National Center For Biotechnology Information Research Articles

Gut microbiota signatures in inflammatory bowel disease.

Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), affect millions of people worldwide with increasing incidence. Several studies have shown a link between gut microbiota composition and IBD, but results are often limited by small sample sizes. We aimed to re-analyze publicly available fecal microbiota data from IBD patients. We extracted original fecal 16S rRNA amplicon sequencing data from 45 cohorts of IBD patients and healthy individuals using the BioProject database at the National Center for Biotechnology Information. Unlike previous meta-analyses, we merged all study cohorts into a single dataset, including sex, age, geography, and disease information, based on which microbiota signatures were analyzed, while accounting for varying technical platforms. Among 2518 individuals in the combined dataset, we discovered a hitherto unseen number of genera associated with IBD. A total of 77 genera associated with CD, of which 38 were novel associations, and a total of 64 genera associated with UC, of which 28 represented novel associations. Signatures were robust across different technical platforms and geographic locations. Reduced alpha diversity in IBD compared to healthy individuals, in CD compared to UC, and altered microbiota composition (beta diversity) in UC and especially in CD as compared to healthy individuals were found. Combining original microbiota data from 45 cohorts, we identified a hitherto unseen large number of genera associated with IBD. Identification of microbiota features robustly associated with CD and UC may pave the way for the identification of new treatment targets.

Docking of vaginal Lactobacillus isolates as a potential bactericidal agent in Kirkuk 2022

Abstract Background: Because the female genital tract is a complex microbial community that plays various roles in disease development. Alternatively, Lactobacilli in the vaginal environment play an important role in maintaining a healthy vaginal ecosystem by preventing pathogenic overgrowth. Objective: Therefore, this study was suggested to isolate vaginal Lactobacilli with antibacterial activity. Materials and Methods: Two hundred and sixty women participated in this study aged between 15 and 50 years divided into two cohorts of bacterial vaginosis (BV): infected and healthy individuals. BV-isolates isolated and identified according to microbiological and biochemical assays. Accordingly, Lactobacillus isolates were further identified through genomic DNA sequencing of the 16S rRNA, and the results were statistically analyzed. Results: A significant increase (P < 0.05) in the BV-infected women in the age range of 21–30 and 31–40 was recorded, with the percentages of 40.62% and 31.88%, respectively. Alternatively, a significant decrease (P > 0.05) in the percentages of vaginal Lactobacillus species between women of Cohort 1 and Cohort 2 recorded the ratios of 3.125% and 31% validating Lactobacilli presence as a sign of a healthy vaginal environment. Accordingly, four Lactobacillus isolates were assigned for their broad spectrum of antibacterial activity against several pathogenic bacteria. Moreover, results of the partial DNA sequencing revealed the isolation of four Limosilactobacillus fermentum strains registered at the National Center for Biotechnology Information (NCBI) under specific gene bank accession numbers. Conclusion: Effective Lactobacillus species with potential bactericidal activity validates vaginal health.

Evaluation of Inoculation with Bradyrhizobium manausense and Bradyrhizobium venae on the Elemental content of Cowpea Plant in Gypsum Soil

