Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE)

BACKGROUND: An important challenge for transcript counting methods such as Serial Analysis of Gene Expression (SAGE), "Digital Northern" or Massively Parallel Signature Sequencing (MPSS), is to carry out statistical analyses that account for the within-class variability, i.e., variability due to the intrinsic biological differences among sampled individuals of the same class, and not only variability due to technical sampling error. RESULTS: We introduce a Bayesian model that accounts for the within-class variability by means of mixture distribution. We show that the previously available approaches of aggregation in pools ("pseudo-libraries") and the Beta-Binomial model, are particular cases of the mixture model. We illustrate our method with a brain tumor vs. normal comparison using SAGE data from public databases. We show examples of tags regarded as differentially expressed with high significance if the within-class variability is ignored, but clearly not so significant if one accounts for it. CONCLUSION: Using available information about biological replicates, one can transform a list of candidate transcripts showing differential expression to a more reliable one. Our method is freely available, under GPL/GNU copyleft, through a user friendly web-based on-line tool or as R language scripts at supplemental web-site

A reliable measure of similarity based on dependency for short time series: an application to gene expression networks

Abstract Background Microarray techniques have become an important tool to the investigation of genetic relationships and the assignment of different phenotypes. Since microarrays are still very expensive, most of the experiments are performed with small samples. This paper introduces a method to quantify dependency between data series composed of few sample points. The method is used to construct gene co-expression subnetworks of highly significant edges. Results The results shown here are for an adapted subset of aSaccharomyces cerevisiaegene expression data set with low temporal resolution and poor statistics. The method reveals common transcription factors with a high confidence level and allows the construction of subnetworks with high biological relevance that reveals characteristic features of the processes driving the organism adaptations to specific environmental conditions. Conclusion Our method allows a reliable and sophisticated analysis of microarray data even under severe constraints. The utilization of systems biology improves the biologists ability to elucidate the mechanisms underlying celular processes and to formulate new hypotheses

Compatibility of neutrino DIS data and global analyses of parton distribution functions

Neutrino\antineutrino deep inelastic scattering (DIS) data provide useful constrains for the flavor decomposition in global fits of parton distribution functions (PDF). The smallness of the cross-sections requires the use of nuclear targets in the experimental setup. Understanding the nuclear corrections is, for this reason, of utmost importance for a precise determination of the PDFs. Here, we explore the nuclear effects in the neutrino\antineutrino-nucleon DIS by comparing the NuTeV, CDHSW, and CHORUS cross-sections to the predictions derived from the latest parton distribution functions and their nuclear modifications. We obtain a good description of these data and find no apparent disagreement between the nuclear effects in neutrino DIS and those in charged lepton DIS. These results also indicate that further improvements in the knowledge of the nuclear PDFs could be obtained by a more extensive use of these sets of neutrino data.Comment: 16 pages, 8 figure

Adult diagnosis of Swyer-James-MacLeod syndrome: a case report

<p>Abstract</p> <p>Introduction</p> <p>Swyer-James-MacLeod syndrome or unilateral hyperlucent lung syndrome is a rare entity associated with postinfectious bronchiolitis obliterans occurring in childhood. It is characterized by hypoplasia and/or agenesis of the pulmonary arteries resulting in pulmonary parenchyma hypoperfusion.</p> <p>Case presentation</p> <p>Here we report the case of a 53-year-old Caucasian woman with Swyer-James-MacLeod syndrome found in the differential diagnosis workup for a new onset of heart failure, secondary to pulmonary arterial hypertension complicated by a patent ductus arteriosus.</p> <p>Conclusion</p> <p>Typically, this disorder is diagnosed in childhood after evaluation for recurrent respiratory infections, but sometimes an indolent course means diagnosis is not made until adulthood.</p

Health trajectories of Immigrant Children (CRIAS)-a prospective cohort study in the metropolitan area of Lisbon, Portugal

