title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=361 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Stress-induced changes in cognitive function and intestinal barrier integrity can be ameliorated by venlafaxine and synbiotic supplementations link: https://peerj.com/articles/17033 last-modified: 2024-02-28 description: Stress profoundly impacts various aspects of both physical and psychological well-being. Our previous study demonstrated that venlafaxine (Vlx) and synbiotic (Syn) treatment attenuated learned fear-like behavior and recognition memory impairment in immobilized-stressed rats. In this study, we further investigated the physical, behavior, and cellular mechanisms underlying the effects of Syn and/or Vlx treatment on brain and intestinal functions in stressed rats. Adult male Wistar rats, aged 8 weeks old were subjected to 14 days of immobilization stress showed a decrease in body weight gain and food intake as well as an increase in water consumption, urinary corticosterone levels, and adrenal gland weight. Supplementation of Syn and/or Vlx in stressed rats resulted in mitigation of weight loss, restoration of normal food and fluid intake, and normalization of corticosterone levels. Behavioral analysis showed that treatment with Syn and/or Vlx enhanced depressive-like behaviors and improved spatial learning-memory impairment in stressed rats. Hippocampal dentate gyrus showed stress-induced neuronal cell death, which was attenuated by Syn and/or Vlx treatment. Stress-induced ileum inflammation and increased intestinal permeability were both effectively reduced by the supplementation of Syn. In addition, Syn and Vlx partly contributed to affecting the expression of the glial cell-derived neurotrophic factor in the hippocampus and intestines of stressed rats, suggesting particularly protective effects on both the gut barrier and the brain. This study highlights the intricate interplay between stress physiological responses in the brain and gut. Syn intervention alleviate stress-induced neuronal cell death and modulate depression- and memory impairment-like behaviors, and improve stress-induced gut barrier dysfunction which were similar to those of Vlx. These findings enhance our understanding of stress-related health conditions and suggest the synbiotic intervention may be a promising approach to ameliorate deleterious effects of stress on the gut-brain axis. creator: Sarawut Lapmanee creator: Nattapon Supkamonseni creator: Sakkarin Bhubhanil creator: Nattakan Treesaksrisakul creator: Chaiyos Sirithanakorn creator: Mattaka Khongkow creator: Katawut Namdee creator: Piyaporn Surinlert creator: Chittipong Tipbunjong creator: Prapimpun Wongchitrat uri: https://doi.org/10.7717/peerj.17033 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lapmanee et al. title: The toxicity assessment of phosmet on development, reproduction, and gene expression in Daphnia magna link: https://peerj.com/articles/17034 last-modified: 2024-02-28 description: The use of pesticides to control pests, weeds, and diseases or to regulate plant growth is indispensable in agricultural production. However, the excessive use of these chemicals has led to significant concern about their potential negative impacts on health and the environment. Phosmet is one such pesticide that is commonly used on plants and animals against cold moth, aphids, mites, suckers, and fruit flies. Here, we investigated the effects of phosmet on a model organism, Daphnia magna using acute and chronic toxicity endpoints such as lethality, mobility, genotoxicity, reproduction, and gene expression. We performed survival experiments in six-well plates at seven different concentrations (0.01, 0.1, 1, 10, 25, 50, 100 μM) as well as the control in three replicates. We observed statistically significant mortality rates at 25 µM and above upon 24 h of exposure, and at 1 µM and above following 48 h of exposure. Genotoxicity analysis, reproduction assay and qPCR analysis were carried out at concentrations of 0.01 and 0.1 μM phosmet as these concentrations did not show any lethality. Comet assay showed that exposure to phosmet resulted in significant DNA damage in the cells. Interestingly, 0.1 μM phosmet produced more offspring per adult compared to the control group indicating a hormetic response. Gene expression profiles demonstrated several genes involved in different physiological pathways, including oxidative stress, detoxification, immune system, hypoxia and iron homeostasis. Taken together, our results indicate that phosmet has negative effects on Daphnia magna in a dose- and time-dependent manner and could also induce lethal and physiological toxicities to other aquatic organisms. creator: Mustafa Ataş creator: Ceyhun Bereketoglu uri: https://doi.org/10.7717/peerj.17034 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ataş and Bereketoglu title: triact package for R: analyzing the lying behavior of cows from accelerometer data link: https://peerj.com/articles/17036 last-modified: 2024-02-28 description: Accelerometers are sensors proven to be useful to analyze the lying behavior of cows. For reasons of algorithm transparency and control, researchers often prefer to use their own data analysis scripts rather than proprietary software. We developed the triact R package that assists animal scientists in analyzing the lying behavior of cows from raw data recorded with a triaxial accelerometer (manufacturer agnostic) attached to a hind leg. In a