Diabetes is associated with increased liver cancer incidence and mortality in adults: A report from Asia Cohort Consortium.

There has been growing evidence suggesting that diabetes may be associated with increased liver cancer risk. However, studies conducted in Asian countries are limited. This project considered data of 968,738 adults pooled from 20 cohort studies of Asia Cohort Consortium to examine the association between baseline diabetes and liver cancer incidence and mortality. Cox proportional hazard model and competing risk approach was used for pooled data. Two-stage meta-analysis across studies was also done. There were 839,194 subjects with valid data regarding liver cancer incidence (5654 liver cancer cases [48.29/100,000 person-years]), follow-up time and baseline diabetes (44,781 with diabetes [5.3%]). There were 747,198 subjects with valid data regarding liver cancer mortality (5020 liver cancer deaths [44.03/100,000 person-years]), follow-up time and baseline diabetes (43,243 with diabetes [5.8%]). Hazard ratio (HR) (95% confidence interval [95%CI]) of liver cancer diagnosis in those with vs. without baseline diabetes was 1.97 (1.79, 2.16) (p < .0001) after adjusting for baseline age, gender, body mass index, tobacco smoking, alcohol use, and heterogeneity across studies (n = 586,072; events = 4620). Baseline diabetes was associated with increased cumulative incidence of death due to liver cancer (adjusted HR (95%CI) = 1.97 (1.79, 2.18); p < .0001) (n = 595,193; events = 4110). A two-stage meta-analytic approach showed similar results. This paper adds important population-based evidence to current literature regarding the increased incidence and mortality of liver cancer in adults with diabetes. The analysis of data pooled from 20 studies of different Asian countries and the meta-analysis across studies with large number of subjects makes the results robust.

Ionic Liquid-Based Immunization Patch for the Transdermal Delivery of Antigens.

Herein, we report a transdermal patch prepared using an ionic liquid-based solid in oil (IL-S/O) nanodispersion and a pressure-sensitive adhesive (PSA) to deliver the macromolecular antigenic protein, ovalbumin (OVA). The IL-S/O nanodispersion and a PSA were first mixed at an equal weight ratio, then coated onto a release liner, and covered with a support film. To evaluate the effect of the PSA, three types of PSAs, DURO-TAK 87-4098, DURO-TAK 87-4287, and DURO-TAK 87-235A, were used to obtain the corresponding IL-S/O patches SP-4098, SP-4287, and SP-235A, respectively. The prepared IL-S/O patches were characterized for surface morphology, viscoelasticity, and moisture content. In vitro skin penetration and in vivo immunization studies of the IL-S/O patches were performed using Yucatan micropig skin and the C57BL/6NJc1 mice model, respectively. The SP-4098 and SP-4287 delivered 5.49-fold and 5.47-fold higher amounts of drug compared with the aqueous formulation. Although both patches delivered a similar amount of drug, SP-4287 was not detached fully from the release liner after 30 days, indicating low stability. Mice immunized with the OVA-containing SP-4098 produced a 10-fold increase in anti-OVA IgG compared with those treated with an aqueous formulation. These findings suggested that the IL-S/O patch may be a good platform for the transdermal delivery of antigen molecules.

Choice of assemblers has a critical impact on de novo assembly of SARS-CoV-2 genome and characterizing variants.

BACKGROUND: Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global pandemic following its initial emergence in China. SARS-CoV-2 has a positive-sense single-stranded RNA virus genome of around 30Kb. Using next-generation sequencing technologies, a large number of SARS-CoV-2 genomes are being sequenced at an unprecedented rate and being deposited in public repositories. For the de novo assembly of the SARS-CoV-2 genomes, a myriad of assemblers is being used, although their impact on the assembly quality has not been characterized for this virus. In this study, we aim to understand the variabilities on assembly qualities due to the choice of the assemblers. RESULTS: We performed 6648 de novo assemblies of 416 SARS-CoV-2 samples using eight different assemblers with different k-mer lengths. We used Illumina paired-end sequencing reads and compared the assembly quality of those assemblers. We showed that the choice of assembler plays a significant role in reconstructing the SARS-CoV-2 genome. Two metagenomic assemblers, e.g. MEGAHIT and metaSPAdes, performed better compared with others in most of the assembly quality metrics including, recovery of a larger fraction of the genome, constructing larger contigs and higher N50, NA50 values, etc. We showed that at least 09% (259/2873) of the variants present in the assemblies between MEGAHIT and metaSPAdes are unique to one of the assembly methods. CONCLUSION: Our analyses indicate the critical role of assembly methods for assembling SARS-CoV-2 genome using short reads and their impact on variant characterization. This study could help guide future studies to determine the best-suited assembler for the de novo assembly of virus genomes.

