Antigen-specific T cells play an essential role in immunoregulation and many diseases such as cancer. Characterizing the T cell receptor (TCR) sequences that encode T cell specificity is critical for elucidating the a...
详细信息
Antigen-specific T cells play an essential role in immunoregulation and many diseases such as cancer. Characterizing the T cell receptor (TCR) sequences that encode T cell specificity is critical for elucidating the antigenic determinants of immunological diseases and designing therapeutic remedies. However, methods of obtaining single-cell TCR sequencing data are labor and cost intensive, typically requiring both cell sorting and full length single-cell RNA-sequencing (scRNA-seq). New high-throughput 3' cell-barcoding scRNA-seq methods can simplify and scale this process;however, they do not routinely capture TCR sequences during library preparation and sequencing. While 5' cell-barcoding scRNA-seq methods can be used to examine TCR repertoire at single-cell resolution, doing so requires specialized reagents which cannot be applied to samples previously processed using 3' cell-barcoding methods. Here, we outline a method for sequencing TCRα and TCRβ transcripts from samples already processed using 3' cell-barcoding scRNA-seq platforms, ensuring TCR recovery at a single-cell resolution. In short, a fraction of the 3' barcoded whole transcriptome amplification (WTA) product typically used to generate a massively parallel 3' scRNA-seq library is enriched for TCR transcripts using biotinylated probes, and further amplified using the same universal primer sequence from WTA. Primer extension using TCR V-region primers and targeted PCR amplification using a second universal primer results in a 3' barcoded single-cell CDR3-enriched library that can be sequenced with custom sequencing primers. Coupled with 3' scRNA-seq of the same WTA, this method enables simultaneous analysis of single-cell transcriptomes and TCR sequences which can help interpret inherent heterogeneity among antigen-specific T cells and salient disease biology. The method presented here can also be adapted readily to enrich and sequence other transcripts of interest from both 3' and 5' barcoded scRNA-seq
—Dominance move (DoM) is a binary quality indicator that can be used in multi-objective and many-objective optimization to compare two solution sets obtained from different algorithms. The DoM indicator can different...
详细信息
COVID-19 has received tremendous attention from scholars worldwide and even being labelled as a black swan event that has disrupted every aspect of human life. Within a short time span of the pandemic, a large volume ...
COVID-19 has received tremendous attention from scholars worldwide and even being labelled as a black swan event that has disrupted every aspect of human life. Within a short time span of the pandemic, a large volume of research pertaining to COVID-19 has been published in diverse research fields. This paper adopts a bibliometric analysis to systematically evaluate the research development in the application of optimization and simulation methods to address COVID-19 physical distancing policy (OSPhyD) using Bibliometrix R package. A textual query on Scopus database using the combination of four classes of keywords; covid-19, optimization, simulation, and physical distance has returned a total of 299 original research articles and reviews published in English. Appropriate visualizations were generated to describe the collaborations between different authors, countries, and institutions, whilst co-word analysis that uses text mining technique has produced a conceptual cluster via co-occurrence network map to underscore the emerging themes in the current research interest. The main findings pinpoint that: 1) OSPhyD as a scientific research field is an emerging multidisciplinary research topic that is growing progressively and steadily in the fields of medicine, engineering, social sciences, mathematics and decision science, 2) The field has attracted the attention of scholars from all over the world particularly from United States of America, United Kingdom, European countries including authors from Asia, and 3) Three dominant themes or research front emerged from the publications including COVID-19 mainstream, medical education and undergraduate.
Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbi...
详细信息
Significance: The thermal analysis of nanofluid in a vertical cylinder (artery) in a magnetized environment holds significant implications in physiological and thermal regulation networks. This research is significant...
详细信息
The explosive spread of Corona Virus Disease-19 (COVID-19) in late December 2019, requires the health authorities worldwide to enforced stricter standard operating procedures (SOP) for mass gathering events, which eve...
The explosive spread of Corona Virus Disease-19 (COVID-19) in late December 2019, requires the health authorities worldwide to enforced stricter standard operating procedures (SOP) for mass gathering events, which eventually caused postponement and cancellation. This has led to a great loss and bankruptcy for most event organizers. As an effort to offer solution to this matter, a professional touch producing “soft landing” such as “Mathematical Modelling of Physical Distancing Policy for Mass Gathering Event Organizer” was proposed. Therefore, a holistic understanding about the issues related to physical distancing in mass gathering event is required. This systematic review paper summarizes current practice of physical distancing among mass gathering event organizers. This study reviewed thirteen articles using two leading databases namely Scopus and Google Scholar. Based on thematic analysis, this review finalized four themes: 1) physical distancing method; 2) the importance of physical distancing; 3) challenges in physical distancing enforcement and 4) approach to monitor the compliance of physical distancing.
Colorectal cancer (CRC) is a leading cause of mortality worldwide. We conducted a genome-wide association study meta-analysis of 100,204 CRC cases and 154,587 controls of European and east Asian ancestry, identifying ...
详细信息
Colorectal cancer (CRC) is a leading cause of mortality worldwide. We conducted a genome-wide association study meta-analysis of 100,204 CRC cases and 154,587 controls of European and east Asian ancestry, identifying 205 independent risk associations, of which 50 were unreported. We performed integrative genomic, transcriptomic and methylomic analyses across large bowel mucosa and other tissues. Transcriptome- and methylome-wide association studies revealed an additional 53 risk associations. We identified 155 high-confidence effector genes functionally linked to CRC risk, many of which had no previously established role in CRC. These have multiple different functions and specifically indicate that variation in normal colorectal homeostasis, proliferation, cell adhesion, migration, immunity and microbial interactions determines CRC risk. Crosstissue analyses indicated that over a third of effector genes most probably act outside the colonic mucosa. Our findings provide insights into colorectal oncogenesis and highlight potential targets across tissues for new CRC treatment and chemoprevention strategies.
This review article provides an overview of structurally oriented, experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy ...
详细信息
Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate harmonisation and interoperability des...
详细信息
暂无评论