A field experiment was conducted during the spring season on 3/25/2022 in the fields of the University of Tikrit / College of Agriculture located in the research station of the Department of Soil Sciences and Water Resources, with the aim of studying the effect of inoculation with Rhizobia bacteria and nitrogen fertilization on the growth and yield of cowpea in gypsum soil, conducted in a randomized complete block design. R. C. B. D With three replications, the experiment included two main factors: inoculation with rhizobium bacteria, and the second factor was nitrogen fertilization. The inoculation factor was three levels (A0 = no inoculation, A1 = inoculation with the first strain, Bradyrhizobium manausense, and A2 = inoculation with the second strain, Bradyrhizobium vignae), and the second factor was nitrogen fertilization. At three levels N0 and N1 = 40 kg / ha and N2 = 80 kg / ha, the process of isolation and development of Rhizobium bacteria was conducted on the optional medium (YEMA), and the two isolates were identified and recorded in the National Center for Biotechnology Information (NCBI) by number Global OP740389 Bradyrhizobium vignae, as for the results of the field experiment, the inoculation treatment with root nodes bacteria Bradyrhizobium vignae was superior to the control treatment and even to the second strain Bradyrhizobium manausense in all studied traits of cowpea plant, and the percentage increase of the inoculation treatment with Bradyrhizobium vignae with 40 kg of nitrogen fertilizer was higher than The control treatment in the number of root nodes and their wet weight (1474.87, 267.101)%, respectively, and the concentration of nitrogen, phosphorus and potassium in the vegetative part (61.300, 1.600, 7.102)%, respectively.

A Systematic Review: Role of miRNA in Gastric Cancer Risk, Onset, and Progression

Abstract Background: Understanding the epidemiological patterns and futuristic trends in gastric cancer (GC) is crucial since the worldwide epidemiological status has altered significantly over time. GC is one of the most prevalent malignancies in terms of becoming an important cause of cancer-related deaths worldwide. However, recent years have seen a remarkable improvement in the study of microRNAs (miRNAs) controlling gene expression where miRNA aberrations have been linked to the development and incidence of GC. Methods: A considerate role of miRNAs in gastric carcinogenesis could deliver great perceptions toward understanding the physiology of tumor development. Therefore, this article reviews the epidemiology, risk factor, classification, and involvement of miRNAs in GC regulation and genes. During the process, more than 150 well-documented articles were reviewed, and collective data information was gathered through search databases such as the World Health Organization, National centre for biotechnology information (NCBI), and Google Scholar. Following this analysis, this review article comprises a number of miRNAs that are associated with types of tumor, stages of the tumor, GC prognosis, their effects on Helicobacter pylori-mediated infection, and potential applications in chemotherapy. Results: This review, thereby, supports a collective and comparative strategic role of miRNA, prominent attention of aberrantly expressed miRNAs, and their associated mechanism of cancer development that have been emphasized on exploiting new anticancer targets, thus effectuating the critical and comparative data for different subtypes, diagnosis, occurrence, and survival rate of GC among men and women.

Effect of Alcoholic Extract of Syntrichia intermedia on some Yeasts Isolated from Mobile Phones and the User’s Finger

Syntrichia intermedia was isolated from the Amadiya region in northern Iraq for the first time, as it was used against the yeast Brettanomyces bruxellensis, Candida krusei and the yeast Meyerozyma caribbica isolated fore the first one and registered as a new strain in the Gen Bank of the National Center for Biotechnology Information (NCBI) with identification number LC723825.1. Three methods were used to determine the effect of the alcoholic extract of S. intermedia at the following concentrations, 1, 2, 4, 6, 8, and 10 mg/ml against yeast isolates, When using the first method-turbidity measurement the concentrations were shown starting from 1 mg/ml an inhibitory effect respectively up to the highest concentration of 10 mg/ml against yeast B. bruxellensis, C. krusei and M. caribbica. and When using the second method-disc diffusion the following concentration showed the highest inhibition percentage the concentration of 2 mg / ml with a diameter of (12.50 mm) against the yeast B. bruxellensis. and The concentrations 1 with a diameter of (11.0 mm) against the yeast C. krusei and The concentrations 4 mg / ml with a diameter of (11.50 mm) Compared with the antibiotic Nystatin which showed a higher percentage of inhibition than the alcoholic extract, While the third method-diffusion by wells was used and the concentration of 4 mg / ml showed the highest percentage of inhibition with a diameter of (23.0 mm) for yeast B. bruxellensis and a concentration of 6 mg / ml showed the highest percentage of inhibition with a diameter of (19.00 mm) against yeast C. krusei. and a concentration of 8 mg / ml showed the highest percentage of inhibition with a diameter of (15.67 mm) against yeast M. caribbica compared with the antibiotic Nystatin, which showed less inhibition than the alcoholic extract, so the yeast B. bruxellensis was more sensitive to the alcoholic extract, followed by the yeast M. caribbica. Then the yeast When using the method of diffusion by discs and digging, either by measuring the turbidity the yeast M. caribbica was the most sensitive to the alcoholic extract followed by C. krusei Then the yeast B. bruxellensis, so the turbidity measurement method is considered one of the best methods that can be used to measure the effect of the alcoholic extract because of measuring the turbidity using a spectrophotometer, followed by the diffusion method by wells, then the method of diffusion by discs.

