OpenHands: An Open-Source Statistical Shape Model of the Finger Bones.

This paper presents statistical shape models of the four fingers of the hand, with an emphasis on anatomic analysis of the proximal and distal interphalangeal joints. A multi-body statistical shape modelling pipeline was implemented on an exemplar training dataset of computed tomography (CT) scans of 10 right hands (5F:5M, 27-37 years, free from disease or injury) imaged at 0.3 mm resolution, segmented, meshed and aligned. Model generated included pose neutralisation to remove joint angle variation during imaging. Repositioning was successful; no joint flexion variation was observed in the resulting model. The first principal component (PC) of morphological variation represented phalanx size in all fingers. Subsequent PCs showed variation in position along the palmar-dorsal axis, and bone breadth: length ratio. Finally, the models were interrogated to provide gross measures of bone lengths and joint spaces. These models have been published for open use to support wider community efforts in hand biomechanical analysis, providing bony anatomy descriptions whilst preserving the security of the underlying imaging data and privacy of the participants. The model describes a small, homogeneous population, and assumptions cannot be made about how it represents individuals outside the training dataset. However, it supplements anthropometric datasets with additional shape information, and may be useful for investigating factors such as joint morphology and design of hand-interfacing devices and products. The model has been shared as an open-source repository ( https://github.com/abel-research/OpenHands ), and we encourage the community to use and contribute to it.

Telehealth Use during COVID-19: An Exploratory Study on Adaptations and Experiences of Providers.

The current exploratory study examines the impact of the rapid acceleration of telehealth during the COVID-19 pandemic from the perspective of healthcare providers. Understanding provider perspectives, particularly in terms of adaptations made during this critical time, is a useful lens into service innovation in times of crisis and can help elucidate successful strategies for continuing the use of telehealth during the postpandemic period. Fourteen providers from 11 different service agencies in a southeastern state were interviewed. Findings identified three themes: (1) dynamic adaptations enacted by healthcare providers at the onset of the pandemic, such as hybrid services, rapid innovations in workflow, collective decision making among providers, and outreach to educate patients; (2) the relaxation of policies by regulators/insurers, focused most often on reimbursement of services; and (3) how patient engagement was impacted via telehealth, including openness to telehealth, more family-level accessibility, and reduced no-show rates. Implications for social workers include heightened professional training on telehealth as well as increasing the critical role that social workers serve in educating providers and patients on telehealth.

Limitations of antifungal prophylaxis in preventing invasive Candida surgical site infections after liver transplant surgery.

Invasive primary Candida surgical site infections (IP-SSIs) are a common complication of liver transplantation, and targeted antifungal prophylaxis is an efficient strategy to limit their occurrence. We performed a retrospective single-center cohort study among adult single liver transplant recipients at Duke University Hospital in the period between 1 January 2015 and 31 December 2020. The study aimed to determine the rate of Candida IP-SSI according to the peri-transplant antifungal prophylaxis received. Of 470 adult single liver transplant recipients, 53 (11.3%) received micafungin prophylaxis, 100 (21.3%) received fluconazole prophylaxis, and 317 (67.4%) did not receive systemic antifungal prophylaxis in the peri-transplant period. Ten Candida IP-SSIs occurred among 5 of 53 (9.4%) micafungin recipients, 1 of 100 (1.0%) fluconazole recipients, and 4 of 317 (1.3%) recipients who did not receive antifungal prophylaxis. Our study highlights the limitations of antifungal prophylaxis in preventing invasive Candida IP-SSI after liver transplant surgery. We hypothesize that pathogen, host, and pharmacokinetic-related factors contributed to the occurrence of Candida IP-SSI despite antifungal prophylaxis. Our study reinforces the need for a risk-based, multi-pronged approach to fungal prevention, including targeted antifungal administration in patients with risks for invasive candidiasis and close monitoring, especially among patients with surgically complex procedures, with timely control of surgical leaks.

CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing.

