title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=416 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning link: https://peerj.com/articles/16129 last-modified: 2023-09-22 description: Metagenome binning is a key step, downstream of metagenome assembly, to group scaffolds by their genome of origin. Although accurate binning has been achieved on datasets containing multiple samples from the same community, the completeness of binning is often low in datasets with a small number of samples due to a lack of robust species co-abundance information. In this study, we exploited the chromatin conformation information obtained from Hi-C sequencing and developed a new reference-independent algorithm, Metagenome Binning with Abundance and Tetra-nucleotide frequencies—Long Range (metaBAT-LR), to improve the binning completeness of these datasets. This self-supervised algorithm builds a model from a set of high-quality genome bins to predict scaffold pairs that are likely to be derived from the same genome. Then, it applies these predictions to merge incomplete genome bins, as well as recruit unbinned scaffolds. We validated metaBAT-LR’s ability to bin-merge and recruit scaffolds on both synthetic and real-world metagenome datasets of varying complexity. Benchmarking against similar software tools suggests that metaBAT-LR uncovers unique bins that were missed by all other methods. MetaBAT-LR is open-source and is available at https://bitbucket.org/project-metabat/metabat-lr. creator: Harrison Ho creator: Mansi Chovatia creator: Rob Egan creator: Guifen He creator: Yuko Yoshinaga creator: Ivan Liachko creator: Ronan O’Malley creator: Zhong Wang uri: https://doi.org/10.7717/peerj.16129 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Ho et al. title: Combining passive acoustic data from a towed hydrophone array with visual line transect data to estimate abundance and availability bias of sperm whales (Physeter macrocephalus) link: https://peerj.com/articles/15850 last-modified: 2023-09-21 description: Visual line transect (VLT) surveys are central to the monitoring and study of marine mammals. However, for cryptic species such as deep diving cetaceans VLT surveys alone suffer from problems of low sample sizes and availability bias where animals below the surface are not available to be detected. The advent of passive acoustic monitoring (PAM) technology offers important opportunities to observe deep diving cetaceans but statistical challenges remain particularly when trying to integrate VLT and PAM data. Herein, we present a general framework to combine these data streams to estimate abundance when both surveys are conducted simultaneously. Secondarily, our approach can also be used to derive an estimate of availability bias. We outline three methods that vary in complexity and data requirements which are (1) a simple distance sampling (DS) method that treats the two datasets independently (DS-DS Method), (2) a fully integrated approach that applies a capture-mark recapture (CMR) analysis to the PAM data (CMR-DS Method) and (3) a hybrid approach that requires only a subset of the PAM CMR data (Hybrid Method). To evaluate their performance, we use simulations based on known diving and vocalizing behavior of sperm whales (Physeter macrocephalus). As a case study, we applied the Hybrid Method to data from a shipboard survey of sperm whales and compared estimates to a VLT only analysis. Simulation results demonstrated that the CMR-DS Method and Hybrid Method reduced bias by >90% for both abundance and availability bias in comparison to the simpler DS -DS Method. Overall, the CMR-DS Method was the least biased and most precise. For the case study, our application of the Hybrid Method to the sperm whale dataset produced estimates of abundance and availability bias that were comparable to estimates from the VLT only analysis but with considerably higher precision. Integrating multiple sources of data is an important goal with clear benefits. As a step towards that goal we have developed a novel framework. Results from this study are promising although challenges still remain. Future work may focus on applying this method to other deep-diving species and comparing the proposed method to other statistical approaches that aim to combine information from multiple data sources. creator: Douglas B. Sigourney creator: Annamaria DeAngelis creator: Danielle Cholewiak creator: Debra Palka uri: https://doi.org/10.7717/peerj.15850 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Genome-wide association analysis of type II resistance to Fusarium head blight