Exon and junction microarrays detect widespread mouse strain- and sex-bias expression differences

Background: Studies have shown that genetic and sex differences strongly influence gene expression in mice. Given the diversity and complexity of transcripts produced by alternative splicing, we sought to use microarrays to establish the extent of variation found in mouse strains and genders. Here, we surveyed the effect of strain and sex on liver gene and exon expression using male and female mice from three different inbred strains. Results: 71 liver RNA samples from three mouse strains - DBA/2J, C57BL/6J and C3H/HeJ - were profiled using a custom-designed microarray monitoring exon and exon-junction expression of 1,020 genes representing 9,406 exons. Gene expression was calculated via two different methods, using the 3'-most exon probe ("3' gene expression profiling") and using all probes associated with the gene ("whole-transcript gene expression profiling"), while exon expression was determined using exon probes and flanking junction probes that spanned across the neighboring exons ("exon expression profiling"). Widespread strain and sex influences were detected using a two-way Analysis of Variance (ANOVA) regardless of the profiling method used. However, over 90% of the genes identified in 3' gene expression profiling or whole transcript profiling were identified in exon profiling, along with 75% and 38% more genes, respectively, showing evidence of differential isoform expression. Overall, 55% and 32% of genes, respectively, exhibited strain- and sex-bias differential gene or exon expression. Conclusion: Exon expression profiling identifies significantly more variation than both 3' gene expression profiling and whole-transcript gene expression profiling. A large percentage of genes that are not differentially expressed at the gene level demonstrate exon expression variation suggesting an influence of strain and sex on alternative splicing and a need to profile expression changes at sub-gene resolution

The Clinical and Economic Impact of Point-of-Care CD4 Testing in Mozambique and Other Resource-Limited Settings: A Cost-Effectiveness Analysis

Background: Point-of-care CD4 tests at HIV diagnosis could improve linkage to care in resource-limited settings. Our objective is to evaluate the clinical and economic impact of point-of-care CD4 tests compared to laboratory-based tests in Mozambique. Methods and Findings: We use a validated model of HIV testing, linkage, and treatment (CEPAC-International) to examine two strategies of immunological staging in Mozambique: (1) laboratory-based CD4 testing (LAB-CD4) and (2) point-of-care CD4 testing (POC-CD4). Model outcomes include 5-y survival, life expectancy, lifetime costs, and incremental cost-effectiveness ratios (ICERs). Input parameters include linkage to care (LAB-CD4, 34%; POC-CD4, 61%), probability of correctly detecting antiretroviral therapy (ART) eligibility (sensitivity: LAB-CD4, 100%; POC-CD4, 90%) or ART ineligibility (specificity: LAB-CD4, 100%; POC-CD4, 85%), and test cost (LAB-CD4, US$10; POC-CD4, US$24). In sensitivity analyses, we vary POC-CD4-specific parameters, as well as cohort and setting parameters to reflect a range of scenarios in sub-Saharan Africa. We consider ICERs less than three times the per capita gross domestic product in Mozambique (US$570) to be cost-effective, and ICERs less than one times the per capita gross domestic product in Mozambique to be very cost-effective. Projected 5-y survival in HIV-infected persons with LAB-CD4 is 60.9$2,440 (95% CI, US$2,440–US$2,450) and increase with POC-CD4 to 10.3 y (95% CI, 10.3–10.3 y) and US$2,800 (95$2,790–US$2,800); the ICER of POC-CD4 compared to LAB-CD4 is US$500/year of life saved (YLS) (95% CI, US$480–US$520/YLS). POC-CD4 improves clinical outcomes and remains near the very cost-effective threshold in sensitivity analyses, even if point-of-care CD4 tests have lower sensitivity/specificity and higher cost than published values. In other resource-limited settings with fewer opportunities to access care, POC-CD4 has a greater impact on clinical outcomes and remains cost-effective compared to LAB-CD4. Limitations of the analysis include the uncertainty around input parameters, which is examined in sensitivity analyses. The potential added benefits due to decreased transmission are excluded; their inclusion would likely further increase the value of POC-CD4 compared to LAB-CD4. Conclusions: POC-CD4 at the time of HIV diagnosis could improve survival and be cost-effective compared to LAB-CD4 in Mozambique, if it improves linkage to care. POC-CD4 could have the greatest impact on mortality in settings where resources for HIV testing and linkage are most limited. Please see later in the article for the Editors' Summar