Extrachromosomal DNA (ecDNA) is a central mechanism for focal oncogene amplification in cancer, occurring in approximately 15% of early stage cancers and 30% of late-stage cancers. EcDNAs drive tumor formation, evolution, and drug resistance by dynamically modulating oncogene copy-number and rewiring gene-regulatory networks. Elucidating the genomic architecture of ecDNA amplifications is critical for understanding tumor pathology and developing more effective therapies. Paired-end short-read (Illumina) sequencing and mapping have been utilized to represent ecDNA amplifications using a breakpoint graph, where the inferred architecture of ecDNA is encoded as a cycle in the graph. Traversals of breakpoint graph have been used to successfully predict ecDNA presence in cancer samples. However, short-read technologies are intrinsically limited in the identification of breakpoints, phasing together of complex rearrangements and internal duplications, and deconvolution of cell-to-cell heterogeneity of ecDNA structures. Long-read technologies, such as from Oxford Nanopore Technologies, have the potential to improve inference as the longer reads are better at mapping structural variants and are more likely to span rearranged or duplicated regions. Here, we propose CoRAL (Complete Reconstruction of Amplifications with Long reads), for reconstructing ecDNA architectures using long-read data. CoRAL reconstructs likely cyclic architectures using quadratic programming that simultaneously optimizes parsimony of reconstruction, explained copy number, and consistency of long-read mapping. CoRAL substantially improves reconstructions in extensive simulations and 9 datasets from previously-characterized cell-lines as compared to previous short-read-based tools. As long-read usage becomes wide-spread, we anticipate that CoRAL will be a valuable tool for profiling the landscape and evolution of focal amplifications in tumors.

Assessing domain match and feasibility of candidate instruments matching with OMERACT endorsed domains to measure flare in knee and hip osteoarthritis.

PURPOSE: To evaluate the domain match (truth) and feasibility of candidate instruments assessing flare in knee and hip osteoarthritis (OA) according to the identified domains. MATERIAL AND METHODS: From a literature review (575 papers), instruments were selected and evaluated using the truth and feasibility elements of the OMERACT Filter 2.2. These were evaluated by 26 experts, including patients, in two Delphi survey rounds. The final selection was obtained by a vote. RESULTS: 44 instruments were identified. In Delphi Round 1, five instruments were selected. In Round 2, all instruments obtained at least 75 % in terms of content match with the endorsed domains and feasibility. In the final selection, the Flare-OA questionnaire obtained 100 % favorable votes. CONCLUSION: Through consensus of the working group, the Flare-OA questionnaire was selected as the best candidate instrument to move into a full assessment of its measurement properties using the OMERACT Filter 2.2.

"You don't put it down to arthritis": A qualitative study of the first symptoms recalled by individuals with knee osteoarthritis.

Objective: As part of the first phase of the OARSI Early-stage Symptomatic Knee Osteoarthritis (EsSKOA) initiative, we explored the first symptoms and experiences recalled by individuals with knee osteoarthritis (OA). Design: This qualitative study, informed by qualitative description, was a secondary analysis of focus groups (n â€‹= â€‹17 groups) and one-on-one interviews (n â€‹= â€‹3) conducted in 91 individuals living with knee OA as part of an international study to better understand the OA pain experience. In each focus group or interview, participants were asked to describe their first symptoms of knee OA. We inductively coded these transcripts and conducted thematic analysis. Results: Mean age of participants was 70 years (range 47-92) and 68 â€‹% were female. We developed four overarching themes: Insidious and Episodic Onset, Diverse Early Symptoms, Must be Something Else, and Adjustments. Participants described the gradual and intermittent way in which symptoms of knee OA developed over many years; many could not identify a specific starting point. Participants described diverse initial knee symptoms, including activity-exacerbated joint pain, stiffness and crepitus. Most participants dismissed early symptoms or rationalized their presence, employing various strategies to enable continued participation in recreational and daily activities. Few sought medical attention until physical functioning was demonstrably impacted. Conclusions: The earliest symptoms of knee OA are frequently insidious in onset, episodic and present long before individuals present to health professionals. These results highlight challenges to identifying people with knee OA early and support the development of specific classification criteria for EsSKOA to capture individuals at an early stage.

