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Preprints allow researchers to make their findings available to the scientific community before they have undergone peer review. Studies on preprints within bioRxiv have been largely focused on article metadata and how often these preprints are downloaded, cited, published, and discussed online. A missing element that has yet to be examined is the language contained within the bioRxiv preprint repository. We sought to compare and contrast linguistic features within bioRxiv preprints to published biomedical text as a whole as this is an excellent opportunity to examine how peer review changes these documents. The most prevalent features that changed appear to be associated with typesetting and mentions of supporting information sections or additional files. In addition to text comparison, we created document embeddings derived from a preprint-trained word2vec model. We found that these embeddings are able to parse out different scientific approaches and concepts, link unannotated preprint–peer-reviewed article pairs, and identify journals that publish linguistically similar papers to a given preprint. We also used these embeddings to examine factors associated with the time elapsed between the posting of a first preprint and the appearance of a peer-reviewed publication. We found that preprints with more versions posted and more textual changes took longer to publish. Lastly, we constructed a web application (https://greenelab.github.io/preprint-similarity-search/) that allows users to identify which journals and articles that are most linguistically similar to a bioRxiv or medRxiv preprint as well as observe where the preprint would be positioned within a published article landscape., Preprints allow researchers to make their findings available to the scientific community before they have undergone peer review This study analyzes the full text content of the bioRxiv preprint repository, identifying field-specific patterns and changes that occur during publication, and providing a search tool that can identify the published papers that are most similar to a given bioRxiv or medRxiv preprint.

Background Coronavirus (COVID-19) has severely impacted lifestyles worldwide. Responses to COVID-19 have intentionally restricted the factors that encourage regular and frequent PA; opportunity, capability and motivation. However, the effects of these restrictions are likely to have differed by gender and age and different intensities of PA. This rapid review builds on previous evidence by synthesising the global impact of COVID-19 on adult PA through specific intensities and types of PA and evaluating this by gender and age. Methods A rapid systematic search of seven electronic databases (PubMed, MEDLINE, CINAHL, SPORTDiscus, Academic Search Complete, APA PsycInfo, and APA PsycArticles) was performed from December 2019 to January 2021. Studies investigating adult change in PA, exercise or sedentary behaviour due to COVID-19 were included. Results From an initial database search identifying 3,863 articles, 66 remained for synthesis after applying eligibility criteria. Results demonstrate decreases among all intensities and types of PA—walking (6 out of 7 papers), moderate-only (5 out of 6 papers), vigorous-only (5 out of 6 papers) and MVPA (4 out of 5 papers); as well as overall PA (14–72% participants reported a decrease). Reflecting that COVID-19 responses were designed to have universal effects, they also achieved whole-society decreases in PA behaviour, accented in older age groups. Conclusion There is a universal need to address the low levels of PA post-COVID-19. The consequences of decreased PA across all intensities has powerful, potentially recoverable, impacts. Universal declines have implications for public health officials and PA advocates for post-COVID-19 initiatives to promote PA.

The widely held assumption that any important scientific information would be available in English underlies the underuse of non-English-language science across disciplines. However, non-English-language science is expected to bring unique and valuable scientific information, especially in disciplines where the evidence is patchy, and for emergent issues where synthesising available evidence is an urgent challenge. Yet such contribution of non-English-language science to scientific communities and the application of science is rarely quantified. Here, we show that non-English-language studies provide crucial evidence for informing global biodiversity conservation. By screening 419,679 peer-reviewed papers in 16 languages, we identified 1,234 non-English-language studies providing evidence on the effectiveness of biodiversity conservation interventions, compared to 4,412 English-language studies identified with the same criteria. Relevant non-English-language studies are being published at an increasing rate in 6 out of the 12 languages where there were a sufficient number of relevant studies. Incorporating non-English-language studies can expand the geographical coverage (i.e., the number of 2° × 2° grid cells with relevant studies) of English-language evidence by 12% to 25%, especially in biodiverse regions, and taxonomic coverage (i.e., the number of species covered by the relevant studies) by 5% to 32%, although they do tend to be based on less robust study designs. Our results show that synthesising non-English-language studies is key to overcoming the widespread lack of local, context-dependent evidence and facilitating evidence-based conservation globally. We urge wider disciplines to rigorously reassess the untapped potential of non-English-language science in informing decisions to address other global challenges. Please see the Supporting information files for Alternative Language Abstracts., A survey of 419,680 peer-reviewed papers in 16 languages reveals that non-English-language studies can expand geographical (by 12-25%) and taxonomic (by 5-32%) coverage of English-language evidence on the effectiveness of biodiversity conservation interventions, especially in biodiverse regions.