Phylogenetic analysis of Aedes species distributed in Taif Province, Saudi Arabia, based on mitochondrial COX1 sequences

AbstractAs Aedes mosquitoes are the predominant carriers of arboviruses responsible for global dengue fever and chikungunya outbreaks, understanding their genetic diversity and population structure can enhance dengue prevention and vector control efforts. Although sympatric cryptic species have been acknowledged in Aedes species subgroups in Southeast Asia, little information is available regarding the occurrence and dispersal of cryptic Aedes species in Saudi Arabia. In the present investigation, we intend to analyze genetic variations and perform a phylogenetic study of sympatric Aedes samples collected from various locations in Taif Province, Saudi Arabia. The locus of mitochondrial DNA cytochrome c oxidase subunit 1 (COX1, analyzed with DNA barcoding) was utilized to determine genetic variance and to build phylogenetic trees. For species identification, the COX1 sequences of Aedes samples from Taif Province were compared with those of Aedes samples from GenBank (National Center for Biotechnology Information, NCBI). To identify phylogenetic relationships and genetic variability, phylogenetic trees were created using Taif Province samples, GenBank A. albopictus samples, and GenBank A. aegypti samples. The phylogenetic analysis revealed that some Taif samples (A3, A7, F2, F4, F1, A4, A1, F9 and F6) were closer to A. aegypti and A. albopictus samples from Africa and East Asia, especially Kenya and Malaysia. Whereas other samples (F9, F6, A4, F1 and A1) were closer to the GenBank A. aegypti samples KP843383 (Thailand), HM399357(Australia), MK533632 (Kenya), KX420460 (Kenya), KU495081 (Australia) and MF179160 (China) than the remaining Taif samples. Overall, our findings demonstrate that examining the genetic diversity and phylogenetic linkages of Aedes samples can aid in understanding the evolution of Aedes cryptic species in the western regions of Saudi Arabia.

RCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R.

The sequencing revolution requires accurate taxonomic classification of DNA sequences. Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of both DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa then are currently curated by professional staff. Thus there is a growing need for an easy to implement computational tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R which, like it's predecessor, relies on sequence homology and PCR primer compatibility instead of keyword-searches to avoid limitations of user-defined metadata. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire a set of sequences analogous to PCR products containing a user-defined set of primer sequences. Next, these seeds are used to iteratively blast search seed sequences against a local copy of the National Center for Biotechnology Information (NCBI) formatted nt database using a taxonomic-rank based stratified random sampling approach ( blast_seeds() ). This results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer-specific reference barcode sequences from NCBI. Databases can then be compared (compare_db()) to determine read and taxonomic overlap. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, fungal ITS, and Leray CO1 loci than CRABS, MetaCurator, RESCRIPt, and ecoPCR reference databases. We then further demonstrate the utility of rCRUX by generating 24 reference databases for 20 metabarcoding loci, many of which lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.

Transposon-aided capture (TRACA) of plasmids from the human gut.

