title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=302 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Use of machine learning to identify protective factors for death from COVID-19 in the ICU: a retrospective study link: https://peerj.com/articles/17428 last-modified: 2024-06-12 description: BackgroundPatients in serious condition due to COVID-19 often require special care in intensive care units (ICUs). This disease has affected over 758 million people and resulted in 6.8 million deaths worldwide. Additionally, the progression of the disease may vary from individual to individual, that is, it is essential to identify the clinical parameters that indicate a good prognosis for the patient. Machine learning (ML) algorithms have been used for analyzing complex medical data and identifying prognostic indicators. However, there is still an urgent need for a model to elucidate the predictors related to patient outcomes. Therefore, this research aimed to verify, through ML, the variables involved in the discharge of patients admitted to the ICU due to COVID-19.MethodsIn this study, 126 variables were collected with information on demography, hospital length stay and outcome, chronic diseases and tumors, comorbidities and risk factors, complications and adverse events, health care, and vital indicators of patients admitted to an ICU in southern Brazil. These variables were filtered and then selected by a ML algorithm known as decision trees to identify the optimal set of variables for predicting patient discharge using logistic regression. Finally, a confusion matrix was performed to evaluate the model’s performance for the selected variables.ResultsOf the 532 patients evaluated, 180 were discharged: female (16.92%), with a central venous catheter (23.68%), with a bladder catheter (26.13%), and with an average of 8.46- and 23.65-days using bladder catheter and submitted to mechanical ventilation, respectively. In addition, the chances of discharge increase by 14% for each additional day in the hospital, by 136% for female patients, 716% when there is no bladder catheter, and 737% when no central venous catheter is used. However, the chances of discharge decrease by 3% for each additional year of age and by 9% for each other day of mechanical ventilation. The performance of the training data presented a balanced accuracy of 0.81, sensitivity of 0.74, specificity of 0.88, and the kappa value was 0.64. The test performance had a balanced accuracy of 0.85, sensitivity 0.75, specificity 0.95, and kappa value of 0.73. The McNemar test found that there were no significant differences in the error rates in the training and test data, suggesting good classification. This work showed that female, the absence of a central venous catheter and bladder catheter, shorter mechanical ventilation, and bladder catheter duration were associated with a greater chance of hospital discharge. These results may help develop measures that lead to a good prognosis for the patient. creator: Lander Dos Santos creator: Lincoln Luis Silva creator: Fernando Castilho Pelloso creator: Vinicius Maia creator: Constanza Pujals creator: Deise Helena Borghesan creator: Maria Dalva Carvalho creator: Raíssa Bocchi Pedroso creator: Sandra Marisa Pelloso uri: https://doi.org/10.7717/peerj.17428 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Dos Santos et al. title: Tick hazard in the South Downs National Park (UK): species, distribution, key locations for future interventions, site density, habitats link: https://peerj.com/articles/17483 last-modified: 2024-06-12 description: BackgroundSouth Downs National Park (SDNP) is UK’s most visited National Park, and a focus of tick-borne Lyme disease. The first presumed UK autochthonous cases of tick-borne encephalitis and babesiosis were recorded in 2019–20. SDNP aims to conserve wildlife and encourage recreation, so interventions are needed that reduce hazard without negatively affecting ecosystem health. To be successful these require knowledge of site hazards.MethodsBritish Deer Society members submitted ticks removed from deer. Key potential intervention sites were selected and six 50 m2 transects drag-sampled per site (mostly twice yearly for 2 years). Ticks were identified in-lab (sex, life stage, species), hazard measured as tick presence, density of ticks (all life stages, DOT), and density of nymphs (DON). Sites and habitat types were analysed for association with hazard. Distribution was mapped by combining our results with records from five other sources.ResultsA total of 87 Ixodes ricinus (all but one adults, 82% F) were removed from 14 deer (10 Dama dama; three Capreolus capreolus; one not recorded; tick burden, 1–35) at 12 locations (commonly woodland). Five key potential intervention sites were identified and drag-sampled 2015–16, collecting 623 ticks (238 on-transects): 53.8% nymphs, 42.5% larvae, 3.7% adults (13 M, 10 F). Ticks were present on-transects at all sites: I. ricinus at three (The Mens (TM); Queen Elizabeth Country Park (QECP); Cowdray Estate (CE)), Haemaphysalis punctata at two (Seven Sisters Country Park (SSCP); Ditchling Beacon Nature Reserve (DBNR)). TM had the highest DOT at 30/300 m2 (DON = 30/300 m2), followed by QECP 22/300 m2 (12/300 m2), CE 8/300 m2 (6/300 m2), and SSCP 1/300 m2 (1/300 m2). For I. ricinus, nymphs predominated in spring, larvae in the second half of summer and early autumn. The overall ranking of site hazard held for DON and DOT from both seasonal sampling periods. DBNR was sampled 2016 only (one adult H. punctata collected). Woodland had significantly greater hazard than downland, but ticks were present at all downland sites. I. ricinus has been identified in 33/37 of SDNPs 10 km2 grid squares, Ixodes hexagonus 10/37, H. punctata 7/37, Dermacentor reticulatus 1/37.ConclusionsMapping shows tick hazard broadly distributed across SDNP. I. ricinus was most common, but H. punctata’s seeming range expansion is concerning. Recommendations: management of small heavily visited high hazard plots (QECP); post-visit precaution signage (all sites); repellent impregnated clothing for deerstalkers; flock trials to control H. punctata (SSCP, DBNR). Further research at TM may contribute to knowledge on ecological dynamics underlying infection density and predator re-introduction/protection as public health interventions. Ecological research on H. punctata would aid control. SDNP Authority is ideally placed to link and champion policies to reduce hazard, whilst avoiding or reducing conflict between public health and ecosystem health. creator: Jo Middleton creator: Ian Cooper creator: Anja S. Rott uri: https://doi.org/10.7717/peerj.17483 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Middleton et al. title: Effects of wind speed and wind direction on crop yield forecasting using dynamic time warping and an ensembled learning model link: https://peerj.com/articles/16538 last-modified: 2024-06-11 description: The cultivation of cashew crops carries numerous economic advantages, and countries worldwide that produce this crop face a high demand. The effects of wind speed and wind direction on crop yield prediction using proficient deep learning algorithms are less emphasized or researched. We propose a combination of advanced deep learning techniques, specifically focusing on long short-term memory (LSTM) and random forest models. We intend to enhance this ensemble model using dynamic time warping (DTW) to assess the spatiotemporal data (wind speed and wind direction) similarities within Jaman North, Jaman South, and Wenchi with their respective production yield. In the Bono region of Ghana, these three areas are crucial for cashew production. The LSTM-DTW-RF model with wind speed and wind direction achieved an R2 score of 0.847 and the LSTM-RF model without these two key features R2 score of (0.74). Both models were evaluated using the augmented Dickey-Fuller (ADF) test, which is commonly used in time series analysis to assess stationarity, where the LSTM-DTW-RF achieved a 90% level of confidence, while LSTM-RF attained an 87.99% level. Among the three municipalities, Jaman South had the highest evaluation scores for the model, with an RMSE of 0.883, an R2 of 0.835, and an MBE of 0.212 when comparing actual and predicted values for Wenchi. In terms of the annual average wind direction, Jaman North recorded (270.5 SW°), Jaman South recorded (274.8 SW°), and Wenchi recorded (272.6 SW°). The DTW similarity distance for the annual average wind speed across these regions fell within specific ranges: Jaman North (±25.72), Jaman South (±25.89), and Wenchi (±26.04). Following the DTW similarity evaluation, Jaman North demonstrated superior performance in wind speed, while Wenchi excelled in