Explore the vast range of titles available.

Full-length spliced RNA isoforms are identified in thousands of single cerebellar cells. Full-length RNA sequencing (RNA-Seq) has been applied to bulk tissue, cell lines and sorted cells to characterize transcriptomes 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , but applying this technology to single cells has proven to be difficult, with less than ten single-cell transcriptomes having been analyzed thus far 12 , 13 . Although single splicing events have been described for ≤200 single cells with statistical confidence 14 , 15 , full-length mRNA analyses for hundreds of cells have not been reported. Single-cell short-read 3′ sequencing enables the identification of cellular subtypes 16 , 17 , 18 , 19 , 20 , 21 , but full-length mRNA isoforms for these cell types cannot be profiled. We developed a method that starts with bulk tissue and identifies single-cell types and their full-length RNA isoforms without fluorescence-activated cell sorting. Using single-cell isoform RNA-Seq (ScISOr-Seq), we identified RNA isoforms in neurons, astrocytes, microglia, and cell subtypes such as Purkinje and Granule cells, and cell-type-specific combination patterns of distant splice sites 6 , 7 , 8 , 9 , 22 , 23 . We used ScISOr-Seq to improve genome annotation in mouse Gencode version 10 by determining the cell-type-specific expression of 18,173 known and 16,872 novel isoforms.

BACKGROUNDThere is a paucity of data on the mental health impact of the Coronavirus disease 2019 (COVID-19) pandemic on United States (US) healthcare workers (HCWs) after the first surge in the spring of 2020.OBJECTIVETo determine the impact of the pandemic on HCWs, and the relationship between HCW mental health and demographics, occupational factors, and COVID-19 concerns.DESIGNCross-sectional survey in an urban medical center (September–November 2020) in Baltimore, MD, in the United States.PARTICIPANTSA total of 605 HCWs (physicians, nurse practitioners, nurses, physician assistants, patient care technicians, respiratory therapists, social workers, mental health therapists, and case managers).MAIN MEASURESMeasures of mental health (Patient Health Questionnaire-2, Generalized Anxiety Disorder-7, PROMIS Sleep Disturbance 4a, Impact of Event Scale-Revised, Maslach Burnout Inventory-2 item, Connor-Davidson Resilience Scale-2 item), demographics, occupational factors, and COVID-19 related concerns.KEY RESULTSFifty-two percent of 1198 HCWs responded to the survey and 14.2% reported depression, 43.1% mild or higher anxiety, 31.6% sleep disturbance, 22.3% posttraumatic stress symptoms, 21.6% depersonalization, 46.0% emotional exhaustion, and 23.1% lower resilience. Relative to HCWs providing in-person care to COVID-19 infected patients none of their working days, those doing so all or most days were more likely to experience worse depression (adjusted odds ratio, 3.9; 95% CI, 1.3–11.7), anxiety (aOR, 3.0; 95% CI, 1.4–6.3), possible PTSD symptoms (aOR, 2.6; 95% CI, 1.1–5.8), and higher burnout (aOR, 2.6; 95% CI, 1.1–6.0). Worse mental health in several domains was associated with higher health fear (aORs ranged from 2.2 to 5.0), job stressors (aORs ranged from 1.9 to 4.0), perceived social stigma/avoidance (aORs ranged from 1.8 to 2.9), and workplace safety concerns (aORs ranged from 1.8 to 2.8).CONCLUSIONSUS HCWs experienced significant mental health symptoms eight months into the pandemic. More time spent providing in-person care to COVID-19-infected patients and greater COVID-19-related concerns were consistently associated with worse mental health.

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.

The maternal-to-zygotic transition (MZT) is a process that occurs in animal embryos at the earliest developmental stages, during which maternally deposited mRNAs and other molecules are degraded and replaced by products of the zygotic genome. The zygotic genome is not activated immediately upon fertilization, and in the pre-MZT embryo post-transcriptional control by RNA-binding proteins (RBPs) orchestrates the first steps of development. To identify relevant Drosophila RBPs organism-wide, we refined the RNA interactome capture method for comparative analysis of the pre- and post-MZT embryos. We determine 523 proteins as high-confidence RBPs, half of which were not previously reported to bind RNA. Comparison of the RNA interactomes of pre- and post-MZT embryos reveals high dynamicity of the RNA-bound proteome during early development, and suggests active regulation of RNA binding of some RBPs. This resource provides unprecedented insight into the system of RBPs that govern the earliest steps of Drosophila development. Early development is controlled by maternally deposited mRNAs and the RNA-binding proteins (RBPs) that regulate them. Here the authors describe the identification of a large number of RBPs bound to polyadenylated RNAs in Drosophila embryos before and after the maternal-to-zygotic transition, revealing changes in RBPs activity during development.

Recently, the electrification and automation of heavy-duty trucks has gained significant attention from both industry and academia, driven by new legislation introduced by the European Union. During a typical drive cycle, the mass of an urban service truck can vary substantially as waste is collected, yet most existing studies rely on a single controller with fixed gains. This limits the ability to adapt to mass changes and results in suboptimal energy usage. Within the framework of the EU-funded OBELICS and ESCALATE projects, this study proposes a novel control strategy for a semi-autonomous refuse truck. The approach combines a particle swarm optimization algorithm to determine optimal controller gains and a multiple model controller to adapt these gains dynamically based on real-time vehicle mass. The main objectives of the proposed method are to (i) optimize controller parameters, (ii) reduce overall energy consumption, and (iii) minimize speed tracking error. A cost function addressing these objectives is formulated for both autonomous and manual driving modes. The strategy is evaluated using a real-world drive cycle from Eskişehir City, Turkiye. Simulation results show that the proposed MMC-based method improves vehicle performance by 5.19% in autonomous mode and 0.534% in manual mode compared to traditional fixed-gain approaches.