Funding Information: This research was financed by the Asylum, Integration and Migration Fund (ref.PT/2018/FAMI/350) under the Multianual Financial Framework 2014/20, by the Portuguese Foundation for Science and Technology (FCT) (ref.RESEARCH4COVID-19-065) and Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine (IHMT), NOVA University of Lisbon, Portugal (ref.UID/04413/2020). The extension of the cohort study is financed by the Portuguese Foundation for Science and Technology (FCT) (ref.PTDC/SAU-SER/4664/2020). Publisher Copyright: © 2022 BMJ Publishing Group. All rights reserved.Purpose The CRIAS (Health trajectories of Immigrant Children in Amadora) cohort study was created to explore whether children exposed to a migratory process experience different health risks over time, including physical health, cognitive, socioemotional and behavioural challenges and different healthcare utilisation patterns. Participants The original CRIAS was set up to include 604 children born in 2015, of whom 50% were immigrants, and their parents. Recruitment of 420 children took place between June 2019 and March 2020 at age 4/5 years, with follow-up carried out at age 5/6 years, at age 6/7 years currently under way. Findings to date Baseline data at age 4/5 years (2019-2020) suggested immigrant children to be more likely to belong to families with less income, compared with non-immigrant children. Being a first-generation immigrant child increased the odds of emotional and behavioural difficulties (adjusted OR 2.2; 95% CI: 1.06 to 4.76); more immigrant children required monitoring of items in the psychomotor development test (38.5% vs 28.3%). The prevalence of primary care utilisation was slightly higher among immigrant children (78.0% vs 73.8%), yet they received less health monitoring assessments for age 4 years. Utilisation of the hospital emergency department was higher among immigrants (53.2% vs 40.6%). Age 5 years follow-up (2020-2021) confirmed more immigrant children requiring monitoring of psychomotor development, compared with non-immigrant children (33.9% vs 21.6%). Economic inequalities exacerbated by post-COVID-19 pandemic confinement with parents of immigrant children 3.2 times more likely to have their household income decreased. Future plans Further follow-up will take place at 8, 10, 12/13 and 15 years of age. Funds awarded by the National Science Foundation will allow 900 more children from four other Lisbon area municipalities to be included in the cohort (cohort-sequential design).publishersversionpublishe

Comparative performance evaluation of hepatitis C virus genotyping based on the 5' untranslated region versus partial sequencing of the NS5B region of brazilian patients with chronic hepatitis C

<p>Abstract</p> <p>Background</p> <p>Genotyping of hepatitis C virus (HCV) has become an essential tool for prognosis and prediction of treatment duration. The aim of this study was to compare two HCV genotyping methods: reverse hybridization line probe assay (LiPA v.1) and partial sequencing of the NS5B region.</p> <p>Methods</p> <p>Plasma of 171 patients with chronic hepatitis C were screened using both a commercial method (LiPA HCV Versant, Siemens, Tarrytown, NY, USA) and different primers targeting the NS5B region for PCR amplification and sequencing analysis.</p> <p>Results</p> <p>Comparison of the HCV genotyping methods showed no difference in the classification at the genotype level. However, a total of 82/171 samples (47.9%) including misclassification, non-subtypable, discrepant and inconclusive results were not classified by LiPA at the subtype level but could be discriminated by NS5B sequencing. Of these samples, 34 samples of genotype 1a and 6 samples of genotype 1b were classified at the subtype level using sequencing of NS5B.</p> <p>Conclusions</p> <p>Sequence analysis of NS5B for genotyping HCV provides precise genotype and subtype identification and an accurate epidemiological representation of circulating viral strains.</p