Detection of pulse trains in the electrically stimulated cochlea: Effects of cochlear health

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/98659/1/JAS003954.pd

Transurethral resection of the prostate in Northern Nigeria, problems and prospects

<p>Abstract</p> <p>Background</p> <p>Benign prostatic hyperplasia (BPH) is the commonest disease of the urinary tract afflicting the ageing male and is the commonest neoplastic disease in men aged 50 years and above.</p> <p>Transurethral prostatectomy (TURP) is the ultimate treatment of choice for benign prostatic hyperplasia (BPH) due mainly to the preference of minimally invasive surgery, long term relief of symptoms and cost effectiveness. It is however not available to the majority of Nigerians in need of prostatic surgery in Public Health Institutions.</p> <p>Methods</p> <p>The records of patients who underwent prostatectomy in Aminu Kano Teaching Hospital, over the period June 2001 to July 2007 were examined. The bio data of patients and laboratory investigations performed were retrieved.</p> <p>Results</p> <p>Five Hundred and forty two patients were operated upon, out of which 40 were excluded due to open prostatectomy (22 patients), bladder neck stenosis (16 patients) or bladder tumour around the trigon (2 patients). The age range of the patients was 47–110 years with a mean of 67.2 years. 289 patients (80.1%) had urethral catheter in situ at presentation and 11 (3%) patients had suprapubic cystostomy of which only 3 (0.85%) had combined urethral stricture and BPH.</p> <p>Only 131 (26%) had their PSA measured which ranged from 2–100 ng/ml out of which 39(29.8% n = 131) patients had more than 4 ng/ml and cancer of the prostate and 1(0.8%, n = 131) patient had a PSA level of 4 ng/ml and malignant prostate.</p> <p>Hospital stay was 1–32 days (mean 7.9) and the mean follow up period was 5.6 months (range 0–60) and there were 17.5% complications comprising of urinary tract infection (UTI) 7.2%, Orchitis 2.2%, urinary incontinence 0.6%, atonic bladder 1%, erectile dysfunction 0.6%, cerebrovascular accident 0.4%, myocardial infarction 0.4%, deep vein thrombosis 0.4% and disseminated intravascular coagulopathy (DIC) 0.6% and 1.2% mortality. The cost of treatment inclusive of pre-admission investigations was US$615.00 (range US$ 300–1,300)</p> <p>Conclusion</p> <p>Despite advances in minimally invasive therapy for LUTH/BPH, TURP is the optimum treatment of choice for the ageing male of sub-Saharan Africa. It is however not available to the majority of patients in this region due to poor health allocation and inadequate facilities and training.</p

The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies

Reproducibility is a fundamental requirement in scientific experiments and clinical contexts. Recent publications raise concerns about the reliability of microarray technology because of the apparent lack of agreement between lists of differentially expressed genes (DEGs). In this study we demonstrate that (1) such discordance may stem from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion, the lists become much more reproducible, especially when fewer genes are selected; and (3) the instability of short DEG lists based on P cutoffs is an expected mathematical consequence of the high variability of the t-values. We recommend the use of FC ranking plus a non-stringent P cutoff as a baseline practice in order to generate more reproducible DEG lists. The FC criterion enhances reproducibility while the P criterion balances sensitivity and specificity

The influence of HLA genotype on the development of metal hypersensitivity following joint replacement

We thank Innovate UK Edge for providing funding to allow this research to be carried out.Background  Over five million joint replacements are performed across the world each year. Cobalt chrome (CoCr) components are used in most of these procedures. Some patients develop delayed type hypersensitivity (DTH) responses to CoCr implants, resulting in tissue damage and revision surgery. DTH is unpredictable and genetic links have yet to be definitively established. Methods At a single site, we carried out an initial investigation to identify HLA alleles associated with development of DTH following metal-on-metal hip arthroplasty. We then recruited patients from other centres to train and validate an algorithm incorporating patient age, gender, HLA genotype44 and blood metal concentrations to predict the development of DTH. Accuracy of the modelling was assessed using performance metrics including time dependent receiver operator curves. Results Using next generation sequencing, here we determine the HLA genotypes of 606 patients. 176 of these patients had experienced failure of their prostheses; the remaining 430 remain asymptomatic at a mean follow up of twelve years. We demonstrate that the development of DTH is associated with patient age, gender, the magnitude of metal exposure and the presence of certain HLA class II alleles. We show that the predictive algorithm developed from this investigation performs to an accuracy suitable for clinical use, with weighted mean survival probability errors of 1.8% and 3.1%53 for pre-operative and post-operative models respectively. Conclusions The development of DTH following joint replacement appears to be determined by the interaction between implant wear and a patient’s genotype. The algorithm described in this paper may improve implant selection and help direct patient surveillance following surgery. Further consideration should be given towards understanding patient specific responses to different biomaterials.Publisher PDFPeer reviewe

