Polygenic architecture of rare coding variation across 394,783 exomes.

Both common and rare genetic variants influence complex traits and common diseases. Genome-wide association studies have identified thousands of common-variant associations, and more recently, large-scale exome sequencing studies have identified rare-variant associations in hundreds of genes1-3. However, rare-variant genetic architecture is not well characterized, and the relationship between common-variant and rare-variant architecture is unclear4. Here we quantify the heritability explained by the gene-wise burden of rare coding variants across 22 common traits and diseases in 394,783 UK Biobank exomes5. Rare coding variants (allele frequency < 1 × 10-3) explain 1.3% (s.e. = 0.03%) of phenotypic variance on average-much less than common variants-and most burden heritability is explained by ultrarare loss-of-function variants (allele frequency < 1 × 10-5). Common and rare variants implicate the same cell types, with similar enrichments, and they have pleiotropic effects on the same pairs of traits, with similar genetic correlations. They partially colocalize at individual genes and loci, but not to the same extent: burden heritability is strongly concentrated in significant genes, while common-variant heritability is more polygenic, and burden heritability is also more strongly concentrated in constrained genes. Finally, we find that burden heritability for schizophrenia and bipolar disorder6,7 is approximately 2%. Our results indicate that rare coding variants will implicate a tractable number of large-effect genes, that common and rare associations are mechanistically convergent, and that rare coding variants will contribute only modestly to missing heritability and population risk stratification.

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets.

COVID-19, which is caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple organ failure1-4, but little is known about its pathophysiology. Here we generated single-cell atlases of 24 lung, 16 kidney, 16 liver and 19 heart autopsy tissue samples and spatial atlases of 14 lung samples from donors who died of COVID-19. Integrated computational analysis uncovered substantial remodelling in the lung epithelial, immune and stromal compartments, with evidence of multiple paths of failed tissue regeneration, including defective alveolar type 2 differentiation and expansion of fibroblasts and putative TP63+ intrapulmonary basal-like progenitor cells. Viral RNAs were enriched in mononuclear phagocytic and endothelial lung cells, which induced specific host programs. Spatial analysis in lung distinguished inflammatory host responses in lung regions with and without viral RNA. Analysis of the other tissue atlases showed transcriptional alterations in multiple cell types in heart tissue from donors with COVID-19, and mapped cell types and genes implicated with disease severity based on COVID-19 genome-wide association studies. Our foundational dataset elucidates the biological effect of severe SARS-CoV-2 infection across the body, a key step towards new treatments.

Peripheral T-cell lymphomas expressing CD30 and CD15 expand the spectrum of anaplastic large cell lymphoma, ALK-negative.

Peripheral T-cell lymphomas (PTCL) are morphologically and biologically heterogeneous and a subset expresses CD30, including anaplastic large cell lymphomas (ALCL) and a minority of PTCL, not otherwise specified (PTCL, NOS). ALCL with ALK translocations (ALCL, ALK+) are readily identified by routine diagnostic methods, but differentiating ALCL without ALK translocation (ALCL, ALK-) and PTCL, NOS expressing CD30 (PTCL CD30+) can be challenging. Furthermore, rare PTCL co-express CD30 and CD15 (PTCL CD30+CD15+); some resemble ALCL, ALK- while others resemble classic Hodgkin lymphoma. To explore the relationship between PTCL CD30+CD15+ and ALCL, ALK-, we analysed 19 cases of PTCL with CD30 expression, previously diagnosed as ALCL, ALK- (nine cases) and PTCL CD30+CD15+ (10 cases) for DUSP22/IRF4 rearrangements, coding RNA expression and selected transcriptome analysis using the NanoString nCounter gene expression analysis platform. Unsupervised clustering showed no clear segregation between ALCL, ALK- and PTCL CD30+CD15+. Three cases previously classified as PTCL CD30+CD15+ showed DUSP22/IRF4 rearrangements, favouring a diagnosis of ALCL, ALK-. Our results suggest that cases previously designated PTCL CD30+CD15+, likely fall within the spectrum of ALCL, ALK-; additionally, a subset of ALCL, ALK- with DUSP22/IRF4 rearrangement expresses CD15, consistent with previous reports and expands the immunophenotypic spectrum of this lymphoma subgroup.