VirusTaxo: Taxonomic classification of viruses from the genome sequence using k-mer enrichment.

Classification of viruses into their taxonomic ranks (e.g., order, family, and genus) provides a framework to organize an abundant population of viruses. Next-generation metagenomic sequencing technologies lead to a rapid increase in generating sequencing data of viruses which require bioinformatics tools to analyze the taxonomy. Many metagenomic taxonomy classifiers have been developed to study microbiomes, but it is particularly challenging to assign the taxonomy of diverse virus sequences and there is a growing need for dedicated methods to be developed that are optimized to classify virus sequences into their taxa. For taxonomic classification of viruses from metagenomic sequences, we developed VirusTaxo using diverse (e.g., 402 DNA and 280 RNA) genera of viruses. VirusTaxo has an average accuracy of 93% at genus level prediction in DNA and RNA viruses. VirusTaxo outperformed existing taxonomic classifiers of viruses where it assigned taxonomy of a larger fraction of metagenomic contigs compared to other methods. Benchmarking of VirusTaxo on a collection of SARS-CoV-2 sequencing libraries and metavirome datasets suggests that VirusTaxo can characterize virus taxonomy from highly diverse contigs and provide a reliable decision on the taxonomy of viruses.

Trend and projection of skilled birth attendants and institutional delivery coverage for adolescents in 54 low- and middle-income countries, 2000-2030.

BACKGROUND: Limitations to accessing delivery care services increase the risks of adverse outcomes during pregnancy and delivery for all pregnant women, particularly among adolescents in LMICs. In order to inform adolescent-specific delivery care initiatives and coverage, we conducted a comprehensive analysis of trends, projections and inequalities in coverage of delivery care services among adolescents at national, urban-rural and socio-economic levels in LMICs. METHODS: Using 224 nationally representative cross-sectional survey data between 2000 and 2019, we estimated the coverage of institutional delivery (INSD) and skilled birth attendants (SBA). Bayesian hierarchical regression models were used to estimate trends, projections and determinants of INSD and SBA. RESULTS: Coverage of delivery care services among adolescents increased substantially at the national level, as well as in both urban and rural areas in most countries between 2000 and 2018. Of the 54 LMICs, 24 countries reached 80% coverage of both INSD and SBA in 2018, and predictions for 40 countries are set to exceed 80% by 2030. The trends in coverage of INSD and SBA of adult mothers mostly align with those for adolescent mothers. Our findings show that urban-rural and wealth-based inequalities to delivery care remain persistent by 2030. In 2018, urban settings across 54 countries had higher rates of coverage exceeding 80% compared to rural for both INSD (45 urban, 16 rural) and SBA (50 urban, 19 rural). Several factors such as household head age ≥ 46 years, household head being female, access to mass media, lower parity, higher education, higher ANC visits and higher socio-economic status could increase the coverage of INSD and SBA among adolescents and adult women. CONCLUSIONS: More than three-quarters of the LMICs are predicted to achieve 80% coverage of INSD and SBA among adolescent mothers in 2030, although with sustained inequalities.

Age-related glomerular lesions with albuminuria in male cotton rats.

