Search

Preprints, versions of scientific manuscripts that precede peer review, are growing in popularity. They offer an opportunity to democratize and accelerate research, as they have no publication costs or a lengthy peer review process. Preprints are often later published in peer-reviewed venues, but these publications and the original preprints are frequently not linked in any way. To this end, we developed a tool, PreprintMatch, to find matches between preprints and their corresponding published papers, if they exist. This tool outperforms existing techniques to match preprints and papers, both on matching performance and speed. PreprintMatch was applied to search for matches between preprints (from bioRxiv and medRxiv), and PubMed. The preliminary nature of preprints offers a unique perspective into scientific projects at a relatively early stage, and with better matching between preprint and paper, we explored questions related to research inequity. We found that preprints from low income countries are published as peer-reviewed papers at a lower rate than high income countries (39.6% and 61.1%, respectively), and our data is consistent with previous work that cite a lack of resources, lack of stability, and policy choices to explain this discrepancy. Preprints from low income countries were also found to be published quicker (178 vs 203 days) and with less title, abstract, and author similarity to the published version compared to high income countries. Low income countries add more authors from the preprint to the published version than high income countries (0.42 authors vs 0.32, respectively), a practice that is significantly more frequent in China compared to similar countries. Finally, we find that some publishers publish work with authors from lower income countries more frequently than others.

Citations play an important role in researchers careers as a key factor in evaluation of scientific impact. Many anecdotes advice authors to exploit this fact and cite prospective reviewers to try obtaining a more positive evaluation for their submission. In this work, we investigate if such a citation bias actually exists: Does the citation of a reviewers own work in a submission cause them to be positively biased towards the submission? In conjunction with the review process of two flagship conferences in machine learning and algorithmic economics, we execute an observational study to test for citation bias in peer review. In our analysis, we carefully account for various confounding factors such as paper quality and reviewer expertise, and apply different modeling techniques to alleviate concerns regarding the model mismatch. Overall, our analysis involves 1,314 papers and 1,717 reviewers and detects citation bias in both venues we consider. In terms of the effect size, by citing a reviewers work, a submission has a non-trivial chance of getting a higher score from the reviewer: an expected increase in the score is approximately 0.23 on a 5-point Likert item. For reference, a one-point increase of a score by a single reviewer improves the position of a submission by 11% on average.

Medical natural language processing (NLP) systems are a key enabling technology for transforming Big Data from clinical report repositories to information used to support disease models and validate intervention methods. However, current medical NLP systems fall considerably short when faced with the task of logically interpreting clinical text. In this paper, we describe a framework inspired by mechanisms of human cognition in an attempt to jump the NLP performance curve. The design centers on a hierarchical semantic compositional model (HSCM), which provides an internal substrate for guiding the interpretation process. The paper describes insights from four key cognitive aspects: semantic memory, semantic composition, semantic activation, and hierarchical predictive coding. We discuss the design of a generative semantic model and an associated semantic parser used to transform a free-text sentence into a logical representation of its meaning. The paper discusses supportive and antagonistic arguments for the key features of the architecture as a long-term foundational framework.

Quantifying the colors of objects is useful in a wide range of applications, including medical diagnosis, agricultural monitoring, and food safety. Accurate colorimetric measurement of objects is a laborious process normally performed through a color matching test in the laboratory. A promising alternative is to use digital images for colorimetric measurement, due to their portability and ease of use. However, image-based measurements suffer from errors caused by the non-linear image formation process and unpredictable environmental lighting. Solutions to this problem often perform relative color correction among multiple images through discrete color reference boards, which may yield biased results due to the lack of continuous observation. In this paper, we propose a smartphone-based solution, that couples a designated color reference board with a novel color correction algorithm, to achieve accurate and absolute color measurements. Our color reference board contains multiple color stripes with continuous color sampling at the sides. A novel correction algorithm is proposed to utilize a first-order spatial varying regression model to perform the color correction, which leverages both the absolute color magnitude and scale to maximize the correction accuracy. The proposed algorithm is implemented as a "human-in-the-loop" smartphone application, where users are guided by an augmented reality scheme with a marker tracking module to take images at an angle that minimizes the impact of non-Lambertian reflectance. Our experimental results show that our colorimetric measurement is device independent and can reduce up to 90% color variance for images collected under different lighting conditions. In the application of reading pH values from test papers, we show that our system performs 200% better than human reading. The designed color reference board, the correction algorithm, and our augmented reality guiding approach form an integrated system as a novel solution to measure color with increased accuracy. This technique has the flexibility to improve color reading performance in systems beyond existing applications, evidenced by both qualitative and quantitative experiments on example applications such as pH-test reading.

The Anticoagulation Length of Therapy and Risk of New Adverse Events In Venous Thromboembolism (ALTERNATIVE) study was designed to compare the benefits and harms of different treatment options for extended treatment of venous thromboembolism (VTE). In this paper, we describe the study cohort, survey data collection, and preliminary results. We identified 39,605 adult patients (age ≥ 18 years) from two large integrated health care delivery systems who were diagnosed with incident VTE and received initial anticoagulation therapy of 3 months or longer. A subset of the cohort (12,737) was invited to participate in a survey. Surveys were completed in English, Spanish or Mandarin via a mailed questionnaire, an online secure web link, or telephone. The survey domains included demographics, personal medical history, anticoagulant treatment history, anticoagulant treatment satisfaction, health-related quality of life and health literacy. A total of 5,017 patients participated in the survey for an overall response rate of 39.4%. The mean (SD) age of the survey respondents was 63.0 (14.5) years and self-reported race was 76.0% White/European, 11.1% Black/African American, and 3.8% Asian/Pacific Islander and 14.0% reported Hispanic ethnicity. Sixty percent of respondents completed the web survey, while 29.0% completed the mail-in paper survey, and 11.0% completed the survey via telephone. The ALTERNATIVE Study will address knowledge gaps by comparing several treatment alternatives for the extended management of VTE so that this information could be used by patients and clinicians to make more informed, patient-centered treatment choices.

The question of whether it is appropriate to attribute authorship to deceased individuals of original studies in the biomedical literature is contentious. Authorship guidelines utilized by journals do not provide a clear consensus framework that is binding on those in the field. To guide and inform the implementation of authorship frameworks it would be useful to understand the extent of the practice in the scientific literature, but studies that have systematically quantified the prevalence of this phenomenon in the biomedical literature have not been performed to date. To address this issue, we quantified the prevalence of publications by deceased authors in the biomedical literature from the period 1990-2020. We screened 2,601,457 peer-reviewed papers from the full text Europe PubMed Central database. We applied natural language processing, stringent filtering and manual curation to identify a final set of 1,439 deceased authors. We then determined these authors published a total of 38,907 papers over their careers with 5,477 published after death. The number of deceased publications has been growing rapidly, a 146-fold increase since the year 2000. This rate of increase was still significant when accounting for the growing total number of publications and pool of authors. We found that more than 50% of deceased author papers were first submitted after the death of the author and that over 60% of these papers failed to acknowledge the deceased authors status. Most deceased authors published less than 10 papers after death but a small pool of 30 authors published significantly more. A pool of 266 authors published more than 90% of their total publications after death. Our analysis indicates that the attribution of deceased authorship in the literature is not an occasional occurrence but a burgeoning trend. A consensus framework to address authorship by deceased scientists is warranted.

Water affordability is central to water access but remains a challenge to measure. California enshrined the human right to safe and affordable water in 2012 but the question remains: how should water affordability be measured across the state? This paper contributes to this question in three steps. First, we identify key dimensions of water affordability measures (including scale, volume of water needed to meet 'basic' needs, and affordability criteria) and a cross-cutting theme (social equity). Second, using these dimensions, we develop three affordability ratios measured at the water system scale for households with median, poverty level, and deep poverty (i.e., half the poverty level) incomes and estimate the corresponding percentage of households at these income levels. Using multiple measures conveys a fuller picture of affordability given the known limitations of specific affordability measures. Third, we analyze our results disaggregated by a key characteristic of water system vulnerability-water system size. We find that water is relatively affordable for median income households. However, we identify high unaffordability for households in poverty in a large fraction of water systems. We identify several scenarios with different policy implications for the human right to water, such as very small systems with high water bills and low-income households within large water systems. We also characterize how data gaps complicate theoretical ideals and present barriers in human right to water monitoring efforts. This paper presents a systematic approach to measuring affordability and represents the first statewide assessment of water affordability within California's community water systems.