The gut microbiota consists of a vast and diverse assemblage of microorganisms that play a pivotal role in maintaining host health. Nevertheless, a significant portion of the human gut microbiota remains uncultivated. Plasmids, a type of MGE, assume a critical function in the biological evolution and adaptation of bacteria to varying environments. To investigate the plasmids present within the gut microbiota community, we used the transposon-aided capture method (TRACA) to explore plasmids derived from the gut microbiota. In this study, fecal samples were collected from two healthy human volunteers and subsequently subjected to the TRACA method for plasmid isolation. Then, the complete sequence of the plasmids was obtained using the genome walking method, and sequence identity was also analyzed. A total of 15 plasmids were isolated. At last, 13 plasmids were successfully sequenced, of which 12 plasmids were highly identical to the plasmids in the National Center for Biotechnology Information (NCBI) database and were all small plasmids. Furthermore, a putative novel plasmid, named pMRPHD, was isolated, which had mobilized elements (oriT and oriV) and a potential type II restriction-modification (R-M) system encoded by DNA cytosine methyltransferase and type II restriction enzyme (Ban I), whose specific functions and applications warrant further exploration.

Prevalence of Leucocytozoon infection in domestic birds in Ghana.

Leucocytozoon is a haemosporidian parasite known to cause leucocytozoonosis in domestic and wild birds in most parts of the world. It is an important pathogen, as some species can be pathogenic, especially in domestic birds. One of the factors affecting poultry health management worldwide is parasitism. However, the study of haemosporidian parasites in Ghana is still lacking. This study sought to assess the prevalence and diversity of Leucocytozoon parasites in domestic birds in Ghana. Blood samples were collected from domestic birds in Ghana's Bono and Eastern regions to screen for Leucocytozoon parasites. Thin blood smears were prepared for microscopy and DNA was extracted from whole blood kept in ethylenediaminetetraacetic acid (EDTA) tubes for PCR. Due to the large number of samples, real-time PCR was performed to amplify the conserved rDNA gene. Two different nested PCR protocols were performed on the positive samples obtained from real-time PCR results, to amplify a partial region of the mitochondrial cytochrome b gene and the amplicons were sequenced. Sequencing revealed six new lineages of Leucocytozoon sp. recovered in 976 individual domestic birds and these sequences were deposited in the National Center for Biotechnology Information (NCBI) GenBank. An overall Leucocytozoon prevalence of 11.6% was reported in all birds sampled. The most prevalent lineage LGHA146 (GenBank accession no. OM643346) (93.8%) was found infecting 3 bird species, Gallus gallus, Meleagris gallopavo, and Anas platyrhynchos. Phylogenetic analysis revealed that the new lineages (GenBank accession nos. OM643342, OM643343, OM643344, OM643345, OM643346, and OM643347), reported in this study were closely related to Leucocytozoon schoutedeni. We suggest that further studies be conducted to evaluate the effect of these parasite species on the general well-being of poultry in Ghana.

The Human Leukemia Immunopeptidome Is Driven By Pathogenic Molecular Variant Biotypes

