title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=331 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: In the social amoeba Dictyostelium discoideum, shortened stalks may limit obligate cheater success even when exploitable partners are available link: https://peerj.com/articles/17118 last-modified: 2024-03-29 description: Cooperation is widespread across life, but its existence can be threatened by exploitation. The rise of obligate social cheaters that are incapable of contributing to a necessary cooperative function can lead to the loss of that function. In the social amoeba Dictyostelium discoideum, obligate social cheaters cannot form dead stalk cells and in chimeras instead form living spore cells. This gives them a competitive advantage within chimeras. However, obligate cheaters of this kind have thus far not been found in nature, probably because they are often enough in clonal populations that they need to retain the ability to produce stalks. In this study we discovered an additional cost to obligate cheaters. Even when there are wild-type cells to parasitize, the chimeric fruiting bodies that result have shorter stalks and these are disadvantaged in spore dispersal. The inability of obligate cheaters to form fruiting bodies when they are on their own combined with the lower functionality of fruiting bodies when they are not represent limits on obligate social cheating as a strategy. creator: James Medina creator: Tyler Larsen creator: David C. Queller creator: Joan E. Strassmann uri: https://doi.org/10.7717/peerj.17118 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Medina et al. title: Bayesian estimation of the measurement of interactions in epidemiological studies link: https://peerj.com/articles/17128 last-modified: 2024-03-29 description: BackgroundInteraction identification is important in epidemiological studies and can be detected by including a product term in the model. However, as Rothman noted, a product term in exponential models may be regarded as multiplicative rather than additive to better reflect biological interactions. Currently, the additive interaction is largely measured by the relative excess risk due to interaction (RERI), the attributable proportion due to interaction (AP), and the synergy index (S), and confidence intervals are developed via frequentist approaches. However, few studies have focused on the same issue from a Bayesian perspective. The present study aims to provide a Bayesian view of the estimation and credible intervals of the additive interaction measures.MethodsBayesian logistic regression was employed, and estimates and credible intervals were calculated from posterior samples of the RERI, AP and S. Since Bayesian inference depends only on posterior samples, it is very easy to apply this method to preventive factors. The validity of the proposed method was verified by comparing the Bayesian method with the delta and bootstrap approaches in simulation studies with example data.ResultsIn all the simulation studies, the Bayesian estimates were very close to the corresponding true values. Due to the skewness of the interaction measures, compared with the confidence intervals of the delta method, the credible intervals of the Bayesian approach were more balanced and matched the nominal 95% level. Compared with the bootstrap method, the Bayesian method appeared to be a competitive alternative and fared better when small sample sizes were used.ConclusionsThe proposed Bayesian method is a competitive alternative to other methods. This approach can assist epidemiologists in detecting additive-scale interactions. creator: Shaowei Lin creator: Chanchan Hu creator: Zhifeng Lin creator: Zhijian Hu uri: https://doi.org/10.7717/peerj.17128 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lin et al. title: Predicting the current fishable habitat distribution of Antarctic toothfish (Dissostichus mawsoni) and its shift in the future under climate change in the Southern Ocean link: https://peerj.com/articles/17131 last-modified: 2024-03-29 description: Global warming continues to exert unprecedented impacts on marine habitats. Species distribution models (SDMs) are proven powerful in predicting habitat distribution for marine demersal species under climate change impacts. The Antarctic toothfish, Dissostichus mawsoni (Norman 1937), an ecologically and commercially significant species, is endemic to the Southern Ocean. Utilizing occurrence records and environmental data, we developed an ensemble model that integrates various modelling techniques. This model characterizes species-environment relationships and predicts current and future fishable habitats of D. mawsoni under four climate change scenarios. Ice thickness, depth and mean water temperature were the top three important factors in affecting the distribution of D. mawsoni. The ensemble prediction suggests an overall expansion of fishable habitats, potentially due to the limited occurrence records from fishery-dependent surveys. Future projections indicate varying degrees of fishable habitat loss in large areas of the Amery Ice Shelf’s eastern and western portions. Suitable fishable habitats, including the spawning grounds in the seamounts around the northern Ross Sea and the coastal waters of the Bellingshausen Sea and Amundsen Sea, were persistent under present and future environmental conditions, highlighting the importance to protect these climate refugia from anthropogenic disturbance. Though data