Healthcare

Multi-drug resistance, inappropriate initial antibiotic therapy and mortality in Gram-negative severe sepsis and septic shock: a retrospective cohort study
The impact of in vitro resistance on initially appropriate antibiotic therapy (IAAT) remains unclear. We elucidated the relationship between non-IAAT and mortality, and between IAAT and multi-drug resistance (MDR) in sepsis due to Gram-negative bacteremia (GNS). We conducted a single-center retrospective cohort study of adult intensive care unit patients with bacteremia and severe sepsis/septic...


Effects of selective ß1-adrenoceptor blockade on cardiovascular and renal function and circulating cytokines in ovine hyperdynamic sepsis
Activation of the sympathetic nervous system has beneficial cardiovascular effects in sepsis, but there is also evidence that sympatholytics have beneficial actions in sepsis. We therefore determined the effect of selective ?1-adrenoceptor blockade on cardiac and renal function and cytokine release in ovine hyperdynamic sepsis. Hyperdynamic sepsis was induced by infusion of live E. Coli for 24?...
Efecto del vendaje neuromuscular sobre el acortamiento de los músculos isquiotibiales
Analizar los efectos del vendaje neuromuscular (VNM) sobre la extensibilidad muscular durante 3 días de aplicación, en sujetos con acortamiento de isquiotibiales (IT). Participaron voluntariamente 54 sujetos jóvenes que presentaban acortamiento de IT, distribuidos aleatoriamente en un grupo experimental (GE), a quienes se les aplicó un VNM, y un grupo control (GC). Se evaluó la extensibili...


The fluid management of adults with severe malaria
Fluid resuscitation has long been considered a key intervention in the treatment of adults with severe falciparum malaria. Profound hypovolemia is common in these patients and has the potential to exacerbate the acidosis and acute kidney injury that are independent predictors of death. However, new microvascular imaging techniques have shown that disease severity correlates more strongly with o...
Endogenous glycosaminoglycan anticoagulation in extracorporeal membrane oxygenation
A heparin-like effect was recently described in infants, children, and adults receiving bivalirudin while supported on extracorporeal membrane oxygenation following cardiopulmonary bypass. This is most likely due to endogenous release of glycosaminoglycans from vascular endothelium and mast cells and is associated with longer duration of extracorporeal membrane oxygenation and an increased inci...


CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites
CRISPRdirect is a simple and functional web server for selecting rational CRISPR/Cas targets from an input sequence. The CRISPR/Cas system is a promising technique for genome engineering which allows target-specific cleavage of genomic DNA guided by Cas9 nuclease in complex with a guide RNA (gRNA), that complementarily binds to a ~20 nt targeted sequence. The target sequence requirements are tw...
NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei
NucleusJ is a simple and user-friendly ImageJ plugin dedicated to the characterization of nuclear morphology and chromatin organization in 3D. Starting from image stacks, the nuclear boundary is delimited by combining the Otsu segmentation method with optimization of nuclear sphericity. Chromatin domains are segmented by partitioning the nucleus using a 3D watershed algorithm and by thresholdin...

Multilevel Regularized Regression for Simultaneous Taxa Selection and Network Construction with Metagenomic Count Data
Identifying disease associated taxa and constructing networks for bacteria interactions are two important tasks usually studied separately. In reality, differentiation of disease associated taxa and correlation among taxa may affect each other. One genus can be differentiated because it is highly correlated with another highly differentiated one. In addition, network structures may vary under d...
A model for the expression of gap genes based on the Jeffreys-type equation
We propose the third-order model equation of the Jeffreys type for concentrations of gap gene proteins in order to take into account particle inertia. Gap genes are responsible for formation of body segments in Drosophila melanogaster embryo during its early development. Usually the expression of the genes is described by the model of protein transport based on conventional diffusion equation. ...

WebPSN: a web server for high-throughput investigation of structural communication in biomacromolecules
We developed a mixed Protein Structure Network (PSN) and Elastic Network Model-Normal Mode Analysis (ENM-NMA)-based strategy (i.e. PSN-ENM) to investigate structural communication in biomacromolecules. The approach starts from a Protein Structure Graph and searches for all shortest communication pathways between user-specified residues. The graph is computed on a single preferably high-resoluti...
Efficient searching and annotation of metabolic networks using chemical similarity
The urgent need for efficient and sustainable biological production of fuels and high-value chemicals has elicited a wave of in silico techniques for identifying promising novel pathways to these compounds in large putative metabolic networks. To date, these approaches have primarily used general graph search algorithms, which are prohibitively slow as putative metabolic networks may exceed one...

Molecular principles of human virus protein-protein interactions
Viruses, from the human protein-protein interaction network perspective, target hubs, bottlenecks and interconnected nodes enriched in certain biological pathways. However, not much is known about the general characteristic features of the human proteins targeted by viral proteins (hVIPs) as well as the motifs and domains utilized by human-virus protein-protein interactions (Hu-Vir PPIs). Our s...
Genomation: a toolkit to summarize, annotate and visualize genomic intervals
Biological insights can be obtained through computational integration of genomics data sets consisting of diverse types of information. The integration is often hampered by a large variety of existing file formats, often containing similar information, and the necessity to use complicated tools to achieve the desired results. We have built an R package, genomation, to expedite the extraction of...
QuasR: Quantification and annotation of short reads in R
QuasR is a package for the integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different experiment types (including RNA-seq, ChIP-seq and Bis-seq) and analysis variants (e.g. paired-end, stranded, spliced and allele-specific), and is integrated in Bioconductor so that its output...
Barriers and Facilitators of Adolescent Health in Rural Kenya
The purpose of this research was to identify perceived barriers and facilitators of health from the perspective of rural Kenyan adolescents and to characterize the cultural context that shapes these barriers and facilitators. Following a semistructured interview guide, qualitative focus group interviews were conducted at day schools with 64 upper-primary and secondary students in rural central ...