NCBI RefSeq: reference sequence standards through 25 years of curation and annotation.

Reference sequences and annotations serve as the foundation for many lines of research today, from organism and sequence identification to providing a core description of the genes, transcripts and proteins found in an organism's genome. Interpretation of data including transcriptomics, proteomics, sequence variation and comparative analyses based on reference gene annotations informs our understanding of gene function and possible disease mechanisms, leading to new biomedical discoveries. The Reference Sequence (RefSeq) resource created at the National Center for Biotechnology Information (NCBI) leverages both automatic processes and expert curation to create a robust set of reference sequences of genomic, transcript and protein data spanning the tree of life.

Antibiotic exposure for culture-negative early-onset sepsis in late-preterm and term newborns: an international study.

Background: Early-life antibiotic exposure is disproportionately high compared to the burden of culture-proven early-onset sepsis (CP-EOS). We assessed the contribution of culture-negative cases to the overall antibiotic exposure in the first postnatal week.

Methods: We conducted a retrospective analysis across eleven countries in Europe, North America, and Australia.

The NCBI Comparative Genome Viewer (CGV) is an interactive visualization tool for the analysis of whole-genome eukaryotic alignments.

We report a new visualization tool for analysis of whole-genome assembly-assembly alignments, the Comparative Genome Viewer (CGV) (https://ncbi.nlm.nih.

Rapid and sensitive detection of genome contamination at scale with FCS-GX.

Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBI's Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant sequences in new genomes. FCS-GX screens most genomes in 0.

Interactive visualization of whole eukaryote genome alignments using NCBI's Comparative Genome Viewer (CGV).

We report a new visualization tool for analysis of whole genome assembly-assembly alignments, the Comparative Genome Viewer (CGV) (https://ncbi.nlm.nih.

Analysis of Antibiotic Exposure and Early-Onset Neonatal Sepsis in Europe, North America, and Australia.

Importance: Appropriate use of antibiotics is life-saving in neonatal early-onset sepsis (EOS), but overuse of antibiotics is associated with antimicrobial resistance and long-term adverse outcomes. Large international studies quantifying early-life antibiotic exposure along with EOS incidence are needed to provide a basis for future interventions aimed at safely reducing neonatal antibiotic exposure.

Objective: To compare early postnatal exposure to antibiotics, incidence of EOS, and mortality among different networks in high-income countries.

Indoleamine-2,3-dioxygenase in murine and human systemic lupus erythematosus: Down-regulation by the tolerogeneic peptide hCDR1.

וֹndoleamine-2,3-dioxygenase (IDO) plays a role in immune regulation. Increased IDO activity was reported in systemic lupus erythematosus (SLE). We investigated the effects of the tolerogenic peptide hCDR1, shown to ameliorate lupus manifestations, on IDO gene expression.

The tolerogenic peptide hCDR1 immunomodulates cytokine and regulatory molecule gene expression in blood mononuclear cells of primary Sjogren's syndrome patients.

Primary Sjogren's syndrome (pSS) is an autoimmune disease characterized by lymphocytic infiltration of exocrine glands. We investigated whether the tolerogenic peptide, hCDR1, that ameliorates lupus manifestations would have beneficial effects on pSS as well. The in vitro effects of hCDR1 on gene expression of pro-inflammatory cytokines and regulatory molecules were tested in peripheral blood mononuclear cells (PBMC) of 16 pSS patients.

Anticitrullinated Protein Antibodies Induce Inflammatory Gene Expression Profile in Peripheral Blood Cells from CCP-positive Patients with RA.

Objective: Anticitrullinated protein antibodies (ACPA) have major diagnostic significance in rheumatoid arthritis (RA). ACPA are directed against different citrullinated antigens, including filaggrin, fibrinogen, vimentin, and collagen. The presence of ACPA is associated with joint damage and extraarticular manifestations, suggesting that ACPA may have a significant role in the pathogenesis of RA.

Conservation of Pollinators in Traditional Agricultural Landscapes - New Challenges in Transylvania (Romania) Posed by EU Accession and Recommendations for Future Research.

Farmland biodiversity is strongly declining in most of Western Europe, but still survives in traditional low intensity agricultural landscapes in Central and Eastern Europe. Accession to the EU however intensifies agriculture, which leads to the vanishing of traditional farming. Our aim was to describe the pollinator assemblages of the last remnants of these landscapes, thus set the baseline of sustainable farming for pollination, and to highlight potential measures of conservation.

Novel approaches to the development of targeted therapeutic agents for systemic lupus erythematosus.

Systemic lupus erythematosus (SLE) is a chronic multisystem disease in which various cell types and immunological pathways are dysregulated. Current therapies for SLE are based mainly on the use of non-specific immunosuppressive drugs that cause serious side effects. There is, therefore, an unmet need for novel therapeutic means with improved efficacy and lower toxicity.

Docosahexaenoic acid reduces amyloid-β induced toxicity in cells of the neurovascular unit.

