Self-administered versus clinician-performed BinaxNOW COVID rapid test: a comparison of accuracy.

We conducted a single-center study at a free community testing site in Baltimore City to assess the accuracy of self-performed rapid antigen tests (RATs) for COVID-19. Self-administered BinaxNOW RATs were compared with clinician-performed RATs and against a reference lab molecular testing as the gold standard. Of the 953 participants, 14.9% were positive for SARS- CoV-2 as determined by RT-PCR. The sensitivity and specificity were similar for both self- and clinician-performed RATs (sensitivity: 83.9% vs 88.2%, P = 0.40; specificity: 99.8% vs 99.6%, P = 0.6). Subgroup comparisons based on age and race yielded similar results. Notably, 5.2% (95% CI: 1.5% to 9.5%) of positive results were potentially missed due to participant misinterpretation of the self-test card. However, the false-positive rate for RATs was reassuringly comparable in accuracy to clinician-administered tests. These findings hold significant implications for physicians prescribing treatment based on patient-reported, self-administered positive test results. Our study provides robust evidence supporting the reliability and utility of patient-performed RATs, underscoring their comparable accuracy to clinician-performed RATs, and endorsing their continued use in managing COVID-19. Further studies using other rapid antigen test brands are warranted.IMPORTANCEAccurate and accessible COVID-19 testing is crucial for effective disease control and management. A recent single-center study conducted in Baltimore City examined the reliability of self-performed rapid antigen tests (RATs) for COVID-19. The study found that self-administered RATs yielded similar sensitivity and specificity to clinician-performed tests, demonstrating their comparable accuracy. These findings hold significant implications for physicians relying on patient-reported positive test results for treatment decisions. The study provides robust evidence supporting the reliability and utility of patient-performed RATs, endorsing their continued use in managing COVID-19. Furthermore, the study highlights the need for further research using different rapid antigen test brands to enhance generalizability. Ensuring affordable and widespread access to self-tests is crucial, particularly in preparation for future respiratory virus seasons and potential waves of reinfection of SARS-CoV-2 variants such as the Omicron variant.

Topical Diclofenac for Prevention of Capecitabine-Associated Hand-Foot Syndrome: A Double-Blind Randomized Controlled Trial.

PURPOSE: Hand-foot syndrome (HFS) is a dose-limiting side effect of capecitabine. Celecoxib prevents HFS by inhibiting cyclooxygenase-2 (COX-2) that is upregulated because of the underlying associated inflammation. However, systemic side effects of celecoxib have limited routine prescription. Topical diclofenac inhibits COX-2 locally with minimal risk of systemic adverse events. Therefore, we conducted this study to assess the efficacy of topical diclofenac in the prevention of capecitabine-induced HFS. METHODS: In this single-site phase III randomized double-blind trial, we enrolled patients with breast or GI cancer who were planned to receive capecitabine-based treatment. Participants were randomly assigned in a 1:1 ratio to receive topical diclofenac or placebo gel for 12 weeks or until the development of HFS, whichever occurred earlier. The primary end point was the incidence of grade 2 or 3 HFS (Common Terminology Criteria for Adverse Events version 5), which was compared between the two groups using simple logistic regression. RESULTS: In total, 264 patients were randomly assigned to receive topical diclofenac gel (n = 131) or placebo (n = 133). Grade 2 or 3 HFS was observed in 3.8% of participants in the diclofenac group compared with 15.0% in the placebo group (absolute difference, 11.2%; 95% CI, 4.3 to 18.1; P = .003). Grade 1-3 HFS was lower in the diclofenac group than in the placebo group (6.1% v 18.1%; absolute risk difference, 11.9%; 95% CI, 4.1 to 19.6). Capecitabine dose reductions because of HFS were less frequent in the diclofenac group (3.8%) than in the placebo group (13.5%; absolute risk difference, 9.7%; 95% CI, 3.0 to 16.4). CONCLUSION: Topical diclofenac prevented HFS in patients receiving capecitabine. This trial supports the use of topical diclofenac to prevent capecitabine-associated HFS.

Physical Restraint Usage in Hospitals Across the United States: 2011-2019.

