Correlation between impact factor and public availability of published research data in Information Science and Library Science journals

The final publication is available at Springer via http://dx.doi.org/10.1007/s11192-016-1868-7[EN] Scientists continuously generate research data but only a few of them are published. If these data were accessible and reusable, researchers could examine them and generate new knowledge. Our purpose is to determine whether there is a relationship between the impact factor and the policies concerning open availability of raw research data in journals of Information Science and Library Science (ISLS) subject category from the Web of Science database. We reviewed the policies related to public availability of papers and data sharing in the 85 journals included in the ISLS category of the Journal Citation Reports in 2012. The relationship between public availability of published data and impact factor of journals is analysed through different statistical tests. The variable "statement of complementary material" was accepted in 50 % of the journals; 65 % of the journals support "reuse"; 67 % of the journals specified "storage in thematic or institutional repositories"; the "publication of the manuscript in a website" was accepted in 69 % of the journals. We have found a 50 % of journals that include the possibility to deposit data as supplementary material, and more than 60 % accept reuse, storage in repositories and publication in websites. There is a clear positive relationship between being a top journal in impact factor ranking of JCR and having an open policy.This work has benefited from assistance by the National R+D+I of the Ministry of Economy and Competitiveness of the Spanish Government (CSO2012-39632-C02).Aleixandre-Benavent, R.; Moreno-Solano, L.; Ferrer Sapena, A.; Sánchez Pérez, EA. (2016). Correlation between impact factor and public availability of published research data in Information Science and Library Science journals. 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A sea of standards for omics data: sink or swim? Journal of the American Medical Informatics Association, 21(2), 200–203.Tenopir, C., Allard, S., Douglass, K., Aydinoglu, A. U., Wu, L., Read, E., et al. (2011). Data sharing by scientists: Practices and perceptions. PLoS One, 6(6), e21101.The Royal Society Publishing. (2015). http://royalsocietypublishing.org/data-sharing . Accessed 15 March 2015Toronto International Data Release Workshop Authors. (2009). Prepublication data sharing. Nature, 461(7261), 168–170.Van Noorden, R. (2013). Data-sharing: Everything on display. Nature, 500, 243–245.Wellcome Trust. (2015). Data sharing. http://www.wellcome.ac.uk/About-us/Policy/Spotlight-issues/Data-sharing/ . Accessed 21 January 201

Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing

BACKGROUND: Rare genetic variation in the human population is a major source of pathophysiological variability and has been implicated in a host of complex phenotypes and diseases. Finding disease-related genes harboring disparate functional rare variants requires sequencing of many individuals across many genomic regions and comparing against unaffected cohorts. However, despite persistent declines in sequencing costs, population-based rare variant detection across large genomic target regions remains cost prohibitive for most investigators. In addition, DNA samples are often precious and hybridization methods typically require large amounts of input DNA. Pooled sample DNA sequencing is a cost and time-efficient strategy for surveying populations of individuals for rare variants. We set out to 1) create a scalable, multiplexing method for custom capture with or without individual DNA indexing that was amenable to low amounts of input DNA and 2) expand the functionality of the SPLINTER algorithm for calling substitutions, insertions and deletions across either candidate genes or the entire exome by integrating the variant calling algorithm with the dynamic programming aligner, Novoalign. RESULTS: We report methodology for pooled hybridization capture with pre-enrichment, indexed multiplexing of up to 48 individuals or non-indexed pooled sequencing of up to 92 individuals with as little as 70 ng of DNA per person. Modified solid phase reversible immobilization bead purification strategies enable no sample transfers from sonication in 96-well plates through adapter ligation, resulting in 50% less library preparation reagent consumption. Custom Y-shaped adapters containing novel 7 base pair index sequences with a Hamming distance of ≥2 were directly ligated onto fragmented source DNA eliminating the need for PCR to incorporate indexes, and was followed by a custom blocking strategy using a single oligonucleotide regardless of index sequence. These results were obtained aligning raw reads against the entire genome using Novoalign followed by variant calling of non-indexed pools using SPLINTER or SAMtools for indexed samples. With these pipelines, we find sensitivity and specificity of 99.4% and 99.7% for pooled exome sequencing. Sensitivity, and to a lesser degree specificity, proved to be a function of coverage. For rare variants (≤2% minor allele frequency), we achieved sensitivity and specificity of ≥94.9% and ≥99.99% for custom capture of 2.5 Mb in multiplexed libraries of 22–48 individuals with only ≥5-fold coverage/chromosome, but these parameters improved to ≥98.7 and 100% with 20-fold coverage/chromosome. CONCLUSIONS: This highly scalable methodology enables accurate rare variant detection, with or without individual DNA sample indexing, while reducing the amount of required source DNA and total costs through less hybridization reagent consumption, multi-sample sonication in a standard PCR plate, multiplexed pre-enrichment pooling with a single hybridization and lesser sequencing coverage required to obtain high sensitivity