In recent decades, animal welfare science has evolved to utilize a multidisciplinary approach to assess the welfare of animals in accredited zoos and aquariums. Science-based animal welfare assessments have become an essential component of management programs and widespread application is expected by animal care professionals. Management practices for bottlenose dolphins in accredited facilities incorporate several programs that potentially impact animal welfare including environmental enrichment and animal training. Additionally, habitat characteristics, such as the dimensions of the habitat, have been proposed to affect welfare. While accredited facilities are required to meet high standards of care, habitat characteristics and management practices are not standardized across locations. Knowledge and subsequent application of these practices and habitat characteristics can enhance our understanding of factors associated with positive welfare. As part of a larger study of dolphin welfare titled "Towards understanding the welfare of cetaceans in zoos and aquariums" (colloquially called the Cetacean Welfare Study), survey data were collected from 86 bottlenose dolphins in 40 habitats at 38 facilities in seven countries. The major aims of this paper are to provide general descriptive information regarding dolphin management in accredited zoos and aquariums and to provide supplemental context to the other research published from the Cetacean Welfare Study data set. This paper provides a review of current habitat characteristics and management practices at those 38 accredited zoos and aquariums. These data enabled the identification and quantification of how cetacean management practices differed between participating facilities accredited by the Alliance for Marine Mammal Parks and Aquariums and the Association of Zoos & Aquariums. Variables were selected based on their potential association with welfare including the physical habitat, environmental enrichment, and training programs. The variables were also used for subsequent research in this collection of related papers to investigate important connections between potential indicators of welfare and habitat characteristics, environmental enrichment, and training programs.

BACKGROUND: 1.8 million Veterans are estimated to need legal services, such as for housing eviction prevention, discharge upgrades, and state and federal Veterans benefits. While having ones legal needs met is known to improve ones health and its social determinants, many Veterans legal needs remain unmet. Public Law 116-315 enacted in 2021 authorizes VA to fund legal services for Veterans (LSV) by awarding grants to legal service providers including nonprofit organizations and law schools legal assistance programs. This congressionally mandated LSV initiative will award grants to about 75 competitively selected entities providing legal services. This paper describes the protocol for evaluating the initiative. The evaluation will fulfill congressional reporting requirements, and inform continued implementation and sustainment of LSV over time. METHODS: Our protocol calls for a prospective, mixed-methods observational study with a repeated measures design, aligning to the Reach Effectiveness Adoption Implementation Maintenance (RE-AIM) and Integrated Promoting Action on Research Implementation in Health Services (i-PARIHS) frameworks. In 2023, competitively selected legal services-providing organizations will be awarded grants to implement LSV. The primary outcome will be the number of Veterans served by LSV in the 12 months after the awarding of the grant. The evaluation has three Aims. Aim 1 will focus on measuring primary and secondary LSV implementation outcomes aligned to RE-AIM. Aim 2 will apply the mixed quantitative-qualitative Matrixed Multiple Case Study method to identify patterns in implementation barriers, enablers, and other i-PARIHS-aligned factors that relate to observed outcomes. Aim 3 involves a mixed-methods economic evaluation to understand the costs and benefits of LSV implementation. DISCUSSION: The LSV initiative is a new program that VA is implementing to help Veterans who need legal assistance. To optimize ongoing and future implementation of this program, it is important to rigorously evaluate LSVs outcomes, barriers and enablers, and costs and benefits. We have outlined the protocol for such an evaluation, which will lead to recommending strategies and resource allocation for VAs LSV implementation.

ObjectivesSurveys can assist in screening oral diseases in populations to enhance the early detection of disease and intervention strategies for children in need. This paper aims to develop short forms of child-report and proxy-report survey screening instruments for active dental caries and urgent treatment needs in school-age children.MethodsThis cross-sectional study recruited 497 distinct dyads of children aged 8-17 and their parents between 2015 to 2019 from 14 dental clinics and private practices in Los Angeles County. We evaluated responses to 88 child-reported and 64 proxy-reported oral health questions to select and calibrate short forms using Item Response Theory. Seven classical Machine Learning algorithms were employed to predict children's active caries and urgent treatment needs using the short forms together with family demographic variables. The candidate algorithms include CatBoost, Logistic Regression, K-Nearest Neighbors (KNN), Naïve Bayes, Neural Network, Random Forest, and Support Vector Machine. Predictive performance was assessed using repeated 5-fold nested cross-validations.ResultsWe developed and calibrated four ten-item short forms. Naïve Bayes outperformed other algorithms with the highest median of cross-validated area under the ROC curve. The means of best testing sensitivities and specificities using both child-reported and proxy-reported responses were 0.84 and 0.30 for active caries, and 0.81 and 0.31 for urgent treatment needs respectively. Models incorporating both response types showed a slightly higher predictive accuracy than those relying on either child-reported or proxy-reported responses.ConclusionsThe combination of Item Response Theory and Machine Learning algorithms yielded potentially useful screening instruments for both active caries and urgent treatment needs of children. The survey screening approach is relatively cost-effective and convenient when dealing with oral health assessment in large populations. Future studies are needed to further leverage the customize and refine the instruments based on the estimated item characteristics for specific subgroups of the populations to enhance predictive accuracy.

Environmental DNA (eDNA) analysis has gained traction as a precise and cost-effective method for species and waterways management. To date, publications on eDNA protocol optimization have focused primarily on DNA yield. Therefore, it has not been possible to evaluate the cost and speed of specific components of the eDNA protocol, such as water filtration and DNA extraction method when designing or choosing an eDNA protocol. At the same time, these two parameters are essential for the experimental design of a project. Here we evaluate and rank 27 different eDNA protocols in the context of Chinook salmon (Oncorhynchus tshawytscha) eDNA detection in an estuarine environment. We present a comprehensive evaluation of multiple eDNA protocol parameters, balancing time, cost and DNA yield. We collected samples composed of 500 mL estuarine water from Deverton Slough (38°11'16.7"N 121°58'34.5"W) and 500 mL from tank water containing 1.3 juvenile Chinook Salmon per liter. Then, we compared extraction methods, filter types, use of inhibitor removal kit for DNA yield, processing time, and protocol cost. Lastly, we used an MCMC algorithm together with machine learning to understand the DNA yield of each step of the protocol as well as the interactions between those steps. Glass fiber filtration was to be the most resilient to high turbidites, filtering the samples in 2.32 ± 0.08 min instead of 14.16 ± 1.86 min and 6.72 ± 1.99 min for nitrocellulose and paper filter N1, respectively. The filtration DNA yield percentages for paper filter N1, glass fiber, and nitrocellulose were 0.00045 ± 0.00013, 0.00107 ± 0.00013, 0.00172 ± 0.00013. The DNA extraction yield percentage for QIagen, dipstick, NaOH, magnetic beads, and direct dipstick ranged from 0.047 ± 0.0388 to 0.475 ± 0.0357. For estuarine waters, which are challenging for eDNA studies due to high turbidity, variable salinity, and the presence of PCR inhibitors, we found that a protocol combining glass filters, magnetic beads, and an extra step for PCR inhibitor removal, is the method that best balances time, cost, and yield. In addition, we provide a generalized decision tree for determining the optimal eDNA protocol for other studies in aquatic systems. Our findings should be applicable to most aquatic environments and provide a clear guide for determining which eDNA protocol should be used under different study constraints.

