Sequencing-guided design of genetically encoded small RNAs targeting CAG repeats for selective inhibition of mutant huntingtin.

Huntington's disease (HD) is an incurable neurodegenerative disorder caused by genetic expansion of a CAG repeat sequence in one allele of the huntingtin (HTT) gene. Reducing expression of the mutant HTT (mutHTT) protein has remained a clear therapeutic goal, but reduction of wild-type HTT (wtHTT) is undesirable, as it compromises gene function and potential therapeutic efficacy. One promising allele-selective approach involves targeting the CAG repeat expansion with steric binding small RNAs bearing central mismatches. However, successful genetic encoding requires consistent placement of mismatches to the target within the small RNA guide sequence, which involves 5' processing precision by cellular enzymes. Here, we used small RNA sequencing (RNA-seq) to monitor the processing precision of a limited set of CAG repeat-targeted small RNAs expressed from multiple scaffold contexts. Small RNA-seq identified expression constructs with high-guide strand 5' processing precision and promising allele-selective inhibition of mutHTT. Transcriptome-wide mRNA-seq also identified an allele-selective small RNA with a favorable off-target profile. These results support continued investigation and optimization of genetically encoded repeat-targeted small RNAs for allele-selective HD gene therapy and underscore the value of sequencing methods to balance specificity with allele selectivity during the design and selection process.

Global mpox lineage discovery and rapid outbreak tracking with nanopore sequencing.

Insufficient tracking of virus introduction, spread, and new lineage emergence for the human monkeypox (mpox) virus 1 (hMPXV1) outbreak of 2022 hindered epidemiological studies and public health response. hMPXV1 mutations accumulated unexpectedly faster than predicted. Thus, new variants with altered pathogenicity could emerge and spread without early detection. Whole genome sequencing addresses this gap when implemented but requires widely accessible and standardized methodologies to be effective both regionally and globally. Here we developed a rapid nanopore whole genome sequencing method complete with working protocols, from DNA extraction to phylogenetic analysis tools. Using this method, we sequenced 84 complete hMPXV1 genomes from Illinois, a Midwestern region of the United States, spanning the first few months of the outbreak. The resulting five-fold increase in hMPXV1 genomes from this region established two previously unnamed global lineages, several mutational profiles not seen elsewhere, multiple separate introductions of the virus into the region, and the likely emergence and spread of new lineages from within this region. These results demonstrate that a dearth of genomic sequencing of hMPXV1 slowed our understanding and response to the mpox outbreak. This accessible nanopore sequencing approach makes near real-time mpox tracking and rapid lineage discovery straightforward and creates a blueprint for how to deploy nanopore sequencing for genomic surveillance of diverse viruses and future outbreaks.

An exploratory study into the relationship between playing at home or away and concussion.

PRIMARY OBJECTIVE: To investigate the effect of home and away game travel on risk of concussion across different levels of rugby union. RESEARCH DESIGN: Exploration study across school, university, and professional rugby teams. METHODS AND PROCEDURES: Retrospective analysis of concussion incidence and symptomology of surveillance data and prospective data collection for potential concussions via surveys. Data was collected from school rugby teams (n = 344 matches, over 2 years), a university rugby (n = 6 matches), and a professional rugby team (n = 64 matches, over two seasons). MAIN OUTCOMES AND RESULTS: School level rugby had an increased prevalence of concussions in away matches (p = 0.02). Likewise, there was a significant increase (p < 0.05) in concussions at away matches in university rugby. In addition, the professional rug by team had significant differences in recovery times and symptoms with away fixtures, including longer recovery times (p < 0.01), more initial symptoms (p < 0.01), as well as greater and more severe symptoms at 48 hours (p < 0.05). CONCLUSIONS: This research highlights an increased prevalence of concussion in school and university-aged rugby players away from home, as well as increased symptoms, symptom severity, and recovery times in professional rugby players.

From eye-blinks to state construction: Diagnostic benchmarks for online representation learning.

We present three new diagnostic prediction problems inspired by classical-conditioning experiments to facilitate research in online prediction learning. Experiments in classical conditioning show that animals such as rabbits, pigeons, and dogs can make long temporal associations that enable multi-step prediction. To replicate this remarkable ability, an agent must construct an internal state representation that summarizes its interaction history. Recurrent neural networks can automatically construct state and learn temporal associations. However, the current training methods are prohibitively expensive for online prediction-continual learning on every time step-which is the focus of this paper. Our proposed problems test the learning capabilities that animals readily exhibit and highlight the limitations of the current recurrent learning methods. While the proposed problems are nontrivial, they are still amenable to extensive testing and analysis in the small-compute regime, thereby enabling researchers to study issues in isolation, ultimately accelerating progress towards scalable online representation learning methods.

