Factors and outcome analysis of emergency peripartum hysterectomy in a tertiary care center catering to hilly terrain for a five-year period: a retrospective study

Background: Emergency peripartum hysterectomy (EPH) is a life-saving surgery associated with significant morbidity and mortality. In the state of Uttarakhand, due to the hilly terrain and poor ante-natal awareness, type 1 and 2 delay is expected in seeking health care. Thus, the present study was conducted in a tertiary care hospital to evaluate the incidence, risk factors, indications, and outcomes of EPH.Methods: Medical records of 63 patients who underwent EPH from January 2015 to December 2019 were retrospectively analyzed for the patient characteristics, high risk factors, indications and type of hysterectomy and outcome.Results: The incidence of EPH at our institute was 2.78 per 1000 deliveries. Most patients (89.89%) were referred cases. There were 4 home deliveries and 4 patients referred for obstructed labour.  The average parity was 2.71±1.13. Thirty-four patients (53.97%) presented in the emergency department in shock. The leading indication was uterine atony (46.03%) followed by rupture uterus (26.98%) and placenta accreta spectrum (23.81%). All patients needed blood transfusion. Intensive care unit admission was required in 88.89%. The maternal mortality was 15.87%.  All the three levels delays contributing to poor outcome were identified. Conclusions: Uterine atony and rupture of non-scarred uterus due to obstructed labour were the prominent indications of EPH. Strengthening of referral system and timely referral of high-risk patients to a setup with facilities for management of high risk obstetric cases can play an important role in decreasing the incidence and morbidity and mortality of EPH

Computing Genomic Signatures Using de Bruijn Chains

Genomic DNA sequences have both deterministic and random aspects and exhibit features at numerous scales, from codons to regions of conserved or divergent gene order. Genomic signatures work by capturing one or more such features efficiently into a compact mathematical structure. We examine the unique manner in which oligonucleotides constitute a genome, within a graph-theoretic setting. A de Bruijn chain (DBC) is a kind of de Bruijn graph that includes a finite Markov chain. By representing a DNA sequence as a walk over a DBC and retaining specific information at nodes and edges, we obtain the de Bruijn chain genomic signature θdbc, based on graph structure and the stationary distribution of the DBC. We demonstrate that the θdbc signature is information-rich, efficient, sufficiently representative of the sequence from which it is derived, and superior to existing genomic signatures such as the dinucleotide odds ratio and word frequency based signatures. We develop a mathematical framework to elucidate the power of the θdbc signature to distinguish between sequences hypothesized to be generated by DBCs of distinct parameters. We study the effect of order of the θdbc signature, genome size, and variation within a genome on accuracy. We illustrate its superior performance over existing genomic signatures in predicting the origin of short DNA sequences.</p

XcisClique: analysis of regulatory bicliques

BACKGROUND: Modeling of cis-elements or regulatory motifs in promoter (upstream) regions of genes is a challenging computational problem. In this work, set of regulatory motifs simultaneously present in the promoters of a set of genes is modeled as a biclique in a suitably defined bipartite graph. A biologically meaningful co-occurrence of multiple cis-elements in a gene promoter is assessed by the combined analysis of genomic and gene expression data. Greater statistical significance is associated with a set of genes that shares a common set of regulatory motifs, while simultaneously exhibiting highly correlated gene expression under given experimental conditions. METHODS: XcisClique, the system developed in this work, is a comprehensive infrastructure that associates annotated genome and gene expression data, models known cis-elements as regular expressions, identifies maximal bicliques in a bipartite gene-motif graph; and ranks bicliques based on their computed statistical significance. Significance is a function of the probability of occurrence of those motifs in a biclique (a hypergeometric distribution), and on the new sum of absolute values statistic (SAV) that uses Spearman correlations of gene expression vectors. SAV is a statistic well-suited for this purpose as described in the discussion. RESULTS: XcisClique identifies new motif and gene combinations that might indicate as yet unidentified involvement of sets of genes in biological functions and processes. It currently supports Arabidopsis thaliana and can be adapted to other organisms, assuming the existence of annotated genomic sequences, suitable gene expression data, and identified regulatory motifs. A subset of Xcis Clique functionalities, including the motif visualization component MotifSee, source code, and supplementary material are available at