in common wheat link: https://peerj.com/articles/15906 last-modified: 2023-09-21 description: BackgroundFusarium head blight (FHB) is a disease affecting wheat spikes caused by some Fusarium species and leads to cases of severe yield reduction and seed contamination. Identifying resistance genes/QTLs from wheat germplasm may help to improve FHB resistance in wheat production.MethodsOur study evaluated 205 elite winter wheat cultivars for FHB resistance. A high-density 90K SNP array was used for genotyping the panel. A genome-wide association study (GWAS) from cultivars from three different environments was performed using a mixed linear model (MLM).ResultsSixty-six significant marker-trait associations (MTAs) were identified (P < 0.001) on fifteen chromosomes that explained the phenotypic variation ranging from 5.4 to 11.2%. Some important new MTAs in genomic regions involving FHB resistance were found on chromosomes 2A, 3B, 5B, 6A, and 7B. Six MTAs at 92 cM on chromosome 7B were found in cultivars from two different environments. Moreover, there were 11 MTAs consistently associated with diseased spikelet rate and diseased rachis rate as pleiotropic effect loci and D_contig74317_533 on chromosome 5D was novel for FHB resistance. Eight new candidate genes of FHB resistance were predicated in wheat in this study. Three candidate genes, TraesCS5D02G006700, TraesCS6A02G013600, and TraesCS7B02G370700 on chromosome 5DS, 6AS, and 7BL, respectively, were perhaps important in defending against FHB by regulating intramolecular transferase activity, GTP binding, or chitinase activity in wheat, but further validation in needed. In addition, a total of five favorable alleles associated with wheat FHB resistance were discovered. These results provide important genes/loci for enhancing FHB resistance in wheat breeding by marker-assisted selection. creator: Dehua Wang creator: Yunzhe Zhao creator: Xinying Zhao creator: Mengqi Ji creator: Xin Guo creator: Jichun Tian creator: Guangfeng Chen creator: Zhiying Deng uri: https://doi.org/10.7717/peerj.15906 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang et al. title: Analysis of influencing factors of anxiety and depression in maintenance hemodialysis patients and its correlation with BDNF, NT-3 and 5-HT levels link: https://peerj.com/articles/16068 last-modified: 2023-09-21 description: ObjectiveThe aim of this study is to examine the factors that contribute to anxiety and depression in individuals undergoing maintenance hemodialysis (MHD), as well as their association with serum levels of brain-derived neurotrophic factor (BDNF), neurotrophin-3 (NT-3), and serotonin (5-HT).MethodsIn May 2020 and June 2022, 120 MHD patients who received MDH treatment at our hospital were enrolled. The control group was composed of 60 healthy adults (>18) who completed the physical examination at the same time. The serum levels of BDNF, NT-3, and 5-HT in patients and clinical data of MHD patients with different degrees of anxiety and depression were compared. The Pearson correlation was used to evaluate the correlation between anxiety and depression scores and serum BDNF, NT-3,5-HT levels in patients with MHD. Multivariate analysis was employed to analyze the risk factors of anxiety and depression in MHD patients.ResultsThe incidence of anxiety and depression in 120 MHD patients was 34.17% (41/120) and 64.17% (77/120), respectively. The levels of serum NT-3 and 5-HT in the anxiety group were higher than those in the non-anxiety and control group, and the levels of serum NT-3 in the non-anxiety group were higher than those in the control group (P < 0.05). The levels of serum BDNF, NT-3 and 5-HT in the depressed group were higher than those in the non-depressed group and control group, and the levels of serum NT-3 in the non-depressed group were higher than those in the control group (P < 0.05). SAS score was positively correlated with serum NT-3 and 5-HT levels, while the SDS score was negatively correlated with serum BDNF and positively correlated with serum NT-3 and 5-HT levels. Female, rural household registration, and restless leg syndrome were independent risk variables for anxiety in patients with MHD (P < 0.05). Rural household registration, economic deterioration, fatigue, insomnia, and vascular pain were independent variables of depression risk in patients with MHD.ConclusionAnxiety and depression in patients with MHD are closely related to the levels of serum BDNF, NT-3, and 5-HT. Female, rural household registration, more than eight dialysis times/month, insomnia, and restless leg syndrome are the risk factors for