Compulsory collisions and corporate interests in school rugby: challenging distortions in the framing of childhood injury.

This article examines how 'framing' is used to resist a proposal to remove rugby tackling from UK schools. It focuses on rugby tackling for UK school children, which is often a compulsory part of many schools' curricula. Specifically, we explore the importance of framing in how the problem is described in various academic publications, how ideas about risk are articulated and how advocates themselves are represented. We show how the corporate interests of rugby governing bodies can become entangled with distortions about injury prevention. These distortions (or framing practices) include omitting arguments, conflating arguments, changing the argument, misrepresenting advocacy positions and skewing advocate identities. Next, the article demonstrates how a combination of recent advocacy, political interventions, research and cultural shifts appears to be changing perceptions about the risks associated with rugby tackling for children in school settings. In conclusion, we argue that while framing can be a useful strategy for policy advocates, there is value in paying attention to how framing is used by different stakeholder groups.

Selecting the best candidates for resurrecting extinct-in-the-wild plants from herbaria.

Resurrecting extinct species is a fascinating and challenging idea for scientists and the general public. Whereas some theoretical progress has been made for animals, the resurrection of extinct plants (de-extinction sensu lato) is a relatively recently discussed topic. In this context, the term 'de-extinction' is used sensu lato to refer to the resurrection of 'extinct in the wild' species from seeds or tissues preserved in herbaria, as we acknowledge the current impossibility of knowing a priori whether a herbarium seed is alive and can germinate. In plants, this could be achieved by germinating or in vitro tissue-culturing old diaspores such as seeds or spores available in herbarium specimens. This paper reports the first list of plant de-extinction candidates based on the actual availability of seeds in herbarium specimens of globally extinct plants. We reviewed globally extinct seed plants using online resources and additional literature on national red lists, resulting in a list of 361 extinct taxa. We then proposed a method of prioritizing candidates for seed-plant de-extinction from diaspores found in herbarium specimens and complemented this with a phylogenetic approach to identify species that may maximize evolutionarily distinct features. Finally, combining data on seed storage behaviour and longevity, as well as specimen age in the novel 'best de-extinction candidate' score (DEXSCO), we identified 556 herbarium specimens belonging to 161 extinct species with available seeds. We expect that this list of de-extinction candidates and the novel approach to rank them will boost research efforts towards the first-ever plant de-extinction.

A Qualitative Exploration of Parents' Perceptions of Risk in Youth Contact Rugby.

The purpose of this study was to explore the understandings and perceptions of risk related to brain trauma amongst parents of children that play contact rugby. A qualitative approach was taken, using semi-structured interviews with 7 mothers and 27 fathers of children that participate in contact rugby. A thematic analysis of data suggests that parents used two primary cognitive strategies to process the risk they consented to with their children's participation in rugby; (1) minimalizing rugby risk to be equivalent to less injurious sports; and (2) elevating physical and social advantages above what they think other sports are capable of providing. From the findings it is suggested that parents who permit their children to play contact rugby are both aware of the high risks of injury in the sport, but simultaneously utilize two cognitive distortion techniques to rectify the dissonance caused between their choice to have their children play, and the salient number of concussions they observe. These results suggest that it will take properly informed consent, inclusive of concussion rates compared to other sports, in order to reduce cognitive distortion and effectively communicate risks associated with participation in contact rugby.

A bead-based method for high-throughput mapping of the sequence- and force-dependence of T cell activation.

Adaptive immunity relies on T lymphocytes that use αß T cell receptors (TCRs) to discriminate among peptides presented by major histocompatibility complex molecules (pMHCs). Identifying pMHCs capable of inducing robust T cell responses will not only enable a deeper understanding of the mechanisms governing immune responses but could also have broad applications in diagnosis and treatment. T cell recognition of sparse antigenic pMHCs in vivo relies on biomechanical forces. However, in vitro screening methods test potential pMHCs without force and often at high (nonphysiological) pMHC densities and thus fail to predict potent agonists in vivo. Here, we present a technology termed BATTLES (biomechanically assisted T cell triggering for large-scale exogenous-pMHC screening) that uses biomechanical force to initiate T cell triggering for peptides and cells in parallel. BATTLES displays candidate pMHCs on spectrally encoded beads composed of a thermo-responsive polymer capable of applying shear loads to T cells, facilitating exploration of the force- and sequence-dependent landscape of T cell responses. BATTLES can be used to explore basic T cell mechanobiology and T cell-based immunotherapies.

