title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=660 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A survey of researchers’ code sharing and code reuse practices, and assessment of interactive notebook prototypes link: https://peerj.com/articles/13933 last-modified: 2022-08-22 description: This research aimed to understand the needs and habits of researchers in relation to code sharing and reuse; gather feedback on prototype code notebooks created by NeuroLibre; and help determine strategies that publishers could use to increase code sharing. We surveyed 188 researchers in computational biology. Respondents were asked about how often and why they look at code, which methods of accessing code they find useful and why, what aspects of code sharing are important to them, and how satisfied they are with their ability to complete these tasks. Respondents were asked to look at a prototype code notebook and give feedback on its features. Respondents were also asked how much time they spent preparing code and if they would be willing to increase this to use a code sharing tool, such as a notebook. As a reader of research articles the most common reason (70%) for looking at code was to gain a better understanding of the article. The most commonly encountered method for code sharing–linking articles to a code repository–was also the most useful method of accessing code from the reader’s perspective. As authors, the respondents were largely satisfied with their ability to carry out tasks related to code sharing. The most important of these tasks were ensuring that the code was running in the correct environment, and sharing code with good documentation. The average researcher, according to our results, is unwilling to incur additional costs (in time, effort or expenditure) that are currently needed to use code sharing tools alongside a publication. We infer this means we need different models for funding and producing interactive or executable research outputs if they are to reach a large number of researchers. For the purpose of increasing the amount of code shared by authors, PLOS Computational Biology is, as a result, focusing on policy rather than tools. creator: Lauren Cadwallader creator: Iain Hrynaszkiewicz uri: https://doi.org/10.7717/peerj.13933 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cadwallader and Hrynaszkiewicz title: Recapitulating human ovarian aging using random walks link: https://peerj.com/articles/13941 last-modified: 2022-08-22 description: Mechanism(s) that control whether individual human primordial ovarian follicles (PFs) remain dormant, or begin to grow, are all but unknown. One of our groups has recently shown that activation of the Integrated Stress Response (ISR) pathway can slow follicular granulosa cell proliferation by activating cell cycle checkpoints. Those data suggest that the ISR is active and fluctuates according to local conditions in dormant PFs. Because cell cycle entry of (pre)granulosa cells is required for PF growth activation (PFGA), we propose that rare ISR checkpoint resolution allows individual PFs to begin to grow. Fluctuating ISR activity within individual PFs can be described by a random process. In this article, we model ISR activity of individual PFs by one-dimensional random walks (RWs) and monitor the rate at which simulated checkpoint resolution and thus PFGA threshold crossing occurs. We show that the simultaneous recapitulation of (i) the loss of PFs over time within simulated subjects, and (ii) the timing of PF depletion in populations of simulated subjects equivalent to the distribution of the human age of natural menopause can be produced using this approach. In the RW model, the probability that individual PFs grow is influenced by regionally fluctuating conditions, that over time manifests in the known pattern of PFGA. Considered at the level of the ovary, randomness appears to be a key, purposeful feature of human ovarian aging. creator: Joshua Johnson creator: John W. Emerson creator: Sean D. Lawley uri: https://doi.org/10.7717/peerj.13941 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Johnson et al. title: Gas chromatography (GC) fingerprinting and immunomodulatory activity of polysaccharide from the rhizome of Menispermum dauricum DC link: https://peerj.com/articles/13946 last-modified: 2022-08-22 description: This research aimed to establish the gas chromatography (GC) fingerprints and examine the immunomodulatory activity of the rhizome of Menispermum dauricum polysaccharides. In this study, the preparation conditions were optimized by the response surface method (RSM). GC is an effective and sensitive technique employed to measure the composition of monosaccharides; the GC fingerprints of total polysaccharides from 10 batches of the rhizome of M. dauricum (tMDP) were established, and chemometrics methods were adopted to examine the differences and similarities of tMDP from distinct regions. The similarity evaluation illustrated that the polysaccharides derived from the rhizome of M. dauricum from different origins were highly similar. The results of principal components analysis (PCA) illustrated that all the tMDPs may be integrated into one group within the 95% confidence interval, but