wind direction. This underscores the potential efficiency of DTW when incorporated into the analysis of environmental factors affecting crop yields, given its invariant nature. The results obtained can guide further exploration of DTW variations in combination with other machine learning models to predict higher cashew yields. Additionally, these findings emphasize the significance of wind speed and direction in vertical farming, contributing to informed decisions for sustainable agricultural growth and development. creator: Bright Bediako-Kyeremeh creator: TingHuai Ma creator: Huan Rong creator: Benjamin Kwapong Osibo creator: Lorenzo Mamelona creator: Isaac Kofi Nti creator: Lord Amoah uri: https://doi.org/10.7717/peerj.16538 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Bediako-Kyeremeh et al. title: Preeclampsia in pregnant women with COVID-19: a prospective cohort study from two tertiary hospitals in Southern Brazil link: https://peerj.com/articles/17481 last-modified: 2024-06-11 description: BackgroundCOVID-19 is an infectious pathology that shows vascular changes during pregnancy, as well as in the placentas. The main objectives of this study were to estimate the prevalence and the risk factors for preeclampsia in hospitalized pregnant women with COVID-19. As well as comparing maternal and perinatal outcomes in hospitalized pregnant women with COVID-19 and preeclampsia with those without preeclampsia.MethodsProspective cohort study of 100 hospitalized pregnant women from two tertiary hospitals, diagnosed with COVID-19, and divided into two groups: PE+ group (pregnant women with COVID-19 and preeclampsia) and PE- group (pregnant women with COVID-19 without preeclampsia). These pregnant women had prevalence, risk factors, maternal and perinatal data analyzed.ResultsThe prevalence of preeclampsia was 11%. Severe COVID-19 was the main risk factor for preeclampsia (OR = 8.18 [CI 1.53–43.52]), as well as fetal growth restriction was the main perinatal outcome (OR = 8.90 [CI 1.52–38.4]). Comorbidities were more frequent in the PE+ group (63.6% vs 31.5%, p = 0.03), as well as prematurity (81.8% vs 41.6%, p = 0.02), low birth weight (63.6% vs 24.7%, p = 0.01), and the need for neonatal intensive care admission of the newborn (63.6% vs 27.0%, p = 0.03). Pregnant women with PE had twice as long a length of stay in the intensive care unit (RR = 2.35 [CI 1.34–4.14]). Although maternal mortality was more frequent among pregnant women with PE, it was not statistically significant.ConclusionsPrevalence of preeclampsia in hospitalized pregnant women with COVID-19 was 11%. Severe COVID-19 was the main risk factor for preeclampsia and associated comorbidities increased the risk for developing preeclampsia. Long length of stay in the intensive care unit was the main maternal outcome and fetal growth restriction was the main perinatal outcome of preeclampsia. creator: Narcizo LEC Sobieray creator: Newton S. Carvalho creator: Cynthia F. Klas creator: Isabella N. Furuie creator: Jullie A. Chiste creator: Cyllian A. Fugaça creator: Jessica S. Longo creator: Juliana D. Oliveira creator: Sérgio L. Padilha uri: https://doi.org/10.7717/peerj.17481 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sobieray et al. title: Using bioluminescence as a tool for studying diversity in marine zooplankton and dinoflagellates: an initial assessment link: https://peerj.com/articles/17516 last-modified: 2024-06-11 description: Bioluminescence is light chemically produced by an organism. It is widespread across all major marine phyla and has evolved multiple times, resulting in a high diversity of spectral properties and first flash kinetic parameters (FFKP). The bioluminescence of a system is often a good proxy for planktonic biomass. The species-specific parameters of bioluminescent displays can be measured to identify species in situ and describe planktonic biodiversity. Most bioluminescent organisms will flash when mechanically stimulated i.e., when subjected to supra-threshold levels of shear stress. Here we compare first flash kinetic parameters such as flash duration, peak intensity, rise time, decay time, first-flash mechanically stimulated light and e-folding time obtained with the commercially available Underwater Bioluminescence Assessment Tool (UBAT). We provide descriptions of the first flash kinetic parameters of several species of