Objective: To determine the change in rates of physical restraint (PR) use and associated outcomes among hospitalized adults. Patients and Methods: Using national inpatient sample databases, we analyzed years 2011-2014 and 2016-2019 to determine trends of PR usage. We also compared the years 2011-2012 and 2018-2019 to investigate rates of PR use, in-hospital mortality, length of stay, and total hospital charges. Results: There were 242,994,110 hospitalizations during the study period. 1,538,791 (0.63%) had coding to signify PRs, compared with 241,455,319 (99.3%), which did not. From 2011 to 2014, there was a significant increase in PR use (p-trend<.01) and a nonsignificant increase in PR rates from 2016-2019 (p-trend=.07). Over time, PR use increased (2011-2012: 0.52% vs 2018-2019: 0.73%; p<.01). Patients with PRs reported a higher adjusted odds for in-hospital mortality in 2011-2012 (adjusted odds ratio [aOR], 3.9; 95% CI, 3.7-4.2; p<.01) and 2018-2019 (aOR, 3.5; 95% CI, 3.4-3.7; p<.01). Length of stay was prolonged for patients with PRs in 2011-2012 (adjusted mean difference [aMD], 4.3 days; 95% CI, 4.1-4.5; p<.01) and even longer in 2018-2019 (aMD, 5.8 days; 95% CI, 5.6-6.0; p<.01). Total hospital charges were higher for patients with PRs in 2011-2012 (aMD, +$55,003; 95% CI, $49,309-$60,679; p<.01). Following adjustment for inflation, total charges remained higher for patients with PRs compared with those without PRs in 2018-2019 (aMD, +$70,018; 95% CI, $65,355-$74,680; p<.01). Conclusion: Overall, PR rates did not decrease across the study period, suggesting that messaging and promulgating best practice guidelines have yet to translate into a substantive change in practice patterns.

DNA-binding protein PfAP2-P regulates parasite pathogenesis during malaria parasite blood stages.

Malaria-associated pathogenesis such as parasite invasion, egress, host cell remodelling and antigenic variation requires concerted action by many proteins, but the molecular regulation is poorly understood. Here we have characterized an essential Plasmodium-specific Apicomplexan AP2 transcription factor in Plasmodium falciparum (PfAP2-P; pathogenesis) during the blood-stage development with two peaks of expression. An inducible knockout of gene function showed that PfAP2-P is essential for trophozoite development, and critical for var gene regulation, merozoite development and parasite egress. Chromatin immunoprecipitation sequencing data collected at timepoints matching the two peaks of pfap2-p expression demonstrate PfAP2-P binding to promoters of genes controlling trophozoite development, host cell remodelling, antigenic variation and pathogenicity. Single-cell RNA sequencing and fluorescence-activated cell sorting revealed de-repression of most var genes in Δpfap2-p parasites. Δpfap2-p parasites also overexpress early gametocyte marker genes, indicating a regulatory role in sexual stage conversion. We conclude that PfAP2-P is an essential upstream transcriptional regulator at two distinct stages of the intra-erythrocytic development cycle.

Prevalence of Workplace Violence and Effects of De-escalation Training Among Hospitalists: A Pilot Study.

Introduction: Workplace violence (WPV) is increasing in healthcare and negatively impacts healthcare worker outcomes. De-escalation training for healthcare workers is recommended to reduce WPV from patients and visitors. Hospitalists may be at high risk for WPV, but the magnitude of WPV and the impact of de-escalation training among hospitalists is not known. Methods: We investigated the baseline prevalence of WPV experienced by 37 hospitalists at a single center. After an in-person de-escalation training, we measured hospitalists' self-reported "Confidence in Coping with Patient Aggression" using a validated scale (score range 10-110). Results: In the 12 months before de-escalation training, 86.5% of participants reported at least one form of WPV: 83.8% verbal abuse, 29.7% racial abuse, 18.9% physical violence, and 16.2% sexual abuse. The mean confidence score increased significantly from pre-training (43.2) to immediately after training (68.5) and remained significantly elevated at three months (57.2), six months (60.2), and after 12 months (59.9) (all P < 0.05; Ptrend <0.05). Conclusion: Hospitalists are at high risk for WPV. Structured in-person de-escalation training may provide the sustained ability for hospitalists to cope with WPV.

Feasibility of and Experience with Free State Funded Telehealth Based Patient Self-referral for COVID-19 Monoclonal Antibody Therapy.