One-pot synthesis of g-C3N4/N-doped CeO2 nanocomposites and their potential visible light-driven photocatalytic degradation of methylene blue dye.

In the pursuit of efficient photocatalytic materials for environmental applications, a new series of g-C3N4/N-doped CeO2 nanocomposites (g-C3N4/N-CeO2 NCs) was synthesized using a straightforward dispersion method. These nanocomposites were systematically characterized to understand their structural, optical, and chemical properties. The photocatalytic performance of g-C3N4/N-CeO2 NCs was evaluated by investigating their ability to degrade methylene blue (MB) dye, a model organic pollutant. The results demonstrate that the integration of g-C3N4 with N-doped CeO2 NCs reduces the optical energy gap compared to pristine N-doped CeO2, leading to enhanced photocatalytic efficiency. It is benefited from the existence of g-C3N4/N-CeO2 NCs not only in promoting the charge separation and inhibits the fast charge recombination but also in improving photocatalytic oxidation performance. Hence, this study highlights the potential of g-C3N4/N-CeO2 NCs as promising candidates for various photocatalytic applications, contributing to the advancement of sustainable environmental remediation technologies.

Institutional end-of-life care policy for inpatients at a tertiary care centre in India: A way forward to provide a system for a dignified death.

India has a high share in the global burden of chronic terminal illnesses. However, there is a lack of a uniform system in providing better end-of-life care (EOLC) for large patients in their terminal stage of life. Institutional policies can be a good alternative as there is no national level policy for EOLC. This article describes the important aspects of the EOLC policy at one of the tertiary care institutes of India. A 15 member institutional committee including representatives from various departments was formed to develop this institutional policy. This policy document is aimed at helping to recognize the potentially non-beneficial or harmful treatments and provide transparency and accountability of the process of limitation of treatment through proper documentation that closely reflects the Indian legal viewpoint on this matter. Four steps are proposed in this direction: (i) recognition of a potentially non-beneficial or harmful treatment by the physicians, (ii) consensus among all the caregivers on a potentially non-beneficial or harmful treatment and initiation of the best supportive care pathway, (iii) initiation of EOLC pathways, and (iv) symptom management and ongoing supportive care till death. The article also focuses on the step-by-step process of formulation of this institutional policy, so that it can work as a blueprint for other institutions of our country to identify the infrastructural needs and resources and to formulate their own policies.

Anterolateral thigh osteomyocutaneous flap in head and neck: Lessons learned.

BACKGROUND: Concerns regarding iatrogenic femur fracture may deter adoption of the anterolateral thigh osteomyocutaneous (ALTO) flap as an alternative reconstructive technique for large composite defects of the head and neck. We describe the evolution of our experience with this flap and the lessons learned in femur management. METHODS: Records from a prospective database (July 2009-January 2020) were reviewed to identify patients with composite osseous free tissue reconstructions. Venous thromboembolic events (VTE), femur fracture, estimated blood loss (EBL), procedure time, blood transfusions, and length of stay (days) were compared for ALTO flaps prior to and after the adoption of intramedullary fixation protocol. RESULTS: ALTO represented 10.5% (n = 23) of total osseus (n = 219) flaps. For large composite reconstructions with either ALTO flap, double flap (n = 2), or subscapular mega flaps (n = 14), ALTO flaps were most frequently used (59%, n = 23/59). There were no differences in operative time prior to and after implementation of prophylactic fixation [median (range): 5.4 (1.7-19.2) vs. 5.8 (1.7-15.0), p = .574]. Additionally, there were no differences in VTE, femur fracture, EBL, blood transfusion, or length of stay (p > .05) with adoption of prophylactic intramedullary fixation. CONCLUSIONS: The ALTO flap represents a useful tool to consider in the armamentarium of reconstructive options for large through and through defects of the head and neck. In our experience, the ALTO flap is a reasonable alternative to subscapular or double flap reconstructions and especially in the setting of unusable fibular flaps or when bone need exceeds that available from the scapula.