International audience; Oxford Nanopore Technologies' (ONT) long read sequencers offer access to longer DNA fragments than previous sequencer generations, at the cost of a higher error rate. While many papers have studied read correction methods, few have addressed the detailed characterization of observed errors, a task complicated by frequent changes in chemistry and software in ONT technology. The MinION sequencer is now more stable and this paper proposes an up-to-date view of its error landscape, using the most mature flowcell and basecaller. We studied Nanopore sequencing error biases on both bacterial and human DNA reads. We found that, although Nanopore sequencing is expected not to suffer from GC bias, it is a crucial parameter with respect to errors. In particular, low-GC reads have fewer errors than high-GC reads (about 6% and 8% respectively). The error profile for homopolymeric regions or regions with short repeats, the source of about half of all sequencing errors, also depends on the GC rate and mainly shows deletions, although there are some reads with long insertions. Another interesting finding is that the quality measure, although overestimated , offers valuable information to predict the error rate as well as the abundance of reads. We supplemented this study with an analysis of a rapeseed RNA read set and shown a higher level of errors with a higher level of deletion in these data. Finally, we have implemented an open source pipeline for long-term monitoring of the error profile, which enables users to easily compute various analysis presented in this work, including for future developments of the sequencing device. Overall, we hope this work will provide a basis for the design of better error-correction methods.

Background mHealth innovations have been proposed as an effective solution to improving adolescent access to and use of Sexual and Reproductive Health (SRH) services; particularly in regions with deeply entrenched traditional social norms. However, research demonstrating the effectiveness and theoretical basis of the interventions is lacking. Aim Our aim was to describe mHealth intervention components, assesses their effectiveness, acceptability, and cost in improving adolescent’s uptake of SRH services in Sub-Saharan Africa (SSA). Methods This paper is based on a systematic review. Twenty bibliographic databases and repositories including MEDLINE, EMBASE, and CINAHL, were searched using pre-defined search terms. Of the 10, 990 records screened, only 10 studies met the inclusion criteria. The mERA checklist was used to critically assess the transparency and completeness in reporting of mHealth intervention studies. The behaviour change components of mHealth interventions were coded using the taxonomy of Behaviour Change Techniques (BCTs). The protocol was registered in the ‘International Prospective Register for Systematic Reviews’ (PROSPERO-CRD42020179051). Results The results showed that mHealth interventions were effective and improved adolescent’s uptake of SRH services across a wide range of services. The evidence was strongest for contraceptive use. Interventions with two-way interactive functions and more behaviour change techniques embedded in the interventions improved adolescent uptake of SRH services to greater extent. Findings suggest that mHealth interventions promoting prevention or treatment adherence for HIV for individuals at risk of or living with HIV are acceptable to adolescents, and are feasible to deliver in SSA. Limited data from two studies reported interventions were inexpensive, however, none of the studies evaluated cost-effectiveness. Conclusion There is a need to develop mHealth interventions tailored for adolescents which are theoretically informed and incorporate effective behaviour change techniques. Such interventions, if low cost, have the potential to be a cost-effective means to improve the sexual and reproductive health outcomes in SSA.