Human embryonic stem cells (hESC), derived from the blastocysts, provide unique cellular models for numerous potential applications. They have great promise in the treatment of diseases such as Parkinson's, Huntington's, diabetes mellitus, etc. hESC are a reliable developmental model for early embryonic growth because of their ability to divide indefinitely (pluripotency), and differentiate, or functionally change, into any adult cell type. Their adaptation to toxicological studies is particularly attractive as pluripotent stem cells can be used to model various stages of prenatal development. Automated detection and classification of human embryonic stem cell in videos is of great interest among biologists for quantified analysis of various states of hESC in experimental work. Currently video annotation is done by hand, a process which is very time consuming and exhaustive. To solve this problem, this paper introduces DeephESC 2.0 an automated machine learning approach consisting of two parts: (a) Generative Multi Adversarial Networks (GMAN) for generating synthetic images of hESC, (b) a hierarchical classification system consisting of Convolution Neural Networks (CNN) and Triplet CNNs to classify phase contrast hESC images into six different classes namely: Cell clusters, Debris, Unattached cells, Attached cells, Dynamically Blebbing cells and Apoptically Blebbing cells. The approach is totally non-invasive and does not require any chemical or staining of hESC. DeephESC 2.0 is able to classify hESC images with an accuracy of 93.23% out performing state-of-the-art approaches by at least 20%. Furthermore, DeephESC 2.0 is able to generate large number of synthetic images which can be used for augmenting the dataset. Experimental results show that training DeephESC 2.0 exclusively on a large amount of synthetic images helps to improve the performance of the classifier on original images from 93.23% to 94.46%. This paper also evaluates the quality of the generated synthetic images using the Structural SIMilarity (SSIM) index, Peak Signal to Noise ratio (PSNR) and statistical p-value metrics and compares them with state-of-the-art approaches for generating synthetic images. DeephESC 2.0 saves hundreds of hours of manual labor which would otherwise be spent on manually/semi-manually annotating more and more videos.

Our world is in the midst of unprecedented change-climate shifts and sustained, widespread habitat degradation have led to dramatic declines in biodiversity rivaling historical extinction events. At the same time, new approaches to publishing and integrating previously disconnected data resources promise to help provide the evidence needed for more efficient and effective conservation and management. Stakeholders have invested considerable resources to contribute to online databases of species occurrences. However, estimates suggest that only 10% of biocollections are available in digital form. The biocollections community must therefore continue to promote digitization efforts, which in part requires demonstrating compelling applications of the data. Our overarching goal is therefore to determine trends in use of mobilized species occurrence data since 2010, as online systems have grown and now provide over one billion records. To do this, we characterized 501 papers that use openly accessible biodiversity databases. Our standardized tagging protocol was based on key topics of interest, including: database(s) used, taxa addressed, general uses of data, other data types linked to species occurrence data, and data quality issues addressed. We found that the most common uses of online biodiversity databases have been to estimate species distribution and richness, to outline data compilation and publication, and to assist in developing species checklists or describing new species. Only 69% of papers in our dataset addressed one or more aspects of data quality, which is low considering common errors and biases known to exist in opportunistic datasets. Globally, we find that biodiversity databases are still in the initial stages of data compilation. Novel and integrative applications are restricted to certain taxonomic groups and regions with higher numbers of quality records. Continued data digitization, publication, enhancement, and quality control efforts are necessary to make biodiversity science more efficient and relevant in our fast-changing environment.

Ideal configuration or layout of highways should resemble the actual demands for the roads represented by Origin-Destination (OD) information. It would be beneficial if existing highways can be evaluated for their configurational fitness against the current demands, and newly planned highways can carefully be designed in terms of their layouts and topologies that would reflect the demands. Analysis techniques used for complex networks in the matured field of network theory can be applied for the highway layout health monitoring against the current OD information. This paper proposes a methodology of measuring the fitness of existing highways by comparing their structural configuration against conceptual OD networks using well-established techniques in network theory for complex networks. In the first phase, this paper conducts an empirical analysis and finds that both structural highway network and OD network follow the "power law" distribution as they are weighted by capacity and traffic volume respectively. It is also found that the power law coefficient of the OD network dynamically changes throughout the day and week. In the second phase, a noble methodology of weighting and measuring the health, of structural highway networks against OD networks by means of comparing their power law coefficients is proposed. It is found that the proposed method is effective at detecting deviations from ideal structural configurations associated with actual demands.

BACKGROUND: The gut-brain axis involves bidirectional communication between the gut-microbiota and central nervous system. This study aimed to investigate whether probiotics and/or prebiotics, known as Microbiome-targeted Therapies (MTTs), improve cognition and prevent postoperative cognitive dysfunction (POCD). METHODS: Relevant animal and human studies were identified using a systematic database search (PubMed, EMBASE, Cochrane Library, and Web of Science), focusing on the effects of MTTs on inflammation, perioperative and non-perioperative cognitive impairment. Screening and data extraction were conducted by two independent reviewers. The Risk of bias was assessed using the SYRCLEs risk of bias tool for animal studies. The revised Cochrane risk of bias tool (RoB 2) was used for human studies. RESULTS: A total of 24 articles were selected; 16 of these involved animal studies, and 8 described studies in humans. In these papers, the use of MTTs consistently resulted in decreased inflammation in perioperative and non-perioperative settings. Out of 16 animal studies, 5 studies (2 associated with delirium and 3 studies related to POCD) were conducted in a perioperative setting. MTTs improved perioperative cognitive behavior and reduced inflammation in all 5 animal studies. Eleven animal studies were conducted in a non-perioperative setting. In all of these studies, MTTs showed improvement in learning and memory function. MTTs showed a positive effect on levels of pro-inflammatory cytokines and biomarkers related to cognitive function. Among the 8 human studies, only one study examined the effects of perioperative MTTs on cognitive function. This study showed a reduced incidence of POCD along with improved cognitive function. Of the remaining 7 studies, 6 suggested that MTTs improved behavioral test results and cognition in non-perioperative environments. One study failed to show any significant differences in memory, biomarkers of inflammation, or oxidative factors. CONCLUSION: In the studies we examined, most showed that MTTs decrease inflammation by down-regulating inflammatory cytokines and oxidative stress in both perioperative and non-perioperative settings. In general, MTTs also seem to have a positive effect on cognition through neural, immune, endocrine, and metabolic pathways. However, these effects have not yet resulted in a consensus regarding preventative strategies or treatments. Based on these current research results, MTTs could be a potential new preventative strategy for cognitive impairment after surgery.

The spread of misinformation and conspiracies has been an ongoing issue since the early stages of the internet era, resulting in the emergence of the field of infodemiology (i.e., information epidemiology), which investigates the transmission of health-related information. Due to the high volume of online misinformation in recent years, there is a need to continue advancing methodologies in order to effectively identify narratives and themes. While machine learning models can be used to detect misinformation and conspiracies, these models are limited in their generalizability to other datasets and misinformation phenomenon, and are often unable to detect implicit meanings in text that require contextual knowledge. To rapidly detect evolving conspiracist narratives within high volume online discourse while identifying nuanced themes requiring the comprehension of subtext, this study describes a hybrid methodology that combines natural language processing (i.e., topic modeling and sentiment analysis) with qualitative content coding approaches to characterize conspiracy discourse related to 5G wireless technology and COVID-19 on Twitter (currently known as X). Discourse that focused on correcting 5G conspiracies was also analyzed for comparison. Sentiment analysis shows that conspiracy-related discourse was more likely to use language that was analytic, combative, past-oriented, referenced social status, and expressed negative emotions. Corrections discourse was more likely to use words reflecting cognitive processes, prosocial relations, health-related consequences, and future-oriented language. Inductive coding characterized conspiracist narratives related to global elites, anti-vax sentiment, medical authorities, religious figures, and false correlations between technology advancements and disease outbreaks. Further, the corrections discourse did not address many of the narratives prevalent in conspiracy conversations. This paper aims to further bridge the gap between computational and qualitative methodologies by demonstrating how both approaches can be used in tandem to emphasize the positive aspects of each methodology while minimizing their respective drawbacks.

INTRODUCTION: Latinos are the fastest growing aging population in the U.S. However, there has been limited attention to conceptualizing successful aging among Latinos, especially those residing in rural communities. Latinos are the largest racial or ethnic group residing in rural underserved communities and rural Latinos experience significant structural barriers to access the conditions they need to age well. The goal of this study is to make unique contributions to the successful aging literature by describing what successful aging means for middle-aged Latinas residing in a rural community. METHODS: This qualitative paper used inductive thematic content analysis to examine definitions of successful aging among Latina women (n = 40) residing in an underserved agricultural community and entering mid-life (mean = 49 years old; age range 40-64). RESULTS: With regards to definitions of successful aging, four themes emerged: 1) Having good health; 2) maintaining an active lifestyle; 3) the wellbeing of ones children; and 4) being independent. DISCUSSION: Participants definitions of successful aging aligned to some extent with existing frameworks, specifically related to health and independence. However, middle-aged Latina participants unique definitions of successful aging also diverged from existing frameworks, especially around the wellbeing of their children and the importance of work as a way of maintaining an active lifestyle. More research is needed to understand the unique social context and circumstances of middle-aged Latinos residing in rural communities and how they influence their aging journeys. This can provide important information for the development of culturally sensitive services, interventions, and policies to help Latinos age well.