Lymphatic and Immune Cell Cross-Talk Regulates Cardiac Recovery After Experimental Myocardial Infarction.

OBJECTIVE: Lymphatics play an essential pathophysiological role in promoting fluid and immune cell tissue clearance. Conversely, immune cells may influence lymphatic function and remodeling. Recently, cardiac lymphangiogenesis has been proposed as a therapeutic target to prevent heart failure after myocardial infarction (MI). We investigated the effects of gene therapy to modulate cardiac lymphangiogenesis post-MI in rodents. Second, we determined the impact of cardiac-infiltrating T cells on lymphatic remodeling in the heart. Approach and Results: Comparing adenoviral versus adeno-associated viral gene delivery in mice, we found that only sustained VEGF (vascular endothelial growth factor)-CC156S therapy, achieved by adeno-associated viral vectors, increased cardiac lymphangiogenesis, and led to reduced cardiac inflammation and dysfunction by 3 weeks post-MI. Conversely, inhibition of VEGF-C/-D signaling, through adeno-associated viral delivery of soluble VEGFR3 (vascular endothelial growth factor receptor 3), limited infarct lymphangiogenesis. Unexpectedly, this treatment improved cardiac function post-MI in both mice and rats, linked to reduced infarct thinning due to acute suppression of T-cell infiltration. Finally, using pharmacological, genetic, and antibody-mediated prevention of cardiac T-cell recruitment in mice, we discovered that both CD4+ and CD8+ T cells potently suppress, in part through interferon-γ, cardiac lymphangiogenesis post-MI. CONCLUSIONS: We show that resolution of cardiac inflammation after MI may be accelerated by therapeutic lymphangiogenesis based on adeno-associated viral gene delivery of VEGF-CC156S. Conversely, our work uncovers a major negative role of cardiac-recruited T cells on lymphatic remodeling. Our results give new insight into the interconnection between immune cells and lymphatics in orchestration of cardiac repair after injury.

Awake Proning for Nonintubated Adult Hypoxic Patients with COVID-19: A Systematic Review of the Published Evidence.

Objective: Awake proning is an intervention that is being advocated for COVID-19 patients and has been suggested to improve the oxygenation, thereby decreasing oxygen requirements. We performed this systematic review with the aim of appraising the latest published evidence on the clinical effectiveness of awake proning in COVID-19 patients. Data sources: PubMed, EMBASE, The Cochrane Central Register of Controlled Trials (CENTRAL), Web of Science, Google Scholar, and one trial registry were searched until September 23, 2020, for studies on the use of awake proning for nonintubated COVID-19 patients. Study selection: Published or in-press peer-reviewed randomized control trials, case-control trials, and prospective or retrospective cohort studies in English language only were sought, assessing the effectiveness of awake proning for nonintubated patients diagnosed with COVID-19. Data results: We included 21 published studies (19 single arm and 2 with comparison group). Twenty-three registered clinical trials were identified. No randomized clinical trial has been published so far. Conclusions: Awake proning is probably safe and effective in enhancing oxygenation in nonintubated COVID-19 patients; however, there is insufficient evidence. Further high-quality clinical trials are urgently needed to assess the effectiveness of awake proning on a variety of patient-centered outcomes. How to cite this article: Parashar S, Karthik AR, Gupta R, Malviya D. Awake Proning for Nonintubated Adult Hypoxic Patients with COVID-19: A Systematic Review of the Published Evidence. Indian J Crit Care Med 2021;25(8):906-916.

AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature.

PURPOSE: Both monogenic pathogenic variant cataloging and clinical patient diagnosis start with variant-level evidence retrieval followed by expert evidence integration in search of diagnostic variants and genes. Here, we try to accelerate pathogenic variant evidence retrieval by an automatic approach. METHODS: Automatic VAriant evidence DAtabase (AVADA) is a novel machine learning tool that uses natural language processing to automatically identify pathogenic genetic variant evidence in full-text primary literature about monogenic disease and convert it to genomic coordinates. RESULTS: AVADA automatically retrieved almost 60% of likely disease-causing variants deposited in the Human Gene Mutation Database (HGMD), a 4.4-fold improvement over the current best open source automated variant extractor. AVADA contains over 60,000 likely disease-causing variants that are in HGMD but not in ClinVar. AVADA also highlights the challenges of automated variant mapping and pathogenicity curation. However, when combined with manual validation, on 245 diagnosed patients, AVADA provides valuable evidence for an additional 18 diagnostic variants, on top of ClinVar's 21, versus only 2 using the best current automated approach. CONCLUSION: AVADA advances automated retrieval of pathogenic monogenic variant evidence from full-text literature. Far from perfect, but much faster than PubMed/Google Scholar search, careful curation of AVADA-retrieved evidence can aid both database curation and patient diagnosis.

Effect of Nation-wide Lockdown on Palliative Care Services in a Tertiary Care Centre in India: A Retrospective Observational Study.

BACKGROUND: The ongoing coronavirus disease 2019 (COVID-19) pandemic has affected all the aspects of life of mankind, posing unique challenges for health-care services. In order to contain the spread of the virus, a countrywide mass lockdown has been imposed in India. Although the lockdown has modified the epidemic trajectory, it has affected the lives of many non-COVID patients. Patients in need of care could not approach hospitals. METHODS: This retrospective observational study was conducted in the Department of Onco-Anaesthesia and Palliative Medicine at a tertiary care center in India. The yearly data of patient flow for the year 2019 was compared with that during the lockdown. RESULTS: The single-day average of out-patients, in-patients, and other department consultation requests requiring palliative care decreased drastically during the lockdown in comparison to the previous year. The single-day average of teleconsultations increased more than double during the lockdown. CONCLUSION: Although lockdown decreases the spread of the epidemic, it increases the suffering of other patients who require medical care. Various steps have to be adopted in the regular working pattern of hospitals to cater to the needs of the patients requiring care, without increasing the risk of contracting COVID-19.

Unraveling the Role of Palliative Surgery in the Era of COVID-19 Pandemic.

Palliative surgery forms an important pillar of palliative treatment to provide holistic care to cancer patients in the form of providing relief from pain, local control of disease, hemorrhage, and for the purpose of rehabilitation. During the COVID-19 pandemic, we report the successful management of two cases of colorectal cancer which came under the category of high priority and underwent palliative surgery to provide relief from pain.

Phrank measures phenotype sets similarity to greatly improve Mendelian diagnostic disease prioritization.

PURPOSE: Exome sequencing and diagnosis is beginning to spread across the medical establishment. The most time-consuming part of genome-based diagnosis is the manual step of matching the potentially long list of patient candidate genes to patient phenotypes to identify the causative disease. METHODS: We introduce Phrank (for phenotype ranking), an information theory-inspired method that utilizes a Bayesian network to prioritize candidate diseases or genes, as a stand-alone module that can be run with any underlying knowledgebase and any variant filtering scheme. RESULTS: Phrank outperforms existing methods at ranking the causative disease or gene when applied to 169 real patient exomes with Mendelian diagnoses. Phrank's greatest improvement is in disease space, where across all 169 patients it ranks only 3 diseases on average ahead of the true diagnosis, whereas Phenomizer ranks 32 diseases ahead of the causal one. CONCLUSIONS: Using Phrank to rank all patient candidate genes or diseases, as they start working through a new case, will save the busy clinician much time in deriving a genetic diagnosis.