Simplified Models for LHC New Physics Searches

This document proposes a collection of simplified models relevant to the design of new-physics searches at the LHC and the characterization of their results. Both ATLAS and CMS have already presented some results in terms of simplified models, and we encourage them to continue and expand this effort, which supplements both signature-based results and benchmark model interpretations. A simplified model is defined by an effective Lagrangian describing the interactions of a small number of new particles. Simplified models can equally well be described by a small number of masses and cross-sections. These parameters are directly related to collider physics observables, making simplified models a particularly effective framework for evaluating searches and a useful starting point for characterizing positive signals of new physics. This document serves as an official summary of the results from the "Topologies for Early LHC Searches" workshop, held at SLAC in September of 2010, the purpose of which was to develop a set of representative models that can be used to cover all relevant phase space in experimental searches. Particular emphasis is placed on searches relevant for the first ~50-500 pb-1 of data and those motivated by supersymmetric models. This note largely summarizes material posted at http://lhcnewphysics.org/, which includes simplified model definitions, Monte Carlo material, and supporting contacts within the theory community. We also comment on future developments that may be useful as more data is gathered and analyzed by the experiments.Comment: 40 pages, 2 figures. This document is the official summary of results from "Topologies for Early LHC Searches" workshop (SLAC, September 2010). Supplementary material can be found at http://lhcnewphysics.or

Gene Set Enrichment in eQTL Data Identifies Novel Annotations and Pathway Regulators

Genome-wide gene expression profiling has been extensively used to generate biological hypotheses based on differential expression. Recently, many studies have used microarrays to measure gene expression levels across genetic mapping populations. These gene expression phenotypes have been used for genome-wide association analyses, an analysis referred to as expression QTL (eQTL) mapping. Here, eQTL analysis was performed in adipose tissue from 28 inbred strains of mice. We focused our analysis on “trans-eQTL bands”, defined as instances in which the expression patterns of many genes were all associated to a common genetic locus. Genes comprising trans-eQTL bands were screened for enrichments in functional gene sets representing known biological pathways, and genes located at associated trans-eQTL band loci were considered candidate transcriptional modulators. We demonstrate that these patterns were enriched for previously characterized relationships between known upstream transcriptional regulators and their downstream target genes. Moreover, we used this strategy to identify both novel regulators and novel members of known pathways. Finally, based on a putative regulatory relationship identified in our analysis, we identified and validated a previously uncharacterized role for cyclin H in the regulation of oxidative phosphorylation. We believe that the specific molecular hypotheses generated in this study will reveal many additional pathway members and regulators, and that the analysis approaches described herein will be broadly applicable to other eQTL data sets

Quantum entanglement and disentanglement of multi-atom systems

We present a review of recent research on quantum entanglement, with special emphasis on entanglement between single atoms, processing of an encoded entanglement and its temporary evolution. Analysis based on the density matrix formalism are described. We give a simple description of the entangling procedure and explore the role of the environment in creation of entanglement and in disentanglement of atomic systems. A particular process we will focus on is spontaneous emission, usually recognized as an irreversible loss of information and entanglement encoded in the internal states of the system. We illustrate some certain circumstances where this irreversible process can in fact induce entanglement between separated systems. We also show how spontaneous emission reveals a competition between the Bell states of a two qubit system that leads to the recently discovered "sudden" features in the temporal evolution of entanglement. An another problem illustrated in details is a deterministic preparation of atoms and atomic ensembles in long-lived stationary squeezed states and entangled cluster states. We then determine how to trigger the evolution of the stable entanglement and also address the issue of a steered evolution of entanglement between desired pairs of qubits that can be achieved simply by varying the parameters of a given system.Comment: Review articl