The increased prevalence of aging-related chronic kidney disease (CKD) among humans is a problem worldwide. Aged cotton rats (Sigmodon hispidus) are considered novel model animals for studying CKD, especially as the females develop severe tubulointerstitial lesions with anemia. To investigate the renal pathologic features in aged male cotton rats and their characteristic glomerular injuries, the animals were divided into young, adult, old-aged, and advanced-aged groups (1-4, 5-8, 9-12, and 13-17 months, respectively) and pathologically analyzed. Anemia and renal dysfunction, as indicated by hematologic and serologic parameters, were significantly milder in the advanced-aged males than in the old-aged females. The males had increased urinary albumin-to-creatinine ratios from the old-age period, with the advanced-aged males having significantly higher levels than those in the old-aged females and young males. The old-aged females did not show clear glomerular injuries, whereas the advanced-aged males showed membranous lesions characterized by irregular and thickened glomerular basement membranes (GBMs). Characteristically, several large-sized projections from the GBM toward the podocytes were observed by microscopy, and podocytes covering these projections effaced their foot processes. The advanced-aged males showed aging-related IgG immune-complex depositions in the paramesangial regions and along the GBM. Furthermore, the positive reaction for podocin (a podocyte molecule) was granulated along the GBM. Thus, we clarified the albuminuria associated with altered glomerular structures in advanced-aged cotton rats, and that these phenotypes were closely associated with aging. These data help to clarify the aging-related pathogenesis of glomerular injury.

Characterization of burn wound healing gel prepared from human amniotic membrane and Aloe vera extract.

BACKGROUND: Skin burn wound is a notable medical burden worldwide. Rapid and effective treatment of burnt skin is vital to fasten wound closure and healing properly. Amniotic graft and Aloe vera are widely used as wound managing biomaterials. Sophisticated processing, high cost, availability, and the requirement of medics for transplantation limit the application of amnion grafts. We aim to prepare a novel gel from amnion combined with the Aloe vera extract for burn wound healing which overcome the limitations of graft. METHODS: Two percent human amniotic membrane (AM), Aloe vera (AV) and AM+AV gels were prepared. In vitro cytotoxicity, biocompatibility, cell attachment, proliferation, wound healing scratch assays were performed in presence of the distinct gels. After skin irritation study, second-degree burns were induced on dorsal region of Wistar rats; and gels were applied to observe the healing potential in vivo. Besides, macroscopical measurement of wound contraction and re-epithelialization; gel treated skin was histologically investigated by Hematoxylin and eosin (H&E) staining. Finally, quantitative assessment of angiogenesis, inflammation, and epithelialization was done. RESULTS: The gels were tested to be non-cytotoxic to nauplii and compatible with human blood and skin cells. Media containing 500 µg/mL AM+AV gel were observed to promote HaCaT and HFF1 cells attachment and proliferation. In vitro scratch assay demonstrated that AM+AV significantly accelerated wound closure through migration of HaCaT cells. No erythema and edema were observed in skin irritation experiments confirming the applicability of the gels. AV and AM+AV groups showed significantly accelerated wound closure through re-epithelialization and wound contraction with P < 0.01. Macroscopically, AM and AM+AV treated wound recovery rates were 87 and 90% respectively with P < 0.05. Histology analysis revealed significant epitheliazation and angiogenesis in AM+AV treated rats compared to control (P < 0.05). AM+AV treated wounds had thicker regenerated epidermis, increased number of blood vessels, and greater number of proliferating keratinocytes within the epidermis. CONCLUSION: We demonstrated that a gel consisting of a combination of amnion and Aloe vera extract has high efficacy as a burn wound healing product. Amniotic membrane combined with the carrier Aloe vera in gel format is easy to produce and to apply.

Ionic liquid-mediated ethosome for transdermal delivery of insulin.

Herein, we report ethosome (ET) formulations composed of a safe amount of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC)-based ionic liquid with various concentrations of ethanol as a carrier for the transdermal delivery of a high molecular weight drug, insulin. The Insulin-loaded ET vesicles exhibited long-term stability compared to conventional DMPC ETs, showing significantly higher drug encapsulation efficiency and increased skin permeation ability.

MiRANN: a reliable approach for improved classification of precursor microRNA using Artificial Neural Network model.