dinoflagellates Pyrocystis fusiformis, Pyrocystis noctiluca, Pyrodinium bahamense, Lingulodinium polyedra, Alexandrium monilatum and two zooplankton (the ctenophore Mnemiopsis leidyi and the larvacean Oikopleura sp.). FFKPs are then compared and discussed using non-parametric analyses of variance (ANOVAs), hierarchical clustering and a linear discriminant analysis to assess the ability to use bioluminescence signatures for identification. Once the first flash kinetic parameters of a bioluminescent species have been described, it is possible to detect its presence using emissions collected by in situ bathyphotometers. Assessing abundance and diversity of bioluminescent species may therefore be possible. creator: Francis Letendre creator: Abigail Blackburn creator: Ed Malkiel creator: Michael Twardowski uri: https://doi.org/10.7717/peerj.17516 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Letendre et al. title: Stress adaptive plasticity from Aegilops tauschii introgression lines improves drought and heat stress tolerance in bread wheat (Triticum aestivum L.) link: https://peerj.com/articles/17528 last-modified: 2024-06-11 description: Aegilops tauchii is a D-genome donor of hexaploid wheat and is a potential source of genes for various biotic and abiotic stresses including heat and drought. In the present study, we used multi-stage evaluation technique to understand the effects of heat and drought stresses on Ae. tauschii derived introgression lines (ILs). Preliminary evaluation (during stage-I) of 369 ILs for various agronomic traits identified 59 agronomically superior ILs. In the second stage (stage-II), selected ILs (i.e., 59 ILs) were evaluated for seedling heat (at 30 °C and 35 °C) and drought (at 20% poly-ethylene glycol; PEG) stress tolerance under growth chambers (stage-II). Heat and drought stress significantly reduced the seedling vigour by 59.29 and 60.37 percent, respectively. Genotype × treatment interaction analysis for seedling vigour stress tolerance index (STI) identified IL-50, IL-56, and IL-68 as high-performing ILs under heat stress and IL-42 and IL-44 as high-performing ILs under drought stress. It also revealed IL-44 and IL-50 as the stable ILs under heat and drought stresses. Furthermore, in the third stage (stage-III), selected ILs were evaluated for heat and drought stress tolerance under field condition over two cropping seasons (viz., 2020–21 and 2021–22), which significantly reduced the grain yield by 72.79 and 48.70 percent, respectively. Stability analysis was performed to identify IL-47, IL-51, and IL-259 as the most stable ILs in stage-III. Tolerant ILs with specific and wider adaptability identified in this study can serve as the potential resources to understand the genetic basis of heat and drought stress tolerance in wheat and they can also be utilized in developing high-yielding wheat cultivars with enhanced heat and drought stress tolerance. creator: Santosh Gudi creator: Mohit Jain creator: Satinder Singh creator: Satinder Kaur creator: Puja Srivastava creator: Gurvinder Singh Mavi creator: Parveen Chhuneja creator: Virinder Singh Sohu creator: Fatmah A. Safhi creator: Diaa Abd El-Moneim creator: Achla Sharma uri: https://doi.org/10.7717/peerj.17528 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Gudi et al. title: A hyaena on stilts: comparison of the limb morphology of Ictitherium ebu (Mammalia: Hyaenidae) from the Late Miocene of Lothagam, Turkana Basin, Kenya with extant Canidae and Hyaenidae link: https://peerj.com/articles/17405 last-modified: 2024-06-10 description: The long, gracile morphology of the limb bones of the Late Miocene hyaenid Ictitherium ebu has led to the hypothesis that this animal was cursorial. The forelimb and femur of the holotype were compared with specimens of extant Hyaenidae and Canidae. Two morphometric methods were used. The first used measurements to calculate indices of different morphological characters. The second method involved capturing photographs of the anterior distal humerus of each specimen, mapping six landmarks on them, and calculating truss distances. These distances represent a schematic reproduction of the elbow. Multivariate statistical analysis primarily separated the data based on taxonomy, yet locomotor and habitat categories were also considered. Ictitherium ebu has an overall morphology similar to that of the maned