deficiency existed in this study, our predictions can provide valuable information for designing climate-adaptive development and conservation strategies in maintaining the sustainability of this species. creator: Jie Liu creator: Ancheng Zhu creator: Xitao Wang creator: Xiangjun Zhou creator: Lu Chen uri: https://doi.org/10.7717/peerj.17131 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: An adaptive data-driven architecture for mental health care applications link: https://peerj.com/articles/17133 last-modified: 2024-03-29 description: BackgroundIn the current era of rapid technological innovation, our lives are becoming more closely intertwined with digital systems. Consequently, every human action generates a valuable repository of digital data. In this context, data-driven architectures are pivotal for organizing, manipulating, and presenting data to facilitate positive computing through ensemble machine learning models. Moreover, the COVID-19 pandemic underscored a substantial need for a flexible mental health care architecture. This architecture, inclusive of machine learning predictive models, has the potential to benefit a larger population by identifying individuals at a heightened risk of developing various mental disorders.ObjectiveTherefore, this research aims to create a flexible mental health care architecture that leverages data-driven methodologies and ensemble machine learning models. The objective is to proficiently structure, process, and present data for positive computing. The adaptive data-driven architecture facilitates customized interventions for diverse mental disorders, fostering positive computing. Consequently, improved mental health care outcomes and enhanced accessibility for individuals with varied mental health conditions are anticipated.MethodFollowing the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, the researchers conducted a systematic literature review in databases indexed in Web of Science to identify the existing strengths and limitations of software architecture relevant to our adaptive design. The systematic review was registered in PROSPERO (CRD42023444661). Additionally, a mapping process was employed to derive essential paradigms serving as the foundation for the research architectural design. To validate the architecture based on its features, professional experts utilized a Likert scale.ResultsThrough the review, the authors identified six fundamental paradigms crucial for designing architecture. Leveraging these paradigms, the authors crafted an adaptive data-driven architecture, subsequently validated by professional experts. The validation resulted in a mean score exceeding four for each evaluated feature, confirming the architecture’s effectiveness. To further assess the architecture’s practical application, a prototype architecture for predicting pandemic anxiety was developed. creator: Aishwarya Sundaram creator: Hema Subramaniam creator: Siti Hafizah Ab Hamid creator: Azmawaty Mohamad Nor uri: https://doi.org/10.7717/peerj.17133 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sundaram et al. title: Forkhead-associated phosphopeptide binding domain 1 (FHAD1) deficiency impaired murine sperm motility link: https://peerj.com/articles/17142 last-modified: 2024-03-29 description: BackgroundGenetic knockout-based studies conducted in mice provide a powerful means of assessing the significance of a gene for fertility. Forkhead-associated phosphopeptide binding domain 1 (FHAD1) contains a conserved FHA domain, that is present in many proteins with phospho-threonine reader activity. How FHAD1 functions in male fertility, however, remains uncertain.MethodsFhad1−/− mice were generated by CRISPR/Cas9-mediated knockout, after which qPCR was used to evaluate changes in gene expression, with subsequent analyses of spermatogenesis and fertility. The testis phenotypes were also examined using immunofluorescence and histological staining, while sperm concentrations and motility were quantified via computer-aided sperm analysis. Cellular apoptosis was assessed using a TUNEL staining assay.ResultsThe Fhad1−/−mice did not exhibit any abnormal changes in fertility or testicular morphology compared to wild-type littermates. Histological analyses confirmed that the testicular morphology of both Fhad1−/−and Fhad1+/+ mice was normal, with both exhibiting intact seminiferous tubules. Relative to Fhad1+/+ mice, however, Fhad1−/−did exhibit reductions in the total and progressive motility of epididymal sperm. Analyses of meiotic division in Fhad1−/−mice also revealed higher levels of apoptotic death during the first wave of spermatogenesis.DiscussionThe findings suggest that FHAD1 is involved in both meiosis and the modulation of sperm motility. creator: Xi Zhang creator: Jiangyang Xue creator: Shan Jiang creator: Haoyu Zheng creator: Chang Wang uri: https://doi.org/10.7717/peerj.17142 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Transcranial magnetic stimulation enhances the specificity of multiple sclerosis diagnostic criteria: a critical narrative review link: https://peerj.com/articles/17155 last-modified: 2024-03-29 description: BackgroundMultiple sclerosis (MS) is an immune-mediated neurodegenerative disease that involves attacks of inflammatory demyelination and axonal damage, with variable but continuous disability accumulation. Transcranial magnetic stimulation (TMS) is a noninvasive method to characterize conduction loss and axonal damage in the corticospinal