anxiety in patients with MHD. Rural household registration, economic deterioration, fatigue, insomnia, and vascular pain are the risk factors for depression in patients with MHD. The clinical implication of these findings suggests that these indexes may perhaps serve as biological indicators of anxiety and depression amongst patients undergoing MHD. Such investigation can hence contribute to early detection, monitoring, and potentially enable the depiction of novel therapeutic strategies for managing these adverse states. creator: Xiaoyan Peng creator: Sujuan Feng creator: Poxuan Zhang creator: Shengmei Sang creator: Yi Zhang uri: https://doi.org/10.7717/peerj.16068 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Peng et al. title: Fishery catch is affected by geographic expansion, fishing down food webs and climate change in Aotearoa, New Zealand link: https://peerj.com/articles/16070 last-modified: 2023-09-21 description: Historical fishing effort has resulted, in many parts of the ocean, in increasing catches of smaller, lower trophic level species once larger higher trophic level species have been depleted. Concurrently, changes in the geographic distribution of marine species have been observed as species track their thermal affinity in line with ocean warming. However, geographic shifts in fisheries, including to deeper waters, may conceal the phenomenon of fishing down the food web and effects of climate warming on fish stocks. Fisheries-catch weighted metrics such as the Mean Trophic Level (MTL) and Mean Temperature of the Catch (MTC) are used to investigate these phenomena, although apparent trends of these metrics can be masked by the aforementioned geographic expansion and deepening of fisheries catch across large areas and time periods. We investigated instances of both fishing down trophic levels and climate-driven changes in the geographic distribution of fished species in New Zealand waters from 1950–2019, using the MTL and MTC. Thereafter, we corrected for the masking effect of the geographic expansion of fisheries within these indices by using the Fishing-in-Balance (FiB) index and the adapted Mean Trophic Level (aMTL) index. Our results document the offshore expansion of fisheries across the New Zealand Exclusive Economic Zone (EEZ) from 1950–2019, as well as the pervasiveness of fishing down within nearshore fishing stock assemblages. We also revealed the warming of the MTC for pelagic-associated fisheries, trends that were otherwise masked by the depth- and geographic expansion of New Zealand fisheries across the study period. creator: Charles Patrick Lavin creator: Daniel Pauly creator: Donna Dimarchopoulou creator: Cui Liang creator: Mark John Costello uri: https://doi.org/10.7717/peerj.16070 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Lavin et al. title: A nomogram model for predicting lower extremity deep vein thrombosis after gynecologic laparoscopic surgery: a retrospective cohort study link: https://peerj.com/articles/16089 last-modified: 2023-09-21 description: ObjectiveTo investigate the risk factors associated with lower extremity deep vein thrombosis (LEDVT) and to establish a predictive model for patients who undergo gynecologic laparoscopic surgery.MethodsA review of clinical data was conducted on patients who underwent gynecologic laparoscopic surgery between November 1, 2020, and January 31, 2022. Patients who developed LEDVT after surgery were included as the observation group, while the control group comprised patients who did not experience complications. Multivariate forward stepwise logistic regression models were used to identify independent risk factors associated with LEDVT. A nomogram model was then developed based on these risk factors.ResultsA total of 659 patients underwent gynecologic laparoscopic surgery during the study period, and 52 (7.89%) of these patients developed postoperative LEDVT. Multivariate logistic regression analysis showed that older age (adjusted OR, 1.085; 95% CI [1.034–1.138]; P < 0.05), longer operation duration (adjusted OR, 1.014; 95% CI [1.009–1.020]; P < 0.05), shorter activated partial thromboplastin time (APTT) (adjusted OR, 0.749; 95% CI [0.635–0.884]; P < 0.05), higher D-dimer (adjusted OR, 4.929; 95% CI [2.369–10.255]; P < 0.05), higher Human Epididymis Protein 4 (HE4) (adjusted OR, 1.007; 95% CI [1.001–1.012]; P < 0.05), and history of hypertension (adjusted OR, 3.732; 95% CI [1.405–9.915]; P < 0.05) were all independent risk factors for LEDVT in patients who underwent gynecologic laparoscopic surgery. A nomogram model was then created, which had an area