BACKGROUND: Monoclonal antibody (mAb) treatment for COVID-19 has been underutilized due to logistical challenges, lack of access and variable treatment awareness among patients and healthcare professionals. The use of telehealth during the pandemic provides an opportunity to increase access to COVID-19 care. METHODS: This is a single-center descriptive study of telehealth-based patient self-referral for mAb therapy between March 1, 2021, to October 31, 2021 at Baltimore Convention Center Field Hospital (BCCFH). RESULTS: Among the 1001 self-referral patients, the mean age was 47, and most were female (57%) white (66%), and had a primary care provider (62%). During the study period, self-referrals increased from 14 per month in March to 427 in October resulting in a 30-fold increase. About 57% of self-referred patients received a telehealth visit, and of those 82% of patients received mAb infusion therapy. The median time from self-referral to onsite infusion was 2 days (1-3 IQR). DISCUSSION: Our study shows the integration of telehealth with a self-referral process improved access to mAb infusion. A high proportion of self-referrals were appropriate and led to timely treatment. This approach helped those without traditional avenues for care and avoided potential delay for patients seeking referral from their PCPs.

A systematic comparison of human mitochondrial genome assembly tools.

BACKGROUND: Mitochondria are the cell organelles that produce most of the chemical energy required to power the cell's biochemical reactions. Despite being a part of a eukaryotic host cell, the mitochondria contain a separate genome whose origin is linked with the endosymbiosis of a prokaryotic cell by the host cell and encode independent genomic information throughout their genomes. Mitochondrial genomes accommodate essential genes and are regularly utilized in biotechnology and phylogenetics. Various assemblers capable of generating complete mitochondrial genomes are being continuously developed. These tools often use whole-genome sequencing data as an input containing reads from the mitochondrial genome. Till now, no published work has explored the systematic comparison of all the available tools for assembling human mitochondrial genomes using short-read sequencing data. This evaluation is required to identify the best tool that can be well-optimized for small-scale projects or even national-level research. RESULTS: In this study, we have tested the mitochondrial genome assemblers for both simulated datasets and whole genome sequencing (WGS) datasets of humans. For the highest computational setting of 16 computational threads with the simulated dataset having 1000X read depth, MitoFlex took the least execution time of 69 s, and IOGA took the longest execution time of 1278 s. NOVOPlasty utilized the least computational memory of approximately 0.098 GB for the same setting, whereas IOGA utilized the highest computational memory of 11.858 GB. In the case of WGS datasets for humans, GetOrganelle and MitoFlex performed the best in capturing the SNPs information with a mean F1-score of 0.919 at the sequencing depth of 10X. MToolBox and NOVOPlasty performed consistently across all sequencing depths with a mean F1 score of 0.897 and 0.890, respectively. CONCLUSIONS: Based on the overall performance metrics and consistency in assembly quality for all sequencing data, MToolBox performed the best. However, NOVOPlasty was the second fastest tool in execution time despite being single-threaded, and it utilized the least computational resources among all the assemblers when tested on simulated datasets. Therefore, NOVOPlasty may be more practical when there is a significant sample size and a lack of computational resources. Besides, as long-read sequencing gains popularity, mitochondrial genome assemblers must be developed to use long-read sequencing data.

Identification of herpesvirus transcripts from genomic regions around the replication origins.

Long-read sequencing (LRS) techniques enable the identification of full-length RNA molecules in a single run eliminating the need for additional assembly steps. LRS research has exposed unanticipated transcriptomic complexity in various organisms, including viruses. Herpesviruses are known to produce a range of transcripts, either close to or overlapping replication origins (Oris) and neighboring genes related to transcription or replication, which possess confirmed or potential regulatory roles. In our research, we employed both new and previously published LRS and short-read sequencing datasets to uncover additional Ori-proximal transcripts in nine herpesviruses from all three subfamilies (alpha, beta and gamma). We discovered novel long non-coding RNAs, as well as splice and length isoforms of mRNAs. Moreover, our analysis uncovered an intricate network of transcriptional overlaps within the examined genomic regions. We demonstrated that herpesviruses display distinct patterns of transcriptional overlaps in the vicinity of or at the Oris. Our findings suggest the existence of a 'super regulatory center' in the genome of alphaherpesviruses that governs the initiation of both DNA replication and global transcription through multilayered interactions among the molecular machineries.

Comparison of hospitalist morale in a COVID-19 alternate care site (ACS) to hospitalist morale in conventional hospitals in Maryland.