Mapping Antimicrobial Stewardship in Undergraduate Medical, Dental, Pharmacy, Nursing and Veterinary Education in the United Kingdom.

OBJECTIVES: To investigate the teaching of antimicrobial stewardship (AS) in undergraduate healthcare educational degree programmes in the United Kingdom (UK). PARTICIPANTS AND METHODS: Cross-sectional survey of undergraduate programmes in human and veterinary medicine, dentistry, pharmacy and nursing in the UK. The main outcome measures included prevalence of AS teaching; stewardship principles taught; estimated hours apportioned; mode of content delivery and teaching strategies; evaluation methodologies; and frequency of multidisciplinary learning. RESULTS: 80% (112/140) of programmes responded adequately. The majority of programmes teach AS principles (88/109, 80.7%). 'Adopting necessary infection prevention and control precautions' was the most frequently taught principle (83/88, 94.3%), followed by 'timely collection of microbiological samples for microscopy, culture and sensitivity' (73/88, 82.9%) and 'minimisation of unnecessary antimicrobial prescribing' (72/88, 81.8%). The 'use of intravenous administration only to patients who are severely ill, or unable to tolerate oral treatment' was reported in ~50% of courses. Only 32/88 (36.3%) programmes included all recommended principles. DISCUSSION: Antimicrobial stewardship principles are included in most undergraduate healthcare and veterinary degree programmes in the UK. However, future professionals responsible for using antimicrobials receive disparate education. Education may be boosted by standardisation and strengthening of less frequently discussed principles

A needs assessment study for optimising prescribing practice in secondary care junior doctors: the Antibiotic Prescribing Education among Doctors (APED).

BACKGROUND: Appropriate antimicrobial prescribing is essential for patient care, yet up to half of antimicrobial prescriptions written in the UK are sub-optimal. Improving prescriber education has recently been promoted as a mechanism to optimise antimicrobial use, but identification of key learning objectives to facilitate this is so far lacking. Using qualitative methods we investigated junior doctor knowledge, attitudes, and behaviours around antimicrobial prescribing to identify key areas to address in future educational programmes. METHODS: A cross-sectional survey of qualified doctors in training in West London was undertaken exploring antimicrobial prescribing practices and educational needs. RESULTS: Among 140 junior doctors from 5 London hospitals, a third (34 %) reported prescribing primarily unsupervised, and two thirds (67 %) reported difficulties obtaining prescribing support outside of hours. 20 % stated not feeling confident in writing an antimicrobial prescription, but confidence was increased through having confirmatory diagnostic results (24) and obtaining advice from a senior doctor (26 %); whether this senior was from their own specialty, or an infection-specialist, varied significantly (p < 0.01) by experience. Only a small percentage (5-13 %; depending on number of years post-qualification) of participants stated their previous antimicrobial education was effective. 60 % of those in their first year post qualification reported wanting further education in antimicrobial prescribing, rising to 74 % among more experienced junior doctors. Specific areas of educational need identified were (i) principles of antimicrobial prescribing, (ii) diagnosis of infections, (iii) clinical review of patients with infections, (iv) prescribing in the context of antimicrobial resistance, and (v) laboratory testing and test results. CONCLUSIONS: A significant proportion of junior doctors report lone prescribing of antimicrobials in the context of low self-perceived confidence and knowledge in this field, and frequent difficulty in accessing help when necessary. Innovative training, targeting five specific areas identified through this needs assessment, is urgently needed by junior doctors practising in secondary care

IGF1R Signaling in Ewing Sarcoma Is Shaped by Clathrin-/Caveolin-Dependent Endocytosis

