title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=587 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Almost nothing is known about the tiger shark in South Atlantic waters link: https://peerj.com/articles/14750 last-modified: 2023-01-20 description: The tiger shark (Galeocerdo cuvier) has been relatively well assessed concerning biology and ecology aspects in both Atlantic and Pacific North America and in Caribbean waters. The amount of data in these regions has led to the species protection under capture quotas and with the creation of sanctuaries. The reality in developing countries, however, is the exact opposite, with scarce information on the species in the southern hemisphere, namely South American and African waters. In these regions, protection measures are insufficient, and studies on tiger shark biology and ecology are scarce, significantly hindering conservation and management efforts. Thus, the aim of this study was to compile scientific literature on the tiger shark in the South Atlantic and discuss the impact of these data (or lack thereof) distributed within a total of ten research categories for guiding management plans. In total, 41 scientific publications on different G. cuvier biology and ecology aspects were obtained. The most studied topics were Feeding Ecology (n = 12), followed by Human Interactions (n = 8), and Movements and Migration (n = 7). Northeastern Brazil (Southwest Atlantic) was the most researched area, probably due to the higher coastal abundance of tiger sharks in this area, alongside a high number of recorded attacks, justifying funding for studies in the region. No studies carried out in other South American or African countries were found. It is important to mention that even though some research topics are relatively well covered, a severe knowledge gap is noted for risk assessments and fisheries management, with a proposition for the implementation of sanctuaries noted. This is, however, particularly worrisome, as the South Atlantic is mostly unexplored in this regard for tiger sharks. It is also important to note how different the attention given to this species is in the North Atlantic when compared to the South region. Lastly, we highlight that the existence of sub-populations, the lack of migratory corridors geographically connecting distinct areas used by the species, and the lack of fisheries statistics on tiger shark landings, all increase the vulnerability of this species in the South Atlantic. creator: Samuel Balanin creator: Rachel Ann Hauser-Davis creator: Eloísa Giareta creator: Patricia Charvet creator: Natascha Wosnick uri: https://doi.org/10.7717/peerj.14750 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Balanin et al. title: A comparative study on third trimester fetal biometric parameters with maternal age link: https://peerj.com/articles/14528 last-modified: 2023-01-19 description: BackgroundAdvanced maternal age is an important parameter associated with increased risk of feto-maternal complications and it is an evolving trend in society for women planning for pregnancy in late ages. However there are no studies done whether advanced maternal age has its effects on expression of growth pattern in the fetus. So this study was done to compare the maternal age with the third trimester fetal biometric parameters.MethodsThis study was done in 100 antenatal women and divided into two groups: Group 1: optimal maternal age group between 21–29 years of age and Group 2: advanced maternal age 30 and above. The pre-pregnant maternal weight, gestational age and third trimester fetal biometrics using ultrasound are noted and compared between the groups.ResultsThe maternal weight gain between the groups was optimal but the third trimester fetal parameters were significantly less in advanced maternal age. The abdominal circumference in optimal age group and head circumference in advanced maternal age group was closer to calculated estimated date of delivery (EDD) and would be specific in calculating the gestational age.ConclusionsThough there is no significant difference in maternal weight gain, there are fetal growth restrictions in advanced maternal age group due to which the third trimester fetal parameters are lesser than the optimal age group. Head circumference would be specific in calculating the estimated date of delivery in advanced maternal age group. creator: Yogitha Poojari creator: Prudhvinath reddy Annapureddy creator: Sharmila Vijayan creator: Vinoth Kumar Kalidoss creator: Yuvaraj Mf creator: Sankaran Pk uri: https://doi.org/10.7717/peerj.14528 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Poojari et al. title: N6-methyladenosine (m6A) reader IGF2BP1 facilitates clear-cell renal cell carcinoma aerobic glycolysis link: https://peerj.com/articles/14591 last-modified: 2023-01-18 description: Emerging articles have reported that N6-methyladenosine (m6A) modification is mainly involved in clear-cell