BACKGROUND: Morale and burnout were concerns for hospitalists prior to the COVID-19 pandemic; these concerns were amplified as COVID-19 spread and hospitals experienced unprecedented stress. In contrast to prior literature, our study assesses both satisfaction and the importance of various factors. This study examines morale of hospitalists early in the COVID-19 pandemic in two settings: conventional hospitals and a COVID-19 Alternate Care site (ACS) in the same geographic region in Maryland. Multiple studies published early in the pandemic show low morale in COVID-19 hospitals. METHODS: In a cross-sectional survey study, we analyze data from the Hospitalist Morale Index (HMI) administered between September 2020 and March 2021 to determine the pandemic's impact on hospitalist morale. RESULTS: Surprisingly, our study found morale in the ACS was better than morale at the conventional hospitals. ACS hospitalists and conventional hospitalists were demographically similar. Our results show that a significantly higher proportion of conventional hospitalists reported burnout compared to the ACS hospitalists. General quality of life was rated significantly higher in the ACS group than the conventional group. Significantly more ACS hospitalists were invested in making their group outstanding. Five main HMI domains were examined with questions on a 5-point rating scale: Clinical Factors, Workload, Material Rewards, Leadership, and Appreciation/Acknowledgement. ACS hospitalists rated most measures higher than conventional hospitalists; largest differences were observed in Clinical Factors and Appreciation/Acknowledgement domains. Narrative comments from ACS hospitalists revealed strong identification with the mission of the ACS and pride in contributing during a crisis. One key difference between the two groups explains these findings: provider autonomy. The ACS staff chose the position and the assignment, while conventional hospitalists caring for COVID-19 patients could not readily opt out of this work. CONCLUSION: Our data suggest that autonomy in assignments with risk has implications for morale and burnout.

A Novel Robust Method Mimicking Human Substratum To Dissect the Heterogeneity of Candida auris Biofilm Formation.

Candida auris is a pathogen of urgent threat level as marked by the CDC. The formation of biofilms is an essential property of this fungus to establish infection and escape drug treatment. However, our understanding of pathogenesis through biofilm is hampered by heterogeneity in C. auris biofilms observed in different studies. It is imperative to replicate in vivo conditions for studying C. auris biofilm formation in vitro. Different methods are standardized, but the surface used to form biofilms lacks consistency as well as the architecture of a typical biofilm. Here, we report an in vitro technique to grow C. auris biofilms on gelatin-coated coverslips. Interestingly, C. auris cells grown on gelatin-coated coverslips either on modified synthetic sweat media or RPMI 1640 resulted in similar multilayer biofilm formation with extracellular polymeric substances (EPS). This method is also consistent with the biofilm formation of other Candida species, such as Candida glabrata and Candida albicans. Biofilms of C. glabrata developed through this method show pseudohyphae and EPS. This method can be used to understand the molecular basis of biofilm formation, associated pathogenesis, and drug tolerance. The technique is cost-effective and would thus serve in rightful screening and repurposing drug libraries for designing new therapeutics against the less-studied high-alarm pathogen C. auris. IMPORTANCE Heterogeneity is seen when multidrug-resistant C. auris biofilm is cultured using different reported methods. Biofilm formed on the gelatin surface mimics the condition of a host environment that has multilayers and EPS. This method has feasibility for drug screening and analyzing biofilms through three-dimensional (3D) reconstruction. This in vitro biofilm formation technique is also exploited to study the formation of biofilm of other Candida species. The biofilms of C. glabrata and C. albicans can also be correctly mimicked using gelatin in the biofilm-forming environment. Thus, the novel in vitro method for biofilm formation reported here can be widely used to understand the mechanism of biofilm formation, related virulence properties, and drug tolerance of C. auris and other Candida species. This simple and low-cost technique is highly suitable for screening novel inhibitors and repurposed libraries and to design new therapeutics against Candida species.

PfAP2-MRP DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages.