MicroRNA (miRNA) is a special class of short noncoding RNA that serves pivotal function of regulating gene expression. The computational prediction of new miRNA candidates involves various methods such as learning methods and methods using expression data. This article has proposed a reliable model - miRANN which is a supervised machine learning approach. MiRANN used known pre-miRNAs as positive set and a novel negative set from human CDS regions. The number of known miRNAs is now huge and diversified that could cover almost all characteristics of unknown miRNAs which increases the quality of the result (99.9% accuracy, 99.8% sensitivity, 100% specificity) and provides a more reliable prediction. MiRANN performs better than other state-of-the-art approaches and declares to be the most potential tool to predict novel miRNAs. We have also tested our result using a previous negative set. MiRANN, opens new ground using ANN for predicting pre-miRNAs with a promise of better performance.

RUNX1 colludes with NOTCH1 to reprogram chromatin in T cell acute lymphoblastic leukemia.

Runt-related transcription factor 1 (RUNX1) is oncogenic in diverse types of leukemia and epithelial cancers where its expression is associated with poor prognosis. Current models suggest that RUNX1 cooperates with other oncogenic factors (e.g., NOTCH1, TAL1) to drive the expression of proto-oncogenes in T cell acute lymphoblastic leukemia (T-ALL) but the molecular mechanisms controlled by RUNX1 and its cooperation with other factors remain unclear. Integrative chromatin and transcriptional analysis following inhibition of RUNX1 and NOTCH1 revealed a surprisingly widespread role of RUNX1 in the establishment of global H3K27ac levels and that RUNX1 is required by NOTCH1 for cooperative transcription activation of key NOTCH1 target genes including MYC, DTX1, HES4, IL7R, and NOTCH3. Super-enhancers were preferentially sensitive to RUNX1 knockdown and RUNX1-dependent super-enhancers were disrupted following the treatment of a pan-BET inhibitor, I-BET151.

Equity in antenatal care visits among adolescent mothers: An analysis of 54 country levels trend and projection of coverage from 2000 to 2030.

Background: Ensuring utilization of antenatal care (ANC) services by adolescent mothers (ages 10-19) is an enormous challenge in low-and middle-income countries (LMICs). This study provides the first comprehensive analysis of ANC visits among adolescent and adult mothers. Methods: Using all available Demographic and Health Survey and Multiple Indicator Cluster Surveys between 2000 and 2019 in 54 LMICs, we estimated proportion of ANC visits among women. Bayesian hierarchical regression models were used to estimate trend, projection, and determinants of single and four ANC visits (ANC1 and ANC4) independently. Equity analysis were performed to assess the magnitude of wealth-based and urban-rural inequalities in access to ANC visits. Results: Compared to women aged 36-49 years, coverage of ANC1 and ANC4 are expected to increase significantly for adolescent mothers and women aged 20-35 years. This increase was observed at the national level, as well as both urban and rural areas in most countries between 2000 and 2030. By 2030, the coverage of ANC1 is predicted to reach 80% or more in all countries except Angola, Central African Republic and Togo, whereas only 16 countries are predicted to reach 80% or more for ANC4. According to wealth quintile, the lowest inequalities with highest coverage of 80% or more ANC4 will be observed in Armenia, Cambodia, Dominican Republic, Ghana, Maldives, Indonesia, and Sao Tome and Principe in 2030. Determinant analysis found increased odds of receiving ANC visits during pregnancy for adolescent mothers with higher educational levels, frequency of listening/watching mass media, and various household socio-economic status factors. Conclusions: This study calls for advanced, innovative and cost-effective approaches to increase ANC coverage among adolescent mothers, particularly in rural areas and/or in low socioeconomic groups.

A Community-Based Cross-Sectional Study about the Knowledge, Attitude, and Practices of Food Safety Measures among Rural Households in Bangladesh.

