Hyldgaardwu3119

The chlorophyll fluorescence excitation spectrum, therefore, could serve as a useful tool to describe specific characteristics of light absorption and energy transfer between light-harvesting pigments.Salmonella enterica serovar Enteritidis (SE) is a foodborne pathogen that can threaten human health through contaminated poultry products. Live poultry, chicken eggs and meat are primary sources of human salmonellosis. To understand the genetic resistance of egg-type chickens in response to SE inoculation, global gene expression in the spleen of 20-week-old White Leghorn was measured using the Agilent 4 × 44 K chicken microarray at 7 and 14 days following SE inoculation (dpi). Results showed that there were 1363 genes significantly differentially expressed between inoculated and non-inoculated groups at 7 dpi (I7/N7), of which 682 were up-regulated and 681 were down-regulated genes. By contrast, 688 differentially expressed genes were observed at 14 dpi (I14/N14), of which 371 were up-regulated genes and 317 were down-regulated genes. There were 33 and 28 immune-related genes significantly differentially expressed in the comparisons of I7/N7 and I14/N14 respectively. Functional annotation revealed that several Gene Ontology (GO) terms related to immunity were significantly enriched between the inoculated and non-inoculated groups at 14 dpi but not at 7 dpi, despite a similar number of immune-related genes identified between I7/N7 and I14/N14. The immune response to SE inoculation changes with different time points following SE inoculation. The complicated interaction between the immune system and metabolism contributes to the immune responses to SE inoculation of egg-type chickens at 14 dpi at the onset of lay. GC, TNFSF8, CD86, CD274, BLB1 and BLB2 play important roles in response to SE inoculation. The results from this study will deepen the current understanding of the genetic response of the egg-type chicken to SE inoculation at the onset of egg laying.

MicroRNAs (miRNAs) play a key role in regulating tumor progression and metastasis. Identifying key miRNAs, defined by their functional activities, can provide a deeper understanding of biology of miRNAs in cancer. However, miRNA expression level cannot accurately reflect miRNA activity.

We developed a computational approach, ActMiR, for identifying active miRNAs and miRNA-mediated regulatory mechanisms. Applying ActMiR to four cancer datasets in The Cancer Genome Atlas (TCGA), we showed that (i) miRNA activity was tumor subtype specific; (ii) genes correlated with inferred miRNA activities were more likely to enrich for miRNA binding motifs; (iii) expression levels of these genes and inferred miRNA activities were more likely to be negatively correlated. For the four cancer types in TCGA we identified 77-229 key miRNAs for each cancer subtype and annotated their biological functions. The miRNA-target pairs, predicted by our ActMiR algorithm but not by correlation of miRNA expression levels, were experimentally validated. The functional activities of key miRNAs were further demonstrated to be associated with clinical outcomes for other cancer types using independent datasets. For ER(-)/HER2(-) breast cancers, we identified activities of key miRNAs let-7d and miR-18a as potential prognostic markers and validated them in two independent ER(-)/HER2(-) breast cancer datasets. Our work provides a novel scheme to facilitate our understanding of miRNA. In summary, inferred activity of key miRNA provided a functional link to its mediated regulatory network, and can be used to robustly predict patient's survival.

the software is freely available at http//research.mssm.edu/integrative-network-biology/Software.html.

jun.zhu@mssm.edu

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.

We present Cas-Designer, a user-friendly program to aid researchers in choosing appropriate target sites in a gene of interest for type II CRISPR/Cas-derived RNA-guided endonucleases, which are now widely used for biomedical research and biotechnology. Cas-Designer rapidly provides the list of all possible guide RNA sequences in a given input DNA sequence and their potential off-target sites including bulge-type sites in a genome of choice. In addition, the program assigns an out-of-frame score to each target site to help users choose appropriate sites for gene knockout. Cas-Designer shows the results in an interactive table and provides user-friendly filter functions.

Free access at http//rgenome.net/cas-designer/.

Free access at http//rgenome.net/cas-designer/.

SeDuS is the first flexible and user-friendly forward-in-time simulator of patterns of molecular evolution within segmental duplications undergoing interlocus gene conversion and crossover. SeDuS introduces known features of interlocus gene conversion such as biased directionality and dependence on local sequence identity. Additionally, it includes aspects such as different selective pressures acting upon copy number and flexible crossover distributions. A graphical user interface allows fast fine-tuning of relevant parameters and straightforward real-time analysis of the evolution of duplicates.

SeDuS is implemented in C++ and can be run via command line or through a graphical user interface developed using Qt C++. Source code and binary executables for Linux, OS X and Windows are freely available at www.biologiaevolutiva.org/sedus/. A tutorial with a detailed description of implementation, parameters and output files is available online.

arcadi.navarro@upf.edu.

arcadi.navarro@upf.edu.

The association between two blocks of 'omics' data brings challenging issues in computational biology due to their size and complexity. Here, we focus on a class of multivariate statistical methods called partial least square (PLS). see more Sparse version of PLS (sPLS) operates integration of two datasets while simultaneously selecting the contributing variables. However, these methods do not take into account the important structural or group effects due to the relationship between markers among biological pathways. link2 Hence, considering the predefined groups of markers (e.g. genesets), this could improve the relevance and the efficacy of the PLS approach.