Applications of drones in emerging economies: a case study of Malaysia

Drones or unmanned aerial vehicles (UAVs) are becoming increasingly popular for commercial and noncommercial uses - especially in fields of environment, surveillance, aerial photography, digital communications, search and rescue operations and military. Drones are in fact low cost aerial robots, that require little preparation and infrastructure and can be equipped with any number of sensors or cameras making them ideal for monitoring the environment. Environmental monitoring plays a major role in analyzing climate and management impacts on natural, agricultural systems, assessing, forecasting and even preventing natural disasters and enhancing hydrological cycle. Monitoring and data collection systems are based upon a combination of ground-based measurements and remote sensing sensors observations. These data however have spatiotemporal constraints. Drones offer an opportunity to bridge the existing gap between field observations and remote sensing by providing high spatial detail over relatively large areas in a cost-effective way. Drones have become popular in several developed countries in recent years. However, the use of drones is still in the infancy stage of development at developing countries such as Malaysia. This paper attempts to review the development of drone applications in Malaysia in order to identify future directions, applications, developments and challenges. We summarize that, to leverage the full potential of drones approaches in Malaysia, measurement protocols, retrieval algorithms, and processing and evaluation techniques need to be harmonized to ensure the sustainability and resiliency of the implementation

Two-year clinical outcome from the Iberian registry patients after left atrial appendage closure

AIMS: The aim of this study was to observe the percentage of thromboembolic and haemorrhagic events over a 2-year follow-up in patients with non-valvular atrial fibrillation (NVAF) undergoing closure of the left atrial appendage (LAA) with an occlusion device. Observed events and CHADS2 (congestive heart failure, hypertension, age, diabetes, stroke history), CHA2DS2-VASc (also adding: vascular disease and sex) and HAS-BLED (hypertension, abnormal liver/renal function, stroke history, bleeding predisposition, labile international normalised ratios, elderly, drugs/alcohol use)-predicted events were compared. METHODS: LAA closure with an occlusion device was performed in 167 NVAF patients contraindicated for oral anticoagulants and recruited from 12 hospitals between 2009 and 2013. At least two transoesophageal echocardiograms were performed in the first 6 months postimplantation. Antithrombotics included clopidogrel and aspirin. Patients were monitored for death, stroke, major and relevant bleeding and hospitalisation for concomitant conditions. Mean age was 74.68±8.58, median follow-up was 24 months, 5.38% had intraoperative complications and implantation was successful in 94.6% of subjects. Mortality during follow-up was 10.8%, mostly (9.5%) non-cardiac related. Bleeding occurred in 10.1% of subjects, 5.7% major and 4.4% minor though relevant, and 4.4% suffered stroke. Major bleeding and stroke/transient ischaemic attack events within 2 years (annual event rates, 290 patients/year) were less frequent than expected from CHADS2 (2.4% vs 9.6%), CHA2DS2-VASc (2.4% vs 8.3%) and HAS-BLED (3.1% vs 6.6%) risk scores (p<0.001, p=0.003, p=0.047, respectively). CONCLUSIONS: LAA closure with an occlusion device in patients contraindicated for oral anticoagulants is a therapeutic option associated with fewer thromboembolic and haemorrhagic events than expected from risk scores, particularly in the second year postimplantation

National inventory of emergency departments in Singapore

Background: Emergency departments (EDs) are the basic units of emergency care. We performed a national inventory of all Singapore EDs and describe their characteristics and capabilities. Methods: Singapore EDs accessible to the general public 24/7 were surveyed using the National ED Inventories instrument ( http://www.emnet-nedi.org). ED staff members were asked about ED characteristics with reference to calendar year 2007. Results: Fourteen EDs participated (100% response). All EDs were located in hospitals, and most (92%) were independent departments. One was a psychiatric ED; the rest were general EDs. Among general EDs, all had a contiguous layout, with medical and surgical care provided in one area. All but two EDs saw both adults and children; one ED was adult-only, and the other saw only children. Six were in the public sector and seven in private health-care institutions, with public EDs seeing the majority (78%) of ED patients. Each private ED had an annual patient census of 60,000. They received 98% of ambulances and had an inpatient admission rate of 30%. Two public EDs reported being overcapacity; no private EDs did. For both public and private EDs, availability of consultant resources in EDs was high, while technological resources varied. Conclusion: Characteristics and capabilities of Singapore EDs varied and were largely dependent on whether they are in public or private hospitals. This initial inventory establishes a benchmark to further monitor the development of emergency care in Singapore