Metasurface optofluidics for dynamic control of light fields.

The ability to manipulate light and liquids on integrated optofluidics chips has spurred a myriad of important developments in biology, medicine, chemistry and display technologies. Here we show how the convergence of optofluidics and metasurface optics can lead to conceptually new platforms for the dynamic control of light fields. We first demonstrate metasurface building blocks that display an extreme sensitivity in their scattering properties to their dielectric environment. These blocks are then used to create metasurface-based flat optics inside microfluidic channels where liquids with different refractive indices can be directed to manipulate their optical behaviour. We demonstrate the intensity and spectral tuning of metasurface colour pixels as well as on-demand optical elements. We finally demonstrate automated control in an integrated meta-optofluidic platform to open up new display functions. Combined with large-scale microfluidic integration, our dynamic-metasurface flat-optics platform could open up the possibility of dynamic display, imaging, holography and sensing applications.

Applying the Bradford Hill Criteria for Causation to Repetitive Head Impacts and Chronic Traumatic Encephalopathy.

Chronic traumatic encephalopathy (CTE) is a neurodegenerative disease associated with a history of repetitive head impacts (RHI). CTE was described in boxers as early as the 1920s and by the 1950s it was widely accepted that hits to the head caused some boxers to become "punch drunk." However, the recent discovery of CTE in American and Australian-rules football, soccer, rugby, ice hockey, and other sports has resulted in renewed debate on whether the relationship between RHI and CTE is causal. Identifying the strength of the evidential relationship between CTE and RHI has implications for public health and medico-legal issues. From a public health perspective, environmentally caused diseases can be mitigated or prevented. Medico-legally, millions of children are exposed to RHI through sports participation; this demographic is too young to legally consent to any potential long-term risks associated with this exposure. To better understand the strength of evidence underlying the possible causal relationship between RHI and CTE, we examined the medical literature through the Bradford Hill criteria for causation. The Bradford Hill criteria, first proposed in 1965 by Sir Austin Bradford Hill, provide a framework to determine if one can justifiably move from an observed association to a verdict of causation. The Bradford Hill criteria include nine viewpoints by which to evaluate human epidemiologic evidence to determine if causation can be deduced: strength, consistency, specificity, temporality, biological gradient, plausibility, coherence, experiment, and analogy. We explored the question of causation by evaluating studies on CTE as it relates to RHI exposure. Through this lens, we found convincing evidence of a causal relationship between RHI and CTE, as well as an absence of evidence-based alternative explanations. By organizing the CTE literature through this framework, we hope to advance the global conversation on CTE mitigation efforts.

Imposing Compulsory Rugby Union on Schoolchildren: An Analysis of English State-Funded Secondary Schools.

Objective: To establish the extent to which Rugby Union was a compulsory physical education activity in state-funded secondary schools in England and to understand the views of Subject Leaders for Physical Education with respect to injury risk. Method: A cross-sectional research study using data obtained under the Freedom of Information Act (2000) from 288 state-funded secondary schools. Results: Rugby Union was delivered in 81% (n = 234 of 288) of state-funded secondary school physical education curricula, including 83% (n = 229 of 275) of state-funded secondary school boys' and 54% (n = 151 of 282) of girls' physical education curricular. Rugby Union was compulsory in 91% (n = 208 of 229) of state-funded secondary schools that delivered it as part of the boys' physical education curriculum and 54% (n = 82 of 151) of state-funded secondary schools that delivered contact Rugby Union as part of the girls' physical education curriculum. Subject Leaders for Physical Education also perceived Rugby Union to have the highest risk of harm of the activities they delivered in their school physical education curriculum. Conclusion: Notwithstanding discussions of appropriate measures (i.e., mandatory concussion training, Rugby Union specific qualifications and CPD) to reduce injury risk, it is recommended that Rugby Union should not be a compulsory activity given that it has a perceived high risk of injury and is an unnecessary risk for children in physical education.

An assessment of current concussion identification and diagnosis methods in sports settings: a systematic review.

