Rare coding variant analysis for human diseases across biobanks and ancestries.

Large-scale sequencing has enabled unparalleled opportunities to investigate the role of rare coding variation in human phenotypic variability. Here, we present a pan-ancestry analysis of sequencing data from three large biobanks, including the All of Us research program. Using mixed-effects models, we performed gene-based rare variant testing for 601 diseases across 748,879 individuals, including 155,236 with ancestry dissimilar to European. We identified 363 significant associations, which highlighted core genes for the human disease phenome and identified potential novel associations, including UBR3 for cardiometabolic disease and YLPM1 for psychiatric disease. Pan-ancestry burden testing represented an inclusive and useful approach for discovery in diverse datasets, although we also highlight the importance of ancestry-specific sensitivity analyses in this setting. Finally, we found that effect sizes for rare protein-disrupting variants were concordant between samples similar to European ancestry and other genetic ancestries (ßDeming = 0.7-1.0). Our results have implications for multi-ancestry and cross-biobank approaches in sequencing association studies for human disease.

A simple technique for percutaneous antegrade retrieval of proximally migrated double J stents after pyeloplasty in infants.

Proximal migration of double J (DJ) stent after pyeloplasty poses a difficult problem in infants whose small ureter renders retrograde ureteroscopic retrieval difficult. Previously described antegrade techniques used large access sheaths or blind removal under fluoroscopic guidance. We describe a technique for antegrade retrieval of the stent under direct vision. A 8F vascular access sheath is placed into the renal pelvis under ultrasound guidance. A 6F nephroscope with 3F forceps placed through the sheath grasps and retrieves the stent under direct visualization. This technique is simple, quick, avoids radiation exposure and was used by us successfully in 2 small infants.

Epidemiology and Management of Pediatric Fractures in Malawi.

BACKGROUND: Pediatric fractures are common in Malawi, and surgical care, when needed, remains inaccessible to many. Understanding which children in Malawi receive surgery or nonsurgical treatment would help set priorities for trauma system development. METHODS: We used multivariate logistic regression to evaluate associations between surgical treatment and age, sex, school enrollment, injury mechanism, fracture type, open fracture, referral status, hospital of presentation, delayed presentation (≥2 days), healthcare provider, and inpatient vs outpatient treatment. RESULTS: From 2016 to 2020, 10,400 pediatric fractures were recorded in the Malawi Fracture Registry. Fractures were most commonly of the wrist (26%), forearm (17%), and elbow (14%). Surgical fixation was performed on 4.0% of patients, and 24 (13.0%) open fractures were treated nonsurgically, without débridement or fixation. Fractures of the proximal and diaphyseal humerus (odds ratio [OR], 3.72; 95% confidence interval [CI], 2.36 to 5.87), knee (OR, 3.16; 95% CI, 1.68 to 5.95), and ankle (OR, 2.63; 95% CI, 1.49 to 4.63) had highest odds of surgery. Odds of surgical treatment were lower for children referred from another facility (OR, 0.62; 95% CI, 0.49 to 0.77). CONCLUSIONS: Most Malawian children with fractures are treated nonsurgically, including many who may benefit from surgery. There is a need to increase surgical capacity, optimize referral patterns, and standardize fracture management in Malawi.

Contractile vacuoles: a rapidly expanding (and occasionally diminishing?) understanding.

Osmoregulation is the homeostatic mechanism essential for the survival of organisms in hypoosmotic and hyperosmotic conditions. In freshwater or soil dwelling protists this is frequently achieved through the action of an osmoregulatory organelle, the contractile vacuole. This endomembrane organelle responds to the osmotic challenges and compensates by collecting and expelling the excess water to maintain the cellular osmolarity. As compared with other endomembrane organelles, this organelle is underappreciated and under-studied. Here we review the reported presence or absence of contractile vacuoles across eukaryotic diversity, as well as the observed variability in the structure, function, and molecular machinery of this organelle. Our findings highlight the challenges and opportunities for constructing cellular and evolutionary models for this intriguing organelle.

Open Exploration and Reduction of Paediatric Supracondylar Humerus Fracture with Pink, Pulseless Hand in Resource-Limited Settings.