tract. TMS as a technique provides indices of corticospinal tract function that may serve as putative MS biomarkers. To date, no reviews have directly addressed the diagnostic performance of TMS in MS. The authors aimed to conduct a critical narrative review on the diagnostic performance of TMS in MS.MethodsThe authors searched the Embase, PubMed, Scopus, and Web of Science databases for studies that reported the sensitivity and/or specificity of any reported TMS technique compared to established clinical MS diagnostic criteria. Studies were summarized and critically appraised for their quality and validity.ResultsSeventeen of 1,073 records were included for data extraction and critical appraisal. Markers of demyelination and axonal damage—most notably, central motor conduction time (CMCT)—were specific, but not sensitive, for MS. Thirteen (76%), two (12%), and two (12%) studies exhibited high, unclear, and low risk of bias, respectively. No study demonstrated validity for TMS techniques as diagnostic biomarkers in MS.ConclusionsCMCT has the potential to: (1) enhance the specificity of clinical MS diagnostic criteria by “ruling in” true-positives, or (2) revise a diagnosis from relapsing to progressive forms of MS. However, there is presently insufficient high-quality evidence to recommend any TMS technique in the diagnostic algorithm for MS. creator: Nicholas J. Snow creator: Hannah M. Murphy creator: Arthur R. Chaves creator: Craig S. Moore creator: Michelle Ploughman uri: https://doi.org/10.7717/peerj.17155 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Snow et al. title: Home range size and habitat selection of owned outdoor domestic cats (Felis catus) in urban southwestern Ontario link: https://peerj.com/articles/17159 last-modified: 2024-03-29 description: Domestic cats (Felis catus) play a dual role in society as both companion animals and predators. When provided with unsupervised outdoor access, cats can negatively impact native wildlife and create public health and animal welfare challenges. The effective implementation of management strategies, such as buffer zones or curfews, requires an understanding of home range size, the factors that influence their movement, and the types of habitats they use. Here, we used a community/citizen scientist approach to collect movement and habitat use data using GPS collars on owned outdoor cats in the Kitchener-Waterloo-Cambridge-Guelph region, southwestern Ontario, Canada. Mean (± SD) 100% minimum convex polygon home range size was 8 ± 8 ha (range: 0.34–38 ha) and was positively associated with road density but not with intrinsic factors such as boldness, sex, or age. With regards to habitat selection, cats used greenspaces, roads, and agricultural land less often than predicted but strongly selected for impervious surfaces (urban areas other than greenspaces or roads). Our results suggest that wildlife near buildings and residential areas are likely at the greatest risk of cat predation and that a buffer size of 840 m would be needed to restrict cats from entering areas of conservation concern. creator: Marlee L. Pyott creator: D. Ryan Norris creator: Greg W. Mitchell creator: Leonardo Custode creator: Elizabeth A. Gow uri: https://doi.org/10.7717/peerj.17159 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Pyott et al. title: Effects of three weeks base training at moderate simulated altitude with or without hypoxic residence on exercise capacity and physiological adaptations in well-trained male runners link: https://peerj.com/articles/17166 last-modified: 2024-03-29 description: ObjectivesTo test the hypothesis that ‘live high-base train high-interval train low’ (HiHiLo) altitude training, compared to ‘live low-train high’ (LoHi), yields greater benefits on performance and physiological adaptations.MethodsSixteen young male middle-distance runners (age, 17.0 ± 1.5 y; body mass, 58.8 ± 4.9 kg; body height, 176.3 ± 4.3 cm; training years, 3–5 y; training distance per week, 30–60 km.wk−1) with a peak oxygen uptake averaging ~65 ml.min−1.kg−1 trained in a normobaric hypoxia chamber (simulated altitude of ~2,500 m, monitored by heart rate ~170 bpm; thrice weekly) for 3 weeks. During this period, the HiHiLo group (n = 8) stayed in normobaric hypoxia (at ~2,800 m; 10 h.day−1), while the LoHi group (n = 8) resided near sea level. Before and immediately after the intervention, peak oxygen uptake and exercise-induced arterial hypoxemia responses (incremental cycle test) as well as running performance and time-domain heart rate variability (5-km time trial) were assessed. Hematological variables were monitored at baseline and on days 1, 7, 14 and 21 during the intervention.ResultsPeak oxygen uptake and running performance did not differ before and after the intervention in either group (all P > 0.05). Exercise-induced arterial hypoxemia responses, measured both at submaximal (240 W) and maximal loads during the incremental test, and log-transformed root mean square of successive R-R intervals during the 4-min post-run recovery period, did not change (all P > 0.05). Hematocrit, mean reticulocyte absolute count and reticulocyte percentage increased above baseline levels on day 21 of the intervention (all P < 0.001), irrespective of group.ConclusionsWell-trained runners undertaking base training at moderate simulated altitude for 3 weeks, with or without hypoxic residence, showed no performance improvement, also with unchanged time-domain heart rate variability and exercise-induced