We propose two PLS extensions called group PLS (gPLS) and sparse gPLS (sgPLS). Our algorithm enables to study the relationship between two different types of omics data (e.g. SNP and gene expression) or between an omics dataset and multivariate phenotypes (e.g. cytokine secretion). We demonstrate the good performance of gPLS and sgPLS compared with the sPLS in the context of grouped data. Then, these methods are compared through an HIV therapeutic vaccine trial. Our approaches provide parsimonious models to reveal the relationship between gene abundance and the immunological response to the vaccine.

The approach is implemented in a comprehensive R package called sgPLS available on the CRAN.

b.liquet@uq.edu.au

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.

To assess the clinical efficacy of the repair of facial nerve defects by allograft transplantation using acellular facial nerves.

Seven patients with facial nerve defects, ranging from damage to 1 facial nerve branch to combined defects of all branches, were enrolled. Defects ranged from 3 to longer than 4cm. All defects were repaired by transplantation of acellular facial nerve allografts. Static and dynamic symmetry and facial expressions were evaluated using the House-Brackmann classification and the functional status of the facial nerve was assessed electromyographically. No patient received immunosuppressive therapy.

All wounds healed well, with no swelling or inflammatory exudation. The patients recovered facial nerve function to various extents. Six months postoperatively, 4 of 7 patients showed static facial asymmetry. Twelve months postoperatively, 3 patients had static facial asymmetry with normal eye closure, and only careful observation could detect slight asymmetry of forehead movement. Two of 7 patients showed moderate facial nerve dysfunction. Ipsilateral facial movement and facial asymmetry were obvious in the patient whose defect affected the common trunk and all facial nerve branches. Two years postoperatively, 5 of 7 patients had mild facial nerve dysfunction, with symmetric faces and incomplete eye occlusion. Six years postoperatively, these patients continued to show symmetric faces and incomplete ipsilateral eye occlusion, but facial muscle function was considerably restored. Follow-up electromyography showed neurologic recovery in all patients.

The repair of a facial nerve defect by transplantation of an acellular facial nerve allograft is feasible.

The repair of a facial nerve defect by transplantation of an acellular facial nerve allograft is feasible.

Several investigators have found that preserving the superior thyroid artery flap can considerably increase the survival rate of the sternocleidomastoid (SCM) flap. Nevertheless, they have recommended not cleaning the lymph nodes above level II for occipital artery preservation, which can leave risky metastatic lymph nodes and restrict the application of the SCM flap in patients with at least stage N1. The authors propose that preserving only the superior thyroid arteriovenous system is sufficient to ensure survival of the SCM flap and preserving the occipital artery is not necessary. They also propose preserving the cranial portion of the external jugular vein for improved venous return of the skin paddle.

This study retrospectively examined 20 patients with oral cancer (18 male, 2 female; 33 to 92yr old; median age, 57.5yr) who underwent SCM flap reconstruction from September 2011 to September 2014. All patients underwent surgical resection and immediate reconstruction with the SCM flap. The primary sita reliable and convenient technique with wide application in the reconstruction of head and neck defects.

Using the SCM flap with modifications is a reliable and convenient technique with wide application in the reconstruction of head and neck defects.Infliximab, a monoclonal antibody directed against tumour necrosis factor, is an effective therapy for moderate-to-severe ulcerative colitis and Crohn's disease. Uncommonly, serious opportunistic infections have occurred in patients after infliximab administration. Here, we describe meningitis caused by Listeria monocytogenes developing in a 37-year-old man with ulcerative colitis refractory to intravenous corticosteroids 10 days after receiving his first infusion of infliximab. With the increasing use of tumour necrosis factor-α-neutralizing agents, clinicians should be aware of the risk of opportunistic infections caused by L. monocytogenes in patients with inflammatory bowel disease following infliximab treatment. The half-life of infliximab is 9.5 days; therefore, patients tend to be more susceptible in the immediate period following infusion. Patients receiving anti-TNF therapy should be advised to avoid foods such as soft cheeses and unpasteurized dairy products.

Sedation uptake rates for oesophagogastroduodenoscopy (OGD) vary greatly. Issues concerning adequate information and consent have been raised. link3 Additionally, patient comprehension of sedation options is inconsistent.

A closed ended questionnaire was created and delivered to assess patient understanding regarding sedation prior to OGD. The questionnaire was based on British Society of Gastroenterology guidelines.

One hundred and eleven patients were recruited. 90% of the sedated and 73% of the unsedated patients were satisfied with their respective decisions (OR 0.283, *p=0.01). 65% were unaware of basic differences between conscious sedation and general anesthesia, and 37% were unaware that driving is permitted after having throat spray alone. The most informed of the age groups had the lowest uptake of sedation and the least informed had the highest uptake.

The decision to undergo gastroscopy with or without sedation is not a sufficiently informed one. This study highlights the need for the widespread dissemination of good quality information to inform patients better regarding sedation prior to OGD.