Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day. This potential for sequencing massive ...numbers of genomes calls for fully automated methods to produce high-quality assemblies and variant calls. We introduce Pilon, a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions. Pilon works with many types of sequence data, but is particularly strong when supplied with paired end data from two Illumina libraries with small e.g., 180 bp and large e.g., 3-5 Kb inserts. Pilon significantly improves draft genome assemblies by correcting bases, fixing mis-assemblies and filling gaps. For both haploid and diploid genomes, Pilon produces more contiguous genomes with fewer errors, enabling identification of more biologically relevant genes. Furthermore, Pilon identifies small variants with high accuracy as compared to state-of-the-art tools and is unique in its ability to accurately identify large sequence variants including duplications and resolve large insertions. Pilon is being used to improve the assemblies of thousands of new genomes and to identify variants from thousands of clinically relevant bacterial strains. Pilon is freely available as open source software.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
What is surveillance, and why should we care? Why are those who use technology susceptible to being both agents and targets of contemporary surveillance practices? Working Through Surveillance and ...Technical Communication addresses these questions, discussing what it means to engage in surveillance, examining why this participation may be problematic, and offering entry points into assessing one's ethical and socially just involvement with surveillance. Further, the book suggests ways to resist both individually and collectively, and it offers pedagogical entry points for those looking to talk about surveillance with others. Led by the central questions, "How are technical communicators also surveillance workers?" and "Why does this matter for technical communication and surveillance scholarship?" the text uses the example of Edward Snowden to illustrate how technical communicators and surveillance workers exist on an often-overlapping range. Sarah Young highlights the potentially discriminatory nature of surveillance and argues that recognizing and evaluating surveillance in is increasingly important in a data-driven world.Open Access funded by Erasmus University Rotterdam Library in support of open science initiatives. It can be found in the SUNY Open Access Repository at https://soar.suny.edu/handle/20.500.12648/8546.
Background
Purposive sampling has a long developmental history and there are as many views that it is simple and straightforward as there are about its complexity. The reason for purposive sampling ...is the better matching of the sample to the aims and objectives of the research, thus improving the rigour of the study and trustworthiness of the data and results. Four aspects to this concept have previously been described: credibility, transferability, dependability and confirmability.
Aims
The aim of this paper is to outline the nature and intent of purposive sampling, presenting three different case studies as examples of its application in different contexts.
Results
Presenting individual case studies has highlighted how purposive sampling can be integrated into varying contexts dependent on study design. The sampling strategies clearly situate each study in terms of trustworthiness for data collection and analysis. The selected approach to purposive sampling used in each case aligns to the research methodology, aims and objectives, thus addressing each of the aspects of rigour.
Conclusions
Making explicit the approach used for participant sampling provides improved methodological rigour as judged by the four aspects of trustworthiness. The cases presented provide a guide for novice researchers of how rigour may be addressed in qualitative research.
New Public Governance theory increases citizen participation and expands bureaucrats' roles in the work of government. Citizen participation creates new mechanisms for citizens to influence the ...policy process. Bureaucrats' expanded roles allow for broader bureaucratic discretion over policy implementation. When citizens' and bureaucrats' views on public management decisions collide, whose views prevail? Do citizen volunteers or bureaucrats have greater influence over public decisions? We answer this question by studying the U.S. Department of Energy's initiative to engage citizens in environmental clean‐up decisions. We assess 10 years of meeting records and administrative decisions using a three‐step, mixed‐method analysis to identify, weigh, and test the influence of citizen participation and bureaucratic discretion. The results indicate that while citizen participation matters, bureaucratic discretion has a more significant influence over administrative decision‐making. The findings expose holes in New Public Governance theory, which has implications for democracy and demands deeper thought into structuring citizen participation.
Awake craniotomies provide unique and invaluable scientific opportunities for neurophysiological experimentation in consenting human subjects. While such experimentation carries a long history, ...rigorous reporting of methodologies focusing on synchronizing data across multiple platforms is not universally reported and often not translatable to across operating rooms, facilities, or behavioral tasks. Therefore, here we detail an intraoperative data synchronization methodology designed to work across multiple commercially available platforms to collect behavioral and surgical field videos, electrocorticography, brain stimulation timing, continuous finger joint angles, and continuous finger force production. Our technique was developed to be nonobstructive to operating room (OR) staff and generalizable to a variety of hand-based tasks. We hope that the detailed reporting of our methods will support the scientific rigor and reproducibility of future studies, as well as aid other groups interested in performing related experiments.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Introduction: Virus-like particle (VLP) vaccines face significant challenges in their translation from laboratory models, to routine clinical administration. While some VLP vaccines thrive and are ...readily adopted into the vaccination schedule, others are restrained by regulatory obstacles, proprietary limitations, or finding their niche amongst the crowded vaccine market. Often the necessity to supplant an existing vaccination regimen possesses an immediate obstacle for the development of a VLP vaccine, despite any preclinical advantages identified over the competition. Novelty, adaptability and formulation compatibility may prove invaluable in helping place VLP vaccines at the forefront of vaccination technology.