arterial hypoxemia responses. creator: Longyan Yi creator: Jian Wu creator: Bing Yan creator: Yang Wang creator: Menghui Zou creator: Yimin Zhang creator: Feifei Li creator: Junqiang Qiu creator: Olivier Girard uri: https://doi.org/10.7717/peerj.17166 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yi et al. title: Attitude towards healthy nutrition and mental toughness: a study of taekwondo athletes link: https://peerj.com/articles/17174 last-modified: 2024-03-29 description: Healthy nutrition is widely considered the cornerstone of optimal athletic performance, both physically and mentally. This study investigates the critical role of healthy nutrition in shaping the physical and mental performance of athletes, with a specific focus on taekwondo. This research aims to explore the potential relationship between taekwondo athletes’ attitudes towards healthy nutrition and their mental toughness. The research group comprised 276 active and licensed taekwondo athletes who voluntarily participated in the study (Age M = 17.18 ± SD = 7.13, N = 125 women, N = 151 men). Ethical approval for the research was obtained prior to the commencement of the study. Data collection instruments included the Healthy Nutrition Attitude Scale, Mental Toughness Scale, and a personal information form. Confirmatory factor analysis was conducted to confirm the validity and reliability of the scales. Descriptive statistics, correlation analysis, and regression analysis were performed to explore the relationship between the variables within the research model. The correlation analysis identified two significant, positive, and moderate correlations: (1) between knowledge about nutrition and mental toughness (r = 0.626) and (2) between positive nutrition and mental toughness (r = 0.672). The regression analysis revealed that both knowledge about nutrition (β = 0.360) and positive nutrition (β = 0.461) significantly contribute to mental toughness. The findings suggest that as athletes’ knowledge of nutrition expands and their attitudes towards healthy eating become more positive, their mental toughness also appears to improve. These results are both important and original, adding significant new insights to the existing research landscape. creator: Arif Özsarı creator: Mehmet Kara creator: Ahmet Naci Dilek creator: Halil Uysal creator: Tolga Tek creator: Şekip Can Deli uri: https://doi.org/10.7717/peerj.17174 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Özsarı et al. title: Identification, validation and quantification of thymoquinone in conjunction with assessment of bioactive possessions and GC-MS profiling of pharmaceutically valuable crop Nigella (Nigella sativa L.) varieties link: https://peerj.com/articles/17177 last-modified: 2024-03-29 description: BackgroundPlants have been pivotal in traditional and modern medicine globally, with historical evidence supporting their therapeutic applications. Nigella (Nigella sativa L.) is an annual herbaceous plant of the Ranunculaceae family and is cultivated in the Middle East, Eastern Europe, and Western and Central Asia. The medicinal use of plants dates back thousands of years, documented in ancient writings from various civilizations. Alkaloids, phenolics, saponins, flavonoids, terpenoids, anthraquinones, and tannins found in plants exhibit antioxidant, immunomodulatory, anti-inflammatory, anticancer, antibacterial, and antidiabetic activities.MethodologyThis study specifically examines the pharmacological potential of Nigella sativa L., emphasizing thymoquinone—a compound with diverse nutraceutical benefits. The extraction, characterization, and quantification of thymoquinone, alongside other physicochemical parameters, were carried out using ethanol through Soxhlet extraction procedures on five nigella varieties. HPLC analysis was performed to determine the maximum accumulation of thymoquinone in the released variety of the plant and the chemical composition of the seed oil isolated from Nigella sativa L., varieties utilized in the study was determined through GC-MS analysis.ResultsThe research revealed that the Ajmer nigella-20 variety stands out, exhibiting elevated levels of thymoquinone (0.20 ± 0.07%), antioxidants (76.18 ± 1.78%), and substantial quantities of total phenols (31.85 ± 0.97 mg GAEg−1 seed) and flavonoids (8.150 ± 0.360 mg QE 100 g−1 seed) compared to other varieties. The GC-MS profiling showed the presence of 11 major compounds in the studied varieties, with p-cymene, longifolene, and myristic acid identified as the major chemical compounds present in the oil.ConclusionThe observed variations among Nigella varieties indicate the Ajmer nigella-20 variety as particularly promising for thymoquinone and bioactive compound extraction. This study underscores Nigella’s potential as a source of pharmacologically active compounds, highlighting the need for further exploration in therapeutic applications. creator: Ravi Y creator: Irene Vethamoni Periyanadar creator: Shailendra Nath Saxena creator: Raveendran Muthurajan creator: Velmurugan Sundararajan creator: Santhanakrishnan Vichangal Pridiuldi creator: Sumer Singh Meena creator: Ashoka Narayana Naik creator: C. B. Harisha creator: Honnappa Asangi creator: Sharda Choudhary creator: Ravindra Singh creator: Yallappa Dengeru creator: Kavan Kumar V creator: Narottam Kumar Meena creator: Ram Swaroop Meena creator: Arvind Kumar Verma uri: https://doi.org/10.7717/peerj.17177 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Y et al.