Background: Supracondylar humerus fractures (SHFs) are common paediatric injuries, with high risk of vascular compromise. Some patients present with a 'pink, pulseless hand', caused by occlusion of brachial artery flow but with collateral circulation preserving distal perfusion. Management of these patients remains controversial, especially when resources may be limited for prolonged hospitalisation and serial monitoring by skilled staff. The aim of this study is to present the intraoperative findings, surgical procedures done and outcomes at 6 weeks for patients with paediatric supracondylar fractures with a pink pulseless hand. Methods: We retrospectively identified 13 patients who presented to a public hospital between January 2019 and May 2023 with a displaced SHF and pink, pulseless hand. All patients underwent an open reduction with an anterior approach allowing for exploration, protection and repair of neurovascular structures. Distal flow was restored in the brachial artery either with topical lidocaine application, thrombectomy or artery reconstruction. Results: Out of 13 patients, all had intact median nerves and 10 had intact arteries (69%), of which seven were interposed at the fracture site and four were in vasospasm. Of the three patients with true arterial injury (23%), two had a crushed artery and one had thrombosis of the artery. Peripheral pulses were restored within an hour of fracture open reduction in all patients. At final follow-up, a mean 6 weeks postoperatively, all patients had recovered without neurovascular deficit, compartment syndrome or Volkmann ischemic contracture. Conclusions: In resource-limited settings, we recommend performing open exploration and reduction for patients with SHFs with pink, pulseless hand. This approach prevents iatrogenic neurovascular injury during closed reduction attempts, allows for immediate repair of a brachial artery injury and avoids unnecessary hospitalisation and serial monitoring. Level of Evidence: Level IV (Therapeutic).

Sex differences in physiological response to increased neuronal excitability in a knockin mouse model of pediatric epilepsy.

BACKGROUND: Epilepsy is a common neurological disease; however, few if any of the currently marketed antiseizure medications prevent or cure epilepsy. Discovery of pathological processes in the early stages of epileptogenesis has been challenging given the common use of preclinical models that induce seizures in physiologically normal animals. Moreover, despite known sex dimorphism in neurological diseases, females are rarely included in preclinical epilepsy models. METHODS: We characterized sex differences in mice carrying a pathogenic knockin variant (p.N1768D) in the Scn8a gene that causes spontaneous tonic-clonic seizures (TCs) at ∼3 months of age and found that heterozygous females are more resilient than males in mortality and morbidity. To investigate the cellular mechanisms that underlie female resilience, we utilized blood-brain barrier (BBB) and hippocampal transcriptomic analyses in heterozygous mice before seizure onset (pre-TC) and in mice that experienced ∼20 TCs (post-TC). RESULTS: In the pre-TC latent phase, both sexes exhibited leaky BBB; however, patterns of gene expression were sexually dimorphic. Females exhibited enhanced oxidative phosphorylation and protein biogenesis, while males activated gliosis and CREB signaling. After seizure onset (chronic phase), females exhibited a metabolic switch to lipid metabolism, while males exhibited increased gliosis and BBB dysfunction and a strong activation of neuroinflammatory pathways. CONCLUSION: The results underscore the central role of oxidative stress and BBB permeability in the early stages of epileptogenesis, as well as sex dimorphism in response to increasing neuronal hyperexcitability. Our results also highlight the need to include both sexes in preclinical studies to effectively translate results of drug efficacy studies.

Purification of retinal ganglion cells using low-pressure flow cytometry.

Purified Retinal Ganglion Cells (RGCs) for in vitro study have been a valuable tool in the study of neural regeneration and in the development of therapies to treat glaucoma. Traditionally, RGCs have been isolated from early postnatal rats and mice, and more recently from human in vitro derived retinal organoids using a two-step immunopanning technique based upon the expression of Thy-1. This technique, however, limits the time periods from which RGCs can be isolated, missing the earliest born RGCs at which time the greatest stage of axon growth occurs, as well as being limited in its use with models of retinal degeneration as Thy-1 is downregulated following injury. While fluorescence associated cell sorting (FACS) in combination with new optogenetically labeled RGCs would be able to overcome this limitation, the use of traditional FACS sorters has been limited to genomic and proteomic studies, as RGCs have little to no survival post-sorting. Here we describe a new method for RGC isolation utilizing a combined immunopanning-fluorescence associated cell sorting (IP-FACS) protocol that initially depletes macrophages and photoreceptors, using immunopanning to enrich for RGCs before using low-pressure FACS to isolate these cells. We demonstrate that RGCs isolated via IP-FACS when compared to RGCs isolated via immunopanning at the same age have similar purity as measured by antibody staining and qRT-PCR; survival as measured by live dead staining; neurite outgrowth; and electrophysiological properties as measured by calcium release response to glutamate. Finally, we demonstrate the ability to isolate RGCs from early embryonic mice prior to the expression of Thy-1 using Brn3b-eGFP optogenetically labeled cells. This method provides a new approach for the isolation of RGCs for the study of early developed RGCs, the study of RGC subtypes and the isolation of RGCs for cell transplantation studies.