Absolute emission intensities of the gamma rays from the decay of 224Ra and 212Pb progenies and the half-life of the 212 Pb decay.

Absolute gamma-ray emission intensities for 36 characteristic gamma rays from the decay of 224Ra, 212Pb, and their progeny were determined by measuring sources calibrated for activity by means of primary methods based on well-defined high-purity germanium (HPGe) detectors at both NIST and NPL. Results from the two laboratories agree with recent data evaluations, except for gamma rays with low emission intensities. The decay schemes have been re-balanced based on the new results. In addition, the half-life for 212Pb was measured using several HPGe detectors, ionization chambers, and a well-type NaI(Tl) detector.

Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair.

Oncogene amplification on extrachromosomal DNA (ecDNA) is a pervasive driver event in cancer, yet our understanding of how ecDNA forms is limited. Here, we couple a CRISPR-based method for induction of ecDNA with extensive characterization of newly formed ecDNA to examine ecDNA biogenesis. We find that DNA circularization is efficient, irrespective of 3D genome context, with formation of a 1 Mb and 1.8 Mb ecDNA both reaching 15%. We show non-homologous end joining and microhomology mediated end joining both contribute to ecDNA formation, while inhibition of DNA-PKcs and ATM have opposing impacts on ecDNA formation. EcDNA and the corresponding chromosomal excision scar form at significantly different rates and respond differently to DNA-PKcs and ATM inhibition. Taken together, our results support a model of ecDNA formation in which double strand break ends dissociate from their legitimate ligation partners prior to joining of illegitimate ends to form the ecDNA and excision scar.

Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma.

Circular extrachromosomal DNA (ecDNA) in patient tumors is an important driver of oncogenic gene expression, evolution of drug resistance and poor patient outcomes. Applying computational methods for the detection and reconstruction of ecDNA across a retrospective cohort of 481 medulloblastoma tumors from 465 patients, we identify circular ecDNA in 82 patients (18%). Patients with ecDNA-positive medulloblastoma were more than twice as likely to relapse and three times as likely to die within 5 years of diagnosis. A subset of tumors harbored multiple ecDNA lineages, each containing distinct amplified oncogenes. Multimodal sequencing, imaging and CRISPR inhibition experiments in medulloblastoma models reveal intratumoral heterogeneity of ecDNA copy number per cell and frequent putative 'enhancer rewiring' events on ecDNA. This study reveals the frequency and diversity of ecDNA in medulloblastoma, stratified into molecular subgroups, and suggests copy number heterogeneity and enhancer rewiring as oncogenic features of ecDNA.

Evaluating the prospective utility of pharmacogenetics reporting among Canadian Armed Forces personnel receiving pharmacotherapy: a preliminary assessment towards precision psychiatric care.

Pharmacological interventions for treating posttraumatic stress disorder in Canadian Armed Forces (CAF) members and Veterans often achieve modest results. The field of pharmacogenetics, or the study of how genes influence an individual's response to different medications, offers insight into how prior knowledge of gene-drug interactions may potentially improve the trial-and-error process of drug selection in pharmacotherapy, thereby improving treatment effects and remission rates. Given the relative recency of pharmacogenetics testing and sparse research in military samples, we used pharmacogenetics testing in a small pilot group (n=23) of CAF members and Veterans who were already engaged in pharmacotherapy for a service-related mental health condition to better understand the associated opportunities and challenges of pharmacogenetics testing in this population. Our preliminary evaluation involved: (1) reporting the prevalence of pharmacogenetics testing 'bin' status according to participants' reports ('green', 'yellow' or 'red'; intending to signal 'go', 'caution' or 'stop', regarding the potential for gene-drug interactions); (2) calculating the percentage of currently prescribed psychotropic medications that were assessed and included in the reports; (3) evaluating whether prescribers used pharmacogenetics testing information according to clinical notes and (4) collecting informal feedback from participating psychiatrists. While pharmacogenetics testing appeared to provide valuable information for a number of clients, a major limitation was the number of commonly prescribed medications not included in the reports.