renal cell carcinoma (ccRCC) tumorigenesis. However, the regulatory mechanisms of m6A reader IGF2BP1 involved in ccRCC tumor energy metabolism are currently unknown. Results showed that the m6A reader IGF2BP1 exhibited significantly higher expression in ccRCC cells. Functionally, results by gain/loss functional assays indicated that IGF2BP1 promoted the glycolytic characteristics, including glucose uptake, lactate production and extracellular acidification rate (ECAR). Mechanistically, IGF2BP1 recognized the m6A modified sites on LDHA mRNA and enhanced its mRNA stability, thereby accelerating tumor energy metabolism. Thus, our work reveals a novel facet of the m6A that promoted mRNA stability and highlighted the functional importance of IGF2BP1 as m6A readers in post-transcriptional gene regulation. creator: Bao Yuan creator: Jin Zhou uri: https://doi.org/10.7717/peerj.14591 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Yuan and Zhou title: Transcriptomic differences between bleached and unbleached hydrozoan Millepora complanata following the 2015-2016 ENSO in the Mexican Caribbean link: https://peerj.com/articles/14626 last-modified: 2023-01-18 description: The 2015-2016 El Niño-southern oscillation or “ENSO” caused many M. complanata colonies that live in the Mexican Caribbean to experience extensive bleaching. The purpose of this work was to analyze the effect of bleaching on the cellular response of M. complanata, employing a transcriptomic approach with RNA-seq. As expected, bleached specimens contained a significantly lower chlorophyll content than unbleached hydrocorals. The presence of algae of the genera Durusdinium and Cladocopium was only found in tissues of unbleached M. complanata, which could be associated to the greater resistance that these colonies exhibited during bleaching. We found that 299 genes were differentially expressed in M. complanata bleached colonies following the 2015-2016 ENSO in the Mexican Caribbean. The differential expression analysis of bleached M. complanata specimens evidenced enriched terms for functional categories, such as ribosome, RNA polymerase and basal transcription factors, chaperone, oxidoreductase, among others. Our results suggest that the heat-shock response mechanisms displayed by M. complanata include: an up-regulation of endogenous antioxidant defenses; a higher expression of heat stress response genes; up-regulation of transcription-related genes, higher expression of genes associated to transport processes, inter alia. This study constitutes the first differential gene expression analysis of the molecular response of a reef-forming hydrozoan during bleaching. creator: Víctor H. Hernández Elizárraga creator: Norma Olguín-López creator: Rosalina Hernández-Matehuala creator: Juan Caballero-Pérez creator: César Ibarra-Alvarado creator: Alejandra Rojas-Molina uri: https://doi.org/10.7717/peerj.14626 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hernández Elizárraga et al. title: Microplastic contamination in canned fish sold in Türkiye link: https://peerj.com/articles/14627 last-modified: 2023-01-18 description: The presence of microplastics (MPs) in processed seafood is a growing concern. In this study, 33 different canned fish brands belonging to seven producers were purchased from the Turkish market and investigated. MPs composition, possible sources, and potential intake were assessed. Light microscopy was used to quantify potential MPs, and micro-Raman microscopy was used to identify the polymer types. The results showed that all the samples had at least one MPs particle, and fragments were the most abundant (57.3%) shape of MPs. Polyolefin (21.88%) was the most common polymer type. The results showed that packaging and the production processes are the main possible sources of MPs. Human intake estimation risk is relatively lower since canned fish consumption is relatively low. The findings suggest that the risk related to MPs in canned fish should be considered one of the components of food safety management systems. creator: Sedat Gündoğdu creator: Ali Riza Köşker uri: https://doi.org/10.7717/peerj.14627 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Gundogdu and Kosker title: Potato bacterial wilt in Ethiopia: history, current status, and future perspectives link: https://peerj.com/articles/14661 last-modified: 2023-01-18 description: BackgroundPotato is an essential food staple and a critical tuber crop for rural livelihoods in Ethiopia, where many pathogenic pests are threatening production. Bacterial wilt, also known as brown rot of potato, ranks among the diseases that most affect many potato farmers in Ethiopia and the disease losses dramatically threatening the vibrant potato sector even in the highlands of the country where it has been uncommon so far.MethodologyTo devise a strategy towards boosting potato productivity in Ethiopia where food insecurity is most prevalent, production constraints