Background Treatment of nerve injuries proves to be a worldwide clinical challenge. Vascularized nerve grafts are suggested to be a promising alternative for bridging a nerve gap to the current gold standard, an autologous non-vascularized nerve graft. However, there is no adequate clinical evidence for the beneficial effect of vascularized nerve grafts and they are still disputed in clinical practice. Objective To systematically review whether vascularized nerve grafts give a superior nerve recovery compared to non-vascularized nerve autografts regarding histological and electrophysiological outcomes in animal models. Material and methods PubMed and Embase were systematically searched. The inclusion criteria were as follows: 1) the study was an original full paper which presented unique data; 2) a clear comparison between a vascularized and a non-vascularized autologous nerve transfer was made; 3) the population study were animals of all genders and ages. A standardized mean difference and 95% confidence intervals for each comparison was calculated to estimate the overall effect. Subgroup analyses were conducted on graft length, species and time frames. Results Fourteen articles were included in this review and all were included in the meta-analyses. A vascularized nerve graft resulted in a significantly larger diameter, higher nerve conduction velocity and axonal count compared to an autologous non-vascularized nerve graft. However, during sensitivity analysis the effect on axonal count disappeared. No significant difference was observed in muscle weight. Conclusion Treating a nerve gap with a vascularized graft results in superior nerve recovery compared to non-vascularized nerve autografts in terms of axon count, diameter and nerve conduction velocity. No difference in muscle weight was seen. However, this conclusion needs to be taken with some caution due to the inherent limitations of this meta-analysis. We recommend future studies to be performed under conditions more closely resembling human circumstances and to use long nerve defects.

Background Digital health (DH) and the benefits of related services are fairly well understood. However, it still is critical to map the digital health care landscape including the key elements that define it as an ecosystem. Particularly, knowing the perspectives of citizens on this digital transformation is an important angle to capture. In this review we aim to analyze the relevant studies to identify how DH is understood and experienced by Australian citizens and what they may require from DH platforms. Materials and methods A scoping literature review was conducted across several electronic databases (ACM Digital Library, OVID, PubMed, Scopus, IEEE, Science Direct, SAGE), as well as grey literature. Additionally, citation mining was conducted to identify further relevant studies. Identified studies were subjected to eligibility criteria and the final set of articles was independently reviewed, analyzed, discussed and interpreted by three reviewers. Results Of 3811 articles, 98 articles met the inclusion criteria with research-based articles–as opposed to review articles or white papers– comprising the largest proportion (72%) of the selected literature. The qualitative analysis of the literature revealed five key elements that capture the essence of the digital health ecosystem interventions from the viewpoint of the Australian citizens. The identified elements were “consumer/user”, “health care”, “technology”, “use and usability”, “data and information”. These elements were further found to be associated with 127 subcategories. Conclusions This study is the first of its kind to analyze and synthesize the relevant literature on DH ecosystems from the citizens’ perspective. Through the lens of two research questions, this study defines the key components that were found crucial to understanding citizens’ experiences with DH. This understanding lays a strong foundation for designing and fostering DH ecosystem. The results provide a solid ground for empirical testing.

Recently, Cicer species have experienced increased research interest due to their economic importance, especially in genetics, genomics, and crop improvement. The Cicer arietinum, Cicer reticulatum, and Cicer echinospermum genomes have been sequenced and provide valuable resources for trait improvement. Since the publication of the chickpea draft genome, progress has been made in genome assembly, functional annotation, and identification of polymorphic markers. However, work is still needed to identify transposable elements (TEs) and make them available for researchers. In this paper, we present CicerSpTEdb, a comprehensive TE database for Cicer species that aims to improve our understanding of the organization and structural variations of the chickpea genome. Using structure and homology-based methods, 3942 C. echinospermum, 3579 C. reticulatum, and 2240 C. arietinum TEs were identified. Comparisons between Cicer species indicate that C. echinospermum has the highest number of LTR-RT and hAT TEs. C. reticulatum has more Mutator, PIF Harbinger, Tc1 Mariner, and CACTA TEs, while C. arietinum has the highest number of Helitron. CicerSpTEdb enables users to search and visualize TEs by location and download their results. The database will provide a powerful resource that can assist in developing TE target markers for molecular breeding and answer related biological questions. Database URL: http://cicersptedb.easyomics.org/index.php