Background: Food handlers have been found to play essential roles in transmitting foodborne diseases and can pose a significant public health problem. Our study aimed to assess the knowledge, attitude, and practices (KAP) of food safety measures among the rural households of Bangladesh. Materials and Methods: We conducted this community-based cross-sectional study among women above 18 years involved with food preparation in rural households of four villages in Bangladesh. A total of 400 respondents were selected using the multistage cluster sampling technique. Data were collected using pretested and predesigned questionnaires based on the World Health Organization's (WHO) five keys for food safety. We used Stata (Version 16) for all statistical analyses. Results: The mean age of the participants was 42.09 ± 12.96 years. The median KAP scores [interquartile range (IQR)] were 7 (21-10), 16 (5-18), and 26 (9-30), respectively. We found the median KAP scores were significantly lower in the age group >55 years than in age groups of 18-25, 26-35, 36-45, and 46-55 years (P < 0.05 for all). In addition, the median KAP scores were significantly higher in respondents who were married, literate, employed/active, living in pakka/semipakka house, and with a monthly family income of >5,000 BDT (P < 0.05 for all). Among all, 33.75%, 80.25%, and 69.00% had good (≥80% of total) KAP scores, respectively. Multivariable regression analysis revealed that monthly family income >5,000 BDT was a significant predictor of good knowledge [Adjusted Odds Ratio (aOR): 3.51, 95%CI: 1.55-7.98], good attitude (aOR: 5.82, 95%CI: 2.80-11.70), and good practice (aOR: 3.18, 95%CI: 1.67-6.07). Age >55 years was a significant predictor of good attitude (aOR: 0.38, 95%CI: 0.17-0.81) and good practice (aOR: 0.48, 95%CI: 0.21-0.89). Having ≤4 members in the family was a significant predictor of good practice (aOR: 1.85, 95%CI: 1.13-3.03) regarding food safety measures. Conclusion: The study found that KAP among rural Bangladeshi women regarding food safety were relatively satisfactory. However, having a poor monthly income and living in a large family were impediments to good food-safety practices where work can be done. The findings of this study may help develop health intervention programs for food handlers to further improve KAP toward food safety, thereby reducing foodborne illness in households.

Whole-genome sequencing of a year-round fruiting jackfruit (Artocarpus heterophyllus Lam.) reveals high levels of single nucleotide variation.

Jackfruit (Artocarpus heterophyllus Lam.) is the national fruit of Bangladesh and produces fruit in the summer season only. However, jackfruit is not commercially grown in Bangladesh because of an extremely high variation in fruit quality, short seasonal fruiting (June-August) and susceptibility to abiotic stresses. Conversely, a year-round high yielding (ca. 4-fold higher than the seasonal variety) jackfruit variety, BARI Kanthal-3 developed by the Bangladesh Agricultural Research Institute (BARI) derived from a wild accession found in Ramgarh of Chattogram Hiltracts of Bangladesh, provides fruits from September to June. This study aimed to generate a draft whole-genome sequence (WGS) of BARI Kanthal-3 to obtain molecular insights including genes associated with year-round fruiting trait of this important unique variety. The estimated genome size of BARI Kanthal-3 was 1.04-gigabase-pair (Gbp) with a heterozygosity rate of 1.62%. De novo assembly yielded a scaffolded 817.7 Mb genome while a reference-guided approach, yielded 843 Mb of genome sequence. The estimated GC content was 34.10%. Variant analysis revealed that BARI Kanthal-3 included 5.7 M (35%) and 10.4 M (65%) simple and heterozygous single nucleotide polymorphisms (SNPs), and about 90% of all these polymorphisms are in inter-genic regions. Through BUSCO assessment, 97.2% of the core genes were represented in the assembly with 1.3% and 1.5% either fragmented or missing, respectively. By comparing identified orthologous gene groups in BARI Kanthal-3 with five closely and one distantly related species of 10,092 common orthogroups were found across the genomes of the six species. The phylogenetic analysis of the shared orthogroups showed that A. heterophyllus was the closest species to BARI Kanthal-3 and orthogroups related to flowering time were found to be more highly prevalent in BARI Kanthal-3 compared to the other Arctocarpus spp. The findings of this study will help better understanding the evolution, domestication, phylogenetic relationships, year-round fruiting of this highly nutritious fruit crop as well as providing a resource for molecular breeding.

Alcohol-based Hand Sanitizers amid COVID-19: Chemical Formulation, Analysis, Safety.