Non-polyadenylated RNA includes a large subset of crucial regulators of RNA expression and constitutes a substantial portion of the transcriptome, playing essential roles in gene regulation. For example, enhancer RNAs are long non-coding RNAs that perform enhancer-like functions, are bi-directionally transcribed, and usually lack polyA tails. This paper presents a novel method, selSeq, that selectively removes mRNA and pre-mRNA from samples enabling the selective sequencing of crucial regulatory elements, including non-polyadenylated RNAs such as long non-coding RNA, enhancer RNA, and non-canonical mRNA.

Many animals take advantage of the shaded, humid, and protected environments in subcortical spaces, i.e., thin spaces under the loosened bark of dead trees. Permanent inhabitants of subcortical spaces often show specialized morphologies, such as a miniaturized or dorsoventrally flattened body. However, the evolutionary consequences of these specialized morphologies on behavioral, ecological, and life-history traits have been little studied. We studied the mating biology and anatomy of Platylabia major (usually placed in the family Anisolabididae), which is an obligate inhabitant of subcortical spaces with a paper-like flattened body, and compared them with those of two thicker, spongiphorid earwigs, Nesogaster amoenus and Paralabellula curvicauda. Mating trials in various settings showed that Pl. major requires thin spaces sandwiched by two planes to accomplish genital coupling and insemination. In contrast, the thicker species, although also frequently found in subcortical spaces, could mate on a single horizontal plane due to the ability of the male to twist its abdomen through approximately 180°. Examination by micro-computed tomography and a reagent-based clearing technique revealed no substantive differences in the configuration of mid-abdominal musculature between the species. The dorsal and lateral muscles of Pl. major, which are almost parallel to the antero-posterior body axis for accommodation within the thin abdomen, seemed incapable of producing the power to twist the abdomen. The abdominal musculature conforms to a simple pattern in both male and female earwigs, which is repeated in each of the pregenital segments. We conclude that small differences in the range of motion of each abdominal segment can result in large differences in possible mating postures and positions. Surgical experiments also demonstrated that both right and left penises of Pl. major are competent and used for insemination with no lateral bias, as in most other earwigs with twin penises studied to date.

Despite extensive debate on the effects of COVID-19 mitigation measures in school settings, little evidence exists on trends in school childrens mental health over the course of the COVID-19 pandemic. The objective of this paper was to identify factors affecting parent reports of school childrens mental health during COVID-19 Omicron variant outbreak in a cohort of high-risk, socially vulnerable children attending public elementary schools. We analyzed four waves of cross-sectional, online-administered surveys completed by parents of children attending public elementary schools in San Diego between November 2021 and March of 2022. Children (n = 684) ranged in age from 2-17 years. We used multilevel linear mixed effects models to assess determinants of parent-reported child mental health status. The outcome was child mental health, as reported by the parent. Parents consistently rated their childrens mental health as very good, though parents who experienced recent COVID-related challenges and who had older children reported lower levels of mental health in their children. Childrens mental health was generally considered to be very good, as judged by their parents during a period of constant in-school masking and the Omicron variant outbreak. Structural support mechanisms aimed at mitigating COVID-related challenges for adults may offer benefit to childrens mental health.

The ongoing COVID-19 pandemic produced far-reaching effects throughout society, and science is no exception. The scale, speed, and breadth of the scientific community's COVID-19 response lead to the emergence of new research at the remarkable rate of more than 250 papers published per day. This posed a challenge for the scientific community as traditional methods of engagement with the literature were strained by the volume of new research being produced. Meanwhile, the urgency of response lead to an increasingly prominent role for preprint servers and a diffusion of relevant research through many channels simultaneously. These factors created a need for new tools to change the way scientific literature is organized and found by researchers. With this challenge in mind, we present an overview of COVIDScholar https://covidscholar.org, an automated knowledge portal which utilizes natural language processing (NLP) that was built to meet these urgent needs. The search interface for this corpus of more than 260,000 research articles, patents, and clinical trials served more than 33,000 users at an average of 2,000 monthly active users and a peak of more than 8,600 weekly active users in the summer of 2020. Additionally, we include an analysis of trends in COVID-19 research over the course of the pandemic with a particular focus on the first 10 months, which represents a unique period of rapid worldwide shift in scientific attention.

BackgroundAdvance care planning (ACP) is influenced by several factors (e.g., patient's readiness to engage, clinician's skills, and the cultural environment). Availability of reliable and valid self-reported measures of the ACP domains is crucial, including cross-cultural equivalence.AimTo culturally adapt into Italian the 19-item Quality of Communication (QOC) and the 4-item ACP Engagement (4-item ACP-E) questionnaires.MethodsWe translated and culturally adapted the two questionnaires and produced a significant other (SO) version of the QOC (QOC-SO). Each questionnaire was field tested via cognitive interviews with users: nine patients (QOC, 4-item ACP-E) and three SOs (QOC-SO) enrolled at three palliative care services.ResultsWe made minor changes to 5/19 QOC items, to improve clarity and internal consistency; we changed the response option 'didn't do' into 'not applicable'. Finally, we slightly revised the QOC to adapt it to the paper/electronic format. QOC debriefing revealed that the section on end of life was emotionally challenging for both patients and SOs. We simplified the 4-item ACP-E layout, added a sentence in the introduction, and revised the wording of one item, to improve coherence with the Italian ACP legislation. ACP-E debriefing did not reveal any major issue.ConclusionsResults were satisfactory in terms of semantic, conceptual and normative equivalence of both questionnaires. Acceptability was satisfactory for the 4-item ACP-E, while findings of the QOC cognitive debriefing informed a major amendment of a pilot trial protocol on ACP in multiple sclerosis (ConCure-SM): use of the interviewer version only, in an adaptive form. Psychometric testing of both questionnaires on a large, independent sample will follow.

We revisit the results of the recent Reproducibility Project: Psychology by the Open Science Collaboration. We compute Bayes factors—a quantity that can be used to express comparative evidence for an hypothesis but also for the null hypothesis—for a large subset (N = 72) of the original papers and their corresponding replication attempts. In our computation, we take into account the likely scenario that publication bias had distorted the originally published results. Overall, 75% of studies gave qualitatively similar results in terms of the amount of evidence provided. However, the evidence was often weak (i.e., Bayes factor < 10). The majority of the studies (64%) did not provide strong evidence for either the null or the alternative hypothesis in either the original or the replication, and no replication attempts provided strong evidence in favor of the null. In all cases where the original paper provided strong evidence but the replication did not (15%), the sample size in the replication was smaller than the original. Where the replication provided strong evidence but the original did not (10%), the replication sample size was larger. We conclude that the apparent failure of the Reproducibility Project to replicate many target effects can be adequately explained by overestimation of effect sizes (or overestimation of evidence against the null hypothesis) due to small sample sizes and publication bias in the psychological literature. We further conclude that traditional sample sizes are insufficient and that a more widespread adoption of Bayesian methods is desirable.

The Protein Data Bank (PDB) is the worldwide repository of 3D structures of proteins, nucleic acids and complex assemblies. The PDB's large corpus of data (> 100,000 structures) and related citations provide a well-organized and extensive test set for developing and understanding data citation and access metrics. In this paper, we present a systematic investigation of how authors cite PDB as a data repository. We describe a novel metric based on information cascade constructed by exploring the citation network to measure influence between competing works and apply that to analyze different data citation practices to PDB. Based on this new metric, we found that the original publication of RCSB PDB in the year 2000 continues to attract most citations though many follow-up updates were published. None of these follow-up publications by members of the wwPDB organization can compete with the original publication in terms of citations and influence. Meanwhile, authors increasingly choose to use URLs of PDB in the text instead of citing PDB papers, leading to disruption of the growth of the literature citations. A comparison of data usage statistics and paper citations shows that PDB Web access is highly correlated with URL mentions in the text. The results reveal the trend of how authors cite a biomedical data repository and may provide useful insight of how to measure the impact of a data repository.

