The transition/transversions bias for nucleotide substitutions models varies from 0.56 to 0.59 in MEGA output. The average nitrogenous bases frequency of U, C, A, and G are 31.74, 19.48, 28.04, and 20.74, respectively in percentages. Overall the genomic data analysis of SARS-CoV-2, SARS-CoV, and MERS-CoV highlights the close genetic relationship.Maize seed pigmentation is one of the important issue to develop maize seed breeding. The differently gene expression was characterized and compared for three inbred lines, such as the pigment accumulated seed (CM22) and non-pigmented seed (CM5 and CM19) at 10 days after pollination. We obtained a total of 63,870, 82,496, and 54,555 contigs by de novo assembly to identify gene expression in the CM22, CM5, and CM19, respectably. In differentially expressed gene analysis, it was revealed that 7,044 genes were differentially expressed by at least two-fold, with 4,067 upregulated in colored maize inbred lines and 2,977 upregulated in colorless maize inbred lines. Of them,18 genes were included to the anthocyanin biosynthesis pathways, while 15 genes were upregulated in both CM22/5 and CM22/19. Additionally, 37 genes were detected in the metabolic pathway concern to the seed pigmentation by BINs analysis using MAPMAN software. Finally, these differently expressed genes may aid in the research on seed pigmentation in maize breeding programs.Streptomyces coelicolor is a gram-positive soil bacterium which is well known for the production of several antibiotics used in various biotechnological applications. But numerous proteins from its genome are considered hypothetical proteins. Therefore, the present study aimed to reveal the functions of a hypothetical protein from the genome of S. coelicolor. Several bioinformatics tools were employed to predict the structure and function of this protein. Sequence similarity was searched through the available bioinformatics databases to find out the homologous protein. The secondary and tertiary structure were predicted and further validated with quality assessment tools. Furthermore, the active site and the interacting proteins were also explored with the utilization of CASTp and STRING server. The hypothetical protein showed the important biological activity having with two functional domain including POD-like_MBL-fold and rhodanese homology domain. The functional annotation exposed that the selected hypothetical protein could show the hydrolase activity. Furthermore, protein-protein interactions of selected hypothetical protein revealed several functional partners those have the significant role for the bacterial survival. At last, the current study depicts that the annotated hypothetical protein is linked with hydrolase activity which might be of great interest to the further research in bacterial genetics.The prevalence of early-onset type 2 diabetes (EOT2D) is increasing in Asian countries. Genome-wide association studies performed in European and various other populations have identified associations of numerous variants with type 2 diabetes in adults. However, the genetic component of EOT2D which is still unexplored could have similarities with late-onset type 2 diabetes. Here in the present study we aim to identify the association of variants with EOT2D in South Indian population. Twenty-five variants from 18 gene loci were genotyped in 1,188 EOT2D and 1,183 normal glucose tolerant subjects using the MassARRAY technology. We confirm the association of the HHEX variant rs1111875 with EOT2D in this South Indian population and also the association of CDKN2A/2B (rs7020996) and TCF7L2 (rs4506565) with EOT2D. Logistic regression analyses of the TCF7L2 variant rs4506565(A/T), showed that the heterozygous and homozygous carriers for allele 'T’ have odds ratios of 1.47 (95% confidence interval [CI], 1.17 to 1.83; p = 0.001) and 1.65 (95% CI, 1.18 to 2.28; p = 0.006) respectively, relative to AA homozygote. For the HHEX variant rs1111875 (T/C), heterozygous and homozygous carriers for allele 'C’ have odds ratios of 1.13 (95% CI, 0.91 to 1.42; p = 0.27) and 1.58 (95% CI, 1.17 to 2.12; p = 0.003) respectively, relative to the TT homozygote. For CDKN2A/2B variant rs7020996, the heterozygous and homozygous carriers of allele 'C’ were protective with odds ratios of 0.65 (95% CI, 0.51 to 0.83; p = 0.0004) and 0.62 (95% CI, 0.27 to 1.39; p = 0.24) respectively, relative to TT homozygote. This is the first study to report on the association of HHEX variant rs1111875 with EOT2D in this population.Single-cell RNA sequencing (scRNA-seq) has been widely applied to provide insights into the cell-by-cell expression difference in a given bulk sample. Accordingly, numerous analysis methods have been developed. As it involves simultaneous analyses of many cell and genes, efficiency of the methods is crucial. The conventional cell type annotation method is laborious and subjective. Here we propose a semi-automatic method that calculates a normalized score for each cell type based on user-supplied cell type-specific marker gene list. The method was applied to a publicly available scRNA-seq data of mouse cardiac non-myocyte cell pool. Annotating the 35 t-stochastic neighbor embedding clusters into 12 cell types was straightforward, and its accuracy was evaluated by constructing co-expression network for each cell type. Gene Ontology analysis was congruent with the annotated cell type and the corollary regulatory network analysis showed upstream transcription factors that have well supported literature evidences. The source code is available as an R script upon request.