BACKGROUND: Concussion in sport is an ongoing global concern. The head injury assessment (HIA) by the field of play is acknowledged as the first step in recognising and identifying concussion. While previous systematic literature reviews have evaluated the sensitivity of side-line screening tools and assessment protocols, no systematic review has evaluated the research designs and assessments used in a field setting. This systematic review investigated existing screening and diagnostic tools used in research as part of the HIA protocol to identify concussion that are currently used in professional, semi-professional and amateur (club) sports settings. METHODS: A systematic searching of relevant databases was undertaken for peer-reviewed literature between 2015 and 2020. RESULTS: Twenty-six studies met the inclusion criteria. Studies were of moderate to good quality, reporting a variety of designs. The majority of studies were undertaken in professional/elite environments with medical doctors and allied health practitioners (e.g., physical therapists) involved in 88% of concussion assessments. While gender was reported in 24 of the 26 studies, the majority of participants were male (77%). There was also a variety of concussion assessments (n = 20) with the sports concussion assessment tool (SCAT) used in less than half of the included studies. CONCLUSION: The majority of studies investigating concussion HIAs are focused on professional/elite sport. With concussion an issue at all levels of sport, future research should be directed at non-elite sport. Further, for research purposes, the SCAT assessment should also be used more widely to allow for consistency across studies.

Efficient Cloning and Sequence Validation of Repetitive and High GC-Content Short Hairpin RNAs.

Short hairpin RNAs, or short hairpin RNAs (shRNAs), are a proven tool for gene knockdown and a promising therapeutic approach for suppression of disease-associated genes. The efficient preparation of shRNA-expressing vectors can sometimes become a bottleneck due to the complexity of shRNA hairpin sequence and structure, especially for repetitive or high GC-content targets. Here, we present improved shRNA cloning and validation methods that enabled efficient and rapid cloning of several shRNAs targeting disease-associated repeat expansions, including GGGGCC, CAG, CTG, CCTG, and CGG into modified pLKO.1 vectors. Improvements included shRNA insert design and preparation, recombination-based cloning, and sequencing-based validation that included Sanger and nanopore long-read sequencing. This improved method should enable practical, efficient cloning of nearly any shRNA sequence.

High throughput nanopore sequencing of SARS-CoV-2 viral genomes from patient samples.

In late 2019, a novel coronavirus began spreading in Wuhan, China, causing a potentially lethal respiratory viral infection. By early 2020, the novel coronavirus, called SARS-CoV-2, had spread globally, causing the COVID-19 pandemic. The infection and mutation rates of SARS-CoV-2 make it amenable to tracking introduction, spread and evolution by viral genome sequencing. Efforts to develop effective public health policies, therapeutics, or vaccines to treat or prevent COVID-19 are also expected to benefit from tracking mutations of the SARS-CoV-2 virus. Here we describe a set of comprehensive working protocols, from viral RNA extraction to analysis using established visualization tools, for high throughput sequencing of SARS-CoV-2 viral genomes using a MinION instrument. This set of protocols should serve as a reliable "how-to" reference for generating quality SARS-CoV-2 genome sequences with ARTIC primer sets and long-read nanopore sequencing technology. In addition, many of the preparation, quality control, and analysis steps will be generally applicable to other sequencing platforms.

Pressure. A Qualitative Analysis of the Perception of Concussion and Injury Risk in Retired Professional Rugby Players.

This study interviewed retired professional rugby union players (≤10 years since retirement) to discuss their careers in the game of rugby union. The primary aim of the study was to document their understanding of concussion knowledge and the analogies they use to describe concussion. In addition, these interviews were used to determine any explicit and implicit pressures of playing professional rugby as described by ex-professional rugby players. Overall, 23 retired professional rugby players were interviewed. The participants had played the game of rugby union (n = 23) at elite professional standard. A semi-structured individual interview design was conducted with participants between June to August 2020. The research team reviewed the transcripts to identify the major themes from the interviews using a reflexive thematic analysis approach. Four major themes were identified: (1) medical and theoretical understanding of concussion, (2) descriptions of concussion and disassociated language, (3) personal concussion experience, and (4) peer influences on concussion within the sport. These were further divided into categories and subcategories. The interviews highlighted that players did not fully understand the ramifications of concussive injury and other injury risk, as it became normalised as part of their sport. This normalisation was supported by trivialising the seriousness of concussions and using dismissive language amongst themselves as players, or with coaching staff. As many of these ex-professional players are currently coaching rugby (48%), these interviews could assist coaches in treating concussion as a significant injury and not downplaying the seriousness of concussion in contact sports.

Dopamine release during psychological stress in euthymic bipolar I disorder: a Positron Emission Tomography study with [11C]raclopride.

