title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=742 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The direct and indirect effects of a global pandemic on US fishers and seafood workers link: https://peerj.com/articles/13007 last-modified: 2022-03-21 description: The United States’ fishing and seafood industries experienced major shifts in consumer demand and social-distancing restrictions starting in March 2020, when the early stages of the COVID-19 pandemic were unfolding. However, the specific effects on fishers and seafood processors are less well known. Fishermen and seafood workers are potentially at risk during a pandemic given existing tight working quarters, seasonal work, and long hours. To address these concerns, and given a lack of data on the sector, we reviewed news articles, scientific articles, and white papers to assess the various effects of COVID-19 on US seafood workers. Here, we show that most COVID-19 cases among seafood workers occurred during summer 2020 and during the beginning of 2021. These cases were documented across coastal areas, with Alaska experiencing the largest number of cases and outbreaks. Seafood workers were about twice as likely to contract COVID-19 as workers in other parts of the overall US food system. We also documented a number of indirect effects of the pandemic. New social-distancing restrictions and policies limited crew size, resulting in longer hours and more physical taxation. Because of changes in demand and the closure of some processing plants because of COVID-19 outbreaks, economic consequences of the pandemic were a primary concern for fishers and seafood workers, and safety measures allowed for seafood price variation and losses throughout the pandemic. We also highlight a number of inequities in COVID-19 responses within the seafood sector, both along racial and gender lines. All of these conditions point to the diverse direct and indirect effects of the COVID-19 pandemic on fishers and seafood workers. We hope this work sets the foundation for future work on the seafood sector in relation to the COVID-19 pandemic, improving the overall workplace, and collecting systematic social and economic data on workers. creator: Easton R. White creator: Jill Levine creator: Amanda Moeser creator: Julie Sorensen uri: https://doi.org/10.7717/peerj.13007 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 White et al. title: Focus on Polish nurses’ health condition: a cross-sectional study link: https://peerj.com/articles/13065 last-modified: 2022-03-21 description: BackgroundThe nursing profession carries with it many negative factors and a high risk of developing chronic diseases, including overweight and obesity. According to statistics, the health condition of this professional group is much worse than that of the average population of the same age. As the largest and most trusted professional group in the world, nurses are critical to the health of any nation. The aim of the study was to assess the Polish nurse’s health condition based on real measurements of parameters important for the occurrence of metabolic diseases.MethodsThis is the cross-sectional, conducted among two age groups of Polish nurses (<50 years and ≥50 years). Study included the measurements with DXA, the assessment of glucose concentration and lipid profile, the measurement of blood pressure and socio-demographic data of the surveyed nurses.ResultsThe majority of respondents above 50 years old were nurses with elevated total cholesterol (79.3%), elevated LDL cholesterol (72.8%), 42.4% of studied nurses had hypertension.ConclusionIndividual, local and national measures to prevent and support the health of this professional group are needed. creator: Anna Bartosiewicz creator: Edyta Łuszczki creator: Pawel Jagielski creator: Lukasz Oleksy creator: Artur Stolarczyk creator: Katarzyna Dereń uri: https://doi.org/10.7717/peerj.13065 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Bartosiewicz et al. title: Cooperation between arbuscular mycorrhizal fungi and plant growth-promoting bacteria and their effects on plant growth and soil quality link: https://peerj.com/articles/13080 last-modified: 2022-03-21 description: The roles of arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) in improving nutrition uptake and soil quality have been well documented. However, few studies have explored their effects on root morphology and soil properties. In this study, we inoculated Elymus nutans Griseb with AMF and/or PGPR in order to explore their effects on plant growth, soil physicochemical properties, and soil enzyme activities. The results showed that AMF and/or PGPR inoculation significantly enhanced aboveground and belowground vegetation biomass. Both single and dual inoculations were beneficial for plant root length, surface area, root branches, stem diameter, height, and the ratio of shoot to root, but decreased root volume and root average diameter. Soil total nitrogen, alkaline phosphatase, and urease activities showed significant growth, and soil electrical conductivity and pH significantly declined under the inoculation treatments. Specific root length showed a negative correlation with belowground biomass, but a positive correlation with root length and root branches. These results indicated that AMF and PGPR had synergetic effects on root morphology, soil nutrient availability, and plant growth. creator: Lu Yu creator: Hui Zhang creator: Wantong Zhang creator: Kesi Liu creator: Miao Liu creator: Xinqing Shao uri: https://doi.org/10.7717/peerj.13080 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yu et al. title: Chikungunya virus time course infection of human macrophages reveals intracellular signaling pathways relevant to repurposed therapeutics link: https://peerj.com/articles/13090 last-modified: 2022-03-21 description: BackgroundChikungunya virus (CHIKV) is a mosquito-borne pathogen, within the Alphavirus genus of the Togaviridae family, that causes ~1.1 million human infections annually. CHIKV uses Aedes albopictus and Aedes aegypti mosquitoes as insect vectors. Human infections can develop arthralgia and myalgia, which results in debilitating pain for weeks, months, and even years after acute infection. No therapeutic treatments or vaccines currently exist for many alphaviruses, including CHIKV. Targeting the phagocytosis of CHIKV by macrophages after mosquito transmission plays an important role in early productive viral infection in humans, and could reduce viral replication and/or symptoms.MethodsTo better characterize the transcriptional response of macrophages during early infection, we generated RNA-sequencing data from a CHIKV-infected human macrophage cell line at eight or 24 hours post-infection (hpi), together with mock-infected controls. We then calculated differential gene expression, enriched functional annotations, modulated intracellular signaling pathways, and predicted therapeutic drugs from these sequencing data.ResultsWe observed 234 pathways were significantly affected 24 hpi, resulting in six potential pharmaceutical treatments to modulate the affected pathways. A subset of significant pathways at 24 hpi includes AGE-RAGE, Fc epsilon RI, Chronic myeloid leukemia, Fc gamma R-mediated phagocytosis, and Ras signaling. We found that the MAPK1 and MAPK3 proteins are shared among this subset of pathways and that Telmisartan and Dasatinib are strong candidates for repurposed small molecule therapeutics that target human processes. The results of our analysis can be further characterized in the wet lab to contribute to the development of host-based prophylactics and therapeutics. creator: Madison Gray creator: Israel Guerrero-Arguero creator: Antonio Solis-Leal creator: Richard A. Robison creator: Bradford K. Berges creator: Brett E. Pickett uri: https://doi.org/10.7717/peerj.13090 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gray et al. title: A machine learning approach for identification of gastrointestinal predictors for the risk of COVID-19 related hospitalization link: https://peerj.com/articles/13124 last-modified: 2022-03-21 description: Background and aimCOVID-19 can be presented with various gastrointestinal symptoms. Shortly after the pandemic outbreak, several machine learning algorithms were implemented to assess new diagnostic and therapeutic methods for this disease. The aim of this study is to assess gastrointestinal and liver-related predictive factors for SARS-CoV-2 associated risk of hospitalization.MethodsData collection was based on a questionnaire from the COVID-19 outpatient test center and from the emergency department at the University Hospital in combination with the data from internal hospital information system and from a mobile application used for telemedicine follow-up of patients. For statistical analysis SARS-CoV-2 negative patients were considered as controls in three different SARS-CoV-2 positive patient groups (divided based on severity of the disease). The data were visualized and analyzed in R version 4.0.5. The Chi-squared or Fisher test was applied to test the null hypothesis of independence between the factors followed, where appropriate, by the multiple comparisons with the Benjamini Hochberg adjustment. The null hypothesis of the equality of the population medians of a continuous variable was tested by the Kruskal Wallis test, followed by the Dunn multiple comparisons test. In order to assess predictive power of the gastrointestinal parameters and other measured variables for predicting an outcome of the patient group the Random Forest machine learning algorithm was trained on the data. The predictive ability was quantified by the ROC curve, constructed from the Out-of-Bag data. Matthews correlation coefficient was used as a one-number summary of the quality of binary classification. The importance of the predictors was measured using the Variable Importance. A 2D representation of the data was obtained by means of Principal Component Analysis for mixed type of data. Findings with the p-value below 0.05 were considered statistically significant.ResultsA total of 710 patients were enrolled in the study. The presence of diarrhea and nausea was significantly higher in the emergency department group than in the COVID-19 outpatient test center. Among liver enzymes only aspartate transaminase (AST) has been significantly elevated in the hospitalized group compared to patients discharged home. Based on the Random Forest algorithm, AST has been identified as the most important predictor followed by age or diabetes mellitus. Diarrhea and bloating have also predictive importance, although much lower than AST.ConclusionSARS-CoV-2 positivity is connected with isolated AST elevation and the level is linked with the severity of the disease. Furthermore, using the machine learning Random