title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=410 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: DisVar: an R library for identifying variants associated with diseases using large-scale personal genetic information link: https://peerj.com/articles/16086 last-modified: 2023-09-28 description: BackgroundGenetic variants may potentially play a contributing factor in the development of diseases. Several genetic disease databases are used in medical research and diagnosis but the web applications used to search these databases for disease-associated variants have limitations. The application may not be able to search for large-scale genetic variants, the results of searches may be difficult to interpret and variants mapped from the latest reference genome (GRCH38/hg38) may not be supported.MethodsIn this study, we developed a novel R library called “DisVar” to identify disease-associated genetic variants in large-scale individual genomic data. This R library is compatible with variants from the latest reference genome version. DisVar uses five databases of disease-associated variants. Over 100 million variants can be simultaneously searched for specific associated diseases.ResultsThe package was evaluated using 24 Variant Call Format (VCF) files (215,054 to 11,346,899 sites) from the 1000 Genomes Project. Disease-associated variants were detected in 298,227 hits across all the VCF files, taking a total of 63.58 m to complete. The package was also tested on ClinVar’s VCF file (2,120,558 variants), where 20,657 hits associated with diseases were identified with an estimated elapsed time of 45.98 s.ConclusionsDisVar can overcome the limitations of existing tools and is a fast and effective diagnostic and preventive tool that identifies disease-associated variations from large-scale genetic variants against the latest reference genome. creator: Khunanon Chanasongkhram creator: Kasikrit Damkliang creator: Unitsa Sangket uri: https://doi.org/10.7717/peerj.16086 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chanasongkhram et al. title: Carbon monoxide poisoning: beyond survival - mortality, morbidities, and risk factors, a Turkey sample link: https://peerj.com/articles/16093 last-modified: 2023-09-28 description: BackgroundWe aimed to investigate the effect of poisoning on mortality leading to new morbidities in people who survived the poisoning.MethodsThe descriptive-retrospective study evaluated all carbon monoxide poisoning cases between 2012 and 2022 in the Adiyaman. For the fatality, all cases were followed up through Turkey’s death notification system until the end of 2022. One-year health records of cases treated as inpatients in Adiyaman hospitals were analyzed for nine diagnoses. A total of 4,395 carbon monoxide cases, recorded over 11 years, were all noted to be accidental cases.ResultsThe rate of carbon monoxide poisoning in Adıyaman was calculated as 63.2 per hundred thousand. A total of 87 (2%) of the cases died. The population’s hospitalization rate was 1.71, while the mortality rate was 1.25 in a hundred thousand. Among the cases, the hospitalization rate was 2.7, and the admission to intensive care rate was 1.7. The fatality rate was 6.5% for those hospitalized and 12.2% for those admitted to the intensive care unit. The highest fatality rate was 65.5% in patients aged 65 and above. One out of five morbidities was developed in 8.4% of cases within one year. The fatality rate of those who developed morbidities (40%) was higher than those who did not (5.5%). Being male posed a 1,886-fold risk for mortality, and each increase in age posed a 1,086-fold risk for mortality.ConclusionIndividuals who had carbon monoxide poisoning should be followed up closely for one year after poisoning due to the possibility of the emergence of new morbidities that increase the risk of mortality. creator: Erdoğan Öz creator: Osman Küçükkelepçe creator: Osman Kurt creator: Aşkı Vural uri: https://doi.org/10.7717/peerj.16093 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Öz et al. title: Areas of spatial overlap between common bottlenose dolphin, recreational boating, and small-scale fishery: management insights from modelling exercises link: https://peerj.com/articles/16111 last-modified: 2023-09-28 description: BackgroundSustainable management requires spatial mapping of both species distribution and human activities to identify potential risk of conflict. The common bottlenose dolphin (Tursiops truncatus) is a priority species of the European Union Habitat Directive, thus, to promote its conservation, the understanding of habitat use and distribution, as well as the identification and spatial trend of the human activities which