Malaria pathogenicity results from the parasite's ability to invade, multiply within and then egress from the host red blood cell (RBC). Infected RBCs are remodeled, expressing antigenic variant proteins (such as PfEMP1, coded by the var gene family) for immune evasion and survival. These processes require the concerted actions of many proteins, but the molecular regulation is poorly understood. We have characterized an essential Plasmodium specific Apicomplexan AP2 (ApiAP2) transcription factor in Plasmodium falciparum (PfAP2-MRP; Master Regulator of Pathogenesis) during the intraerythrocytic developmental cycle (IDC). An inducible gene knockout approach showed that PfAP2-MRP is essential for development during the trophozoite stage, and critical for var gene regulation, merozoite development and parasite egress. ChIP-seq experiments performed at 16 hour post invasion (h.p.i.) and 40 h.p.i. matching the two peaks of PfAP2-MRP expression, demonstrate binding of PfAP2-MRP to the promoters of genes controlling trophozoite development and host cell remodeling at 16 h.p.i. and antigenic variation and pathogenicity at 40 h.p.i. Using single-cell RNA-seq and fluorescence-activated cell sorting, we show de-repression of most var genes in Δpfap2-mrp parasites that express multiple PfEMP1 proteins on the surface of infected RBCs. In addition, the Δpfap2-mrp parasites overexpress several early gametocyte marker genes at both 16 and 40 h.p.i., indicating a regulatory role in the sexual stage conversion. Using the Chromosomes Conformation Capture experiment (Hi-C), we demonstrate that deletion of PfAP2-MRP results in significant reduction of both intra-chromosomal and inter-chromosomal interactions in heterochromatin clusters. We conclude that PfAP2-MRP is a vital upstream transcriptional regulator controlling essential processes in two distinct developmental stages during the IDC that include parasite growth, chromatin structure and var gene expression.

Outcomes among hospitalized patients with dementia and behavioral disturbances when physical restraints are introduced.

BACKGROUND: Physical restraint use among patients hospitalized with dementia and behavioral disturbances has not been studied nationally in the United States. METHODS: National Inpatient Sample database years 2016 through 2020 were used to compare physically restrained and unrestrained patients with dementia and behavioral disturbances. Multivariable regression analyses were used to assess patient outcomes. RESULTS: There were 991,605 patients coded for dementia with behavioral disturbances. Among these, physical restraints were used with 64,390 (6.5%) and not with 927,215 (93.5%). Patients in the restrained group were younger (mean age ± standard error: 78.7 ± 0.25 vs. 79.9 ± 0.34 ; p < 0.01) and more often male (59.0% vs. 45.8%; p < 0.01) compared to the unrestrained group. A higher proportion of Black patients were in the restrained group (15.2% vs. 11.8%; p < 0.01). Larger hospitals also made up a more significant proportion of restrained versus unrestrained patients (53.3% vs. 45.1%; p < 0.01). Those with physical restraints had longer lengths of stays (adjusted mean difference [aMD] = 2.6 days CI [2.2-3.0]; p < 0.01) and higher total hospital charges (aMD = $13,150 CI [10,827-15,472]; p < 0.01). There were similar adjusted odds for in-hospital mortality (adjusted odds ratio [aOR] = 1.0 [CI 0.95-1.1]; p = 0.28) and lower odds of being discharged to home after hospitalization (aOR = 0.74 [0.70-0.79]; <0.01) for patients with physical restraints compared to those without. CONCLUSION: Among patients hospitalized with dementia and behavioral disturbances, those with physical restraints had greater hospital resource utilization outcomes. Attempts to limit physical restraint use whenever possible may improve outcomes in this vulnerable population.

Draft Genome Sequence of a Delftia sp., a Member of an Electroactive Community Enriched from Wastewater from the Indian Institute of Technology Delhi, India.

The draft genome sequence of Delftia sp. is reported here. The genome was recovered from a mixed-species electroactive community in a microbial fuel cell that had been inoculated with wastewater from the Indian Institute of Technology Delhi, India. Sequencing was performed using Nanopore technology.

Outcomes for Hospitalized Aggressive and Violent Patients When Physical Restraints Are Introduced.