Background Historically, acute myelogenous leukemia (AML) has been characterized as having a low somatic mutational burden and is predicted to have low neoantigen levels compared to solid tumors. However, recent data has shown that AML is an immunogenic malignancy and oncogenic driver mutations promote immune escape through immunoediting. Downregulation of human leukocyte antigen (HLA) class II HLA-DRB1, HLA-DQB1, HLA-DPA1 and HLA-DPB1 gene expression on leukemia cells has previously been associated with immune escape in AML following allogeneic hematopoietic stem cell transplantation (allo-HCT). While allo-HCT and cellular therapies are well-known potentially curative treatment options in AML, the human leukemia immunopeptidome has still not been well characterized. Here, we sought to uncover the human leukemia immunopeptidome by detecting differential major histocompatibility complex (MHC) class I neopeptide expression using molecular biotype subgroups. Methods We conducted retrospective analysis on 31 patients with hematopoietic malignancies including AML, chronic myelomonocytic leukemia (CMML), myelodysplastic syndrome/myeloproliferative neoplasm (MDS/MPN), MDS, chronic myelogenous leukemia (CML) and other hematopoietic malignancies (i.e. NK cell leukemia) at MedStar Georgetown University Hospital. Mutations were identified using next generation sequencing and separated into the following annotated molecular biotypes based on the mechanism of pathogenesis: Group 0 (G0) DNA repair, G1 splicing, G2 transcription factor, G3 kinase activation, G4 epigenetic modification, G5 chromatin remodeling, G6 cohesin, G7 tumor suppressor (i.e. p53), G8 telomere maintenance, G9 histone modification, G10 nucleotransport (i.e. NPM1) and G11 cell cycle regulation. FASTA nucleotide sequences were obtained by subjecting mutations to transcript expression and cDNA alignment in the National Center for Biotechnology Information (NCBI) gene database. MHC class I binding neopeptides were identified by mapping patient FASTA nucleotide sequences and HLA class I alleles in the Net MHC pan 4.1 database. Neopeptides were grouped by % Rank and categorized as weak binding (WB) if > 0.5 and strong binding (SB) if ≤0.5. Descriptive and inferential statistics were performed using SAS. Results Thirty-one patients were evaluated including 17 AML (54.8%), 5 MDS (16.1%), 3 CMML (9.7%), 2 MDS/MPN (6.5%), 1 CML (3.2%) and 3 hematopoietic malignancies (9.7%). The median age was 65 years (range 28 -89); 43.8% were female and 43.3% were African American (AA). 144mutations were identified; thus far, 82 mutations have been subjected to FASTA NP_ protein extraction. The G3 biotype had the highest frequency of neopeptide bindings (n=59) followed by G2 (n=50) and G4 biotypes (n=42) ( Fig.1). Among patients with MDS, smokers were more likely to exhibit neopeptide binding compared to non-smokers (p=0.032). Patients with neopeptide binding had a longer median overall survival (mOS) compared to patients without neopeptide binding (mOS = 566 vs 114 days, p=0.0174) (Fig 2). Data exploration allowed isolation of a 54-year-old Asian male with Li-Fraumeni syndrome and p53 mutated AML who demonstrated high affinity neopeptide binding to HLA-B*39:01 with %Rank 0.08. Additionally, a 34 -year-old AA female with FLT3 mutated AML showed very high affinity neopeptide binding to HLA-A*29:02 with %Rank 0.007 as well as evidence of somatic HLA-A*03:01 deletion. Conclusions Pathogenic molecular variant biotypes constitute a novel immune signature, the human leukemia immunopeptidome. Smoking increased the likelihood of MHC class I neopeptide binding among patients with MDS. The presence of neopeptide binding predicted improved mOS in patients with myeloid malignancies. Further investigation of the human leukemia immunopeptidome may provide additional prognostic significance above that of standard molecular and cytogenetic risk stratification.

Production and characterization of plantaricin Y11 from <i>Lactiplantibacillus Plantarum</i> strain y11 (MW642245.1) isolated from Nigerian food samples and their applications in preserving milk

Bacteriocin from lactic acid bacterium (LAB) was characterized and its biopreservation assay carried out using conventional methods and integrative approaches. About 66.7% (n=180) of the bacterial strains isolated from twelve different fermented/non-fermented food products were potential LAB strains by biochemical characterization. The highest bacteriocin producing strain was selected and confirmed with 16S rRNA sequencing and submitted to GenBank of National Center for Biotechnology Information as Lactiplantibacillus plantarum strain Y11 (Accession number: MW642245.1). Polymerase Chain Reaction (PCR) revealed the presence of virulence genes (cytotoxin K and haemolysin C) in L. plantarum Y11. The bacteriocin produced was labelled as plantaricin Y11 with molecular weight of 1540 Da, amino acid sequence was NSHGTADYCVMWLIXK, and possessed the merits of wide pH stability (2–10), high thermal stability and sensitivity to protease. The bacteriocin showed wide spectrum of activity against bacterial reference strains with bacteriocin activity ranging from 3200Au/mL to 6400Au/mL. Preservative potentials of the bacteriocin compared favourably with sodium benzoate in milk, inhibiting bacterial and fungal load compared to the control. There was log reduction of aerobic mesophilic bacterial count of 8.02±0.15 and 8.43±0.21 Log 10 CFU/mL in milk treated with plantaricin Y11 and sodium benzoate, respectively. The log reductions of fungal count in plantaricin Y11 and sodium benzoate treated milk ≥4.41±0.11 and ≥3.1±0.2 Log 10 CFU/mL respectively. The plantaricin Y11 was then classified as class IIa in bacteriocin classification schemes and it sustained some organoleptic conditions of milk making it a promising candidate for safe bio-preservatives.