Genome sequence of Ensifer arboris strain LMG 14919T: a microsymbiont of the legume Prosopis chilensis growing in Kosti, Sudan

Ensifer arboris LMG 14919T is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of several species of legume trees. LMG 14919T was isolated in 1987 from a nodule recovered from the roots of the tree Prosopis chilensis growing in Kosti, Sudan. LMG 14919T is highly effective at fixing nitrogen with P. chilensis (Chilean mesquite) and Acacia senegal (gum Arabic tree or gum acacia). LMG 14919T does not nodulate the tree Leucena leucocephala, nor the herbaceous species Macroptilium atropurpureum, Trifolium pratense, Medicago sativa, Lotus corniculatus and Galega orientalis. Here we describe the features of E. arboris LMG 14919T, together with genome sequence information and its annotation. The 6,850,303 bp high-quality-draft genome is arranged into 7 scaffolds of 12 contigs containing 6,461 protein-coding genes and 84 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project

ProDeGe: a computational protocol for fully automated decontamination of genomes

Single amplified genomes and genomes assembled from metagenomes have enabled the exploration of uncultured microorganisms at an unprecedented scale. However, both these types of products are plagued by contamination. Since these genomes are now being generated in a high-throughput manner and sequences from them are propagating into public databases to drive novel scientific discoveries, rigorous quality controls and decontamination protocols are urgently needed. Here, we present ProDeGe (Protocol for fully automated Decontamination of Genomes), the first computational protocol for fully automated decontamination of draft genomes. ProDeGe classifies sequences into two classes—clean and contaminant—using a combination of homology and feature-based methodologies. On average, 84% of sequence from the non-target organism is removed from the data set (specificity) and 84% of the sequence from the target organism is retained (sensitivity). The procedure operates successfully at a rate of ~0.30 CPU core hours per megabase of sequence and can be applied to any type of genome sequence

High-quality permanent draft genome sequence of Bradyrhizobium sp Th.b2, a microsymbiont of Amphicarpaea bracteata collected in Johnson City, New York

Bradyrhizobium sp. Th.b2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Amphicarpaea bracteata collected in Johnson City, New York. Here we describe the features of Bradyrhizobium sp. Th.b2, together with high-quality permanent draft genome sequence information and annotation. The 10,118,060 high-quality draft genome is arranged in 266 scaffolds of 274 contigs, contains 9,809 protein-coding genes and 108 RNA-only encoding genes. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project

High-quality permanent draft genome sequence of Bradyrhizobium sp Tv2a.2, a microsymbiont of Tachigali versicolor discovered in Barro Colorado Island of Panama

Bradyrhizobiumsp. Tv2a.2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Tachigali versicolor collected in Barro Colorado Island of Panama. Here we describe the features of Bradyrhizobiumsp. Tv2a.2, together with high-quality permanent draft genome sequence information and annotation. The 8,496,279 bp high-quality draft genome is arranged in 87 scaffolds of 87 contigs, contains 8,109 protein-coding genes and 72 RNA-only encoding genes. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project

High-quality permanent draft genome sequence of Bradyrhizobium sp Ai1a-2; a microsymbiont of Andira inermis discovered in Costa Rica

Bradyrhizobium sp. Ai1a-2 is is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen fixing root nodule of Andira inermis collected from Tres Piedras in Costa Rica. In this report we describe, for the first time, the genome sequence information and annotation of this legume microsymbiont. The 9,029,266 bp genome has a GC content of 62.56% with 247 contigs arranged into 246 scaffolds. The assembled genome contains 8,482 protein-coding genes and 102 RNA-only encoding genes. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal

Genome sequence of Burkholderia mimosarum strain LMG 23256T: a Mimosa pigra microsymbiont from Anso, Taiwan

Burkholderia mimosarum strain LMG 23256T is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Mimosa pigra (giant sensitive plant). LMG 23256T was isolated from a nodule recovered from the roots of the M. pigra growing in Anso, Taiwan. LMG 23256T is highly effective at fixing nitrogen with M. pigra. Here we describe the features of B. mimosarum strain LMG 23256T, together with genome sequence information and its annotation. The 8,410,967 bp high-quality-draft genome is arranged into 268 scaffolds of 270 contigs containing 7,800 protein-coding genes and 85 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project