under the curve of 0.927 (95% CI [0.893–0.961]; P < 0.05), a sensitivity of 96.1%, and a specificity of 79.5%.ConclusionsA nomogram model that incorporates information on age, operation duration, APTT, D-dimer, history of hypertension, and HE4 could effectively predict the risk of LEDVT in patients undergoing gynecologic laparoscopic surgery, potentially helping to prevent the development of this complication. creator: Yuping Zhao creator: Renyu Wang creator: Shuiling Zu creator: Yanbin Lin creator: Ying Fu creator: Na Lin creator: Xiumei Fang creator: Chenyin Liu uri: https://doi.org/10.7717/peerj.16089 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2023 Zhao et al. title: Influence of engaging female caregivers in households with adolescent girls on adopting equitable family eating practices: a quasi-experimental study link: https://peerj.com/articles/16099 last-modified: 2023-09-21 description: BackgroundIn patriarchal societies, female caregivers decide on food allocation within a family based on prevailing gender and age norms, which may lead to inequality that does not favor young adolescent girls. This study evaluated the effect of a community-based social norm intervention involving female caregivers in West Hararghe, Ethiopia. The intervention was engaging female caregivers along with other adult influential community members to deliberate and act on food allocation social norms in a process referred to as Social Analysis and Action (SAA).MethodWe used data from a large quasi-experimental study to compare family eating practices between those who participated in the Social Analyses and Action intervention and those who did not. The respondents were female caregivers in households with young adolescent girls (ages 13 and 14 years). The study’s outcome was the practice of family eating together from the same dish. The difference in difference (DID) analysis with the mixed effect logistic regression model was used to examine the effect of the intervention.ResultThe results showed improved family eating practices in both groups, but the improvement was greater in the intervention group. The DID analysis showed an 11.99 percentage points greater improvement in the intervention arm than in the control arm. The mixed-effect regression produced an adjusted odds ratio of 2.08 (95% CI [1.06–4.09]) after controlling selected covariates, p-value 0.033.ConclusionsThe involvement of influential adult community members significantly improves the family practice of eating together in households where adolescent girls are present in our study. The intervention has great potential to minimize household food allocation inequalities and thus improve the nutritional status of young adolescents. Further studies are necessary to evaluate the effectiveness of the intervention in different social norm contexts to formulate policy and guidelines for scale-up. creator: Hanna Gulema creator: Meaza Demissie creator: Alemayehu Worku creator: Tesfaye Assebe Yadeta creator: Yemane Berhane uri: https://doi.org/10.7717/peerj.16099 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Gulema et al. title: Deciphering pathological behavior of pediatric medullary thyroid cancer from single-cell perspective link: https://peerj.com/articles/15546 last-modified: 2023-09-20 description: BackgroundPediatric medullary thyroid cancer (MTC) is one of the rare pediatric endocrine neoplasms. Derived from C cells of thyroid glands, MTC is more aggressive and more prompt to metastasis than other types of pediatric thyroid cancer. The mechanism remains unclear.MethodsWe performed single-cell transcriptome sequencing on the samples of the primary tumor and metastases lymph nodes from one patient diagnosed with MTC, and it is the first single-cell transcriptome sequencing data of pediatric MTC. In addition, whole exome sequencing was performed and peripheral blood was regarded as a normal reference. All cells that passed quality control were merged and analyzed in R to discover the association between tumor cells and their microenvironment as well as tumor pathogenesis.ResultsWe first described the landscape of the single-cell atlas of MTC and studied the interaction between the tumor cell and its microenvironment. C cells, identified as tumor cells, and T cells, as the dominant participant in the tumor microenvironment, were particularly discussed in their development and interactions. In addition, the WES signature of tumor cells and their microenvironment were also described. Actively immune interactions were found, indicating B cells, T cells and myeloid cells were all actively