Molecular detection and characterization of Clostridium perfringens toxin genes causing necrotic enteritis in broiler chickens.

A total of 464 samples comprising of cloacal swabs from necrotic enteritis suspected live birds (191), intestinal scrapings from dead birds with symptoms of necrotic enteritis (91), and apparently healthy birds (182) were collected from selected districts of AP. The samples were subjected to multiplex PCR for simultaneous detection of α, ß, and ß2 toxin genes and uniplex PCR for the detection of NetB gene. Multiplex PCR screening of samples reveled α toxin gene positives from (cpa) 248/282 (87.94%) necrotic enteritis suspected and 40/182 (21.97%) apparently healthy samples. Among cpa positives 142/248 (57.25%) and 3/40 (7.5%) were positive for ß2 toxin gene in necrotic enteritis suspected and apparently healthy birds respectively, indicating the involvement of C. perfringens type A, with minor pore forming toxin gene cpb2 in causing necrotic enteritis in poultry. None of the sample was positive for ß toxin gene. The present research indicates C. perfringens type A along with ß2 toxin gene was responsible for causing necrotic enteritis in broiler chickens in some parts of Andhra Pradesh in India. Phylogenetic relationship of amplified cpa and cpb2 amino acids sequences from present C. perfringens isolates were studied. The analysis reveals the sequence identity of cpb2 gene of the present isolates and variations at both nucleotide and amino acid level with the published sequences of cpb2 gene of C. perfringens isolates from different animal species of the USA, Iran, Netherlands, and Japan.

Biallelic loss-of-function WNT5A mutations in an infant with severe and atypical manifestations of Robinow syndrome.

Robinow syndrome (RS) is a well-recognized Mendelian disorder known to demonstrate both autosomal dominant and autosomal recessive inheritance. Typical manifestations include short stature, characteristic facies, and skeletal anomalies. Recessive inheritance has been associated with mutations in ROR2 while dominant inheritance has been observed for mutations in WNT5A, DVL1, and DVL3. Through trio whole genome sequencing, we identified a homozygous frameshifting single nucleotide deletion in WNT5A in a previously reported, deceased infant with a unique constellation of features comprising a 46,XY disorder of sex development with multiple congenital malformations including congenital diaphragmatic hernia, ambiguous genitalia, dysmorphic facies, shortened long bones, adactyly, and ventricular septal defect. The parents, who are both heterozygous for the deletion, appear clinically unaffected. In conjunction with published observations of Wnt5a double knockout mice, we provide evidence for the possibility of autosomal recessive inheritance in association with WNT5A loss-of-function mutations in RS.

GATA2 deficiency-associated bone marrow disorder differs from idiopathic aplastic anemia.

Germ-line GATA2 gene mutations, leading to haploinsufficiency, have been identified in patients with familial myelodysplastic syndrome/acute myeloid leukemia, monocytopenia and mycobacterial infections, Emberger syndrome, and dendritic cell, monocyte, B-, and NK-cell deficiency. GATA2 mutations have also been reported in a minority of patients with congenital neutropenia and aplastic anemia (AA). The bone marrow (BM) from patients with GATA2 deficiency is typically hypocellular, with varying degrees of dysplasia. Distinguishing GATA2 patients from those with AA is critical for selecting appropriate therapy. We compared the BM flow cytometric, morphologic, and cytogenetic features of 28 GATA2 patients with those of 32 patients being evaluated for idiopathic AA. The marrow of GATA2 patients had severely reduced monocytes, B cells, and NK cells; absent hematogones; and inverted CD4:CD8 ratios. Atypical megakaryocytes and abnormal cytogenetics were more common in GATA2 marrows. CD34(+) cells were comparably reduced in GATA2 and AA. Using these criteria, we prospectively identified 4 of 32 patients with suspected AA who had features suspicious for GATA2 mutations, later confirmed by DNA sequencing. Our results show that routine BM flow cytometry, morphology, and cytogenetics in patients who present with cytopenia(s) can identify patients for whom GATA2 sequencing is indicated.