BACKGROUND: Neurochemical mechanisms underlying stress induced relapse of mood episodes in Bipolar I Disorder (BD) remain unknown. This study investigated whether euthymic BD patients have a greater dopamine release in ventral striatum, caudate and putamen in response to psychological stress using Positron Emission Tomography (PET) scanning with the radiotracer [11C]raclopride. METHODS: Euthymic patients with BD (n = 10) and 10 matched healthy controls underwent two [11C]raclopride PET scans, one during a "stress" and the other in a "no stress" condition separated by at least 24 h. Montreal Imaging Stress Test (MIST) was used to induce stress during stress condition. Participants received an injection of [11C]raclopride over one minute followed by PET scan for 60 min. Participants were assessed for mood symptom severity at baseline, and before and after each scan. The reduction in [11C]raclopride binding in stress condition compared with non-stress rest condition for each subject provided an estimate of dopamine release due to stress. RESULTS: There was a significant effect of stress in reducing the [11C]raclopride binding in the ventral striatum, caudate and putamen; however, no significant effects of group or condition x group interaction were found. LIMITATIONS: Small sample size and recruitment of euthymic patients who may be less vulnerable to stress may limit the generalizability of findings. CONCLUSIONS: Our findings showed that psychological stress led to dopamine release in the basal ganglia for all participants but the magnitude of dopamine release during a stress task was not different between euthymic BD patients and healthy controls.

Effects of Stricter Management Guidelines on Return-to-Competition Timeframes Following Concussion in Professional Australian Rules Football: An Exploratory Analysis.

BACKGROUND: Management of concussion remains a serious issue for professional sports, particularly with the growing knowledge on the consequences of repetitive concussion. One primary concern is the subjective assessment of recovery that dictates the time until a concussed athlete is returned-to-competition. In response to this concern, the Australian Football League (AFL) changed its policy in 2020 such that medical clearance for return-to-competition was extended from 1 day, to a minimum of 5 days, prior to the next scheduled match. OBJECTIVE: We sought to explore the impact of the AFL policy change by asking whether time to return-to-competition after concussion was increased in the 2020 season relative to previous years. METHODS: Retrospective data on injury and return-to-competition were sourced from publicly available tables published by the AFL. Our primary exploration compared the number of matches missed and the number of days missed in concussed players across 2017-2020 inclusive, with secondary exploration analysing the proportion of players returning to play 12 days or longer. RESULTS: Analysis of data from 166 concussed players revealed no increase in the number of matches missed in 2020 relative to previous years as would have been expected from an extended recovery protocol. Comparing 2020 relative to 2017-2019, we found that there was an overall moderate reduction in median time to return-to-competition (RTC) in 2020 (10 vs 13 days, respectively d = - 0.345) and a significant reduction in players taking more than 12 days to RTC (p = 0.046). CONCLUSION: This exploratory study demonstrates that clubs may not have followed policy change around concussion management designed to increase time to RTC. Ongoing auditing is required to ensure player clearance meets policy goals, highlighting the need for objective measures for RTC after concussion.

Potential Benefits of Limited Clinical and Radiographic Follow-up After Surgical Treatment of Ankle Fractures.

INTRODUCTION: Ankle fractures are one of the most prevalent musculoskeletal injuries, with a significant number requiring surgical treatment. Postoperative complications requiring additional interventions frequently occur during the early postoperative period. We hypothesize that there is a limited need for routine clinical and radiographic follow-up once the fracture is deemed healed. METHODS: IRB approval was obtained at four academic trauma centers. A retrospective chart review was done to identify adults with healed unimalleolar and bimalleolar ankle fractures treated surgically with at least 12 months of follow-up. Based on postoperative radiographs, changes in fracture alignment and implant position from radiographic union to final follow-up were documented. The average reimbursement for a final follow-up clinic visit and a set of ankle radiographs were estimated. RESULTS: A total of 140 patients met inclusion criteria. The mean age at injury was 49.5 years, and 67.9% of patients were female. The mean time to healing was 82.2 days (±33.5 days). After radiographic healing, one patient had radiographic changes but was asymptomatic and full weight bearing at their final follow-up. On average, our institution was reimbursed $46 to $49 for a follow-up clinic visit and $364 to $497 for a set of ankle radiographs. CONCLUSION: Given the average time to healing, there is limited utility in routine radiographic and clinical follow-up beyond 16 weeks in asymptomatic patients. In our series, this would result in a savings of $950 to $1,200 per patient. However, after ankle fractures were deemed healed, 0.7% patients had radiographic evidence of a change in implant position. Documenting this change did not modify the immediate course of fracture treatment. Surgeons will need to balance the need for routine follow-up with the potential economic benefits in reducing costs to the healthcare system.