Coordinated inheritance of extrachromosomal DNA species in human cancer cells.

The chromosomal theory of inheritance has dominated human genetics, including cancer genetics. Genes on the same chromosome segregate together while genes on different chromosomes assort independently, providing a fundamental tenet of Mendelian inheritance. Extrachromosomal DNA (ecDNA) is a frequent event in cancer that drives oncogene amplification, dysregulated gene expression and intratumoral heterogeneity, including through random segregation during cell division. Distinct ecDNA sequences, herein termed ecDNA species, can co-exist to facilitate intermolecular cooperation in cancer cells. However, how multiple ecDNA species within a tumor cell are assorted and maintained across somatic cell generations to drive cancer cell evolution is not known. Here we show that cooperative ecDNA species can be coordinately inherited through mitotic co-segregation. Imaging and single-cell analyses show that multiple ecDNAs encoding distinct oncogenes co-occur and are correlated in copy number in human cancer cells. EcDNA species are coordinately segregated asymmetrically during mitosis, resulting in daughter cells with simultaneous copy number gains in multiple ecDNA species prior to any selection. Computational modeling reveals the quantitative principles of ecDNA co-segregation and co-selection, predicting their observed distributions in cancer cells. Finally, we show that coordinated inheritance of ecDNAs enables co-amplification of specialized ecDNAs containing only enhancer elements and guides therapeutic strategies to jointly deplete cooperating ecDNA oncogenes. Coordinated inheritance of ecDNAs confers stability to oncogene cooperation and novel gene regulatory circuits, allowing winning combinations of epigenetic states to be transmitted across cell generations.

Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells.

Extrachromosomal DNAs (ecDNAs) are common in cancer, but many questions about their origin, structural dynamics and impact on intratumor heterogeneity are still unresolved. Here we describe single-cell extrachromosomal circular DNA and transcriptome sequencing (scEC&T-seq), a method for parallel sequencing of circular DNAs and full-length mRNA from single cells. By applying scEC&T-seq to cancer cells, we describe intercellular differences in ecDNA content while investigating their structural heterogeneity and transcriptional impact. Oncogene-containing ecDNAs were clonally present in cancer cells and drove intercellular oncogene expression differences. In contrast, other small circular DNAs were exclusive to individual cells, indicating differences in their selection and propagation. Intercellular differences in ecDNA structure pointed to circular recombination as a mechanism of ecDNA evolution. These results demonstrate scEC&T-seq as an approach to systematically characterize both small and large circular DNA in cancer cells, which will facilitate the analysis of these DNA elements in cancer and beyond.

The AAV capsid can influence the epigenetic marking of rAAV delivered episomal genomes in a species dependent manner.

Recombinant adeno-associated viral vectors (rAAVs) are among the most commonly used vehicles for in vivo based gene therapies. However, it is hard to predict which AAV capsid will provide the most robust expression in human subjects due to the observed discordance in vector-mediated transduction between species. In our study, we use a primate specific capsid, AAV-LK03, to demonstrate that the limitation of this capsid towards transduction of mouse cells is unrelated to cell entry and nuclear transport but rather due to depleted histone H3 chemical modifications related to active transcription, namely H3K4me3 and H3K27ac, on the vector DNA itself. A single-amino acid insertion into the AAV-LK03 capsid enables efficient transduction and the accumulation of active-related epigenetic marks on the vector chromatin in mouse without compromising transduction efficiency in human cells. Our study suggests that the capsid protein itself is involved in driving the epigenetic status of the vector genome, most likely during the process of uncoating. Programming viral chromatin states by capsid design may enable facile DNA transduction between vector and host species and ultimately lead to rational selection of AAV capsids for use in humans.

Librarian and Researcher Assessments of Search Result Relevance: How Well Do They Align?