should be investigated and properly addressed. Hence, we have used existing reviews and reports on the subjects, such as textbooks, and proceeding and conference abstracts in Plant Protection Society of Ethiopia; Web of Science; Google Scholar; Research Gate and CIP’s database to document most relevant information on the occurrence, distribution, and disease management of bacterial wilt in Ethiopia.ResultsProvision of comprehensive information on potato bacterial wilt occurrence, distribution, and management techniques are crucial for potato growers, researchers and stakeholders engaged on potato industry. In this review, we provided insights on the history, status, and future perspectives of potato bacterial wilt in Ethiopia.ConclusionsAwareness of potato bacterial wilt and integrated disease management approaches could bring a fundamental impact to the farming community mostly to smallholder farmers in developing countries. This document compiled such imperative information targeting bacterial wilt management techniques to ensure food security. creator: Gebrehanna Lemma Tessema creator: Hussen Ebrahim Seid uri: https://doi.org/10.7717/peerj.14661 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Gebrehanna and Hussen title: The energetic effect of hip flexion and retraction in walking at different speeds: a modeling study link: https://peerj.com/articles/14662 last-modified: 2023-01-18 description: In human walking, power for propulsion is generated primarily via ankle and hip muscles. The addition of a ‘passive’ hip spring to simple bipedal models appears more efficient than using only push-off impulse, at least, when hip spring associated energetic costs are not considered. Hip flexion and retraction torques, however, are not ‘free’, as they are produced by muscles demanding metabolic energy. Studies evaluating the inclusion of hip actuation costs, especially during the swing phase, and the hip actuation’s energetic benefits are few and far between. It is also unknown whether these possible benefits/effects may depend on speed. We simulated a planar flat-feet model walking stably over a range of speeds. We asked whether the addition of independent hip flexion and retraction remains energetically beneficial when considering work-based metabolic cost of transport (MCOT) with different efficiencies of doing positive and negative work. We found asymmetric hip actuation can reduce the estimated MCOT relative to ankle actuation by up to 6%, but only at medium speeds. The corresponding optimal strategy is zero hip flexion and some hip retraction actuation. The reason for this reduced MCOT is that the decrease in collision loss is larger than the associated increase in hip negative work. This leads to a reduction in total positive mechanical work, which results in an overall lower MCOT. Our study shows how ankle actuation, hip flexion, and retraction actuation can be coordinated to reduce MCOT. creator: Jian Jin creator: Dinant Kistemaker creator: Jaap H. van Dieën creator: Andreas Daffertshofer creator: Sjoerd M. Bruijn uri: https://doi.org/10.7717/peerj.14662 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Jin et al. title: A geospatial risk analysis graphical user interface for identifying hazardous chemical emission sources link: https://peerj.com/articles/14664 last-modified: 2023-01-18 description: BackgroundPerforming back trajectory and forward trajectory using the Hybrid Single-Particle Lagrangian Integrated Trajectory Model (HYSPLIT) is a reliable approach for assessing particle transport after release among mid-field atmospheric models. HYSPLIT has an externally facing online interface that allows non-expert users to run the model trajectories without requiring extensive training or programming. However, the existing HYSPLIT interface is limited if simulations have a large amount of meteorological data and timesteps that are not coincident. The objective of this study is to design and develop a more robust tool to rapidly evaluate hazard transport conditions and to perform risk analysis, while still maintaining an intuitive and user-friendly interface.MethodsHYSPLIT calculates forward and backward trajectories of particles based on wind speed, wind direction, and the corresponding location, timestamp, and Pasquill stability classes of the regions of the atmosphere in terms of the wind speed, the amount of solar radiation, and the fractional cloud cover. The computed particle transport trajectories, combined with the online Proton Transfer Reaction-Mass Spectrometry (PTR-MS) data (https://figshare.com/articles/dataset/ARL_Data_from_PROS_station_at_Hanford_site/19993964), can be used to identify and quantify the sources and affected area of the hazardous chemicals’ emission using the potential source distribution function (PSDF). PSDF is an improved statistical function based on the well-known potential source contribution function (PSCF) in establishing the air pollutant