may directly affect populations traits, is pivotal.MethodsA MaxEnt modeling approach was applied to predict the seasonal (from April to September) habitat use of a small population of bottlenose dolphins in the north-western Sardinia (Mediterranean Sea) in relation to environmental variables and the likelihoods of boat and fishing net presence. Then, the overlapping areas between dolphin, fishing net and boat presence were identified to provide insights for the marine spatial management of this area.ResultsThree of the main factors influencing the seasonal distribution of bottlenose dolphins in the area are directly (boating and fishing) or indirectly (ocean warming) related to human activities. Furthermore, almost half of the most suitable area for dolphins overlapped with areas used by fishing and boating. Finally, relying on fishing distribution models, we also shed light on the potential impact of fishing on the Posidonia oceanica beds, a protected habitat, which received higher fishing efforts than other habitat types.DiscussionModelling the spatial patterns of anthropogenic activities was fundamental to understand the ecological impacts both on cetacean habitat use and protected habitats. A greater research effort is suggested to detect potential changes in dolphin habitat suitability, also in relation to ocean warming, to assess dolphin bycatch and the status of target fish species, and to evaluate sensitive habitats conditions, such as the Posidonia oceanica meadow. creator: Gabriella La Manna creator: Fabio Ronchetti creator: Francesco Perretti creator: Giulia Ceccherelli uri: https://doi.org/10.7717/peerj.16111 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 La Manna et al. title: Systematic bioprospection for cellulolytic actinomycetes in the Chihuahuan Desert: isolation and enzymatic profiling link: https://peerj.com/articles/16119 last-modified: 2023-09-28 description: The quest for microbial cellulases has intensified as a response to global challenges in biofuel production. The efficient deconstruction of lignocellulosic biomass holds promise for generating valuable products in various industries such as food, textile, and detergents. This article presents a systematic bioprospection aimed at isolating actinomycetes with exceptional cellulose deconstruction capabilities. Our methodology explored the biodiverse oligotrophic region of Cuatro Cienegas, Coahuila, within the Chihuahuan Desert. Among the evaluated actinomycetes collection, 78% exhibited cellulolytic activity. Through a meticulous screening process based on enzymatic index evaluation, we identified a highly cellulolytic Streptomyces strain for further investigation. Submerged fermentation of this strain revealed an endoglucanase enzymatic activity of 149 U/mg. Genomic analysis of strain Streptomyces sp. STCH565-A revealed unique configurations of carbohydrate-active enzyme (CAZyme) genes, underscoring its potential for lignocellulosic bioconversion applications. These findings not only highlight the significance of the Chihuahuan Desert as a rich source of cellulolytic microorganisms but also offer insights into the systematic exploration and selection of high-performing cellulolytic microorganisms for application in diverse environmental contexts. In conclusion, our bioprospecting study lays a foundation for harnessing the cellulolytic potential of actinomycetes from the Chihuahuan Desert, with implications for advancing cellulose deconstruction processes in various industries. The findings can serve as a blueprint for future bioprospecting efforts in different regions, facilitating the targeted discovery of microorganisms with exceptional cellulosic deconstruction capabilities. creator: Janneth Escudero-Agudelo creator: Juan Martínez-Villalobos creator: Hector Arocha-Garza creator: Luis Jesús Galán-Wong creator: Hamlet Avilés-Arnaut creator: Susana De la Torre-Zavala uri: https://doi.org/10.7717/peerj.16119 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Escudero-Agudelo et al. title: Differences in and associations between belief in just deserts and human rights restrictions over a 3-year period in five countries during the COVID-19 pandemic link: https://peerj.com/articles/16147 last-modified: 2023-09-28 description: Discrimination, which arose during the coronavirus disease 2019 outbreak, is a global public health issue. This study aimed to provide fundamental knowledge in proposing control measures to mitigate discrimination. We focused on two psychological variables: belief in just deserts (BJD, i.e., the belief that the infected individual deserves to be infected), a psychological factor that potentially promotes discrimination and prejudice, and human