The paper-based immunoassay for point-of-care diagnostics is widely used due to its low cost and portability over traditional lab-based assays. Lateral-flow immunoassay (LFA) is the most well-established paper-based assay since it is rapid and easy to use. However, the disadvantage of LFA is its lack of sensitivity in some cases where a large sample volume is required, limiting its use as a diagnostic tool. To improve the sensitivity of LFA, we previously reported on the concentration of analytes into one of the two bulk phases of an aqueous two-phase system (ATPS) prior to detection. In this study, we preserved the advantages of LFA while significantly improving upon our previous proof-of-concept studies by employing a novel approach of concentrating gold nanoparticles, a common LFA colorimetric indicator. By conjugating specific antibodies and polymers to the surfaces of the particles, these gold nanoprobes (GNPs) were able to capture target proteins in the sample and subsequently be concentrated within 10 min at the interface of an ATPS solution comprised of polyethylene glycol, potassium phosphate, and phosphate-buffered saline. These GNPs were then extracted and applied directly to LFA. By combining this prior ATPS interface extraction with LFA, the detection limit of LFA for a model protein was improved by 100-fold from 1 ng/μL to 0.01 ng/μL. Additionally, we examined the behavior of the ATPS system in fetal bovine serum and synthetic urine to more closely approach real-world applications. Despite using more complex matrices, ATPS interface extraction still improved the detection limit by 100-fold within 15 to 25 min, demonstrating the system's potential to be applied to patient samples.

The local neighborhood forms an integral part of our lives. It provides the context through which social networks are nurtured and the foundation from which a sense of attachment and cohesion with fellow residents can be established. Whereas much of the previous research has examined the role of social and demographic characteristic in relation to the level of neighboring and cohesion, this paper explores whether particular environmental features in the neighborhood affect social porosity. We define social porosity as the degree to which social ties flow over the surface of a neighborhood. The focus of our paper is to examine the extent to which a neighborhood's environmental features impede the level of social porosity present among residents. To do this, we integrate data from the census, topographic databases and a 2010 survey of 4,351 residents from 146 neighborhoods in Australia. The study introduces the concepts of wedges and social holes. The presence of two sources of wedges is measured: rivers and highways. The presence of two sources of social holes is measured: parks and industrial areas. Borrowing from the geography literature, several measures are constructed to capture how these features collectively carve up the physical environment of neighborhoods. We then consider how this influences residents' neighboring behavior, their level of attachment to the neighborhood and their sense of neighborhood cohesion. We find that the distance of a neighborhood to one form of social hole-industrial areas-has a particularly strong negative effect on all three dependent variables. The presence of the other form of social hole-parks-has a weaker negative effect. Neighborhood wedges also impact social interaction. Both the length of a river and the number of highway fragments in a neighborhood has a consistent negative effect on neighboring, attachment and cohesion.

IntroductionRespondent-driven sampling (RDS) offers a recruitment strategy for hard-to-reach populations. However, RDS faces logistical and theoretical challenges that threaten efficiency and validity in settings worldwide. We present innovative adaptations to conventional RDS to overcome barriers encountered in recruiting a large, representative sample of men who have sex with men (MSM) who travel internationally.MethodsNovel methodological adaptations for the "International Travel Research to Inform Prevention" or "I-TRIP" study were offering participants a choice between electronic and paper coupons referrals for recruitment and modifying the secondary incentives structure from small cash amounts to raffle entries for periodic large cash prize raffle drawings. Staged referral limit increases from 3 to 10 referrals and progressive addition of 70 seeds were also implemented.ResultsThere were 501 participants enrolled in up to 13 waves of growth. Among participants with a choice of referral methods, 81% selected electronic referrals. Of participants who were recruited electronically, 90% chose to remain with electronic referrals when it was their turn to recruit. The mean number of enrolled referrals was 0.91 for electronic referrals compared to 0.56 for paper coupons. Median referral lag time, i.e., the time interval between when recruiters were given their referrals and when a referred individual enrolled in the study, was 20 days (IQR 10-40) for electronic referrals, 20 days (IQR 8-58) for paper coupons, 20 days (IQR 10-41) for raffle entries and 33 days (IQR 16-148) for small cash incentives.ConclusionsThe recruitment of MSM who travel internationally required maximizing known flexible tools of RDS while at the same time necessitating innovations to increase recruitment efficiency. Electronic referrals emerged as a major advantage in recruiting this hard-to-reach population who are of high socio-economic status, geographically diffuse and highly mobile. These enhancements may improve the performance of RDS in target populations with similar characteristics.

Although a tremendous amount of modern interaction is electronic, our understanding of everyday digital communications-including what they look like and how their properties vary by medium and relationship type-is still growing. In this paper, we examine digital exchange in two of its simplest forms: email and SMS. Specifically, our data consist of 2,004 messages provided by a diverse sample of college students, supplemented by in-depth interviews with their authors. These data were collected in 2010-a time when both mediums were widespread but devoid of most of their modern complexity. Based on these data, we make two contributions: First, we develop an empirically grounded typology of the basic properties of text-based digital communication; second, we document the distribution of these properties across five common relationship types. Respectively, these findings provide a starting point to understanding the substance of digital exchange in all its many forms and an empirical benchmark for comparison.

This collection provides a contemporary excerpt of Cities as complex systems. The contributions have been submitted between April and October 2020. We briefly discuss example papers addressing the themes urban scaling, urban mobility, flows in cities, spatial analysis, information technology and cities, and cities in time. After motivating the intersection of cities and complexity, we provide an introduction and additional thoughts on urban scaling.

Given increased prevalence of direct-to-consumer (DTC) genetic health tests in recent years, this paper delves into discourses among researchers at professional genomics conferences and lay DTC genetic test users on popular discussion website Reddit to understand the contested value of genetic knowledge and its direct implications for health management. Harnessing ethnographic observations at five conferences and a text -analysis of 52 Reddit threads, we find both experts and lay patient-consumers navigate their own versions of "productive uncertainty." Experts develop genetic technologies to legitimize unsettled genomics as medical knowledge and mobilize resources and products, while lay patient-consumers turn to Internet forums to gain clarity on knowledge gaps that help better manage their genetic risk states. By showing how the uncertain nature of genomics serves as a productive force placing both parties within a mutually cooperative cycle, we argue that experts and patient-consumers co-produce a form of relational medicalization that concretizes "risk" itself as a disease state.

Nurse, Midwives and Allied Health Professionals (AHPs), along with other health and social care colleagues are the backbone of healthcare services. They have played a key role in responding to the increased demands on healthcare during the COVID-19 pandemic. This paper compares cross-sectional data on quality of working life, wellbeing, coping and burnout of nurses, midwives and AHPs in the United Kingdom (UK) at two time points during the COVID-19 pandemic. An anonymous online repeated cross-sectional survey was conducted at two timepoints, Phase 1 (7th May 2020-3rd July 2020); Phase 2 (17th November 2020-1st February 2021). The survey consisted of the Short Warwick-Edinburgh Mental Wellbeing Scale, the Work-Related Quality of Life Scale, and the Copenhagen Burnout Inventory (Phase 2 only) to measure wellbeing, quality of working life and burnout. The Brief COPE scale and Strategies for Coping with Work and Family Stressors scale assessed coping strategies. Descriptive statistics and multiple linear regressions examined the effects of coping strategies and demographic and work-related variables on wellbeing and quality of working life. A total of 1839 nurses, midwives and AHPs responded to the first or second survey, with a final sample of 1410 respondents -586 from Phase 1; 824 from Phase 2, (422 nurses, 192 midwives and 796 AHPs). Wellbeing and quality of working life scores were significantly lower in the Phase 2 sample compared to respondents in Phase 1 (p

Little is known about longitudinal patterns of welfare program participation among single mothers after they transition from employment to unemployment. To better understand how utilization patterns of these welfare programs may change during the 12 months after a job loss, we used the 2008 Survey of Income and Program Participation to examine the patterns of participation in Medicaid, the Supplemental Nutrition Assistance Program, Temporary Assistance for Needy Families, and unemployment insurance among 342 single mothers who transitioned from employment to unemployment during the Great Recession. Using sequence analysis and cluster analysis, this paper identified four distinct patterns of program participation: (a) constantly receiving in-kind benefits; (b) primarily but not solely receiving food stamps; (c) inconsistent unemployment insurance or Medicaid-based benefits; and (d) limited or no benefits. Almost two-fifths of our sample of single mothers received inconsistent, limited, or no benefits. Results of the multinomial regression revealed that race, work disability, poverty, homeownership, and region of residence were significant factors that influenced whether study subjects participated in or had access to social safety net programs. Our findings illustrate the heterogeneity in patterns of multiple program participation among single mothers transitioning from employment to unemployment. Better understanding these varied patterns may inform decisions that increase the accessibility of US social safety net programs for single mothers during periods of personal economic hardship.