Areas covered: The purpose of this review is to outline the diversity of VLP vaccines, VLP-specific immune responses, and to explore how modern formulation and delivery techniques can enhance the clinical relevance and overall success of VLP vaccines.
Expert commentary: The role of formation science, with an emphasis on the diversity of immune responses induced by VLP, is underrepresented amongst clinical trials for VLP vaccines. Harnessing such diversity, particularly through the use of combinations of select excipients and adjuvants, will be paramount in the development of VLP vaccines.
The COVID-19 pandemic has dramatically transformed the U.S. healthcare landscape. Within psychiatry, a sudden relaxing of insurance and regulatory barriers during the month of March 2020 enabled ...clinicians practicing in a wide range of settings to quickly adopt virtual care in order to provide critical ongoing mental health supports to both existing and new patients struggling with the pandemic's impact. In this article, we briefly review the extensive literature supporting the effectiveness of telepsychiatry relative to in-person mental health care, and describe how payment and regulatory challenges were the primary barriers preventing more widespread adoption of this treatment modality prior to COVID-19. We then review key changes that were implemented at the federal, state, professional, and insurance levels over a one-month period that helped usher in an unprecedented transformation in psychiatric care delivery, from mostly in-person to mostly virtual. Early quality improvement data regarding virtual visit volumes and clinical insights from our outpatient psychiatry department located within a large, urban, tertiary care academic medical center reflect both the opportunities and challenges of virtual care for patients and providers. Notable benefits have included robust clinical volumes despite social distancing mandates, reduced logistical barrieres to care for many patients, and decreased no-show rates. Finally, we provide clinical suggestions for optimizing telepsychiatry based on our experience, make a call for advocacy to continue the reduced insurance and regulatory restrictions affecting telepsychiatry even once this public health crisis has passed, and pose research questions that can help guide optimal utilization of telepsychiatry as mainstay or adjunct of outpatient psychiatric treatment now and in the future.
Magnetite-binding proteins are in high demand for the functionalization of magnetic nanoparticles. Binding analysis of six previously uncharacterized proteins from the magnetotactic
BW-1 identified ...two new magnetite-binding proteins (Mad10, Mad11). These proteins can be utilized as affinity tags for the immobilization of recombinant fusion proteins to magnetite.
Numerous claims have been made about the benefits of activity-based working (ABW) on workers' health and work performance. Yet, it is unclear if these claims are proven. This systematic review aims ...to establish whether there is an evidence base for the effects of ABW on health, work performance and perceptions of the work environment. Eight databases were searched in September 2016. Three reviewers independently screened titles and abstracts and assessed the studies and extracted the data. Seventeen studies involving 36,039 participants were included. The study designs varied in rigorousness from qualitative studies to pre-post-trials and in sample size ranging from 12 to 11,799. This review found that ABW has positive merits in the areas of interaction, communication, control of time and space, and satisfaction with the workspace; however, it is unfavourable for concentration and privacy. For physical and mental health, the evidence is equivocal. ABW seems to be a promising concept that can be implemented and promoted based on some benefits for work performance and perceptions of the work environment when it is coupled with appropriate management support and organization. More high-quality research is needed to strengthen the evidence base further and establish its health effects.
To examine trends in leisure time physical activity and inactivity in Australians aged 15 years or older from 1989 to 2011.
We used data from six Australian National Health Surveys conducted from ...1989/90 to 2011/12 in which physical activity was assessed using comparable questions. Analyses examined trends in the prevalence of sufficient physical activity (≥150 minutes/week moderate‐to‐vigorous physical activity) and of inactivity (<30 minutes/week moderate‐to‐vigorous physical activity).
The proportion of sufficiently active adults was 39.2% in 1989 and 40.7% in 2011 with an overall declining trend of 0.2% per year (p=0.012). The prevalence of inactivity was 38.7% in 1989 and 37.3% in 2011; the overall time trend by year was stable (OR=0.999, p=0.242). In women, sufficient physical activity decreased by 0.3% per year from 35.5% in 1989 (p=0.025); inactivity increased from 39.5% by 0.3% per year (p=0.004). In men, sufficient physical activity prevalence was 43.1% in 1989 with a steady trend; inactivity decreased from 37.9% by 0.5% per year (p<0.0001).
The prevalence of sufficient physical activity remains low and inactivity high. Women appear to be a key target group for intervention. Public health efforts have been ineffective over two decades for improving physical activity among Australian adults.
This research supports calls for a national physical activity action plan given the multitude of benefits from sufficient physical activity. Maintenance of consistent physical activity questions in future National Health Surveys will facilitate long term tracking of physical activity levels in the Australian population.
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