rights restrictions (HRR; i.e., the degree of individuals’ agreement with government restrictions on citizens’ behavior during emergencies). Differences in these items, as well as their annual trends from 2020 to 2022, were examined in Japan, the United States (US), the United Kingdom (UK), Italy, and China. In addition, the associations between BJD and HRR by country and year and the direction of the associations between them in Japan and Italy were analyzed. Online surveys were conducted annually, with 392–518 participants per country and year. The BJD was higher in Japan and lower in the UK. BJD increased significantly from 2020 to 2021 in all countries, except in China. Meanwhile, HRR was higher in China and lower in Japan. The HRR decreased from 2020 to 2021 in Japan and decreased from 2020 to 2022 in the US, the UK, and Italy. There were significant positive associations between BJD and HRR in Japan and Italy. Cross-lagged panel models revealed positive bidirectional associations between BJD and HRR in Japan and Italy, respectively, indicating that the HRR declined among those with weak BJD and that the BJD increased among those with high HRR. In Japan and Italy, the dissemination of public messages targeting those with a high HRR in the early stages of an infectious disease outbreak could potentially mitigate the adverse impact of the BJD, eventually reducing discrimination, especially when the infection is not attributed to the fault of the infected individuals. creator: Michio Murakami creator: Kai Hiraishi creator: Mei Yamagata creator: Daisuke Nakanishi creator: Andrea Ortolani creator: Nobuhiro Mifune creator: Yang Li creator: Asako Miura uri: https://doi.org/10.7717/peerj.16147 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Murakami et al. title: Identification of CDT1 as a prognostic marker in human lung adenocarcinoma using bioinformatics approaches link: https://peerj.com/articles/16166 last-modified: 2023-09-28 description: BackgroundLung cancer has the highest cancer-related mortality worldwide. Lung adenocarcinoma (LUAD) is the most common histological subtype of non-small cell lung cancer (NSCLC). Chromatin licensing and DNA replication factor 1 (CDT1), a key regulator of cell cycle control and replication in eukaryotic cells, has been implicated in various cancer-related processes. Given its significant role in cancer, the focus on CDT1 in this study is justified as it holds promise as a potential biomarker or therapeutic target for cancer treatment. However, its prognostic value in lung adenocarcinoma (LUAD) remains unclear.MethodsBioinformatics analysis was conducted using data obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were utilized to predict biological processes and signaling pathways, respectively. The LinkedOmics database was employed to identify differentially expressed genes (DEGs) associated with CDT1. Nomograms and Kaplan-Meier plots were generated to assess the survival rates of patients with lung adenocarcinoma (LUAD). To determine the RNA and protein expression levels of CDT1 in LUAD and adjacent normal tissues, quantitative polymerase chain reaction (qPCR) and immunohistochemistry techniques were employed, respectively.ResultsCDT1 was upregulated in the vast majority of cancer tissues, based on pan-cancer analysis in TCGA and GEO datasets, as to lung cancer, the level of CDT1 expression was much higher in LUAD tissue than in healthy lung tissue. Our clinical data supported these findings. In our study, we used a specific cutoff value to dichotomize the patient samples into high and low CDT1 expression groups. The Kaplan–Meier survival curve revealed poor survival rates in CDT1 high expression group than the low expression group. To determine if CDT1 expression was an independent risk factor in LUAD patients, univariate and multivariate Cox regression analyses were performed. The result showed that CDT1 was a potential novel prognosis factor for LUAD patients, whose prognosis was poorer when CDT1 expression was higher. Based on functional enrichment analysis, highly expressed DEGs of CDT1-high patients were predicted to be involved in the cell cycle. According to our analysis of immune infiltration, CDT1 exhibited a strong correlation with specific immune cell subsets and was found to be a significant predictor of poor survival in patients with LUAD.ConclusionsOur research found that CDT1 was upregulated in LUAD and that high CDT1 expression predicted poor prognosis. We comprehensively and systematically analyzed the expression level in the datasets as well as in our own clinical samples, we also evaluated the prognostic and diagnostic value of CDT1, and finally, the potential mechanisms of CDT1 