Purification of Retinal Ganglion Cells from Differentiation Through Adult via Immunopanning and Low-Pressure Flow Cytometry.

The isolation and culturing of rodent retinal ganglion cells (RGC) is a key step in studying the function and cellular response of this crucial cell type. Typical methods used for isolation of RGCs include immunopanning or magnetic bead separation with antibodies targeting RGC specific protein markers. However, in developmental research, many of the most common markers, such as Thy-1, are not expressed in early stages of development. To help study these crucial early stage RGCs, we have developed a novel method that utilizes a transgenic mouse with a GFP tag on the protein BRN3 and a low-pressure fluorescence-activated cell sorter (FACS) system.

High-normal versus low-normal mean arterial pressure thresholds in critically ill patients: a systematic review and meta-analysis of randomized trials.

PURPOSE: Targeted blood pressure thresholds remain unclear in critically ill patients. Two prior systematic reviews have not shown differences in mortality with a high mean arterial pressure (MAP) threshold, but there have been new studies published since. Thus, we conducted an updated systematic review and meta-analysis of randomized controlled trials (RCTs) that compared the effect of a high-normal vs low-normal MAP on mortality, favourable neurologic outcome, need for renal replacement therapy, and adverse vasopressor-induced events in critically ill patients. SOURCE: We searched six databases from inception until 1 October 2022 for RCTs of critically ill patients targeted to either a high-normal vs a low-normal MAP threshold for at least 24 hr. We assessed study quality using the revised Cochrane risk-of-bias 2 tool and the risk ratio (RR) was used as the summary measure of association. We used the Grading of Recommendations Assessment, Development, and Evaluation framework to assess the certainty of evidence. PRINCIPAL FINDINGS: We included eight RCTs with 4,561 patients. Four trials were conducted in patients following out-of-hospital cardiac arrest, two in patients with distributive shock requiring vasopressors, one in patients with septic shock, and one in patients with hepatorenal syndrome. The pooled RRs for mortality (eight RCTs; 4,439 patients) and favourable neurologic outcome (four RCTs; 1,065 patients) were 1.06 (95% confidence interval [CI], 0.99 to 1.14; moderate certainty) and 0.99 (95% CI, 0.90 to 1.08; moderate certainty), respectively. The RR for the need for renal replacement therapy (four RCTs; 4,071 patients) was 0.97 (95% CI, 0.87 to 1.08; moderate certainty). There was no statistical between-study heterogeneity across all outcomes. CONCLUSION: This updated systematic review and meta-analysis of RCTs found no differences in mortality, favourable neurologic outcome, or the need for renal replacement therapy between critically ill patients assigned to a high-normal vs low-normal MAP target. STUDY REGISTRATION: PROSPERO (CRD42022307601); registered 28 February 2022.