wolf and a distal humerus reminiscent of that of the aardwolf. The long, gracile limb bones of I. ebu are suggested to be adaptations for pouncing on prey, for locomotor efficiency, and for looking over the tall grass of the open environments the animal lived in, much like the present-day maned wolf. creator: Julien van der Hoek creator: Lars Werdelin uri: https://doi.org/10.7717/peerj.17405 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 van der Hoek and Werdelin title: Phenethyl isothiocyanate inhibits the carcinogenic properties of hepatocellular carcinoma Huh7.5.1 cells by activating MAPK/PI3K-Akt/p53 signaling pathways link: https://peerj.com/articles/17532 last-modified: 2024-06-10 description: BackgroundHepatocellular carcinoma (HCC) is an aggressive malignancy with limited effective treatment options. Phenethyl isothiocyanate (PEITC) is a bioactive substance present primarily in the cruciferous vegetables. PEITC has exhibited anti-cancer properties in various cancers, including lung, bile duct, and prostate cancers. It has been demonstrated that PEITC can inhibit the proliferation, invasion, and metastasis of SK-Hep1 cells, while effectively inducing apoptosis and cell cycle arrest in HepG2 cells. However, knowledge of its anti-carcinogenic effects on Huh7.5.1 cells and its underlying mechanism remains elusive. In the present study, we aim to evaluate the anti-carcinogenic effects of PEITC on human HCC Huh7.5.1 cells.MethodsMTT assay and colony formation assay was performed to investigate the anti-proliferative effects of PEITC against Huh7.5.1 cells. The pro-apoptosis effects of PEITC were determined by Annexin V-FITC/PI double staining assay by flow cytometry (FCM), mitochondrial transmembrane potential (MMP) measurement, and Caspase-3 activity detection. A DAPI staining and terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) assay was conducted to estimate the DNA damage in Huh7.5.1 cells induced by PEITC. Cell cycle progression was determined by FCM. Transwell invasion assay and wound healing migration assay were performed to investigate the impact of PEITC on the migration and invasion of Huh7.5.1 cells. In addition, transcriptome sequencing and gene set enrichment analysis (GSEA) were used to explore the potential molecular mechanisms of the inhibitory effects of PEITC on HCC. Quantitative real-time PCR (qRT-PCR) analysis was performed to verify the transcriptome data.ResultsMTT assay showed that treatment of Huh7.5.1 cells with PEITC resulted in a dose-dependent decrease in viability, and colony formation assay further confirmed its anti-proliferative effect. Furthermore, we found that PEITC could induce mitochondrial-related apoptotic responses, including a decrease of mitochondrial transmembrane potential, activation of Caspase-3 activity, and generation of intracellular reactive oxygen species. It was also observed that PEITC caused DNA damage and cell cycle arrest in the S-phase in Huh7.5.1 cells. In addition, the inhibitory effect of PEITC on the migration and invasion ability of Huh7.5.1 cells was assessed. Transcriptome sequencing analysis further suggested that PEITC could activate the typical MAPK, PI3K-Akt, and p53 signaling pathways, revealing the potential mechanism of PEITC in inhibiting the carcinogenic properties of Huh7.5.1 cells.ConclusionPEITC exhibits anti-carcinogenic activities against human HCC Huh7.5.1 cells by activating MAPK/PI3K-Akt/p53 signaling pathways. Our results suggest that PEITC may be useful for the anti-HCC treatment. creator: Jiao Du creator: Yuting Zhang creator: Jiajia Chen creator: Libo Jin creator: Liying Pan creator: Pengyu Lei creator: Sue Lin uri: https://doi.org/10.7717/peerj.17532 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Du et al. title: Adoption of CRISPR-Cas for crop production: present status and future prospects link: https://peerj.com/articles/17402 last-modified: 2024-06-07 description: BackgroundGlobal food systems in recent years have been impacted by some harsh environmental challenges and excessive anthropogenic activities. The increasing levels of both biotic and abiotic stressors have led to a decline in food production, safety, and quality. This has also contributed to a low crop production rate and difficulty in meeting the requirements of the ever-growing population. Several biotic stresses have developed above natural