharan African countries based on sociobehavioural characteristics and associated HIV incidence link: https://peerj.com/articles/10660 last-modified: 2021-01-15 description: IntroductionHIV incidence varies widely between sub-Saharan African (SSA) countries. This variation coincides with a substantial sociobehavioural heterogeneity, which complicates the design of effective interventions. In this study, we investigated how sociobehavioural heterogeneity in sub-Saharan Africa could account for the variance of HIV incidence between countries.MethodsWe analysed aggregated data, at the national-level, from the most recent Demographic and Health Surveys of 29 SSA countries (2010–2017), which included 594,644 persons (183,310 men and 411,334 women). We preselected 48 demographic, socio-economic, behavioural and HIV-related attributes to describe each country. We used Principal Component Analysis to visualize sociobehavioural similarity between countries, and to identify the variables that accounted for most sociobehavioural variance in SSA. We used hierarchical clustering to identify groups of countries with similar sociobehavioural profiles, and we compared the distribution of HIV incidence (estimates from UNAIDS) and sociobehavioural variables within each cluster.ResultsThe most important characteristics, which explained 69% of sociobehavioural variance across SSA among the variables we assessed were: religion; male circumcision; number of sexual partners; literacy; uptake of HIV testing; women’s empowerment; accepting attitude toward people living with HIV/AIDS; rurality; ART coverage; and, knowledge about AIDS. Our model revealed three groups of countries, each with characteristic sociobehavioural profiles. HIV incidence was mostly similar within each cluster and different between clusters (median (IQR); 0.5/1000 (0.6/1000), 1.8/1000 (1.3/1000) and 5.0/1000 (4.2/1000)).ConclusionsOur findings suggest that the combination of sociobehavioural factors play a key role in determining the course of the HIV epidemic, and that similar techniques can help to predict the effects of behavioural change on the HIV epidemic and to design targeted interventions to impede HIV transmission in SSA. creator: Aziza Merzouki creator: Janne Estill creator: Erol Orel creator: Kali Tal creator: Olivia Keiser uri: https://doi.org/10.7717/peerj.10660 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2021 Merzouki et al. title: A new caimanine alligatorid from the Middle Eocene of Southwest Texas and implications for spatial and temporal shifts in Paleogene crocodyliform diversity link: https://peerj.com/articles/10665 last-modified: 2021-01-15 description: Dramatic early Cenozoic climatic shifts resulted in faunal reorganization on a global scale. Among vertebrates, multiple groups of mammals (e.g., adapiform and omomyiform primates, mesonychids, taeniodonts, dichobunid artiodactyls) are well known from the Western Interior of North America in the warm, greenhouse conditions of the early Eocene, but a dramatic drop in the diversity of these groups, along with the introduction of more dry-tolerant taxa, occurred near the Eocene–Oligocene boundary. Crocodyliforms underwent a striking loss of diversity at this time as well. Pre-Uintan crocodyliform assemblages in the central Western Interior are characterized by multiple taxa, whereas Chadronian assemblages are depauperate with only Alligator prenasalis previously known. Crocodyliform diversity through the intervening Uintan and Duchesnean is not well understood. The middle Eocene Devil’s Graveyard Formation (DGF) of southwest Texas provides new data from southern latitudes during that crucial period. A new specimen from the middle member of the DGF (late Uintan–Duchesnean) is the most complete cranial material of an alligatorid known from Paleogene deposits outside the Western Interior. We identify this specimen as a caimanine based on notched descending laminae of the pterygoids posterior to the choanae and long descending processes of the exoccipitals that are in contact with the basioccipital tubera. Unlike Eocaiman cavernensis, the anterior palatine process is rounded rather than quadrangular. The relationships and age of this new taxon support the hypothesis that the modern distribution of caimanines represents a contraction of a more expansive early Cenozoic distribution. We hypothesize that the range of caimanines tracked shifting warm, humid climatic conditions that contracted latitudinally toward the hothouse-icehouse transition later in the Eocene. creator: Michelle R. Stocker creator: Christopher A. Brochu creator: E. Christopher Kirk uri: https://doi.org/10.7717/peerj.10665 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Stocker et al.