Porcine reproductive and respiratory syndrome (PRRS) is an extremely contagious disease that causes great damage to the U.S. pork industry. PRRS is not subject to official control in the U.S., but most producers adopt control strategies, including vaccination. However, the PRRS virus mutates frequently, facilitating its ability to infect even vaccinated animals. In this paper we analyze how increased vaccination on sow farms reduces PRRS losses and when vaccination is profitable. We develop a SIR model to simulate the spread of an outbreak between and within swine farms located in a region of Minnesota. Then, we estimate economic losses due to PRRS and calculate the benefits of vaccination. We find that increased vaccination of sow farms increases the private profitability of vaccination, and also transmits positive externalities to farms that do not vaccinate. Although vaccination reduces industry losses, a low to moderate vaccine efficacy implies that large PRRS losses remain, even on vaccinated farms. Our approach provides useful insight into the dynamics of an endemic animal disease and the benefits of different vaccination regimens.

BackgroundPersons with submicroscopic malaria infection are a major reservoir of gametocytes that sustain malaria transmission in sub-Saharan Africa. Despite recent decreases in the national malaria burden in Kenya due to vector control interventions, malaria transmission continues to be high in western regions of the country bordering Lake Victoria. The objective of this study was to advance knowledge of the topographical, demographic and behavioral risk factors associated with submicroscopic malaria infection in the Lake Victoria basin in Kisumu County.MethodsCross-sectional community surveys for malaria infection were undertaken in three eco-epidemiologically distinct zones in Nyakach sub-County, Kisumu. Adjacent regions were topologically characterized as lakeshore, hillside and highland plateau. Surveys were conducted during the 2019 and 2020 wet and dry seasons. Finger prick blood smears and dry blood spots (DBS) on filter paper were collected from 1,777 healthy volunteers for microscopic inspection and real time-PCR (RT-PCR) diagnosis of Plasmodium infection. Persons who were PCR positive but blood smear negative were considered to harbor submicroscopic infections. Topographical, demographic and behavioral risk factors were correlated with community prevalence of submicroscopic infections.ResultsOut of a total of 1,777 blood samples collected, 14.2% (253/1,777) were diagnosed as submicroscopic infections. Blood smear microscopy and RT-PCR, respectively, detected 3.7% (66/1,777) and 18% (319/1,777) infections. Blood smears results were exclusively positive for P. falciparum, whereas RT-PCR also detected P. malariae and P. ovale mono- and co-infections. Submicroscopic infection prevalence was associated with topographical variation (χ2 = 39.344, df = 2, p

This paper introduces a series of high resolution (100-meter) population grids for eight different sociodemographic variables across the state of California using data from the 2020 census. These layers constitute the 'CA-POP' dataset, and were produced using dasymetric mapping methods to downscale census block populations using fine-scale residential tax parcel boundaries and Microsoft's remotely-sensed building footprint layer as ancillary datasets. In comparison to a number of existing gridded population products, CA-POP shows good concordance and offers a number of benefits, including more recent data vintage, higher resolution, more accurate building footprint data, and in some cases more sophisticated but parsimonious and transparent dasymetric mapping methodologies. A general accuracy assessment of the CA-POP dasymetric mapping methodology was conducted by producing a population grid that was constrained by population observations within block groups instead of blocks, enabling a comparison of this grid's population apportionment to block-level census values, yielding a median absolute relative error of approximately 30% for block group-to-block apportionment. However, the final CA-POP grids are constrained by higher-resolution census block-level observations, likely making them even more accurate than these block group-constrained grids over a given region, but for which error assessments of population disaggregation is not possible due to the absence of observational data at the sub-block scale. The CA-POP grids are freely available as GeoTIFF rasters online at github.com/njdepsky/CA-POP, for total population, Hispanic/Latinx population of any race, and non-Hispanic populations for the following groups: American Indian/Alaska Native, Asian, Black/African-American, Native Hawaiian and other Pacific Islander, White, other race or multiracial (two or more races) and residents under 18 years old (i.e. minors).

The increasing concern about the degradation of water-dependent ecosystems calls for considering ecosystems benefits in water management decision-making. Sustainable water management requires adequate economic and biophysical information on water systems supporting both human activities and natural ecosystems. This information is essential for assessing the impact on social welfare of water allocation options. This paper evaluates various alternative water management policies by including the spatial and sectoral interrelationships between the economic and environmental uses of water. A hydroeconomic model is developed to analyze water management policies for adaptation to reduced water availability in the Ebro Basin of Spain. The originality in our contribution is the integration of environmental benefits across the basin, by using endemic biophysical information that relates stream flows and ecosystem status in the Ebro Basin. The results show the enhancement of social welfare that can be achieved by protecting environmental flows, and the tradeoffs between economic and environmental benefits under alternative adaptation strategies. The introduction of water markets is a policy that maximizes the private benefits of economic activities, but disregards environmental benefits. The results show that the current institutional policy where stakeholders cooperate inside the water authority, provides lower private benefits but higher environmental benefits compared to those obtained under water markets, especially under severe droughts. However, the water authority is not allocating enough environmental flows to optimize social welfare. This study informs strategies for protection of environmental flows in the Ebro Basin, which is a compelling decision under the imminent climate change impacts on water availability in coming decades.

BackgroundThe reopening of college and university campuses was seen as presenting a high risk for transmission of COVID-19. Thus, these institutions faced with a new public health challenge never heretofore faced on this scale. To magnify the problem, they needed to rapidly develop and implement re-opening plans in an environment filled with uncertainty and for a population that was significantly less likely to observe COVID-19 mitigation behaviors. In response, within three weeks of opening, as part of its COVID-19 public health strategy, a West Coast university created and trained a public health workforce comprised of 282 undergraduates tasked with encouraging compliance with COVID-19 mitigating healthy behaviors.Main objectivesThis paper describes the use and outcomes of a practicum framework to quickly create a university-based public health workforce. It addresses two questions: (1) Using a practicum framework, what are important considerations in designing and building a public health workforce for a university campus? and (2) What are the benefits to the workforce in terms of public health education and professional growth?MethodsProgram administrative data were used to describe the workforce and their learning outcomes.ResultsThe majority of students indicated that through the practicum, they learned new skills/developed new attitudes (71.7%) and became aware of their own strengths and opportunities for professional growth (73.7%). The types of new skills and attitudes learned included communication (49.2%), conflict management (20.4%), time management (7.5%), and open-mindedness/less judgmental attitude (14.6%). In terms of public health, they gained an understanding of infectious disease prevention (40.9%) that is multi-disciplinary (20.5%), and involves a community effort (36.8%).ConclusionsThese findings demonstrate an effective way of rapidly addressing public health concerns that allowed for on the job training and opportunities for young adults to learn and grow. The practicum framework allowed the expeditious development of a public health workforce that ensured a fit between student interests and the role. This led to high retention with the majority of students continuing into the winter quarter. Only 5% of students reported not being satisfied with their position. None of the students contracted job-related COVID-19. The role gave students a sense of purpose during the pandemic's uncertain times that helped to protect them from the negative effects of stress. The practicum structure and support fostered a safe environment in which students were able to feel part of the larger community while gaining valuable work experience and skills and serve their community.