user-friendly workflow, triact allows the determination of common measures for lying behavior including total lying duration, the number of lying bouts, and the mean duration of lying bouts. Further capabilities are the description of lying laterality and the calculation of proxies for the level of physical activity of the cow. In this publication we describe the functionality of triact and the rationales behind the implemented algorithms. The triact R package is developed as an open-source project and freely available via the CRAN repository. creator: Michael Simmler creator: Stijn P. Brouwers uri: https://doi.org/10.7717/peerj.17036 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Simmler and Brouwers title: Raised water temperature enhances benthopelagic links via intensified bioturbation and benthos-mediated nutrient cycling link: https://peerj.com/articles/17047 last-modified: 2024-02-28 description: Sediment reworking by benthic infauna, namely bioturbation, is of pivotal importance in expansive soft-sediment environments such as the Wadden Sea. Bioturbating fauna facilitate ecosystem functions such as bentho-pelagic coupling and sediment nutrient remineralization capacities. Yet, these benthic fauna are expected to be profoundly affected by current observed rising sea temperatures. In order to predict future changes in ecosystem functioning in soft-sediment environments like the Wadden Sea, knowledge on the underlying processes such as sediment reworking, is crucial. Here, we tested how temperature affects bioturbation and its associated ecosystem processes, such as benthic nutrient fluxes and sediment oxygen consumption, using luminophore tracers and sediment incubation cores. We used a controlled mesocosm experiment set-up with key Wadden Sea benthos species: the burrowing polychaetes Arenicola marina and Hediste diversicolor, the bivalve Cerastoderma edule, and the tube-building polychaete Lanice conchilega. The highest bioturbation rates were observed from A. marina, reaching up to 375 cm2yr−1; followed by H. diversicolor, with 124 cm2yr−1 being the peak bioturbation rate for the ragworm. Additionally, the sediment reworking activity of A. marina facilitated nearly double the amount of silicate efflux compared to any other species. Arenicola marina and H. diversicolor accordingly facilitated stronger nutrient effluxes under a warmer temperature than L. conchilega and C. edule. The oxygen uptake of A. marina and H. diversicolor within the sediment incubation cores was correspondingly enhanced with a higher temperature. Thus, increases in sea temperatures may initially be beneficial to ecosystem functioning in the Wadden Sea as faunal bioturbation is definitely expedited, leading to a tighter coupling between the sediment and overlying water column. The enhanced bioturbation activity, oxygen consumption, and facilitated nutrient effluxes from these invertebrates themselves, will aid in the ongoing high levels of primary productivity and organic matter production. creator: Eilish M. Farrell creator: Andreas Neumann creator: Jan Beermann creator: Alexa Wrede uri: https://doi.org/10.7717/peerj.17047 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Farrell et al. title: Relationship between accelerometer-measured sleep duration and Stroop performance: a functional near-infrared spectroscopy study among young adults link: https://peerj.com/articles/17057 last-modified: 2024-02-28 description: ObjectivesShort sleep is becoming more common in modern society. This study aimed to explore the relationship between accelerometer-measured sleep duration and cognitive performance among young adults as well as the underlying hemodynamic mechanisms.MethodsA total of 58 participants were included in this study. Participants were asked to wear an ActiGraph GT3X+ accelerometer to identify their sleep duration for 7 consecutive days. Cognitive function was assessed by the Stroop test. Two conditions, including the congruent and incongruent Stroop, were set. In addition, stratified analyses were used to examine sensitivity. 24-channel functional near-infrared spectroscopy (fNIRS) equipment was applied to measure hemodynamic changes of the prefrontal cortex (PFC) during cognitive tasks.ResultsResults showed that sleep duration was positively associated with accuracy of the incongruent Stroop test (0.001 (0.000, 0.002), p = 0.042). Compared with the regular sleep (≥7 h) group, lower accuracy of the incongruent Stroop test (−0.012 (−0.023, −0.002), p = 0.024) was observed in the severe short sleep (<6 h). Moreover, a stratified analysis was conducted to examining gender, age, BMI, birthplace, and education’s impact on sleep duration and the incongruent Stroop test accuracy, confirming a consistent correlation across all demographics. In the severe short sleep group, the activation of left middle frontal gyri and right dorsolateral superior frontal gyri were negatively associated with the cognitive performance.ConclusionsThis study emphasized the importance of maintaining enough sleep schedules in young college students from a fNIRS perspective. The findings of this study could potentially be used to guide sleep time in young adults and help them make sleep schemes. creator: Yanwei You creator: Jianxiu Liu creator: Xingtian Li creator: Peng Wang creator: Ruidong Liu creator: Xindong Ma uri: https://doi.org/10.7717/peerj.17057 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 You et al. title: Use of Callistemon citrinus