Genetic Diversity of Bamboo (Yushinia alpina) Borer Larvae in the Mau Forest Complex, Kenya

Bamboo borer larvae have caused major losses of bamboo cover in natural forests and plantations. Lack of information on the fauna of bamboo trees has been cited as the contributing factor to poor management of bamboo stands. Genetic diversity information helps understand the effects of different fauna in guiding management plans. Genetic diversity information has recently become an important tool in conservation science. This paper aimed to determine the genetic diversity of the bamboo borer larvae in the Mau Forest complex in order to generate information that could guide the management and conservation of bamboo trees (Yushinia Alpina) in the Mau Forest Complex. The mitochondrial C oxidase Subunit 1 (COI) of 12 isolates was sequenced and analyzed. A similarity search of the bamboo borer larvae was carried out using the National Center for Biotechnology Information (NCBI) BLAST search to identify the larvae species. The genetic diversity and genetic pairwise distances were determined, and Tajimas D and Nei’s FU Fs statistics were calculated to estimate the population expansion that has occurred. The results showed genetic diversity (haplotype diversity 0.956) in the bamboo borer larvae population of the Mau Forest Complex. The nucleotide diversity (0.283) was found to be low. The similarity search showed that the bamboo borer larvae of Yushinia alpina belonged to four (4) species of noctuid larvae (Lepidoptera). The identity matches to the similar species scored an average of 94%. The Tajimas D (0.374) and FUs Fs (5.547) collectively indicated no rare excess mutations in the population. The results reveal high genetic diversity, which is key in the management of forest species

Ancient Roman bacterium against current issues: strain Aquil_B6, Paenisporosarcina quisquiliarum, or Psychrobacillus psychrodurans?

Since 1988, through the United States government's founding, the National Center for Biotechnology Information (NCBI) has provided an invaluable service to scientific advancement. The universality and total freedom of use if on the one hand allow the use of this database on a global level by all researchers for their valuable work, on the other hand, it has the disadvantage of making it difficult to check the correctness of all the materials present. It is, therefore, of fundamental importance for the correctness and ethics of research to improve the databases at our disposal, identifying and amending the critical issues. This work aims to provide the scientific community with a new sequence for the type strain Paenisporosarcina quisquiliarum SK 55 and broaden the knowledge of the Psychrobacillus psychrodurans species, in particular, considering the ancient strain Aquil_B6 found in an ancient Roman amphora.

ARDS (Acute Respiratory Distress Syndrome) in Pediatric and Adult

Acute Respiratory Distress Syndrome (ARDS) is a serious medical condition that occurs when lungs become severely inflamed, which inhibits the ability to take in the oxygen and eliminate carbon dioxide. The purpose of this article is to find out more about the clinical manifestation, pathophysiology, diagnosis, and treatment of ARDS. The literatures that used for this literature review are from National Center for Biotechnology Information (NCBI), Google scholar, and Proquest. The result for this literature review is the development of ARDS is associated with inflammation in lung’s epithelium, endothelium, and interstitium which consist three phases which is exudative, proliferative, and fibrotic phases. The Berlin Criteria issued by the American-European Consensus Conference (AECC) in 2021 used for ARDS diagnosis. The treatments for ARDS could used pharmacotherapy and non-pharmacotherapy.