Kernel density estimation is a widely used method for estimating a distribution based on a sample of points drawn from that distribution. Generally, in practice some form of error contaminates the sample of observed points. Such error can be the result of imprecise measurements or observation bias. Often this error is negligible and may be disregarded in analysis. In cases where the error is non-negligible, estimation methods should be adjusted to reduce resulting bias. Several modifications of kernel density estimation have been developed to address specific forms of errors. One form of error that has not yet been addressed is the case where observations are nominally placed at the centers of areas from which the points are assumed to have been drawn, where these areas are of varying sizes. In this scenario, the bias arises because the size of the error can vary among points and some subset of points can be known to have smaller error than another subset or the form of the error may change among points. This paper proposes a “contingent kernel density estimation” technique to address this form of error. This new technique adjusts the standard kernel on a point-by-point basis in an adaptive response to changing structure and magnitude of error. In this paper, equations for our contingent kernel technique are derived, the technique is validated using numerical simulations, and an example using the geographic locations of social networking users is worked to demonstrate the utility of the method.

To date, the effect of both fixed and time-varying individual, social, psychological, environmental, and behavioral characteristics on temporal growth trends in physical activity (PA) among younger individuals remains an under-studied topic. In this paper, we address this gap in previous work by examining how temporal growth trends in PA respond to changing social, environmental, and behavioral characteristics using a large sample of college students (N = 692) who participated in the NetHealth project at the University of Notre Dame and from which fine-grained longitudinal data on physical activity and social interaction were collected unobtrusively via the use of wearables for 637 days (August 16, 2015 to May 13, 2017). These data are augmented by periodic survey data on fixed sociodemographic and psychological variables. We estimate latent growth-curve models for daily activity status, steps, active minutes, and activity calories. We find evidence of both a generalized friendship paradox and a peer effect for PA, with the average PA level of study participants' contacts being on average larger than their own, and with this average level exerting a statistically significant effect on individual PA levels. Notably, there was limited evidence of temporal growth in PA across the 637 days of observation with null temporal effects for three out of the four PA indicators, except for daily steps taken. Finally, we find that social, psychological, and behavioral factors (e.g., large network size, high extroversion levels, and more courses taken) are systematically associated with higher PA levels in this sample. Overall, our findings highlight the importance of social, environmental, and behavioral factors (such as peer networks and daily sociability) in modulating the dynamics of PA levels among college students.

Undocumented status is widely recognized as an important social determinant of health. While undocumented immigrants have lower levels of health care access, they do not have consistently poorer physical health than the US-born or other immigrant groups. Furthermore, heterogeneity by race/ethnicity has been largely ignored in this growing literature. This paper used the 2001, 2004, 2008 panels of the restricted Survey of Income and Program Participation (SIPP), one of the only representative surveys equipped to adequately identify Asian undocumented immigrants, to compare health patterns between Asians and Latinos by immigration status. We examined three general measures of health/health access: self-rated health, disability, and current health insurance. Latino undocumented immigrants displayed some advantages in self-rated health and disability but had lower insurance coverage compared to US-born Latinos. In contrast, Asian undocumented immigrants did not differ from US-born Asians in any of the three outcomes. While undocumented status has been proposed as a fundamental cause of disease, we found no evidence that Latino and Asian undocumented immigrants consistently fare worse in health access or physical health outcomes than immigrants in other status categories. Different racial groups also appeared to have unique patterns between immigration status and health outcomes from one another.

BackgroundThe development of mobile computing technology has enabled the delivery of psychological interventions while people go about their everyday lives. The original visions of the potential of these "ecological momentary interventions" were presented over a decade ago, and the widespread adoption of smartphones in the intervening years has led to a variety of research studies exploring the feasibility of these aspirations. However, there is a dearth of research describing the different dimensions, characteristics, and features of these interventions, as constructed.ObjectiveTo provide an overview of the definitions given for "ecological momentary interventions" in the treatment of common mental health disorders, and describe the set of technological and interaction possibilities which have been used in the design of these interventions.MethodsA systematic search identified relevant literature published between 2009 and 2020 in the PubMed, PsycInfo, and ACM Guide to the Computing Literature databases. Following screening, data were extracted from eligible articles using a standardized extraction worksheet. Selected articles were then thematically categorized.ResultsThe search identified 583 articles of which 64 met the inclusion criteria. The interventions target a range of mental health problems, with diverse aims, intervention designs and evaluation approaches. The studies employed a variety of features for intervention delivery, but recent research is overwhelmingly comprised of studies based on smartphone apps (30 of 42 papers that described an intervention). Twenty two studies employed sensors for the collection of data in order to provide just-in-time support or predict psychological states.ConclusionsWith the shift towards smartphone apps, the vision for EMIs has begun to be realised. Recent years have seen increased exploration of the use of sensors and machine learning, but the role of humans in the delivery of EMI is also varied. The variety of capabilities exhibited by EMIs motivates development of a more precise vocabulary for capturing both automatic and human tailoring of these interventions.

A crucial question in the governance of infectious disease outbreaks is how to ensure that people continue to adhere to mitigation measures for the longer duration. The present paper examines this question by means of a set of cross-sectional studies conducted in the United States during the COVID-19 pandemic, in May, June, and July of 2020. Using stratified samples that mimic the demographic characteristics of the U.S. population, it seeks to understand to what extent Americans continued to adhere to social distancing measures in the period after the first lockdown ended. Moreover, it seeks to uncover which variables sustained (or undermined) adherence across this period. For this purpose, we examined a broad range of factors, relating to people's (1) knowledge and understanding of the mitigation measures, (2) perceptions of their costs and benefits, (3) perceptions of legitimacy and procedural justice, (4) personal factors, (5) social environment, and (6) practical circumstances. Our findings reveal that adherence was chiefly shaped by three major factors: respondents adhered more when they (a) had greater practical capacity to adhere, (b) morally agreed more with the measures, and (c) perceived the virus as a more severe health threat. Adherence was shaped to a lesser extent by impulsivity, knowledge of social distancing measures, opportunities for violating, personal costs, and descriptive social norms. The results also reveal, however, that adherence declined across this period, which was partly explained by changes in people's moral alignment, threat perceptions, knowledge, and perceived social norms. These findings show that adherence originates from a broad range of factors that develop dynamically across time. Practically these insights help to improve pandemic governance, as well as contributing theoretically to the study of compliance and the way that rules come to shape behavior.

Distance learning in response to the COVID-19 pandemic presented tremendous challenges for many families. Parents were expected to support children's learning, often while also working from home. Students with Attention Deficit Hyperactivity Disorder (ADHD) are at particularly high risk for setbacks due to difficulties with organization and increased risk of not participating in scheduled online learning. This paper explores how smartwatch technology, including timing notifications, can support children with ADHD during distance learning due to COVID-19. We implemented a 6-week pilot study of a Digital Health Intervention (DHI) with ten families. The DHI included a smartwatch and a smartphone. Google calendars were synchronized across devices to guide children through daily schedules. After the sixth week, we conducted parent interviews to understand the use of smartwatches and the impact on children's functioning, and we collected physiological data directly from the smartwatch. Our results demonstrated that children successfully adopted the use of the smartwatch, and parents believed the intervention was helpful, especially in supporting the development of organizational skills in their children. Overall, we illustrate how even simple DHIs, such as using smartwatches to promote daily organization and task completion, have the potential to support children and families, particularly during periods of distance learning. We include practical suggestions to help professionals teach children with ADHD to use smartwatches to improve organization and task completion, especially as it applies to supporting remote instruction.

Cybersecurity affects us all in our daily lives. New knowledge on best practices, new vulnerabilities, and timely fixes for cybersecurity issues is growing super-linearly, and is spread across numerous, heterogeneous sources. Because of that, community contribution-based, question and answer sites have become clearinghouses for cybersecurity-related inquiries, as they have for many other topics. Historically, Stack Overflow has been the most popular platform for different kinds of technical questions, including for cybersecurity. That has been changing, however, with the advent of Security Stack Exchange, a site specifically designed for cybersecurity-related questions and answers. More recently, some cybersecurity-related subreddits of Reddit, have become hubs for cybersecurity-related questions and discussions. The availability of multiple overlapping communities has created a complex terrain to navigate for someone looking for an answer to a cybersecurity question. In this paper, we investigate how and why people choose among three prominent, overlapping, question and answer communities, for their cybersecurity knowledge needs. We aggregated data of several consecutive years of cybersecurity-related questions from Stack Overflow, Security Stack Exchange, and Reddit, and performed statistical, linguistic, and longitudinal analysis. To triangulate the results, we also conducted user surveys. We found that the user behavior across those three communities is different, in most cases. Likewise, cybersecurity-related questions asked on the three sites are different, more technical on Security Stack Exchange and Stack Overflow, and more subjective and personal on Reddit. Moreover, there appears to have been a differentiation of the communities along the same lines, accompanied by overall popularity trends suggestive of Stack Overflow's decline and Security Stack Exchange's rise within the cybersecurity community. Reddit is addressing the more subjective, discussion type needs of the lay community, and is growing rapidly.