Background Understanding the molecular mechanisms of the malarial parasites in hosts is crucial for developing effective treatments. Epitranscriptomic research on pathogens has unveiled the significance of RNA methylation in gene regulation and pathogenesis. This is the first report investigating methylation signatures and alternative splicing events using Nanopore Direct RNA Sequencing to single-base resolution in Plasmodium falciparum and Plasmodium vivax clinical isolates with hepatic dysfunction complications. Methods Direct RNA Sequencing using Nanopore from clinical isolates of P. falciparum and P. vivax showing hepatic dysfunction manifestation was performed. Subsequently, transcriptome reconstruction using FLAIR and transcript classification using SQANTI3, followed by methylation detection using CHEUI and m6Anet to identify N6-methyladenosine (m6A) and 5-methylcytosine (m5C) methylation signatures, was done. The alternative splicing events from both the datasets were documented. Results The reference genome of Plasmodium reports > 5000 genes out of which ~ 50% was identified as expressed in the two sequenced isolates, including novel isoforms and intergenic transcripts, highlighting extensive transcriptome diversity. The distinct RNA methylation profiles of m6A and m5C from the expressed transcripts were observed in sense, Natural Antisense Transcripts (NATs) and intergenic categories hinting at species-specific regulatory mechanisms. Dual modification events were observed in a significant number of transcripts in both the parasites. Modified transcripts originating from apicoplast and mitochondrial genomes have also been detected. These modifications are unevenly present in the annotated regions of the mRNA, potentially influencing mRNA export and translation. Several splicing events were observed, with alternative 3′ and 5′ end splicing predominating in the datasets suggesting differences in translational kinetics and possible protein characteristics in these disease conditions. Conclusion The data shows the presence of modified sense, NATs and alternatively spliced transcripts. These phenomena together suggest the presence of multiple regulatory layers which decides the post-translational proteome of the parasites in particular disease conditions. Studies like these will help to decipher the post-translational environments of malaria parasites in vivo and elucidate their inherent proteome plasticity, thus allowing the conceptualization of novel strategies for interventions.

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.

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. 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. 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. Our data suggest that autonomy in assignments with risk has implications for morale and burnout.

To elucidate the molecular mechanisms that manifest lung abnormalities during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, we performed whole-transcriptome sequencing of lung autopsies from 31 patients with severe COVID-19 and ten uninfected controls. Using metatranscriptomics, we identified the existence of two distinct molecular signatures of lethal COVID-19. The dominant ‘classical’ signature (n=23) showed upregulation of the unfolded protein response, steroid biosynthesis and complement activation, supported by massive metabolic reprogramming leading to characteristic lung damage. The rarer signature (n=8) that potentially represents ‘cytokine release syndrome’ (CRS) showed upregulation of cytokines such as IL1 and CCL19, but absence of complement activation. We found that a majority of patients cleared SARS-CoV-2 infection, but they suffered from acute dysbiosis with characteristic enrichment of opportunistic pathogens such as Staphylococcus cohnii in ‘classical’ patients and Pasteurella multocida in CRS patients. Our results suggest two distinct models of lung pathology in severe COVID-19 patients, which can be identified through complement activation, presence of specific cytokines and characteristic microbiome. These findings can be used to design personalized therapy using in silico identified drug molecules or in mitigating specific secondary infections.

Introduction Hand-foot syndrome (HFS) is a common cutaneous side effect of capecitabine therapy. Apart from oral cyclooxygenase-2 (COX-2) inhibitor (celecoxib), there are no proven strategies for the prevention of HFS. However, celecoxib is associated with significant cardiotoxicity. To date, no study has evaluated the role of topical COX inhibitor, diclofenac. In this study, we aim to compare topical 1% diclofenac gel with placebo in the prevention of capecitabine-induced HFS. Methods This is a randomized, placebo-controlled, double-blind, parallel-group superiority trial: the Diclofenac Topical in Reducing Capecitabine induced HFS (D-TORCH) study. A total of 264 patients with breast and gastrointestinal malignancies will be randomly allocated (stratified by sex and type of therapy [monotherapy or combination regimen with capecitabine]) to receive either 1% topical diclofenac or placebo that will be applied over the palmar and dorsal surface of the hands twice daily whilst taking capecitabine for 12 weeks. The patients will be followed up until the end of four cycles. The primary objective of this study is to compare the effect of topical diclofenac with placebo in preventing HFS (incidence of NCI CTCAEv5.0 grade 2 or higher HFS). The secondary objective is to compare the effect of topical diclofenac with placebo on preventing all grades of HFS (incidence of NCI CTCv5.0 all grade HFS), time to develop HFS (from the start of capecitabine), patient-reported outcomes (PROs) (HF-HRQoL questionnaire), adherence with the application (self-reported), capecitabine dose changes (number of patients with dose modifications due to HFS) and safety profile (NCICTCv5.0 all grade HFS) Discussion The D-TORCH study aims to determine if 1% topical diclofenac reduces the incidence of grade 2 or higher HFS in patients receiving capecitabine. To date, there have been a lot of trials for hand-foot syndrome prevention using agents like pyridoxine, vitamin E, carvedilol, and various polyherbal formulations, but none has been found successful. If the trial meets the primary end point, 1% topical diclofenac will be the new standard of care for HFS prevention. Trial registration Clinical Trials Registry of India  CTRI/2021/01/030592 . Prospectively registered on January 19, 2021