in the progression of LUAD. These results suggested that CDT1 may be a prognostic marker and therapeutic target for LUAD. creator: Jing Jiang creator: Yu Zhang creator: Jun Wang creator: Xuefei Yang creator: Xingchang Ren creator: Hai Huang creator: Jue Wang creator: Jinhua Lu creator: Yazhen Zhong creator: Zechen Lin creator: Xianlei Lin creator: Yewei Jia creator: Shengyou Lin uri: https://doi.org/10.7717/peerj.16166 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Jiang et al. title: Ecological engineering in low land rice for brown plant hopper, Nilaparvata lugens (Stål) management link: https://peerj.com/articles/15531 last-modified: 2023-09-27 description: Rice field bunds and edges can act as near crop habitats, available for planting flowering plants to attract and conserve the natural enemies. We evaluated the effect of ecological engineering on the incidence of Brown Planthopper (BPH), Nilaparvata lugens (Stål) (Hemiptera; Delphacidae) and the abundance of its predators in the rice variety Pusa Basmati-1121. Plots included the oilseed crops viz. sesamum, sunflower and soybean, with plantings of flowering crops marigold, balsam and gaillardia as bund flora around the edges of rice plots. Ecologically engineered plots contained both crops+flowers and resulted in a significantly reduced BPH population per hill in rice plots for 2019 (6.3) and 2020 (9.4) compared to the control plots (9.8 and 14.4). Ecologically engineered plots also witnessed the delayed appearance of BPH during each growing season. Peak BPH populations are lower in the ecologically engineered plots than in the control grounds. Furthermore, the activity of natural enemies, viz., spiders, mirid bugs and rove beetles was the highest in rice fields planted with oilseed crops like sesamum, sunflower and soybean. Olfactory response studies showed that the attraction response of spiders toward sesamum and balsam leaves was more significant than in other crop plants. Rice yield was enhanced in plots planted with crops+flowers during both seasons compared to control plots. Planting of oilseed crops plants such as sesamum, sunflower and soybean with flowering crops such as marigold, balsam and gaillardia as bund flora on the bunds around the main rice field enhanced the natural enemy activity, suppressed the planthopper population, and increased yields. Based on the results, we recommend including ecological engineering techniques as one of the management components in the Integrated Pest Management programme for rice crops. creator: Yogesh Yele creator: Subhash Chander creator: Sachin S. Suroshe creator: Suresh Nebapure creator: Prabhulinga Tenguri creator: Arya Pattathanam Sundaran uri: https://doi.org/10.7717/peerj.15531 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yele et al. title: CESCProg: a compact prognostic model and nomogram for cervical cancer based on miRNA biomarkers link: https://peerj.com/articles/15912 last-modified: 2023-09-27 description: Cervical squamous cell carcinoma, more commonly cervical cancer, is the fourth common cancer among women worldwide with substantial burden of disease, and less-invasive, reliable and effective methods for its prognosis are necessary today. Micro-RNAs are increasingly recognized as viable alternative biomarkers for direct diagnosis and prognosis of disease conditions, including various cancers. In this work, we addressed the problem of systematically developing an miRNA-based nomogram for the reliable prognosis of cervical cancer. Towards this, we preprocessed public-domain miRNA -omics data from cervical cancer patients, and applied a cascade of filters in the following sequence: (i) differential expression criteria with respect to controls; (ii) significance with univariate survival analysis; (iii) passage through dimensionality reduction algorithms; and (iv) stepwise backward selection with multivariate Cox modeling. This workflow yielded a compact prognostic DEmiR signature of three miRNAs, namely hsa-miR-625-5p, hs-miR-95-3p, and hsa-miR-330-3p, which were used to construct a risk-score model for the classification of cervical cancer patients into high-risk and low-risk groups. The risk-score model was subjected to evaluation on an unseen test dataset, yielding a one-year AUROC of 0.84 and five-year AUROC of 0.71. The model was validated on an out-of-domain, external dataset yielding significantly worse prognosis for high-risk patients. The risk-score was combined with significant features of the clinical profile to establish a predictive prognostic nomogram. Both the miRNA-based risk score model and the integrated nomogram are freely available for academic and not-for-profit use at CESCProg, a web-app (https://apalania.shinyapps.io/cescprog). creator: Sangeetha Muthamilselvan creator: Ashok Palaniappan uri: https://doi.org/10.7717/peerj.15912 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Muthamilselvan et al. title: Clinical value of hemoglobin, albumin, lymphocyte, and platelet indexes in predicting lymph node metastasis and recurrence of endometrial cancer: a retrospective study link: https://peerj.com/articles/16043 last-modified: 2023-09-27 description: ObjectiveTo study the clinical importance of hemoglobin, albumin, lymphocyte, and platelet (HALP) indexes in predicting lymph node metastasis and recurrence of endometrial cancer.MethodsFrom July 2016 to July 2020, 158 patients suffering from endometrial cancer who visited the gynecology department of General Hospital of Ningxia Medical University from were collected. Employing the X-Tiles program, the ideal HALP cut-off value was established, and the patients were separated into low and high HALP groups. Univariate and multivariate analysis were used to determine the relationship between HALP score and lymph node metastasis and recurrence of endometrial cancer.ResultsThe optimal cut-off value of HALP score was established to be 22.2 using X-Tiles software, and the patients were separated into high HALP group (HALP score > 22.2, with 43 cases) and low HALP group (HALP score ≤ 22.2, 115 cases). Endometrial cancer patients’ HALP scores were strongly connected with differentiation, the degree of myometrial invasion, and lymph node metastasis (P < 0.05), although not with age, menopausal status, or stage (P > 0.05). Multivariate logistic regression analysis revealed that the HALP score (OR = 2.087) was the influencing factor for lymph node metastasis (P < 0.05). The ROC curve suggested that the AUC of HALP score in predicting lymph node metastasis was 0.871, which had high diagnostic value. When compared to patients without recurrence, HALP scores of patients with recurrence were considerably lower (P < 0.05). Multivariate logistic regression analysis showed that HALP score (OR = 2.216) was the influencing factor for the occurrence of lymph node metastasis (P < 0.05). The ROC curve suggested that the AUC of HALP score in predicting relapse was 0.855, with high diagnostic value.ConclusionThe HALP score shows good predictive performance in predicting lymph node metastasis and recurrence of endometrial cancer, and has high clinical value, which helps in improving the accuracy and effectiveness of clinical diagnosis and prognosis research. creator: Ying Xiong creator: Yuanyuan Yong creator: Yanhua Wang uri: https://doi.org/10.7717/peerj.16043 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Xiong et al. title: Gut content metabarcoding of specialized feeders is not a replacement for environmental DNA assays of seawater in reef environments link: https://peerj.com/articles/16075 last-modified: 2023-09-27 description: In tropical marine ecosystems, the coral-based diet of benthic-feeding reef fishes provides a window into the composition and health of coral reefs. In this study, for the first time, we compare multi-assay metabarcoding sequences of environmental DNA (eDNA) isolated from seawater and partially digested gut items from an obligate corallivore butterflyfish (Chaetodon lunulatus) resident to coral reef sites in the South China Sea. We specifically tested the proportional and statistical overlap of the different approaches (seawater vs gut content metabarcoding) in characterizing eukaryotic community composition on coral reefs. Based on 18S and ITS2 sequence data, which differed in their taxonomic sensitivity, we found that gut content detections were only partially representative of the eukaryotic communities detected in the seawater based on low levels of taxonomic overlap (3 to 21%) and significant differences between the sampling approaches. Overall, our results indicate that dietary metabarcoding of specialized feeders can be complimentary to, but is no replacement for, more comprehensive environmental DNA assays of reef environments that might include the processing of different substrates (seawater, sediment, plankton) or traditional observational surveys. These molecular assays, in tandem, might be best suited to highly productive but cryptic oceanic environments (kelp forests, seagrass meadows) that contain an abundance of organisms that are often small, epiphytic, symbiotic, or cryptic. creator: Joseph D. DiBattista creator: Shang Yin Vanson Liu creator: Maarten De Brauwer creator: Shaun P. Wilkinson creator: Katrina West creator: Adam Koziol creator: Michael Bunce uri: https://doi.org/10.7717/peerj.16075 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 DiBattista et al.