Complex IT outsourcing relationships aptitude several benefits such as increased cost likelihood and lowered costs, higher scalability and flexibility upon demand. However, by virtue of its complexity, the complex outsourcing typically necessitates the interactions among various stakeholders from diverse regions and cultures, making it significantly more challenging to manage than traditional outsourcing. Furthermore, when compared to other types of outsourcing, complex outsourcing is extremely difficult because it necessitates a variety of control and coordination mechanisms for project management, which proportionally increases the risk of project failure. In order to overcome the failure of projects in complex outsourcing relationships, there is a need of robust systematic research to identify the key challenges and practices in this area. Therefore, this research implements systematic literature review as a research method and works as a pioneer attempt to accomplish the aforementioned objectives. Upon furnishing the SLR results, the authors identified 11 major challenges with 67 practices in hand from a total of 85 papers. Based on these findings, the authors intend to construct a comprehensive framework in the future by incorporating robust methodologies such as AHP and fuzzy logic, among others. Qatar National Library and Qatar University - grant No. IRCC- 2021-010.

There has been a spate of interest in association networks in biological and medical research, for example, genetic interaction networks. In this paper, we propose a novel method, the extended joint hub graphical lasso (EDOHA), to estimate multiple related interaction networks for high dimensional omics data across multiple distinct classes. To be specific, we construct a convex penalized log likelihood optimization problem and solve it with an alternating direction method of multipliers (ADMM) algorithm. The proposed method can also be adapted to estimate interaction networks for high dimensional compositional data such as microbial interaction networks. The performance of the proposed method in the simulated studies shows that EDOHA has remarkable advantages in recognizing class-specific hubs than the existing comparable methods. We also present three applications of real datasets. Biological interpretations of our results confirm those of previous studies and offer a more comprehensive understanding of the underlying mechanism in disease., Author summary Reconstruction of multiple association networks from high dimensional omics data is an important topic, especially in biology. Previous studies focused on estimating different networks and detecting common hubs among all classes. Integration of information over different classes of data while allowing the difference in the hub nodes is also biologically plausible. Therefore, we propose a method, EDOHA, to jointly construct multiple interaction networks with the capacity in finding different hub networks for each class of data. Simulation studies show better performance over conventional methods. The method has been demonstrated in three real-world data.

8 pages.-- This is an open access article distributed under the terms of the Creative Commons Attribution License, A recent paper published in PLOS Computational Biology [1] introduces the Scaling Invariance Method (SIM) for analysing structural local identifiability and observability. These two properties define mathematically the possibility of determining the values of the parameters (identifiability) and states (observability) of a dynamic model by observing its output. In this note we warn that SIM considers scaling symmetries as the only possible cause of non-identifiability and non-observability. We show that other types of symmetries can cause the same problems without being detected by SIM, and that in those cases the method may lead one to conclude that the model is identifiable and observable when it is actually not, AFV has received funding from a Ramón y Cajal Fellowship (RYC-2019-027537-I) and from the Spanish Ministry of Science, Innovation and Universities and the European Union FEDER under project grant SYNBIOCONTROL (DPI2017-82896-C2-2-R). GM was funded by the CSIC intramural project grant MOEBIUS (PIE 202070E062)

To our knowledge, no published systematic review has described the effects of mindful walking on mental and cardiovascular health. We have aimed to fill this gap by first establishing our systematic review protocol. Our protocol was adapted from the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) and is registered in PROSPERO (Registration Number: CRD42021241180). The protocol is described step-by-step in this paper, which we wrote to achieve three objectives: to adhere to the best practices stated in the PRISMA guidelines, to ensure procedural transparency, and to enable readers to co-opt our protocol for future systematic reviews on mindful walking and related topics. To achieve our third objective, we provide and explain a novel tool we created to track the sources we will find and screen for our review. Ultimately, the protocol and novel tool will lead to the first published systematic review about mindful walking and will also facilitate future systematic reviews.