source and receptor relationship. Performing this analysis requires a range of meteorological and pollutant concentration measurements to be statistically meaningful. The existing HYSPLIT graphical user interface (GUI) does not easily permit computations of trajectories of a dataset of meteorological data in high temporal frequency. To improve the performance of HYSPLIT computations from a large dataset and enhance risk analysis of the accidental release of material at risk, a geospatial risk analysis tool (GRAT-GUI) is created to allow large data sets to be processed instantaneously and to provide ease of visualization.ResultsThe GRAT-GUI is a native desktop-based application and can be run in any Windows 10 system without any internet access requirements, thus providing a secure way to process large meteorological datasets even on a standalone computer. GRAT-GUI has features to import, integrate, and convert meteorological data with various formats for hazardous chemical emission source identification and risk analysis as a self-explanatory user interface. The tool is available at https://figshare.com/articles/software/GRAT/19426742. creator: Hongfei Hou creator: Huiying Ren creator: Patrick Royer creator: Xiao-Ying Yu uri: https://doi.org/10.7717/peerj.14664 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hou et al. title: Patterns and controlling factors of soil carbon sequestration in nitrogen-limited and -rich forests in China—a meta-analysis link: https://peerj.com/articles/14694 last-modified: 2023-01-18 description: Soil organic carbon (SOC) management has the potential to contribute to climate change mitigation by reducing atmospheric carbon dioxide (CO2). Understanding the changes in forest nitrogen (N) deposition rates has important implications for C sequestration. We explored the effects of N enrichment on soil carbon sequestration in nitrogen-limited and nitrogen-rich Chinese forests and their controlling factors. Our findings reveal that N inputs enhanced net soil C sequestration by 5.52–18.46 kg C kg−1 N, with greater impacts in temperate forests (8.37–13.68 kg C kg−1 N), the use of NH4NO3 fertilizer (7.78 kg Ckg−1 N) at low N levels (<30 kg Ckg−1 N; 9.14 kg Ckg−1 N), and in a short period (<3 years; 12.95 kg C kg−1 N). The nitrogen use efficiency (NUE) varied between 0.24 and 13.3 (kg C kg−1 N) depending on the forest type and was significantly controlled by rainfall, fertilizer, and carbon-nitrogen ratio rates. Besides, N enrichment increased SOC concentration by an average of 7% and 2% for tropical and subtropical forests, respectively. Although soil carbon sequestration was higher in the topsoil compared to the subsoil, the relative influence indicated that nitrogen availability strongly impacts the SOC, followed by dissolved organic carbon concentration and mean annual precipitation. This study highlights the critical role of soil NUE processes in promoting soil C accumulation in a forest ecosystem. creator: Mbezele Junior Yannick Ngaba creator: Yves Uwiragiye creator: Jianbin Zhou uri: https://doi.org/10.7717/peerj.14694 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ngaba et al. title: HLA-A*01:01 allele diminishing in COVID-19 patients population associated with non-structural epitope abundance in CD8+ T-cell repertoire link: https://peerj.com/articles/14707 last-modified: 2023-01-18 description: In mid-2021, the SARS-CoV-2 Delta variant caused the third wave of the COVID-19 pandemic in several countries worldwide. The pivotal studies were aimed at studying changes in the efficiency of neutralizing antibodies to the spike protein. However, much less attention was paid to the T-cell response and the presentation of virus peptides by MHC-I molecules. In this study, we compared the features of the HLA-I genotype in symptomatic patients with COVID-19 in the first and third waves of the pandemic. As a result, we could identify the diminishing of carriers of the HLA-A*01:01 allele in the third wave and demonstrate the unique properties of this allele. Thus, HLA-A*01:01-binding immunoprevalent epitopes are mostly derived from ORF1ab. A set of epitopes from ORF1ab was tested, and their high immunogenicity was confirmed. Moreover, analysis of the results of single-cell phenotyping of T-cells in recovered patients showed that the predominant phenotype in HLA-A*01:01 carriers is central memory T-cells. The predominance of T-lymphocytes of this phenotype may contribute to forming long-term T-cell immunity in carriers of this allele. Our results can be the basis for highly effective vaccines based on ORF1ab peptides. creator: Maxim Shkurnikov creator: Stepan Nersisyan creator: Darya Averinskaya creator: Milena Chekova creator: Fedor Polyakov creator: Aleksei Titov creator: Dmitriy Doroshenko creator: Valery Vechorko creator: Alexander Tonevitsky uri: https://doi.org/10.7717/peerj.14707 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Shkurnikov et al.