the rhizome of M. dauricum from different origins could also be distinguished in the plot of PCA scores. Then, the major bioactive fraction MDP was purified and obtained by column chromatography. Our previous study showed that MDP exhibited significant immunomodulatory activity, but the mechanism of the in vitro immunomodulatory activity of MDP is unclear. The macrophage activation induced by MDP was abolished when Toll-like receptor 4 (TLR4) signaling was knocked down by the TLR4 inhibitor. Furthermore, western blot analysis illustrated that MDP activated RAW264.7 cells through MAPKs and NFκB pathways induced by TLR4. This research offers a theoretical foundation for quality control and additional study as a potential immunomodulator of MDP. creator: Pei Yang creator: Yang Zhai creator: Yan Ma creator: Beibei Mao creator: Fengshan Wang creator: Li Li creator: Lijuan Luan creator: Yuhong Liu uri: https://doi.org/10.7717/peerj.13946 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yang et al. title: Daylight savings time transition and the incidence of femur fractures in the older population: a nationwide registry-based study link: https://peerj.com/articles/13672 last-modified: 2022-08-19 description: BackgroundDaylight Savings Time (DST) transition is known to cause sleep disruption, and thus may increase the incidence of injuries and accidents during the week following the transition. The aim of this study was to assess the incidence of femur fractures after DST transition.MethodsWe conducted retrospective population-based register study. All Finnish patients 70 years or older who were admitted to hospital due to femur fracture between 1997 and 2020 were gathered from the Finnish National Hospital Discharge Register. Negative binomial regression with 95% confidence intervals (CI) was used to evaluate the incidence of femur fractures after DST transition.ResultsThe data included a total of 112,658 femur fractures during the study period between 1997 and 2020, with an annual mean (SD) of 4,694 (206) fractures. The incidence of femur fractures decreased at the beginning of the study period from 968 to 688 per 100,000 person-years between 1997 and 2007. The weekly mean of femur fractures remained lower during the summer (from 130 to 150 per 100,000 person-weeks) than in winter (from 160 to 180 per 100,000 person-weeks). Incidence rate ratio for the Monday following DST transition was 1.10 (CI [0.98–1.24]) in spring and 1.10 (CI [0.97–1.24]) in fall, and for the whole week 1.07 (CI [1.01–1.14]) in spring and 0.97 (CI [0.83–1.13]) in fall.ConclusionWe found weak evidence that the incidence of femur fractures increases after DST transition in the spring. creator: Ville Ponkilainen creator: Topias Koukkula creator: Mikko Uimonen creator: Ville M. Mattila creator: Ilari Kuitunen creator: Aleksi Reito uri: https://doi.org/10.7717/peerj.13672 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ponkilainen et al. title: Somatization symptoms—prevalence and risk, stress and resilience factors among medical and dental students at a mid-sized German university link: https://peerj.com/articles/13803 last-modified: 2022-08-19 description: ObjectivePrevious studies have shown that an increased prevalence of mental illness can be found among medical and dental students. Among these, somatization symptoms are severely understudied. The present study examined the prevalence of somatization symptoms in a subpopulation of medical and dental students and aimed at finding associated risk and resilience factors.MethodsA cross-sectional survey was conducted using a self-reporting questionnaire, including the SOMS-2, the Becks-Depression-Inventory-II (BDI-II), the NEO-Five-Factor-Inventory, and a questionnaire on socio-demographics for possible risk and resilience factors. A total of 271 medical and dental students of a mid-sized German university completed the questionnaire.ResultsThe Somatization index yielded a mean of 9.12 symptoms for the total sample, which is 1.2 SD higher than the reported norm. A total of 50.7% of the medical students and 63.6% of the dental students transcend a critical somatization score. Significant positive associations for eight general risk factors, four university related stress factors, and a significant negative association for seven resilience factors were found.ConclusionMedical and even more dental students at the studied university showed a high burden of somatoform complaints. Also, factors were found that could be of etiological relevance and others that could be used to enhance resilience. Both could present an opportunity for the prevention of somatization disorders but prospective and multicenter studies with an aged-matched comparison group are needed to obtain a more accurate overview. creator: Oskar Feussner creator: Carolin Rehnisch creator: Nadja Rabkow creator: Stefan Watzke uri: https://doi.org/10.7717/peerj.13803 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Feussner et al. title: Users’ needs for a digital smoking cessation application and how to address them: A mixed-methods study link: https://peerj.com/articles/13824 last-modified: 2022-08-19 description: BackgroundDespite their increasing prevalence and potential, eHealth applications