Alzheimer's disease (AD) is characterized by the accumulation of amyloid-β peptides (Aβ) as perivascular deposits and senile plaques in the brain. The intake of the polyunsaturated fatty acid docosahexaenoic acid (DHA) has been associated with decreased amyloid deposition and reduced risk in AD in several epidemiological trials; however the exact underlying molecular mechanism remains to be elucidated. The aim of the study was to test whether DHA can exert a direct protective effect on the elements of the neurovascular unit, such as neurons, glial cells, brain endothelial cells, and pericytes, treated with Aβ42 (15 μM).

16/6-idiotype expressing antibodies induce brain inflammation and cognitive impairment in mice: the mosaic of central nervous system involvement in lupus.

Background: The 16/6-idiotype (16/6-Id) of the human anti-DNA antibody was found to induce experimental lupus in naïve mice, manifested by production of autoantibodies, leukopenia and elevated inflammatory markers, as well as kidney and brain involvement. We assessed behavior and brain pathology of naive mice injected intra-cerebra-ventricularly (ICV) with the 16/6-Id antibody.

Methods: C3H female mice were injected ICV to the right hemisphere with the human 16/6-Id antibody or commercial human IgG antibodies (control).

The tolerogenic peptide, hCDR1, down-regulates the expression of interferon-α in murine and human systemic lupus erythematosus.

Background: The tolerogenic peptide, hCDR1, ameliorated manifestations of systemic lupus erythematosus (SLE) via the immunomodulation of pro-inflammatory and immunosuppressive cytokines and the induction of regulatory T cells. Because type I interferon (IFN-α) has been implicated to play a role in SLE pathogenesis, we investigated the effects of hCDR1 on IFN-α in a murine model of SLE and in human lupus.

Methodology Principal Findings: (NZBxNZW)F1 mice with established SLE were treated with hCDR1 (10 weekly injections).

Proteome-wide study of endoplasmic reticulum stress induced by thapsigargin in N2a neuroblastoma cells.

Disturbances in intraluminal endoplasmic reticulum (ER) Ca(2+) concentration leads to the accumulation of unfolded proteins and perturbation of intracellular Ca(2+) homeostasis, which has a huge impact on mitochondrial functioning under normal and stress conditions and can trigger cell death. Thapsigargin (TG) is widely used to model cellular ER stress as it is a selective and powerful inhibitor of sarcoplasmic/endoplasmic reticulum Ca(2+) ATPases. Here we provide a representative proteome-wide picture of ER stress induced by TG in N2a neuroblastoma cells.

A novel method for the rapid determination of beta-amyloid toxicity on acute hippocampal slices using MTT and LDH assays.

It is difficult task to measure precisely the toxic effect of beta-amyloid (Aβ 1-42) peptides and also the protective effect of novel drug candidates against Aβ-peptides. The widely used MTT-assay in cell lines or primary cell cultures could be insensitive against Aβ-peptides. We describe here an easy and relevant method for testing Aβ 1-42 toxicity on acute hippocampal slices derived from rat.

A novel application of the fluorescent dye bis-ANS for labeling neurons in acute brain slices.

The cell-impermeant oligomer-(e.g. beta-amyloid-, or tubulin-) specific fluorescent dye, bis-ANS (4,4'-bis-1-anilinonaphtalene-8-sulfonate), was successfully used for labeling mechanically damaged but still viable neuron bodies, neurites and neurite cross sections in acute brain slices.

[Bacterial strains isolated from systemic infections and reported for evaluation and antibiotic resistance surveillance by the "Dr. Victor Babeş" Clinical Hospital for Infectious and Tropical Diseases, Bucharest].

Aim: Testing antibiotic resistance of bacterial strains (compulsor, reported for EARSS surveillance) isolated from patients hospitalised for systemic infection in the "Dr. V. Babe" Hospital for Infectious and Tropical Diseases during 01.

Induction of hippocampal neurogenesis by a tolerogenic peptide that ameliorates lupus manifestations.

To determine the effect of the tolerogenic peptide hCDR1 on hippocampal neurogenesis, we treated SLE-afflicted (NZBxNZW)F1 mice with hCDR1 (once a week for 10weeks). The treatment resulted in the up-regulation of neurogenesis in the dentate gyrus and restored the NeuN immunoreactivity in brain hippocampi of the mice in association with increased gene expression of IGF-1, NGF and BDNF. Furthermore, hCDR1 treatment significantly up-regulated p-ERK and p-Akt that are suggested to be key components in mediating growth factor-induced neurogenesis.

An integrated approach to uncover drivers of cancer.

Systematic characterization of cancer genomes has revealed a staggering number of diverse aberrations that differ among individuals, such that the functional importance and physiological impact of most tumor genetic alterations remain poorly defined. We developed a computational framework that integrates chromosomal copy number and gene expression data for detecting aberrations that promote cancer progression. We demonstrate the utility of this framework using a melanoma data set.

A role for the B-cell CD74/macrophage migration inhibitory factor pathway in the immunomodulation of systemic lupus erythematosus by a therapeutic tolerogenic peptide.

Systemic lupus erythematosus (SLE) is an autoimmune disease that involves dysregulation of B and T cells. A tolerogenic peptide, designated hCDR1, ameliorates disease manifestations in SLE-afflicted mice. In the present study, the effect of treatment with hCDR1 on the CD74/macrophage migration inhibitory factor (MIF) pathway was studied.