BACKGROUND: Hospital outcomes among patients acting aggressively or violently have not been extensively studied in the United States. OBJECTIVES: The aims of the study are to determine rates of physical restraint use among hospitalized patients who are aggressive/violent and to characterize associations with mortality and utilization metrics. DESIGN/SETTING/PARTICIPANTS: National Inpatient Sample databases from 2016 to 2019 were analyzed with multivariable regression to compare aggressive/violent patients in whom physical restraints were or were not used. MEASURES: Prevalence of physical restraint use, in-hospital mortality, length of stay, and total hospital charges were measures. RESULTS: A total of 40,309 hospitalized patients were coded as having aggressive/violent behavior, of whom 4475 (11.1%) were physically restrained. Physically restrained patients were younger (mean age ± standard error, 42.6 ± 0.64 versus 45.7± 0.41; P < 0.01), more frequently male (71.0% versus 65.4%; P < 0.01), and had less comorbidity (Charlson Index score >3: 7.9% versus 12.5%; P < 0.01) than unrestrained patients. Patients with physical restraints had higher odds of in-hospital mortality (adjusted odds ratio, 2.4, confidence interval [CI], 1.0-5.7; P = 0.04) and lower odds of being discharged to home (adjusted odds ratio, 0.46; CI, 0.38-0.56; P < 0.01) compared with unrestrained patients. Longer hospital stays (adjusted mean difference, 4.1 days CI, 2.1-6.0; P < 0.01) and higher hospitalization charges (adjusted mean difference, $16,996; CI, 6883-27,110; P < 0.01) were observed for those who were physically restrained. CONCLUSIONS: Physically restrained aggressive/violent patients had worse in-hospital outcomes compared with their unrestrained counterparts. Avoiding physical restraints whenever possible should be considered when managing this confrontational yet vulnerable patient population. When restraints are needed, providers must thoughtfully bear in mind heightened risks for worse outcomes.

Rapamycin and Torin2 inhibit Candida auris TOR: Insights through growth profiling, docking, and MD simulations.

The fungus Candida auris is a pathogen of utmost concern due to its rapid emergence across the globe, acquired antifungal drug tolerance, thermotolerance, and ability to survive in hospital settings and preserved foods. Recent incidences of comorbidity of corona patients with its infection in hospital settings highlighted the importance of understanding the pathobiology and drug tolerance of this fungus on priority. The Target of rapamycin (TOR) is a central regulator of growth across eukaryotes with an illustrated role in fungal pathology. The role of the TOR signalling pathway in the growth of C. auris is yet to be described. In-silico, analysis revealed the presence of highly conserved Tor kinase, components of TORC, and key downstream components in C. auris. Rapamycin and Torin2, the specific inhibitors of Tor reduce the growth of C. auris. An inhibition of Tor leads to cell cycle arrest at the G1 phase with a defect in cytokinesis. Interestingly, with an insignificant difference in growth at 30 and 37 °C, a sharp decline in growth is seen with Torin2 at 37 °C. The heterogeneous response emphasizes the importance of physiology-based differential cellular response at different temperatures. In addition, the inhibition of Tor suppresses the biofilm formation. In silico studies through docking and simulations showed rapamycin and torin2 as specific inhibitors of C. auris Tor kinase (CauTor kinase) and hence can be exploited for a thorough understanding of the TOR signalling pathway in pathobiology and drug tolerance of C. auris. HIGHLIGHTSConservation of TOR signalling pathway in Candida aurisRapamycin and torin2 are specific inhibitors of Cau TorUnderstanding of the role of TOR signalling pathway through the use of inhibitors rapamycin and torin2.Heterogenous response of C. auris to torin2 at different physiological conditions.Communicated by Ramaswamy H. Sarma.

RNA Pol II Assembly Affects ncRNA Expression.

RNA pol II assembly occurs in the cytoplasm before translocation of the enzyme to the nucleus. Affecting this assembly influences mRNA transcription in the nucleus and mRNA decay in the cytoplasm. However, very little is known about the consequences on ncRNA synthesis. In this work, we show that impairment of RNA pol II assembly leads to a decrease in cryptic non-coding RNAs (preferentially CUTs and SUTs). This alteration is partially restored upon overcoming the assembly defect. Notably, this drop in ncRNAs is only partially dependent on the nuclear exosome, which suggests a major specific effect of enzyme assembly. Our data also point out a defect in transcription termination, which leads us to propose that CTD phosphatase Rtr1 could be involved in this process.

A Comprehensive narrative review of transcriptomics and epigenomics of gallbladder cancer.

ABSTRACTS: Gallbladder cancer (GBC) is one of the quiet prevalent and aggressive biliary tract malignant neoplasms distinguished by significant cellular heterogeneity, metastatic activity, and a poor prognosis, with varied frequency worldwide. Most cases are detected incidentally while routine screening imaging or pathological investigation of cholecystectomy tissues and usually present with advanced disease. The surgical resection is usually done in the initial clinical stage having limited spread. Despite the surgical therapy, the death rate is significant. Furthermore, the molecular mechanisms affecting the clinical course of inflammatory gallbladder to carcinogenesis remain poorly understood. There is an impending need for developing diagnostic biomarkers and targeted approaches for GBC. The newer molecular platform, such as next-generation sequencing (NGS), such as RNA-sequencing (RNAseq), single-cell sequencing, and microarray technology, has revolutionized the field of genomics, opened a new perspective in defining genetic and epigenetic characteristics identifying molecules as possible therapeutic targets. Therefore, in this review, we would analyze transcriptomic and epigenomics profiles of GBC using already published high-throughput sequencing-based studies published between 2010 and 2023. The review would also analyze the possible impact of the technological advancement on the patient management strategy and overall survival. This may also help identify target genes and pathways linked to GBC, which may help establish molecular biomarkers, for early GBC diagnosis, personalized therapy, and management.