RéSUMé: OBJECTIF: Les seuils de pression artérielle ciblés demeurent incertains chez les patient·es gravement malades. Deux revues systématiques antérieures n'ont pas montré de différences dans la mortalité avec un seuil élevé de pression artérielle moyenne (PAM), mais de nouvelles études ont été publiées depuis. Pour cette raison, nous avons réalisé une revue systématique mise à jour et une méta-analyse d'études randomisées contrôlées (ERC) comparant l'effet d'une PAM normale élevée vs normale faible sur la mortalité, les devenirs neurologiques favorables, la nécessité d'un traitement substitutif de l'insuffisance rénale et les événements indésirables induits par les vasopresseurs chez les patient·es gravement malades. SOURCES: Nous avons effectué des recherches dans six bases de données depuis leur création jusqu'au 1er octobre 2022 pour trouver des ERC portant sur des patient·es gravement malades chez lesquel·les un seuil de PAM normale élevée ou normale faible a été ciblé pendant au moins 24 heures. Nous avons évalué la qualité des études à l'aide de l'outil de risque de biais 2 révisé de Cochrane, et le risque relatif (RR) a été utilisé comme mesure sommaire de l'association. Nous avons utilisé le système de notation GRADE (Grading of Recommendations Assessment, Development, and Evaluation) pour évaluer la certitude des données probantes. CONSTATATIONS PRINCIPALES: Nous avons inclus huit ERC portant sur 4561 personnes traitées. Quatre études ont été menées chez des patient·es à la suite d'un arrêt cardiaque hors de l'hôpital, deux chez des patient·es présentant un choc distributif nécessitant des vasopresseurs, une chez des patient·es présentant un choc septique et une chez des patient·es atteint·es d'un syndrome hépato-rénal. Les RR combinés pour la mortalité (huit ERC; 4439 personnes) et les devenirs neurologiques favorables (quatre ERC; 1065 personnes) étaient respectivement de 1,06 (intervalle de confiance [IC] à 95 %, 0,99 à 1,14; certitude modérée) et de 0,99 (IC 95 %, 0,90 à 1,08; certitude modérée). Le RR pour le besoin de traitement substitutif de l'insuffisance rénale (quatre ERC; 4071 patient·es) était de 0,97 (IC 95 %, 0,87 à 1,08; certitude modérée). Il n'y avait pas d'hétérogénéité statistique entre les études pour tous les critères d'évaluation. CONCLUSION: Ces revue systématique et méta-analyse mises à jour des ERC n'ont révélé aucune différence dans la mortalité, les devenirs neurologiques favorables ou la nécessité d'un traitement substitutif de l'insuffisance rénale entre les patient·es gravement malades assigné·es à une cible de PAM normale élevée vs normale faible. ENREGISTREMENT DE L'éTUDE: PROSPERO (CRD42022307601); enregistrée le 28 février 2022.

Mobilizing registry data for quality improvement: A convergent mixed-methods analysis and application to spinal cord injury.

Introduction: The rising prevalence of complex chronic conditions and growing intricacies of healthcare systems emphasizes the need for interdisciplinary partnerships to advance coordination and quality of rehabilitation care. Registry databases are increasingly used for clinical monitoring and quality improvement (QI) of health system change. Currently, it is unclear how interdisciplinary partnerships can best mobilize registry data to support QI across care settings for complex chronic conditions. Purpose: We employed spinal cord injury (SCI) as a case study of a highly disruptive and debilitating complex chronic condition, with existing registry data that is underutilized for QI. We aimed to compare and converge evidence from previous reports and multi-disciplinary experts in order to outline the major elements of a strategy to effectively mobilize registry data for QI of care for complex chronic conditions. Methods: This study used a convergent parallel-database variant mixed design, whereby findings from a systematic review and a qualitative exploration were analyzed independently and then simultaneously. The scoping review used a three-stage process to review 282 records, which resulted in 28 articles reviewed for analysis. Concurrent interviews were conducted with multidisciplinary-stakeholders, including leadership from condition-specific national registries, members of national SCI communities, leadership from SCI community organizations, and a person with lived experience of SCI. Descriptive analysis was used for the scoping review and qualitative description for stakeholder interviews. Results: There were 28 articles included in the scoping review and 11 multidisciplinary-stakeholders in the semi-structured interviews. The integration of the results allowed the identification of three key learnings to enhance the successful design and use of registry data to inform the planning and development of a QI initiative: enhance utility and reliability of registry data; form a steering committee lead by clinical champions; and design effective, feasible, and sustainable QI initiatives. Conclusion: This study highlights the importance of interdisciplinary partnerships to support QI of care for persons with complex conditions. It provides practical strategies to determine mutual priorities that promote implementation and sustained use of registry data to inform QI. Learnings from this work could enhance interdisciplinary collaboration to support QI of care for rehabilitation for persons with complex chronic conditions.

Clinical and genetic associations of deep learning-derived cardiac magnetic resonance-based left ventricular mass.