resistance in crops coupled with alarming contamination rates. In particular, the multiple antibiotic resistance in bacteria and some other plant pathogens has been a hot topic over recent years since the food system is often exposed to contamination at each of the farm-to-fork stages. Therefore, a system that prioritizes the safety, quality, and availability of foods is needed to meet the health and dietary preferences of everyone at every time.MethodsThis review collected scattered information on food systems and proposes methods for plant disease management. Multiple databases were searched for relevant specialized literature in the field. Particular attention was placed on the genetic methods with special interest in the potentials of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and Cas (CRISPR associated) proteins technology in food systems and security.ResultsThe review reveals the approaches that have been developed to salvage the problem of food insecurity in an attempt to achieve sustainable agriculture. On crop plants, some systems tend towards either enhancing the systemic resistance or engineering resistant varieties against known pathogens. The CRISPR-Cas technology has become a popular tool for engineering desired genes in living organisms. This review discusses its impact and why it should be considered in the sustainable management, availability, and quality of food systems. Some important roles of CRISPR-Cas have been established concerning conventional and earlier genome editing methods for simultaneous modification of different agronomic traits in crops.ConclusionDespite the controversies over the safety of the CRISPR-Cas system, its importance has been evident in the engineering of disease- and drought-resistant crop varieties, the improvement of crop yield, and enhancement of food quality. creator: Akinlolu Olalekan Akanmu creator: Michael Dare Asemoloye creator: Mario Andrea Marchisio creator: Olubukola Oluranti Babalola uri: https://doi.org/10.7717/peerj.17402 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Akanmu et al. title: Baseline haematological parameters in three common Australian frog species link: https://peerj.com/articles/17406 last-modified: 2024-06-07 description: Amphibians are experiencing declines globally, with emerging infectious diseases as one of the main causes. Haematological parameters present a useful method for determining the health status of animals and the effects of particular diseases, but the interpretation of differential cell counts relies on knowing the normal ranges for the species and factors that can affect these counts. However, there is very little data on either normal haematological parameters or guides for blood cell types for free-ranging frog species across the world. This study aims to 1) create a visual guide for three different Australian frog species: Litoria paraewingi, Limnodynastes dumerilii, and Crinia signifera, 2) determine the proportions of erythrocytes to leukocytes and 3) differential leukocytes within blood smears from these three species and 4) assess the association between parasites and differential counts. We collected blood samples from free-ranging frogs and analysed blood smears. We also looked for ectoparasites and tested for the fungal disease chytridiomycosis. Overall, we found that the differentials of erythrocytes to leukocytes were not affected by species, but the proportions of different leukocytes did vary across species. For example, while lymphocytes were the most common type of leukocyte across the three species, eosinophils were relatively common in Limnodynastes dumerilii but rarely present in the other two species. We noted chytridiomycosis infection as well as ectoparasites present in some individuals but found no effect of parasites on blood parameters. Our results add baseline haematological parameters for three Australian frog species and provide an example of how different frog species can vary in their differential blood cell counts. More information is needed on frog haematological data before these parameters can be used to determine the health status of wild or captive frogs. creator: Tara Jadwani-Bungar creator: Nicholas P. Doidge creator: Danielle K. Wallace creator: Laura A. Brannelly uri: https://doi.org/10.7717/peerj.17406 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Jadwani-Bungar et al.