BACKGROUND:Studies estimate that the number of cancer survivors will double by 2050 due to improvements in diagnostic accuracy and treatment efficacy. Despite the growing population of cancer survivors, there is a paucity of research regarding how these individuals experience the transition from active treatment to long-term surveillance. While research has explored this transition from more organized venues, such as support groups for cancer survivors, this paper explores the discourses surrounding cancer survivorship on social media, paying particular attention to how individuals who identify as cancer survivors represent their experience. METHODS:We identified social media posts relating to cancer survivorship on Twitter and Instagram in early June 2018, in order to coincide with National Cancer Survivorship Day on June 3, 2018. We used nine pre-selected hashtags to identify content. For each hashtag, we manually collected the 150 most recent posts from Twitter and the 100 most recent plus the top 9 posts from Instagram. Our preliminary sample included 1172 posts; after eliminating posts from one hashtag due to irrelevance, we were left with 1063 posts. We randomly sampled 200 of these to create a subset for analysis; after review for irrelevant posts, 193 posts remained for analysis (118 from Instagram and 75 from Twitter). We utilized a grounded theory approach to analyze the posts, first open-coding a subset to develop a codebook, then applying the codebook to the rest of the sample and finally memo writing to develop themes. RESULTS:Overall, there is substantial difference in the tone and thematic content between Instagram and Twitter posts, Instagram takes on a more narrative form that represents journeys through cancer treatment and subsequent survivorship, whereas Twitter is more factual, leaning towards advocacy, awareness and fundraising. In terms of content type, 120 posts (62%) of the sample were images, of which 42 (35%) were images of the individual posting and 28 (23%) were images of patients posted by family or friends. Of the remaining images, 14 (12%) were of support groups and 7 (6%) were of family or friends. We identified four salient themes through analysis of the social media posts from Twitter and Instagram: social support, celebrating milestones and honoring survivors, expressing identity, and renewal vs. rebirth. DISCUSSION:We observed a marked relationship between physical appearance, functional status and survivorship. Additionally, our findings suggest the importance of social support for cancer patients and survivors as well as the role social media can pay in identity formation. CONCLUSION:Our findings suggest that individuals who identify as survivors on social media define their identity fluidly, incorporating elements of physical, emotional and psychological health as well as autonomy.

We examine how solitary confinement correlates with self-reported adverse physical health outcomes, and how such outcomes extend the understanding of the health disparities associated with incarceration. Using a mixed methods approach, we find that solitary confinement is associated not just with mental, but also with physical health problems. Given the disproportionate use of solitary among incarcerated people of color, these symptoms are most likely to affect those populations. Drawing from a random sample of prisoners (n = 106) in long-term solitary confinement in the Washington State Department of Corrections in 2017, we conducted semi-structured, in-depth interviews; Brief Psychiatric Rating Scale (BPRS) assessments; and systematic reviews of medical and disciplinary files for these subjects. We also conducted a paper survey of the entire long-term solitary confinement population (n = 225 respondents) and analyzed administrative data for the entire population of prisoners in the state in 2017 (n = 17,943). Results reflect qualitative content and descriptive statistical analysis. BPRS scores reflect clinically significant somatic concerns in 15% of sample. Objective specification of medical conditions is generally elusive, but that, itself, is a highly informative finding. Using subjective reports, we specify and analyze a range of physical symptoms experienced in solitary confinement: (1) skin irritations and weight fluctuation associated with the restrictive conditions of solitary confinement; (2) un-treated and mis-treated chronic conditions associated with the restrictive policies of solitary confinement; (3) musculoskeletal pain exacerbated by both restrictive conditions and policies. Administrative data analyses reveal disproportionate rates of racial/ethnic minorities in solitary confinement. This analysis raises the stakes for future studies to evaluate comparative prevalence of objective medical diagnoses and potential causal mechanisms for the physical symptoms specified here, and for understanding differential use of solitary confinement and its medically harmful sequelae.

Water buffalo (Bubalus bubalis) is an important source of meat and milk in countries with relatively warm weather. Compared to the cattle genome, a little has been done to reveal its genome structure and genomic traits. This is due to the complications stemming from the large genome size, the complexity of the genome, and the high repetitive content. In this paper, we introduce a high-quality draft assembly of the Egyptian water buffalo genome. The Egyptian breed is used as a dual purpose animal (milk/meat). It is distinguished by its adaptability to the local environment, quality of feed changes, as well as its high resistance to diseases. The genome assembly of the Egyptian water buffalo has been achieved using a reference-based assembly workflow. Our workflow significantly reduced the computational complexity of the assembly process, and improved the assembly quality by integrating different public resources. We also compared our assembly to the currently available draft assemblies of water buffalo breeds. A total of 21,128 genes were identified in the produced assembly. A list of milk virgin-related genes; milk pregnancy-related genes; milk lactation-related genes; milk involution-related genes; and milk mastitis-related genes were identified in the assembly. Our results will significantly contribute to a better understanding of the genetics of the Egyptian water buffalo which will eventually support the ongoing breeding efforts and facilitate the future discovery of genes responsible for complex processes of dairy, meat production and disease resistance among other significant traits.

In radioactive source surveying protocols, a number of task-inherent features degrade the quality of collected gamma ray spectra, including: limited dwell times, a fluctuating background, a large distance to the source, weak source activity, and the low sensitivity of mobile detectors. Thus, collected gamma ray spectra are expected to be sparse and noise dominated. For extremely sparse spectra, direct background subtraction is infeasible and many background estimation techniques do not apply. In this paper, we present a statistical algorithm for source estimation and anomaly detection under such conditions. We employ a fixed-hyperparameter Gaussian processes regression methodology with a linear innovation sequence scheme in order to quickly update an ongoing source distribution estimate with no prior training required. We have evaluated the effectiveness of this approach for anomaly detection using background spectra collected with a Kromek D3S and simulated source spectrum and hyperparameters defined by detector characteristics and information derived from collected spectra. We attained an area under the ROC curve of 0.902 for identifying sparse source peaks within a sparse gamma ray spectrum and achieved a true positive rate of 93% when selecting the optimum thresholding value derived from the ROC curve.

Currently, injection sites of probes, cannula, and optic fibers in stereotactic neurosurgery are typically located manually. This step involves location estimations based on human experiences and thus introduces errors. In order to reduce localization error and improve repeatability of experiments and treatments, we investigate an automated method to locate injection sites. This paper proposes a localization framework, which integrates a region-based convolutional network and a fully convolutional network, to locate specific anatomical points on skulls of rodents. Experiment results show that the proposed localization framework is capable of identifying and locatin bregma and lambda in rodent skull anatomy images with mean errors less than 300 μm. This method is robust to different lighting conditions and mouse orientations, and has the potential to simplify the procedure of locating injection sites.

Primary symptoms of adults with autism spectrum disorder (ASD), such as pervasive social deficits in social interaction and communication, cause adults with ASD to adopt a sedentary lifestyle. Meanwhile, gamified and behavioral theory-based interventions have been shown to improve physical activity in a fun and unobtrusive way. In this paper, we describe the iterative design inquiry process of PuzzleWalk, a gamified, physical activity-promoting mobile app designed for adults with ASD. We report the design rationales and lessons learned across four user-centered design phases with ASD experts and adults with ASD, including user requirement gathering, iterative participatory design, usability evaluation, and field deployment. The design insights generated from this work could inform future research focusing on designing sociotechnical systems, games, and interventions for people with ASD.