for behavior change suffer from a lack of adherence and from dropout. Advances in virtual coach technology provide new opportunities to improve this. However, these applications still do not always offer what people need. We, therefore, need a better understanding of people’s needs and how to address these, based on both actual experiences of users and their reflections on envisioned scenarios.MethodsWe conducted a longitudinal study in which 671 smokers interacted with a virtual coach in five sessions. The virtual coach assigned them a new preparatory activity for quitting smoking or increasing physical activity in each session. Participants provided feedback on the activity in the next session. After the five sessions, participants were asked to describe barriers and motivators for doing their activities. In addition, they provided their views on videos of scenarios such as receiving motivational messages. To understand users’ needs, we took a mixed-methods approach. This approach triangulated findings from qualitative data, quantitative data, and the literature.ResultsWe identified 14 main themes that describe people’s views of their current and future behaviors concerning an eHealth application. These themes relate to the behaviors themselves, the users, other parties involved in a behavior, and the environment. The most prevalent theme was the perceived usefulness of behaviors, especially whether they were informative, helpful, motivating, or encouraging. The timing and intensity of behaviors also mattered. With regards to the users, their perceived importance of and motivation to change, autonomy, and personal characteristics were major themes. Another important role was played by other parties that may be involved in a behavior, such as general practitioners or virtual coaches. Here, the themes of companionableness, accountability, and nature of the other party (i.e., human vs AI) were relevant. The last set of main themes was related to the environment in which a behavior is performed. Prevalent themes were the availability of sufficient time, the presence of prompts and triggers, support from one’s social environment, and the diversity of other environmental factors. We provide recommendations for addressing each theme.ConclusionsThe integrated method of experience-based and envisioning-based needs acquisition with a triangulate analysis provided a comprehensive needs classification (empirically and theoretically grounded). We expect that our themes and recommendations for addressing them will be helpful for designing applications for health behavior change that meet people’s needs. Designers should especially focus on the perceived usefulness of application components. To aid future work, we publish our dataset with user characteristics and 5,074 free-text responses from 671 people. creator: Nele Albers creator: Mark A. Neerincx creator: Kristell M. Penfornis creator: Willem-Paul Brinkman uri: https://doi.org/10.7717/peerj.13824 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Albers et al. title: CCL25/CCR9 interaction promotes the malignant behavior of salivary adenoid cystic carcinoma via the PI3K/AKT signaling pathway link: https://peerj.com/articles/13844 last-modified: 2022-08-19 description: BackgroundCC chemokine receptor 9 (CCR9), an organ-specific chemokine receptor, interacts with its exclusive ligand CCL25 to promote tumor proliferation and metastasis. However, the effect of CCR9 on salivary adenoid cystic carcinoma (SACC) malignant behavior remains unknown. This study aimed to investigate the specific molecular mechanism by which CCR9/CCL25 modulates malignant progression in SACC.MethodsImmunohistochemistry staining and RT–qPCR analyses were performed to detect the correlation of CCR9 expression and tumor progression-associated markers in SACC. In vitro, SACC cell proliferation and apoptosis were evaluated using Cell Counting Kit-8 and colon formation, and cell migration and invasion were detected by wound healing and transwell assays. Vercirnon was used as an inhibitor of CCR9, and LY294002 was used as an inhibitor of the PI3K/AKT pathway in this study. Western blot and RT–qPCR assays were carried out to measure the downstream factors of the interaction of CCL25 and CCR9. The effect of CCL25 on the development of SACC in vivo was examined by a xenograft tumor model in nude mice following CCL25, Vercirnon and LY294002 treatment.ResultsCCR9 was highly expressed in SACC compared with adjacent salivary gland tissues, and its level was associated with tumor proliferation and metastases. CCL25 enhanced cell proliferation, migration, and invasion through its interaction with CCR9 and exerted an antiapoptotic effect on SACC cells. Targeting CCR9 via Vercirnon significantly reduced the phosphorylation level of AKT induced by CCL25. CCL25/CCR9 could activate its downstream factors through the PI3K/AKT signaling pathway, such as cyclin D1, BCL2 and SLUG, thus promoting SACC cell proliferation, antiapoptosis, invasion and metastasis. The in vivo data from the xenograft mouse models further proved that CCL25 administration promoted malignant tumor progression by activating the PI3K/AKT pathway.ConclusionThe interaction of CCL25 and CCR9 promotes tumor growth and