Indolent T- and NK-cell lymphoproliferative disorders of the gastrointestinal tract: a review and update.

Primary gastrointestinal (GI) T- and NK-cell lymphomas are usually aggressive neoplasms associated with high morbidity and mortality. Over the past two decades, however, cases of primary GI lymphoproliferative disorders (LPDs) or lymphomas of T- or NK-cell derivation with indolent behavior have been reported. These LPDs are rare and they can be challenging to diagnose as they share clinical and pathological features with both, inflammatory disorders and aggressive T- and NK-cell lymphomas. Primary, indolent clonal T-cell proliferations of the GI tract, which can be CD4+, CD8+ or CD4- CD8-, have been included as a provisional entity in the newly revised World Health Organization (WHO) classification of lymphoid neoplasms and designated 'indolent T-cell LPD of the GI tract'. It is currently unclear whether the indolent NK-cell LPDs represent reactive or neoplastic proliferations. In this review, we describe the clinical, morphologic, immunophenotypic and genetic features of indolent GI T- and NK-cell LPDs and provide guidance in differentiating them from other inflammatory and neoplastic diseases. We believe that greater awareness of these LPDs amongst physicians and the research community will lead to timely and accurate diagnoses, stimulate investigations into the pathogenetic mechanisms underlying different entities thereby enhancing our understanding of disease biology and enable the development of effective therapeutic regimens. Copyright © 2016 John Wiley & Sons, Ltd.

Identification and characterization of Dichelobacter nodosus serogroup H from ovine footrot in India.

A total of 56 foot swabs were collected from inter digital spaces of sheep with footrot lesions were screened for 16 rRNA of Dichelobacter nodosus by PCR. Out of the 56 samples, 38(67.85%) were found to be positive. All the positive samples were subjected to multiplex PCR targeting fimA gene for identification of serogroups of D. nodosus. Serogroup H was found along with serogroup B in 12 (55.26%) samples and with serogroup I in 8 (22.2%) samples. The serogroup H was identified for the first time from the Indian subcontinent. The phylogenetic analysis of the present sequence with the available serogroup H sequences of GenBank revealed to be in close association with the serotype H1.

Early lymphoid lesions: conceptual, diagnostic and clinical challenges.

There are no "benign lymphomas", a fact due to the nature of lymphoid cells to circulate and home as part of their normal function. Thus, benign clonal expansions of lymphocytes are only rarely recognized when localized. Recent studies have identified a number of lymphoid proliferations that lie at the interface between benign and malignant. Some of these are clonal proliferations that carry many of the molecular hallmarks of their malignant counterparts, such as BCL2/IGH and CCND1/IGH translocations associated with the in situ forms of follicular lymphoma and mantle cell lymphoma, respectively. There are other clonal B-cell proliferations with low risk of progression; these include the pediatric variants of follicular lymphoma and marginal zone lymphoma. Historically, early or incipient forms of T/NK-cell neoplasia also have been identified, such as lymphomatoid papulosis and refractory celiac disease. More recently an indolent form of T-cell lymphoproliferative disease affecting the gastrointestinal tract has been described. Usually, CD8(+), the clonal cells are confined to the mucosa. The clinical course is chronic, but non-progressive. NK-cell enteropathy is a clinically similar condition, composed of cytologically atypical NK-cells that may involve the stomach, small bowel or colon. Breast implant-associated anaplastic large cell lymphoma is a cytologically alarming lesion that is self-limited if confined to the seroma cavity. Atypical lymphoid proliferations that lie at the border of benign and malignant can serve as instructive models of lymphomagenesis. It is also critical that they be correctly diagnosed to avoid unnecessary and potentially harmful therapy.