as a gastroprotective and anti-inflammatory agent on indomethacin-induced gastric ulcers in obese rats link: https://peerj.com/articles/17062 last-modified: 2024-02-28 description: BackgroundObesity leads to an elevated risk of developing gastrointestinal disease such as gastric ulcers. Callistemon citrinus leaf extract has shown antioxidant, antimicrobial, hepatoprotective, and chemoprotective effects against colon cancer. The aim of this study is to evaluate the gastroprotective effect of C. citrinus leaf extract on indomethacin-induced gastric ulcers in obese rats.MethodsGastric ulcers were induced in female obese Wistar rats using a single oral dose of indomethacin (IND). In the first stage, the rats were fed with a high fat sugar diet (HFSD) for 15 weeks to induce obesity and, at the same time, the diet of the other group of animals included daily administration of ethanolic C. citrinus leaf extract (250 mg/kg) in addition to HFSD. In the second stage, gastric ulcers were induced with IND (30 mg/kg). The gastroprotective activity of C. citrinus, the inflammatory enzyme activities, and cytokines in the stomach were determined.ResultsC. citrinus produced a reduction of gastric lesions caused by IND. Myeloperoxidase (MPO), cyclooxygenase-2 (COX-2), and 5-lipoxygenase (5-LOX) activities also decreased. Although inflammatory biomarkers such as TNFα, IL-6, AOPP, and leptin were significantly decreased by C. citrinus, adiponectin levels increased. Moreover, C. citrinus decreased weight gain and morphological and biochemical parameters.ConclusionThe use of indomethacin in rats fed with a high fat-sugar diet increased gastric ulcers. Gastroprotective effect of C. citrinus in obese rats is attributed to the reduction of pro-inflammatory cytokines and the inflammatory enzymes. creator: Jonathan Saúl Piñón-Simental creator: Luis Alberto Ayala-Ruiz creator: Luis Gerardo Ortega-Pérez creator: Oliver Rafid Magaña-Rodríguez creator: Esperanza Meléndez-Herrera creator: Asdrubal Aguilera-Méndez creator: Patricia Rios-Chavez uri: https://doi.org/10.7717/peerj.17062 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Piñón-Simental et al. title: Prognostic factors and outcomes of invasive pulmonary aspergillosis, a retrospective hospital-based study link: https://peerj.com/articles/17066 last-modified: 2024-02-28 description: ObjectiveInvasive pulmonary aspergillosis (IPA) affects immunocompromised hosts and is associated with higher risks of respiratory failure and mortality. However, the clinical outcomes of different IPA types have not been identified.MethodsBetween September 2002 and May 2021, we retrospectively enrolled patients with IPA in Taichung Veterans General Hospital, Taiwan. Cases were classified as possible IPA, probable IPA, proven IPA, and putative IPA according to EORTC/MSGERC criteria and the AspICU algorithm. Risk factors of respiratory failure, kidney failure, and mortality were analyzed by logistic regression. A total of 3-year survival was assessed by the Kaplan-Meier method with log-rank test for post-hoc comparisons.ResultsWe included 125 IPA patients (50: possible IPA, 47: probable IPA, 11: proven IPA, and 17: putative IPA). Comorbidities of liver cirrhosis and solid organ malignancy were risk factors for respiratory failure; diabetes mellitus and post-liver or kidney transplantation were related to kidney failure. Higher galactomannan (GM) test optical density index (ODI) in either serum or bronchoalveolar lavage fluid was associated with dismal outcomes. Probable IPA and putative IPA had lower 3-year respiratory failure-free survival compared to possible IPA. Probable IPA and putative IPA exhibited lower 3-year renal failure-free survival in comparison to possible IPA and proven IPA. Putative IPA had the lowest 3-year overall survival rates among the four IPA groups.ConclusionPatients with putative IPA had higher mortality rates than the possible, probable, or proven IPA groups. Therefore, a prompt diagnosis and timely treatment are warranted for patients with putative IPA. creator: Wei-Che Chen creator: I-Chieh Chen creator: Jun-Peng Chen creator: Tsai-Ling Liao creator: Yi-Ming Chen uri: https://doi.org/10.7717/peerj.17066 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Discovering unknown Madagascar biodiversity: integrative taxonomy of raft spiders (Pisauridae: Dolomedes) link: https://peerj.com/articles/16781 last-modified: 2024-02-27 description: Madagascar is a global biodiversity hotspot, but its biodiversity continues to be underestimated and understudied. Of raft spiders, genus Dolomedes Latreille, 1804, literature only reports two species on Madagascar. Our single expedition to humid forests of eastern and northern Madagascar, however, yielded a series of Dolomedes exemplars representing both sexes of five morphospecies. To avoid only using morphological diagnostics, we devised and tested an integrative taxonomic model for Dolomedes based on the unified species concept. The model first determines morphospecies within a morphometrics framework, then tests their validity via species delimitation using COI. It then incorporates habitat preferences, geological barriers, and dispersal related traits to form hypotheses about gene flow limitations. Our results reveal four new Dolomedes species that we describe from both sexes as Dolomedes gregoricsp. nov., D. bedjanicsp. nov., D. hydatostellasp. nov., and D. rotundussp. nov. The range of D. kalanoro Silva & Griswold, 2013, now also known from