Single-Cell DNA Methylation Analysis in Cancer.

Morphological, transcriptomic, and genomic defects are well-explored parameters of cancer biology. In more recent years, the impact of epigenetic influences, such as DNA methylation, is becoming more appreciated. Aberrant DNA methylation has been implicated in many types of cancers, influencing cell type, state, transcriptional regulation, and genomic stability to name a few. Traditionally, large populations of cells from the tissue of interest are coalesced for analysis, producing averaged methylome data. Considering the inherent heterogeneity of cancer, analysing populations of cells as a whole denies the ability to discover novel aberrant methylation patterns, identify subpopulations, and trace cell lineages. Due to recent advancements in technology, it is now possible to obtain methylome data from single cells. This has both research and clinical implications, ranging from the identification of biomarkers to improved diagnostic tools. As with all emerging technologies, distinct experimental, bioinformatic, and practical challenges present themselves. This review begins with exploring the potential impact of single-cell sequencing on understanding cancer biology and how it could eventually benefit a clinical setting. Following this, the techniques and experimental approaches which made this technology possible are explored. Finally, the present challenges currently associated with single-cell DNA methylation sequencing are described.

Characteristics & outcomes of cancer patients with COVID-19: A multicentre retrospective study from India.

Background & objectives: High mortality has been observed in the cancer population affected with COVID-19 during this pandemic. We undertook this study to determine the characteristics and outcomes of cancer patients with COVID-19 and assessed the factors predicting outcome. Methods: Patients of all age groups with a proven history of malignancy and a recent diagnosis of SARS-CoV-2 infection based on nasal/nasopharyngeal reverse transcriptase (RT)-PCR tests were included. Demographic, clinical and laboratory variables were compared between survivors and non-survivors groups, with respect to observed mortality. Results: Between May 11 and August 10, 2020, 134 patients were included from the three centres and observed mortality was 17.1 per cent. The median age was 53 yr (interquartile range 39-61 yr) and thirty four patients (25%) were asymptomatic. Solid tumours accounted for 69.1 per cent and breast cancer was the most common tumour type (20%). One hundred and five patients (70.5%) had received chemotherapy within the past four weeks and 25 patients (19.3%) had neutropenia at presentation. On multivariate analysis, age [odds ratio (OR) 7.99 (95% confidence interval [CI] 1.18-54.00); P=0.033], haemoglobin [OR 6.28 (95% CI 1.07-37.04); P=0.042] neutrophil-lymphocyte ratio [OR 12.02 (95% CI 2.08-69.51); P=0.005] and baseline serum albumin [OR 18.52 (95% CI 2.80-122.27); P=0.002], were associated with higher mortality. Recent chemotherapy, haematological tumours type and baseline neutropenia did not affect the outcome. Interpretation & conclusions: Higher mortality in moderate and severe infections was associated with baseline organ dysfunction and elderly age. Significant proportion of patients were asymptomatic and might remain undetected.

Construing the metaxin-2 mediated simultaneous localization between mitochondria and nucleolus using molecular viscometry.

Fluorescent probes for specific inter-organelle communication are of massive significance as such communication is essential for a diverse range of cellular events. Here, we present the microviscosity-sensitive fluorescence marker, Quinaldine Red (QR), and its dual organelle targeting light-up response in live cells. This biocompatible probe was able to localize in mitochondria and nucleolus simultaneously. While QR was able to sense the viscosity change inside these compartments under the induced effect of an ionophore and ROS-rich microenvironment, the probe's ability to stain mitochondria remained unperturbed even after protonophore-induced depolarization. Consequently, a systematic quantification was performed to understand the alteration of microviscosity. Similar behavior in two distinct organelles implied that QR binds to metaxin-2 protein, common to mitochondrial and nucleolar proteomes. We believe this is the first of its kind investigation that identifies the inter-organelle communications marker and opens up a new dimension in this field.