Alcohol-based hand sanitizers (ABHSs) containing ethanol (EtOH) or isopropyl alcohol (IPA) to inactivate microorganisms help prevent the spread of respiratory diseases. These products have become very popular during the COVID-19 pandemic. Apart from vaccines or other preventative antiseptic measures, the majority of consumers have relied on different types of ABHSs to disinfect their hands. As a result, there has been a global rush in the demand for these ABHSs and other antiseptic hygiene products. This has resulted in the formation of many new commercial sanitizer producers. There are around fifty companies of varying sizes that have been marketing their ABHSs in Bangladesh, most of which have only been manufacturing their products for the first time since the COVID-19 pandemic. To monitor the quality and components of these products, the Bangladesh Council of Scientific and Industrial Research (BCSIR) analyzed approximately 200 different hand sanitizer samples using GC-FID method. All samples were alcohol-based except for 3 which were alcohol-free aqueous hand sanitizers. Of the supplied formulated ABHSs, 80 samples were found to contain only IPA and 54 contained only EtOH. However, 28 samples were found to be contaminated with methanol (MeOH), 7 samples contained only MeOH and 18 samples contained both EtOH and IPA. This is the first study to explore the analysis of alcohol content in formulated ABHSs and their marketing status in Bangladesh, but the findings could be of use in other jurisdictions as similar issues have been raised in many parts of the world.

Single-cell profiling reveals a memory B cell-like subtype of follicular lymphoma with increased transformation risk.

Follicular lymphoma (FL) is an indolent cancer of mature B-cells but with ongoing risk of transformation to more aggressive histology over time. Recurrent mutations associated with transformation have been identified; however, prognostic features that can be discerned at diagnosis could be clinically useful. We present here comprehensive profiling of both tumor and immune compartments in 155 diagnostic FL biopsies at single-cell resolution by mass cytometry. This revealed a diversity of phenotypes but included two recurrent patterns, one which closely resembles germinal center B-cells (GCB) and another which appears more related to memory B-cells (MB). GCB-type tumors are enriched for EZH2, TNFRSF14, and MEF2B mutations, while MB-type tumors contain increased follicular helper T-cells. MB-type and intratumoral phenotypic diversity are independently associated with increased risk of transformation, supporting biological relevance of these features. Notably, a reduced 26-marker panel retains sufficient information to allow phenotypic profiling of future cohorts by conventional flow cytometry.

Association between body mass index and oesophageal cancer mortality: a pooled analysis of prospective cohort studies with >800 000 individuals in the Asia Cohort Consortium.

BACKGROUND: The association between body mass index (BMI) and oesophageal cancer (OC) has been consistently negative among Asians, whereas different associations based on histological OC subtypes have been observed in Europeans and North Americans. We examined the association between BMI and OC mortality in the Asia Cohort Consortium. METHODS: We performed a pooled analysis to evaluate the association between BMI and OC mortality among 842 630 Asians from 18 cohort studies. Cox regression models were used to estimate hazard ratios (HRs) and 95% CIs. RESULTS: A wide J-shaped association between BMI and overall OC mortality was observed. The OC mortality risk was increased for underweight (BMI <18.5 kg/m2: HR = 2.20, 95% CI 1.80-2.70) and extreme obesity (BMI ≥35 kg/m2: HR = 4.38, 95% CI 2.25-8.52) relative to the reference BMI (23-25 kg/m2). This association pattern was confirmed by several alternative analyses based on OC incidence and meta-analysis. A similar wide J-shaped association was observed in oesophageal squamous cell carcinoma (OSCC). Smoking and alcohol synergistically increased the OC mortality risk in underweight participants (HR = 6.96, 95% CI 4.54-10.67) relative to that in reference BMI participants not exposed to smoking and alcohol. CONCLUSION: Extreme obesity and being underweight were associated with an OC mortality risk among Asians. OC mortality and BMI formed a wide J-shaped association mirrored by OSCC mortality. Although the effect of BMI on OSCC and oesophageal adenocarcinoma mortality can be different in Asians, further research based on a large case-control study is recommended.

CRIS: complete reconstruction of immunoglobulin V-D-J sequences from RNA-seq data.