Medullary thyroid carcinoma (MTC) is an aggressive malignancy originating from the parafollicular C cells. Preoperatively, thyroid nodule fine-needle aspiration cytology (FNAC) and pathogenic gene mutations are definitive in approximately one-half of cases. MicroRNAs (miRNAs) are endogenous, noncoding, single-stranded RNAs that regulate gene expression, a characteristic that confers the potential for identifying malignancy. In the current study, the authors hypothesized that differential pairwise (diff-pair) analysis of miRNA expression levels would reliably identify MTC in FNA samples.

The relative abundance of 10 different miRNAs in total nucleic acids was obtained from ThyraMIR test results. Diff-pair analysis was performed by subtracting the critical threshold value of one miRNA from the critical threshold values of other miRNAs. Next-generation sequencing with the ThyGeNEXT panel identified oncogenic gene alterations. The discovery cohort consisted of 30 formalin-fixed, paraffin-embedded benign and mte FNAC findings.

This study was designed to test the hypothesis that the effectiveness of intensive treatment for locoregionally advanced head and neck cancer (LAHNC) depends on the proportion of patients’ overall event risk attributable to cancer.

This study analyzed 22,339 patients with LAHNC treated in 81 randomized trials testing altered fractionation (AFX; Meta-Analysis of Radiotherapy in Squamous Cell Carcinomas of Head and Neck [MARCH] data set) or chemotherapy (Meta-Analysis of Chemotherapy in Head and Neck Cancer [MACH-NC] data set). Generalized competing event regression was applied to the control arms in MARCH, and patients were stratified by tertile according to the ω score, which quantified the relative hazard for cancer versus competing events. The classifier was externally validated on the MACH-NC data set. The study tested for interactions between the ω score and treatment effects on overall survival (OS).

Factors associated with a higher ω score were a younger age, a better performance status, an oral cavity site, higher T and N categories, and a p16-negative/unknown status. The effect of AFX on OS was greater in patients with high ω scores (hazard ratio [HR], 0.92; 95% confidence interval [CI], 0.85-0.99) and medium ω scores (HR, 0.91; 95% CI, 0.84-0.98) versus low ω scores (HR, 0.97; 95% CI, 0.90-1.05; P for interaction = .086). The effect of chemotherapy on OS was significantly greater in patients with high ω scores (HR, 0.81; 95% CI, 0.75-0.88) and medium ω scores (HR, 0.86; 95% CI, 0.78-0.93) versus low ω scores (HR, 0.96; 95% CI, 0.86-1.08; P for interaction = .011).

LAHNC patients with a higher risk of cancer progression relative to competing mortality, as reflected by a higher ω score, selectively benefit from more intensive treatment.

LAHNC patients with a higher risk of cancer progression relative to competing mortality, as reflected by a higher ω score, selectively benefit from more intensive treatment.

Many group-living primate species have evolved the capacity for some individuals to live alone for part of their lives, but this solitary life stage has rarely been the subject of focused research. The mantled howler monkey (Alouatta palliata) is a social primate species with bisexual dispersal that lives in mixed-sex groups with low male-to-female sex ratios. Consequently, males often spend a long period of their lives as solitary individuals. This study compares the tree use, feeding, and long-distance vocalization behavior of solitary and group-living mantled howler monkey males living within a fragmented rainforest in Costa Rica, La Suerte Biological Research Station. Based on differences in competitive ability between solitary and group-living males, we predicted that lone males would be found in significantly smaller feeding and resting trees, consume more low-quality foods, and produce shorter howling bouts made at lower rates than group-living males.

We collected data on tree use and feeding during 30-min focal samples on male focal animals, recording data at 2-min intervals. We measured the trees in which the monkeys fed and rested for two or more intervals, and recorded the plant parts consumed. We recorded howling behavior using all-occurrences sampling.

Lone males used significantly smaller feeding and resting trees, consumed more low-quality foods, and howled at lower rates but had longer howling bouts triggered by anthropogenic noise more than group-living males.

Our results demonstrate that lone males differ in their behavioral ecology compared to group-living males, thus improving understanding of the solitary male life stage in primates.

Our results demonstrate that lone males differ in their behavioral ecology compared to group-living males, thus improving understanding of the solitary male life stage in primates.

This study explores whether ancient Atacama Desert populations in northern Chile were exposed to endemic boron contamination.

Using Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry (LA-ICP-MS), we studied 144 strands of ancient mummy hair, ranging from 3000 B.C. to 1500 A.D., excavated from the Lluta, Azapa, and Camarones valleys in northern Chile. We tested whether these ancient populations showed signs of significant boron concentration in hair tissue.

On average, all individuals from these valleys showed high boron concentrations, ranging from 1.5 to 4 times above the average boron concentration in contemporary hair (baseline <0.85 μg/g). The boron concentration in mummy hair varied according to the main geographic areas mentioned above.

The rivers of northern Chile have high geogenic boron concentrations. They contain 38 times above the recommended limit for human consumption. Geogenic boron contamination likely played a role in population morbidity and the types of crops that were cultivated in antiquity.