Conducting comprehensive but efficient literature searches for complex evidence syntheses involves selecting databases that will retrieve the greatest number of relevant results on the question. Lack of a comprehensive single database on allied health educational topics challenges those seeking such literature. In this study, six participants contributed research questions on instructional methods and materials for allied health patients, caregivers, and future health professionals. Two health sciences librarians created search strategies for these questions and searched eleven databases. Both the librarians and the six participants evaluated the search results using a rubric based on PICO to assess extent of alignment between the librarians' and requestors' relevance judgments. Intervention, Outcome, and Assessment Method constituted the most frequent bases for assessments of relevance by both librarians and participants. The librarians were more restrictive in all of their assessments except in a preliminary search yielding twelve citations without abstracts. The study's results could be used to identify effective techniques for reference interviewing, selecting databases, and weeding search results.

Physician's Knowledge and Practices Surrounding Low-Dose Aspirin for Preeclampsia Risk Reduction.

OBJECTIVE: Preeclampsia is a leading cause of pregnancy-related deaths. Up to 60% of maternal deaths associated with preeclampsia may be prevented. Clinical trials have shown that low-dose aspirin reduces preeclampsia up to 30% among women at increased risk. Since 2014, multiple professional societies and the U.S. Preventive Services Task Force have released guidelines on the use of low-dose aspirin to reduce the risk of preeclampsia. We aimed to evaluate physician's knowledge and practices surrounding low-dose aspirin for preeclampsia risk reduction. STUDY DESIGN: We distributed an anonymous electronic survey to licensed physicians in the Rio Grande Valley of Texas who provide prenatal care, including general obstetrician-gynecologists, maternal fetal medicine subspecialists, and family medicine physicians. The survey consisted of 20 items assessing demographics, provider practices, and knowledge on the use of low-dose aspirin for preeclampsia risk reduction. RESULTS: We received 48 surveys with a response rate of 55%. More than 90% of physicians reported recommending low-dose aspirin for preeclampsia risk reduction, of which 98% correctly identified the dose. Of the physicians recommending aspirin, 83% initiate dosing between 12 and 16 weeks, but only 52% continue it until the day of delivery. Nearly 80% of respondents identified that one high-risk factor for preeclampsia is an indication for prophylaxis, but only 56% identified that two or more moderate risk factors should prompt aspirin recommendation. CONCLUSION: Despite clear professional guidelines, physicians demonstrated gaps in knowledge and differences in practices. Enhancing screening tools to assess patient's risk of developing preeclampsia and tailored medical education on moderate risk factors are needed to identify patients who may benefit from this intervention. Increasing the use of aspirin in patients at risk is critical given the benefits of low-dose aspirin in the reduction of poor maternal and neonatal outcomes related to preeclampsia. KEY POINTS: · Low-dose aspirin reduces preeclampsia in patients up to 30%.. · Physicians have gaps in knowledge despite guidelines.. · Following guidelines reduces poor outcomes associated with preeclampsia..

TURN-IT: a novel turning intervention program to improve quality of turning in daily life in people with Parkinson's disease.

BACKGROUND: People with Parkinson's disease (PD) have a high fall rate and many falls are associated with turns. Despite this, there is minimal research on effects of rehabilitation on the quality of turns. Further, quantifying turns in the home may have broader implications since rehabilitation of turns would ideally improve turning in real world mobility. METHODS: Sixty people with PD and a history of falls will be randomized to receive either a novel TURNing InTervention (TURN-IT) or no intervention (control group). The TURN-IT group will be seen for 6 weeks (18 visits) for an individualized, progressive program that is based on the specific constraints of turning in PD. Wearable sensors will be used to measure 7 days of mobility, including turns, before and after intervention or control period. In addition, blinded assessments of gait, mobility and turns will occur before and after intervention for both groups and falls will be monitored for twelve months post intervention with bimonthly email questionnaires. DISCUSSION: This study has the potential to change how we rehabilitate and assess turning in people with PD and falls. There are several novel aspects to our study including a comprehensive turning-focused intervention that is tailored to the underlying constraints that impair turning in people with PD. Further, our outcome measure of turning quality during 7 days of daily life is novel and has implications for determining real-life changes after rehabilitation. The ultimate goal of this rehabilitation intervention is to improve how patients turn in daily life and to reduce falls. TRIALS REGISTRATION: This protocol is registered at clinicaltrials.gov; #NCT04897256; https://clinicaltrials.gov/ct2/show/NCT04897256?term=Horak&cond=Parkinson+Disease&draw=2&rank=4 .