CTIVA: Censored time interval variable analysis.

Traditionally, datasets with multiple censored time-to-events have not been utilized in multivariate analysis because of their high level of complexity. In this paper, we propose the Censored Time Interval Analysis (CTIVA) method to address this issue. It estimates the joint probability distribution of actual event times in the censored dataset by implementing a statistical probability density estimation technique on the dataset. Based on the acquired event time, CTIVA investigates variables correlated with the interval time of events via statistical tests. The proposed method handles both categorical and continuous variables simultaneously-thus, it is suitable for application on real-world censored time-to-event datasets, which include both categorical and continuous variables. CTIVA outperforms traditional censored time-to-event data handling methods by 5% on simulation data. The average area under the curve (AUC) of the proposed method on the simulation dataset exceeds 0.9 under various conditions. Further, CTIVA yields novel results on National Sample Cohort Demo (NSCD) and proteasome inhibitor bortezomib dataset, a real-world censored time-to-event dataset of medical history of beneficiaries provided by the National Health Insurance Sharing Service (NHISS) and National Center for Biotechnology Information (NCBI). We believe that the development of CTIVA is a milestone in the investigation of variables correlated with interval time of events in presence of censoring.

Precocious Puberty: Etiology and Current Treatment

Precocious puberty also known as premature puberty is an abnormal pubertal development that can affect a child's growth and development. The clinical manifestations of precocious puberty are generally diverse and based on etiology are classified into central precocious puberty (GnRH dependent) and peripheral precocious puberty (GnRH independent). The main concern with precocious puberty is that precocious puberty can be a clinical symptom of an underlying serious disease such as a brain tumor, adrenal or gonadal tumor and others. Early identification of etiology plays an important role in prevention, diagnosis, and treatment of this disease. This literature review aims to determine the etiology and current management of precocious puberty. This literature review uses the keywords "Precocious Puberty AND etiology AND treatment" through the National Center for Biotechnology Information (NCBI) and Google Scholar databases. This article uses 11 articles that were used as references in its preparation. In conclusion, it is necessary to know the etiology of precocious puberty using imaging examinations for optimal management and excluding malignant abnormalities. The current treatment for central precocious puberty is GnRH agonists (gold-standard) and surgery in cases of intracranial lesions and peripheral precocious puberty using a combination of androgen antagonists (spironolactone) and aromatase inhibitors (anastrozole, testolactone) and surgery is indicated for gonadal and adrenal tumors. The role of parents is very important in early detection of precocious puberty, because the earlier the therapy, the better the prognosis.

DDBJ update in 2023: the MetaboBank for metabolomics data and associated metadata.

The Bioinformation and DNA Data Bank of Japan (DDBJ) Center (https://www.ddbj.nig.ac.jp) provides database archives that cover a wide range of fields in life sciences. As a founding member of the International Nucleotide Sequence Database Collaboration (INSDC), DDBJ accepts and distributes nucleotide sequence data as well as their study and sample information along with the National Center for Biotechnology Information in the United States and the European Bioinformatics Institute (EBI). Besides INSDC databases, the DDBJ Center provides databases for functional genomics (GEA: Genomic Expression Archive), metabolomics (MetaboBank) and human genetic and phenotypic data (JGA: Japanese Genotype-phenotype Archive). These database systems have been built on the National Institute of Genetics (NIG) supercomputer, which is also open for domestic life science researchers to analyze large-scale sequence data. This paper reports recent updates on the archival databases and the services of the DDBJ Center, highlighting the newly redesigned MetaboBank. MetaboBank uses BioProject and BioSample in its metadata description making it suitable for multi-omics large studies. Its collaboration with MetaboLights at EBI brings synergy in locating and reusing public data.