Left ventricular mass is a risk marker for cardiovascular events, and may indicate an underlying cardiomyopathy. Cardiac magnetic resonance is the gold-standard for left ventricular mass estimation, but is challenging to obtain at scale. Here, we use deep learning to enable genome-wide association study of cardiac magnetic resonance-derived left ventricular mass indexed to body surface area within 43,230 UK Biobank participants. We identify 12 genome-wide associations (1 known at TTN and 11 novel for left ventricular mass), implicating genes previously associated with cardiac contractility and cardiomyopathy. Cardiac magnetic resonance-derived indexed left ventricular mass is associated with incident dilated and hypertrophic cardiomyopathies, and implantable cardioverter-defibrillator implant. An indexed left ventricular mass polygenic risk score ≥90th percentile is also associated with incident implantable cardioverter-defibrillator implant in separate UK Biobank (hazard ratio 1.22, 95% CI 1.05-1.44) and Mass General Brigham (hazard ratio 1.75, 95% CI 1.12-2.74) samples. Here, we perform a genome-wide association study of cardiac magnetic resonance-derived indexed left ventricular mass to identify 11 novel variants and demonstrate that cardiac magnetic resonance-derived and genetically predicted indexed left ventricular mass are associated with incident cardiomyopathy.

Emergence of a novel genotype of class II New Castle Disease virus in North Eastern States of India.

Outbreaks of New Castle Disease from three north eastern states of India were confirmed by clinico-pathological examination followed by reverse transcription-PCR detection of F gene of ND Virus (NDV). Irrespective of vaccination, the outbreaks resulted 90-100% mortality in the affected flocks. The analysis of fusion protein sequences from ten field isolates revealed them as the velogenic or highly virulent strain. Phylogenetic analyses based on the complete F gene nucleotide sequences of the isolates have characterized only one of the isolate (OK149201) in the genotype XIII.2.2. The rest of the nine isolates are depicted in a distinct monophyletic group with average nucleotide distances from the other 20 genotypes ranged from 10.90 - 20.70. The nine isolates were further divided into two sub branches with the bootstrap support value of 100% at the nodes that define the two subgroups with an average evolutionary nucleotide distance of 6.00between the isolates in the two subgroups. As per the recommendation put forth in recently updated unified phylogenetic classification system for NDV, our findings clearly indicates emergence of a novel genotype of class II NDV in the biodiversity hot spot region of NER, India. The isolates in the newly identified genotype is designated with next available Roman numerals XXII. Further, the two subgroups within the genotype are designated as XXII.1 and XXII.2.

The Socioeconomic consequences of femoral shaft fracture for patients in Malawi.

Background: Femoral shaft fractures are common in Malawi, with an annual incidence of 44 per 100,000 people. Inadequate treatment and delayed presentation often result in functional, biopsychosocial, and financial challenges for patients. The purpose of this study was to examine the socioeconomic consequences of femoral shaft fractures for patients in Malawi. Methods: This study of 42 patients was part of a larger study that prospectively examined quality of life. Questionnaires were distributed to patients at 1-year follow-up following femoral shaft fracture treatment. Patients reported pre- and post-injury standard of living and financial well-being. Results: Patients reported relatively high transportation costs to and from the hospital. One year after injury, 17 patients (40%) had not returned to work. Of the 25 (60%) who had returned, 5 (20%) changed jobs due to their injury, all reported decreased productivity. Household income decreased for 29% of patients. 20 (49%) of 41 patients reported food insecurity in the week prior to questionnaire completion. Many patients reported changing their residence, borrowing money, selling personal property, and unenrolling children from school due to financial hardship caused by their injury. Conclusion: While the Malawian public healthcare system is free at the point of care, it lacks the financial risk protection that is essential to universal health coverage (UHC). In this study, we found that the indirect costs of care due to femoral shaft fractures had substantial socioeconomic consequences on the majority of patients and their families. Increased investment of financial and human capital should be made into capacity building and preventative measures to decrease the burden of injury, increase access to care, improve care delivery, and provide financial risk protection for patients with traumatic injuries in Malawi.

A comparative study on COVID-19 disease severity and outcome among patients admitted before and after vaccination at tertiary care hospital.