Ex vivo engineered human plasma cells exhibit robust protein secretion and long-term engraftment in vivo.

Due to their unique longevity and capacity to secrete high levels of protein, plasma B cells have the potential to be used as a cell therapy for protein replacement. Here, we show that ex vivo engineered human plasma cells exhibit single-cell RNA profiles, scanning electron micrograph ultrastructural features, and in vivo homing capacity of long-lived plasma cells. After transferring human plasma cells to immunodeficient mice in the presence of the human cytokines BAFF and IL-6, we observe increases in retention of plasma cells in the bone marrow, with engraftment exceeding a year. The most profound in vivo effects of human IL-6 are observed within 20 days of transfer and could be explained by decreased apoptosis in newly differentiated plasma cells. Collectively, these results show that ex vivo engineered and differentiated human plasma cells have the potential for long-lived in vivo protein secretion, which can be modeled in small animals.

Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH.

Extrachromosomal DNA (ecDNA) is a common mode of oncogene amplification but is challenging to analyze. Here, we adapt CRISPR-CATCH, in vitro CRISPR-Cas9 treatment and pulsed field gel electrophoresis of agarose-entrapped genomic DNA, previously developed for bacterial chromosome segments, to isolate megabase-sized human ecDNAs. We demonstrate strong enrichment of ecDNA molecules containing EGFR, FGFR2 and MYC from human cancer cells and NRAS ecDNA from human metastatic melanoma with acquired therapeutic resistance. Targeted enrichment of ecDNA versus chromosomal DNA enabled phasing of genetic variants, identified the presence of an EGFRvIII mutation exclusively on ecDNAs and supported an excision model of ecDNA genesis in a glioblastoma model. CRISPR-CATCH followed by nanopore sequencing enabled single-molecule ecDNA methylation profiling and revealed hypomethylation of the EGFR promoter on ecDNAs. We distinguished heterogeneous ecDNA species within the same sample by size and sequence with base-pair resolution and discovered functionally specialized ecDNAs that amplify select enhancers or oncogene-coding sequences.

Prevalence and correlates of stocking up on drugs during the COVID-19 pandemic: Data from the C3PNO Consortium.

BACKGROUND: Data from the COVID-19 pandemic describes increases in drug use and related harms, especially fatal overdose. However, evidence is needed to better understand the pathways from pandemic-related factors to substance use behaviours. Thus, we investigated stockpiling drugs among people who use drugs (PWUD) in five cities in the United States and Canada. METHODS: We used data from two waves of interviews among participants in nine prospective cohorts to estimate the prevalence and correlates of stockpiling drugs in the previous month. Longitudinal correlates were identified using bivariate and multivariate generalized linear mixed-effects modeling analyses. RESULTS: From May 2020 to February 2021, we recruited 1873 individuals who completed 2242 interviews, of whom 217 (11.6%) reported stockpiling drugs in the last month at baseline. In the multivariate model, stockpiling drugs was significantly and positively associated with reporting being greatly impacted by COVID-19 (Adjusted Odds Ratio [AOR]= 1.21, 95% CI: 1.09-1.45), and at least daily use of methamphetamine (AOR = 4.67, 95% CI: 2.75-7.94) in the past month. CONCLUSIONS: We observed that approximately one-in-ten participants reported stocking up on drugs during the COVID-19 pandemic. This behaviour was associated with important drug-related risk factors including high-intensity methamphetamine use. While these correlations need further inquiry, it is possible that addressing the impact of COVID-19 on vulnerable PWUD could help limit drug stockpiling, which may lower rates of high-intensity stimulant use.