Cloning and in silico investigation of a putative voltage-gated calcium channel gene and protein in Astacus leptodactylus

Abstract Objectives Voltage-gated calcium channels are essential elements in development of many cellular processes like electrical signaling, contraction secretion and gene expression. There has been a fair amount of information about the functional and structural properties of the calcium channels in mammalian species. Crayfish serves as a model animal for many types of experiments. However, there has been no information related to the molecular and genetic properties of the calcium channels in the crayfish. Methods Conventional cloning methods, three-dimensional structural calculations, docking experiments have been conducted. Results An mRNA 7,791 bp in size has been cloned. The coding region has been translated into an alpha peptide with 1,942 residues. The cloned protein sequence has similarity to other L-type voltage-gated calcium channel sequences from the neighboring species. Three-dimensional structure, in reference to human L-type voltage-gated calcium channel, has been calculated. Known calcium channel blockers, nifedipine, verapamil and diltiazem have been successfully docked on the calculated three-dimensional model. Conclusions Considering the similarity assay in the National Center for Biotechnology Information (NCBI) platform, the three-dimensional structural calculations and the docking experiments it was concluded that the cloned mRNA codes an alpha peptide for a putative voltage-gated calcium channel protein in the crayfish. In the present work by using the conventional molecular biology methods a complete mRNA coding a putative calcium channel has been de novo cloned. Three-dimensional structure of the related protein has been calculated and several pharmacological agents blocking the channel have been docked to the identified receptor sites.

Minimally-invasive and non-invasive methods of thermal destruction in the treatment of patients with aggressive fibromatosis

The purpose of the study was to characterize various methods of local physical destruction used in the treatment of patients with aggressive fibromatosis and demonstrate international experience of their use.Material and Methods. literature search was conducted in the electronic databases Rsci (Russian science citation index) and NcBi (National centre for Biotechnology information) in the interval time between 2002 and 2022. The review was devoted to the thermal ablation modalities (radiofrequency, microwave ablation, cryodestruction, high-intensity focused ultrasound ablations) used in therapy of patients with desmoid fibromas of various locations, as well as their safety and efficacy.Results. The review presents the current data on safety and efficacy of minimally-invasive and non-invasive methods of hypo- and hyperthermic local destruction in patients with aggressive fibromatosis, gives the characteristics of exposure and biological effects when performing radiofrequency and microwave ablation, cryodestruction, high-intensity focused ultrasound therapy, describes the main limitations of the methods, indications and contraindications for their application, as well as the methods of prevention of the development of desmoid fibromas.Conclusion. The described methods of local destruction are used in clinical practice mainly for palliative and symptomatic purposes, in case of persistent tumor growth or recurrence, ineffectiveness of other treatment options or contraindications to them due to concomitant somatic pathology or functional status of the patient. Inclusion of these methods in the treatment plan of patients with aggressive fibromatosis can contribute to the reduction of pain syndrome, improvement of functional status of patients as well as long survival with no evidence of tumor progression.

Viral proteins length distributions: A comparative analysis

In this work, we perform a comparative analysis of length distributions of proteins belonging to two virus families, namely Flaviviridae and Coronaviridae. Both families of viruses are highly contagious and represent severe threats to global health systems. To perform the comparative analysis, we retrieved data from the databases Virus Pathogen Database and Analysis Resource (ViPR) and National Center for Biotechnology Information (NCBI). In our investigation, we have considered four distinct Cumulative Distribution Functions (CDFs) of protein length: q-Exponential-CDF and q-Gaussian-CDF, q-Weibull-CDF, and κ-Maxwellian-CDF. Our results show that q-Weibull-CDF is the least appropriate for length distributions among the four CDFs. Also, the q-Exponential, q-Gaussian, and κ-Maxwellian distribution functions fit the cumulative distributions of viral protein lengths with remarkable agreement. Furthermore, our findings suggest that the correlations for viral protein lengths are identical for both species, even though their average lengths differ.