Forest algorithm, we have identified the elevated AST as the most important predictor for COVID-19 related hospitalizations. creator: Peter Lipták creator: Peter Banovcin creator: Róbert Rosoľanka creator: Michal Prokopič creator: Ivan Kocan creator: Ivana Žiačiková creator: Peter Uhrik creator: Marian Grendar creator: Rudolf Hyrdel uri: https://doi.org/10.7717/peerj.13124 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Lipták et al. title: An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2 link: https://peerj.com/articles/13136 last-modified: 2022-03-21 description: Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures. creator: Sk. Sarif Hassan creator: Vaishnavi Kodakandla creator: Elrashdy M. Redwan creator: Kenneth Lundstrom creator: Pabitra Pal Choudhury creator: Tarek Mohamed Abd El-Aziz creator: Kazuo Takayama creator: Ramesh Kandimalla creator: Amos Lal creator: Ángel Serrano-Aroca creator: Gajendra Kumar Azad creator: Alaa A.A. Aljabali creator: Giorgio Palù creator: Gaurav Chauhan creator: Parise Adadi creator: Murtaza Tambuwala creator: Adam M. Brufsky creator: Wagner Baetas-da-Cruz creator: Debmalya Barh creator: Vasco Azevedo creator: Nikolas G. Bazan creator: Bruno Silva Andrade creator: Raner José Santana Silva creator: Vladimir N. Uversky uri: https://doi.org/10.7717/peerj.13136 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hassan et al. title: State of biodiversity documentation in the Philippines: Metadata gaps, taxonomic biases, and spatial biases in the DNA barcode data of animal and plant taxa in the context of species occurrence data link: https://peerj.com/articles/13146 last-modified: 2022-03-21 description: Anthropogenic changes in the natural environment have led to alarming rates of biodiversity loss, resulting in a more urgent need for conservation. Although there is an increasing cognizance of the importance of incorporating biodiversity data into conservation, the accuracy of the inferences generated from these records can be highly impacted by gaps and biases in the data. Because of the Philippines’ status as a biodiversity hotspot, the assessment of potential gaps and biases in biodiversity documentation in the country can be a critical step in the identification of priority research areas for conservation applications. In this study, we systematically assessed biodiversity data on animal and plant taxa found in the Philippines by examining the extent of metadata gaps, taxonomic biases, and spatial biases in DNA barcode data while using species occurrence data as a backdrop of the ‘Philippines’ biodiversity. These barcode and species occurrence datasets were obtained from public databases, namely: GenBank, Barcode of Life Data System and Global Biodiversity Information Facility. We found that much of the barcode data had missing information on either records and publishing, geolocation, or taxonomic metadata, which consequently, can limit the usability of barcode data for further analyses. We also observed that the amount of barcode data can be directly associated with the amount of species occurrence data available for a particular taxonomic group and location–highlighting the potential sampling biases in the barcode data. While the majority of barcode data came from foreign institutions, there has been an increase in local efforts in recent decades. However, much of the contribution to biodiversity documentation only come from institutions based in Luzon. creator: Carmela Maria P. Berba creator: Ambrocio Melvin A. Matias uri: https://doi.org/10.7717/peerj.13146 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Berba and Matias title: Computational bioacoustics with deep learning: a review and roadmap link: https://peerj.com/articles/13152 last-modified: 2022-03-21 description: Animal vocalisations and natural soundscapes are fascinating objects of study, and contain valuable evidence about animal behaviours, populations and ecosystems. They are studied in bioacoustics and ecoacoustics, with signal processing and analysis an important component. Computational bioacoustics has accelerated in recent decades due to the growth of affordable digital sound recording devices, and to huge progress in informatics such as big data, signal processing and machine learning. Methods are inherited from the wider field of deep learning, including speech and image processing. However, the tasks, demands and data characteristics are often different from those addressed in speech or music analysis. There remain unsolved problems, and tasks for which evidence is surely present in many acoustic signals, but not yet realised. In this paper I perform a review of the state of the art in deep learning for computational bioacoustics, aiming to clarify key concepts and identify and analyse knowledge gaps. Based on this, I offer a subjective but principled roadmap for computational bioacoustics with deep learning: topics that the community should aim to address, in order to make the most of future developments in AI and informatics, and to use audio data in answering zoological and ecological questions. creator: Dan Stowell uri: https://doi.org/10.7717/peerj.13152 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Stowell title: Immediate and cumulative effects of upper-body isometric exercise on the cornea and anterior segment of the human eye link: https://peerj.com/articles/13160 last-modified: 2022-03-21 description: ObjectivesThe execution of isometric resistance training has demonstrated to cause changes in the ocular physiology. The morphology of the cornea and anterior chamber is of paramount importance in the prevention and management of several ocular diseases, and thus, understating the impact of performing isometric exercise on the eye physiology may allow a better management of these ocular conditions. We aimed to determine the short-term effects of 2-minutes upper-body isometric effort at two different intensities on corneal and anterior eye morphology.MethodsEighteen healthy young adults performed a 2-minutes isometric biceps-curl exercise against two loads relative to their maximum strength capacity (high-intensity and low-intensity) in a randomized manner. An Oculus Pentacam was used to measure the corneal morphology and anterior chamber parameters in both experimental conditions at baseline, during the isometric effort (after 30, 60, 90 and 120 seconds), and after 30 and 120 seconds of passive recovery.ResultsWe found that isometric effort causes an increase in pupil size (P < 0.001), and a decrease in the iridocorneal angle (P = 0.005), anterior chamber volume (P < 0.001) and K-flat (P < 0.001) during isometric effort, with these effects being more accentuated in high-intensity condition (P < 0.005 in all cases).Performing 2-minutes upper-body isometric effort did not alter anterior chamber depth, central corneal thickness, corneal volume, and K-steep (P > 0.05 in all cases).ConclusionsOur data exhibit that performing 2-minutes of upper-body isometric exercise modifies several parameters of the corneal morphology and anterior eye biometrics, with these changes being greater for the high-intensity exercise condition. The findings of this study may be of relevance for the prevention and management of corneal ectasias and glaucoma. creator: Jesus Vera creator: Beatriz Redondo creator: Rubén Molina creator: Amador García-Ramos creator: Raimundo Jiménez uri: https://doi.org/10.7717/peerj.13160 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Vera et al. title: Relationship between circadian genes and memory impairment caused by sleep deprivation link: https://peerj.com/articles/13165 last-modified: 2022-03-21 description: BackgroundSleep deprivation (SD)-induced cognitive impairment is highly prevalent worldwide and has attracted widespread attention. The temporal and spatial oscillations of circadian genes are severely disturbed after SD, leading to a progressive loss of their physiological rhythms, which in turn affects memory function. However, there is a lack of research on the role of circadian genes and memory function after SD. Therefore, the present study aims to investigate the relationship between circadian genes and memory function and provide potential therapeutic insights into the mechanism of SD-induced memory impairment.MethodsGene expression profiles of GSE33302 and GSE9442 from the Gene Expression Omnibus (GEO) were applied to identify differentially expressed genes (DEGs). Subsequently, both datasets were subjected to Gene Set Enrichment Analysis (GSEA) to determine the overall gene changes in the hippocampus and brain after SD. A Gene Oncology (GO) analysis and Protein-Protein Interaction (PPI) analysis were employed to explore the genes related to circadian rhythm, with their relationship and importance determined through a correlation analysis and a receiver operating characteristic curve (ROC), respectively. The water maze experiments detected behavioral changes related to memory function in SD rats. The expression of circadian genes in several critical organs such as the brain, heart, liver, and lungs and their correlation with memory function was investigated using several microarrays. Finally, changes in the hippocampal immune environment after SD were analyzed using the CIBERSORT in R software.ResultsThe quality of the two datasets was very good. After SD, changes were seen primarily in genes related to memory impairment and immune function. Genes related to circadian rhythm were highly correlated with engagement in muscle structure development and circadian rhythm. Seven circadian genes showed their potential therapeutic value in SD. Water maze experiments confirmed that SD exacerbates memory impairment-related behaviors, including prolonged escape latencies and reduced numbers of rats crossing the platform. The expression of circadian genes was verified, while some genes were also significant in the heart, liver, and lungs. All seven circadian genes were also associated with memory markers in SD. The contents of four immune cells in the hippocampal immune environment changed after SD. Seven circadian genes were related to multiple immune cells.ConclusionsIn the present study, we found that SD leads to memory impairment accompanied by changes in circadian rhythm-related genes. Seven circadian genes play crucial roles in memory impairment after SD. Naïve B cells and follicular helper T cells are closely related to SD. These findings provide new insights into the treatment of memory impairment caused by SD. creator: Peng Ke creator: Chengjie Zheng creator: Feng Liu creator: LinJie Wu creator: Yijie Tang creator: Yanqin Wu creator: Dongdong Lv creator: Huangli Chen creator: Lin Qian creator: Xiaodan Wu creator: Kai Zeng uri: https://doi.org/10.7717/peerj.13165 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ke et al.