MOTIVATION: B cells display remarkable diversity in producing B-cell receptors through recombination of immunoglobulin (Ig) V-D-J genes. Somatic hypermutation (SHM) of immunoglobulin heavy chain variable (IGHV) genes are used as a prognostic marker in B-cell malignancies. Clinically, IGHV mutation status is determined by targeted Sanger sequencing which is a resource-intensive and low-throughput procedure. Here, we describe a bioinformatic pipeline, CRIS (Complete Reconstruction of Immunoglobulin IGHV-D-J Sequences) that uses RNA sequencing (RNA-seq) datasets to reconstruct IGHV-D-J sequences and determine IGHV SHM status. RESULTS: CRIS extracts RNA-seq reads aligned to Ig gene loci, performs assembly of Ig transcripts and aligns the resulting contigs to reference Ig sequences to enumerate and classify SHMs in the IGHV gene sequence. CRIS improves on existing tools that infer the B-cell receptor repertoire from RNA-seq data using a portion IGHV gene segment by de novo assembly. We show that the SHM status identified by CRIS using the entire IGHV gene segment is highly concordant with clinical classification in three independent chronic lymphocytic leukemia patient cohorts. AVAILABILITY AND IMPLEMENTATION: The CRIS pipeline is available under the MIT License from https://github.com/Rashedul/CRIS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.

Cholinesterase inhibitory activity of tinosporide and 8-hydroxytinosporide isolated from Tinospora cordifolia: In vitro and in silico studies targeting management of Alzheimer's disease.

Tinosporide and 8-hydroxytinosporide isolated from Tinospora cordifolia were evaluated for acetylcholinesterase (AChE) and butylcholinesterase (BuChE) inhibitory activities. The structure of the compound was confirmed by spectroscopic analysis, whereas cholinesterase inhibition was investigated by Ellman method using donepezil as standard drug and the data were presented as IC50 (µg/ml ± SEM). Furthermore, donepezil, tinosporide and 8-hydroxytinosporide were executed for docking analysis. The results from the isolated compounds TC-16R confirmed as tinosporide promisingly inhibited AChE with IC50 value of 13.45 ± 0.144, whereas TC-19R confirmed as 8-hydroxytinosporide moderately inhibited AChE with IC50 value of 46.71 ± 0.511. In case of BuChE inhibition, the IC50 values were found to be 408.50 ± 17.197 and 317.26 ± 6.918 for tinosporide and 8-hydroxytinosporide, respectively. The in silico studies revealed that the ligand tinosporide fit with the binding sites and inhibited AChE. Overall, the study findings suggested that tinosporide would be a complementary noble molecule of donepezil which is correlated with its pharmacological activity through in vitro studies, while 8-hydroxytinosporide modestly inhibited BuChE and the results are very close to the standard donepezil.

Genome Sequences of Two Novel Coronavirus (SARS-CoV-2) Isolates from Dhaka, Bangladesh.

This study reports the genome sequences of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains detected in the nasopharyngeal swab specimens of two coronavirus disease 2019 (COVID-19) patients from Dhaka, Bangladesh.

RUNX1 promotes cell growth in human T-cell acute lymphoblastic leukemia by transcriptional regulation of key target genes.

RUNX1 is frequently mutated in T-cell acute lymphoblastic leukemia (T-ALL). The spectrum of RUNX1 mutations has led to the notion that it acts as a tumor suppressor in this context; however, other studies have placed RUNX1, along with transcription factors TAL1 and NOTCH1, as core drivers of an oncogenic transcriptional program. To reconcile these divergent roles, we knocked down RUNX1 in human T-ALL cell lines and deleted Runx1 or Cbfb in primary mouse T-cell leukemias. RUNX1 depletion consistently resulted in reduced cell proliferation and increased apoptosis. RUNX1 upregulated variable sets of target genes in each cell line, but consistently included a core set of oncogenic effectors including insulin-like growth factor 1 receptor (IGF1R) and NRAS. Our results support the conclusion that RUNX1 has a net positive effect on cell growth in the context of established T-ALL.