both sexes, is expanded to eastern Madagascar. By increasing the known raft spider diversity from one valid species to five, our results merely scratch the surface of the true Dolomedes species diversity on Madagascar. Our integrative taxonomic model provides the framework for future revisions of raft spiders anywhere. creator: Kuang-Ping Yu creator: Matjaž Kuntner uri: https://doi.org/10.7717/peerj.16781 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yu and Kuntner title: Does it pay to pay? A comparison of the benefits of open-access publishing across various sub-fields in biology link: https://peerj.com/articles/16824 last-modified: 2024-02-27 description: Authors are often faced with the decision of whether to maximize traditional impact metrics or minimize costs when choosing where to publish the results of their research. Many subscription-based journals now offer the option of paying an article processing charge (APC) to make their work open. Though such “hybrid” journals make research more accessible to readers, their APCs often come with high price tags and can exclude authors who lack the capacity to pay to make their research accessible. Here, we tested if paying to publish open access in a subscription-based journal benefited authors by conferring more citations relative to closed access articles. We identified 146,415 articles published in 152 hybrid journals in the field of biology from 2013–2018 to compare the number of citations between various types of open access and closed access articles. In a simple generalized linear model analysis of our full dataset, we found that publishing open access in hybrid journals that offer the option confers an average citation advantage to authors of 17.8 citations compared to closed access articles in similar journals. After taking into account the number of authors, Journal Citation Reports 2020 Quartile, year of publication, and Web of Science category, we still found that open access generated significantly more citations than closed access (p < 0.0001). However, results were complex, with exact differences in citation rates among access types impacted by these other variables. This citation advantage based on access type was even similar when comparing open and closed access articles published in the same issue of a journal (p < 0.0001). However, by examining articles where the authors paid an article processing charge, we found that cost itself was not predictive of citation rates (p = 0.14). Based on our findings of access type and other model parameters, we suggest that, in the case of the 152 journals we analyzed, paying for open access does confer a citation advantage. For authors with limited budgets, we recommend pursuing open access alternatives that do not require paying a fee as they still yielded more citations than closed access. For authors who are considering where to submit their next article, we offer additional suggestions on how to balance exposure via citations with publishing costs. creator: Amanda D. Clark creator: Tanner C. Myers creator: Todd D. Steury creator: Ali Krzton creator: Julio Yanes creator: Angela Barber creator: Jacqueline Barry creator: Subarna Barua creator: Katherine Eaton creator: Devadatta Gosavi creator: Rebecca Nance creator: Zahida Pervaiz creator: Chidozie Ugochukwu creator: Patricia Hartman creator: Laurie S. Stevison uri: https://doi.org/10.7717/peerj.16824 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Clark et al. title: The interplay of motor adaptation and groupitizing in numerosity perception: Insights from visual motion adaptation and proprioceptive motor adaptation link: https://peerj.com/articles/16887 last-modified: 2024-02-27 description: Groupitizing is a well-established strategy in numerosity perception that enhances speed and sensory precision. Building on the ATOM theory, Anobile proposed the sensorimotor numerosity system, which posits a strong link between number and action. Previous studies using motor adaptation technology have shown that high-frequency motor adaptation leads to underestimation of numerosity perception, while low-frequency adaptation leads to overestimation. However, the impact of motor adaptation on groupitizing, and whether visual motion adaptation produces similar effects, remain unclear. In this study, we investigate the persistence of the advantage of groupitizing after motor adaptation and explore the effects of visual motion adaptation. Surprisingly, our findings reveal that proprioceptive motor adaptation weakens the advantage of groupitizing, indicating a robust effect of motor adaptation even when groupitizing is employed. Moreover, we observe a bidirectional relationship, as groupitizing also weakens the adaptation effect. These results highlight the complex interplay between motor adaptation and groupitizing in numerosity perception. Furthermore, our study provides evidence that visual motion adaptation also has an adaptation effect, but does not fully replicate the effects of proprioceptive motor adaptation on groupitizing. In conclusion, our research underscores the importance of groupitizing as a valuable strategy in numerosity perception, and sheds light on the influence of motion adaptation on this strategy. creator: Huanyu Yang creator: Liangzhi Jia creator: Jun Zhu creator: Jian Zhang creator: Mengmeng Li creator: Chenli Li creator: Yun Pan uri: https://doi.org/10.7717/peerj.16887 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yang et al.