Background: Coronavirus disease 2019 (COVID-19) is a novel infectious disease caused by SARS CoV-2 that emerged in Wuhan, China, and has rapidly spread worldwide. The mortality rate of critically ill COVID-19 patients is high. The objective of the study was to assess the COVID-19 disease severity and outcome among COVID-19 positive patients admitted before and after vaccination. Methodology: A prospective observational study conducted among all patients aged more than 18 years were included in the study. The patients who were positive before vaccination and received at least one dose of vaccine and positive after receiving two doses of vaccination included in the study. Disease severity was assessed in terms of high-resolution computed tomography (HRCT) score, intensive care unit (ICU) admission, SpO2 maintained, oxygen, plasma exchange, steroids received and on mechanical ventilation, and outcome was assessed on prognosis and stabilized/discharged to home. Results: A total of 172 were participated in the study with 101 (58.7%) males and 71 (41.3) females, respectively. Amongst them, 92 were affected before vaccination and 80 were affected before vaccination. The patients admitted in the ICU were 56 (32.6%) and 116 (67.4%) were not admitted in the ICU; among the patient admitted in ICU 42 (45.7%) before vaccination, and 14 (17.5%) were after vaccination, and difference was statistically significant with P- value <0.001. SPO2, steroids given, plasma exchange, oxygen >10 litres given and mechanical ventilation were positively associated with the vaccine received and disease severity with P- value <0.05. Conclusion: The severe COVID-19 had the worst outcome in the unvaccinated patients in terms of severity. Most partially vaccinated patients got infected before developing immunity; receiving at least one vaccination dose significantly reduced illness severity.

Genome-wide association and multi-trait analyses characterize the common genetic architecture of heart failure.

Heart failure is a leading cause of cardiovascular morbidity and mortality. However, the contribution of common genetic variation to heart failure risk has not been fully elucidated, particularly in comparison to other common cardiometabolic traits. We report a multi-ancestry genome-wide association study meta-analysis of all-cause heart failure including up to 115,150 cases and 1,550,331 controls of diverse genetic ancestry, identifying 47 risk loci. We also perform multivariate genome-wide association studies that integrate heart failure with related cardiac magnetic resonance imaging endophenotypes, identifying 61 risk loci. Gene-prioritization analyses including colocalization and transcriptome-wide association studies identify known and previously unreported candidate cardiomyopathy genes and cellular processes, which we validate in gene-expression profiling of failing and healthy human hearts. Colocalization, gene expression profiling, and Mendelian randomization provide convergent evidence for the roles of BCKDHA and circulating branch-chain amino acids in heart failure and cardiac structure. Finally, proteome-wide Mendelian randomization identifies 9 circulating proteins associated with heart failure or quantitative imaging traits. These analyses highlight similarities and differences among heart failure and associated cardiovascular imaging endophenotypes, implicate common genetic variation in the pathogenesis of heart failure, and identify circulating proteins that may represent cardiomyopathy treatment targets.

Economic burden of chronic pain in Alberta, Canada.

BACKGROUND: Although chronic pain (CP) is common, little is known about its economic burden in Alberta, Canada. AIMS: To estimate incremental (as compared to the general population or people without CP) societal (healthcare and lost productivity) costs of CP in Alberta. METHODS: We applied the prevalence estimated from the Canadian Community Health Survey data to the population retrieved from the Statistics Canada to estimate the number of people with CP in Alberta in 2019. We analyzed the Alberta Health administrative databases to estimate the healthcare costs of person with CP. Finally, we multiplied the number of people with the cost per person. RESULTS: The prevalence of any CP was 20.1% and of activity-preventing CP was 14.5% among people aged > = 12 years. Incremental cost per person with CP per year was CA$2,217 for healthcare services (among people aged > = 12 years) and CA$8,412 for productivity losses (among people aged 18-64 years). Of the healthcare cost, prescription drugs accounted for the largest share (32.8%), followed by inpatient services (31.0%), outpatient services (13.1%), physician services (9.8%), other services (7.4%), and diagnostic imaging (5.8%). Provincially, total incremental cost of CP ranges from CA$1.2 to 1.7 billion for healthcare services (6% to 8% of total provincial health expenditure); and CA$3.4 to 4.7 billion for productivity losses. Considering costs for long-term care services, the total societal cost of CP in Alberta was CA$6.3 to 8.3 billion per year, reflecting 2.0% to 2.7% of Alberta's GDP. CONCLUSIONS: Interventions improving CP prevention and management to reduce this substantial economic burden are urgently needed.