metastasis in SACC by activating the PI3K/AKT signaling pathway, offering a promising strategy for SACC treatment. creator: Songling Chai creator: Zhihao Wen creator: Rongxin Zhang creator: Yuwen Bai creator: Jing Liu creator: Juanjuan Li creator: Wenyao Kongling creator: Weixian Chen creator: Fu Wang creator: Lu Gao uri: https://doi.org/10.7717/peerj.13844 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chai et al. title: Regional impact of large-scale climate oscillations on ice out variability in New Brunswick and Maine link: https://peerj.com/articles/13741 last-modified: 2022-08-18 description: The available ice out (the date of disappearance of ice from a water body) records were analyzed from four relatively closely spaced lakes in southwestern New Brunswick (Harvey, Oromocto, Skiff) and eastern Maine (West Grand Lake), with the longest set of available observations being for Oromocto Lake starting in 1876. Results of a coherence analysis carried out on the ice out data from the four lakes indicates that there is regional coherence and correspondingly, that regional drivers influence ice out. These results also indicate that ice out dates for lakes from the region where records have not been kept can also be interpolated from these results. As the ice out record was coherent, further analysis was done for only Oromocto Lake on the basis of it having the longest ice out record. Cross-wavelet analysis was carried out between the ice out record and a variety of cyclic climate teleconnections and the sunspot record to identify which phenomena best explain the observed ice out trends. The most important observed contributors to ice out were the North Atlantic Oscillation (NAO) and the El Niño Southern Oscillation (ENSO), with observed periodicities at the interannual scale. At the decadal scale the Pacific Decadal Oscillation (PDO) and the 11-year solar cycle were the only patterns observed to significantly contribute to ice out. creator: Carling R. Walsh creator: R. Timothy Patterson uri: https://doi.org/10.7717/peerj.13741 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Walsh and Patterson title: Identifying important ecosystem service areas based on distributions of ecosystem services in the Beijing–Tianjin–Hebei region, China link: https://peerj.com/articles/13881 last-modified: 2022-08-18 description: Water conservation, soil conservation, biodiversity importance, and sandstorm prevention are important ecosystem services (ES) and the core challenges to sustainable economic and societal development in the Beijing–Tianjin–Hebei (BTH) region. Using the Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) model and observation data, we identified high-value ES areas in the BTH region. The high-value ES areas were mainly found in the northern and southwestern parts of the region, like the Yanshan Mountain Range and the Taihang Mountain Range. The ecosystem in the northern mountains is dominated by forest and grassland, and generally provides more valuable ES than does the eastern agricultural plain. Greater species richness was mainly found in the northern mountains with low human activity intensity. Due to its proximity, the Yanshan Mountain Range is critical to the health of the local ecosystem of Beijing. High biodiversity was present in the vicinity of the national nature reserves. Compared with other regions of China, changes in the BTH region are highly intense. Reinforcement of biodiversity conservation and ecosystem restoration in areas with a high degree of ES in the BTH region are capable of effectively improving habitat quality and regional ES. creator: Cuiyun Cheng creator: Shuping Zhang creator: Meichun Zhou creator: Yanchun Du creator: Chazhong Ge uri: https://doi.org/10.7717/peerj.13881 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cheng et al. title: A simple hierarchical model for heterogeneity in the evolutionary correlation on a phylogenetic tree link: https://peerj.com/articles/13910 last-modified: 2022-08-18 description: Numerous questions in phylogenetic comparative biology revolve around the correlated evolution of two or more phenotypic traits on a phylogeny. In many cases, it may be sufficient to assume a constant value for the evolutionary correlation between characters across all the clades and branches of the tree. Under other circumstances, however, it is desirable or necessary to account for the possibility that the evolutionary correlation differs through time or in different sections of the phylogeny. Here, we present a method designed to fit a hierarchical series of models for heterogeneity in the evolutionary rates and correlation of two quantitative traits on a phylogenetic tree. We apply the method to two datasets: one for different attributes of the buccal morphology in sunfishes (Centrarchidae); and a second for overall body length and relative body depth in rock- and non-rock-dwelling South American iguanian lizards. We also examine the performance of the method for parameter estimation and model selection using a small set of numerical simulations. creator: Liam J. Revell creator: Ken S. Toyama creator: D. Luke Mahler uri: https://doi.org/10.7717/peerj.13910 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Revell et al.