participating in immune reaction in MTC. T cells, as the major components of the tumor microenvironment, proliferated in MTC and could be divided into clusters that expressed proliferation, immune effectiveness, and naive markers separately. creator: De-qian Chen creator: En-qing Zhou creator: Hui-fen Chen creator: Yong Zhan creator: Chun-Jing Ye creator: Yi Li creator: Shu-yang Dai creator: Jun-feng Wang creator: Lian Chen creator: Kui-ran Dong creator: Rui Dong uri: https://doi.org/10.7717/peerj.15546 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chen et al. title: Preoperative lymphocyte count, neutrophil to lymphocyte and platelet to lymphocyte ratio predict the recurrence with progression and cancerization in vocal fold lesions—retrospective study link: https://peerj.com/articles/15642 last-modified: 2023-09-20 description: BackgroundsThis study explored the contribution of peripheral blood markers in diagnosis and prognosis estimation of different stages of laryngeal dysplasia and early glottic cancer.MethodsRetrospective analysis of clinical, histopathological and laboratory data of 220 patients including hemoglobin, neutrophil, lymphocyte, monocyte and platelet counts, neutrophil to lymphocyte ratio (NLR), platelet to lymphocyte ratio (PLR).ResultsThe mean hemoglobin level and platelets count showed differences between histopathological stages of lesions (p = 0.041 and 0.046, respectively). In patients with recurrent lesions mean level of lymphocyte count, NLR and PLR were significant in assessing progression and cancerization (p = 0.005, 0.028 and 0.023, respectively). The univariate analysis recognized level of PLR ≥ 141.74 as significant risk factor of the recurrence of vocal fold hypertrophic lesions (OR = 1.963).ConclusionsThe levels of blood cells and their ratios seem to be effective in predicting the recurrence of lesion and even more their potential role in indicating malignant progression. creator: Anna Rzepakowska creator: Wioletta Pietruszewska creator: Michał Żurek creator: Maria Molga-Magusiak creator: Michał Leszczyński creator: Kazimierz Niemczyk uri: https://doi.org/10.7717/peerj.15642 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Rzepakowska et al. title: Modelling and analysis of the complement system signalling pathways: roles of C3, C5a and pro-inflammatory cytokines in SARS-CoV-2 infection link: https://peerj.com/articles/15794 last-modified: 2023-09-20 description: The complement system is an essential part of innate immunity. It is activated by invading pathogens causing inflammation, opsonization, and lysis via complement anaphylatoxins, complement opsonin’s and membrane attack complex (MAC), respectively. However, in SARS-CoV-2 infection overactivation of complement system is causing cytokine storm leading to multiple organs damage. In this study, the René Thomas kinetic logic approach was used for the development of biological regulatory network (BRN) to model SARS-CoV-2 mediated complement system signalling pathways. Betweenness centrality analysis in cytoscape was adopted for the selection of the most biologically plausible states in state graph. Among the model results, in strongly connected components (SCCs) pro-inflammatory cytokines (PICyts) oscillatory behaviour between recurrent generation and downregulation was found as the main feature of SARS-CoV-2 infection. Diversion of trajectories from the SCCs leading toward hyper-inflammatory response was found in agreement with in vivo studies that overactive innate immunity response caused PICyts storm during SARS-CoV-2 infection. The complex of negative regulators FI, CR1 and DAF in the inhibition of complement peptide (C5a) and PICyts was found desirable to increase immune responses. In modelling role of MAC and PICyts in lowering of SARS-CoV-2 titre was found coherent with experimental studies. Intervention in upregulation of C5a and PICyts by C3 was found helpful in back-and-forth variation of signalling pattern linked with the levels of PICyts. Moreover, intervention in upregulation of PICyts by C5a was found productive in downregulation of all activating factors in the normal SCCs. However, the computational model predictions require experimental studies to be validated by exploring the activation role of C3 and C5a which could change levels of PICyts at various phases of SARS-CoV-2 infection. creator: Didar Murad creator: Rehan Zafar Paracha creator: Muhammad Tariq Saeed creator: Jamil Ahmad creator: Ammar Mushtaq creator: Maleeha Humayun uri: https://doi.org/10.7717/peerj.15794 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Murad et al.