Receptor endocytosis is critical for cell signaling. IGF1R mediates an autocrine loop that is de-regulated in Ewing Sarcoma (ES) cells. Here we study the impact of IGF1R internalization, mediated by clathrin and caveolin-1 (CAV1), in ES signaling. We used clathrin and CAV1-siRNA to interfere in clathrin- and caveolin-dependent endocytosis. Chlorpromazine (CPMZ) and methyl-beta-cyclo-dextrin (MCD) were also used in order to inhibit clathrin- and caveolin-dependent endocytosis, respectively. We analyzed IGF1R internalization and co-localization with clathrin and CAV1 upon ligand binding, as well as the status of the IGF1R pathway, cellular proliferation, and the apoptosis of interfered and inhibited ES cells. We performed a high-throughput tyrosine kinase phosphorylation assay to analyze the effects of combining the IGF1R tyrosine kinase inhibitor AEW541 (AEW) with CPMZ or MCD on the intracellular phospho-proteome. We observed that IGF1R is internalized upon ligand binding in ES cells and that this process is dependent on clathrin or CAV1. The blockage of receptor internalization inhibited AKT and MAPK phosphorylation, reducing the proliferative rate of ES cells and increasing the levels of apoptosis. Combination of AEW with CPMZ or MCD largely enhanced these effects. CAV1 and clathrin endocytosis controls IGF1R internalization and signaling and has a profound impact on ES IGF1R-promoted survival signaling. We propose the combination of tyrosine-kinase inhibitors with endocytosis inhibitors as a new therapeutic approach to achieve a stronger degree of receptor inhibition in this, or other neoplasms dependent on IGF1R signaling

Eficácia do exercício físico na fadiga dos pacientes com câncer durante o tratamento ativo: revisão sistemática e meta-análise

El objetivo del estudio fue determinar la efectividad del ejercicio físico en la fatiga de pacientes con cáncer durante el tratamiento activo. Las bases de datos de PubMed Central, EMBASE y OVID fueron consultadas hasta abril de 2014 para identificar ensayos clínicos aleatorizados, que evaluaran el efecto del ejercicio en la fatiga de pacientes con cáncer sometidos a tratamiento activo. Once estudios (n = 1.407) fueron incluidos. La quimioterapia fue el tratamiento más común (n = 1.028). Los estudios tuvieron bajo riesgo de sesgo y alta calidad metodológica. Las estimaciones de efecto mostraron que el ejercicio físico mejoró significativamente la fatiga (SMD = -3,0; IC95%: -5,21; -0,80), p < 0,0001. Se encontraron efectos similares para el entrenamiento de resistencia (SMD = -4,5; IC95%: -7,24; -1,82), p = 0,001. Se encontraron mejoras significativas en pacientes con cáncer de mama y de próstata (p < 0,05). El ejercicio es una intervención segura y eficaz en el control de la fatiga en pacientes sometidos a tratamiento activoThis study aimed to determine the effectiveness of physical exercise in decreasing fatigue in cancer patients during active treatment. The PubMed Central, EMBASE, and OVID databases were consulted up to April 2014 to identify randomized clinical trials that evaluated the effect of exercise on fatigue in cancer patients undergoing active treatment. Eleven studies (n = 1,407) were included. Chemotherapy was the most common form of treatment (n = 1,028). The studies showed a low risk of bias and high methodological quality. Effect estimates showed that physical exercise significantly improved fatigue (SMD = -3.0; 95%CI: -5.21; -0.80), p < 0.0001. Similar effects were found for resistance training (SMD = -4.5; 95%CI: -7.24; -1.82), p = 0.001. Significant improvements were found in breast and prostate cancer patients (p < 0.05). Exercise is a safe and effective intervention in the management fatigue in cancer patients undergoing active treatmentO objetivo foi determinar a efetividade do exercício físico sobre a fadiga em pacientes com câncer durante o tratamento ativo. As bases de dados PubMed Central, EMBASE e OVID foram consultadas até abril de 2014 para identificar ensaios clínicos randomizados que avaliaram o efeito do exercício sobre a fadiga em pacientes com câncer em tratamento ativo. Onze estudos (n = 1.407) foram incluídos. A quimioterapia foi o tratamento mais comum (n = 1.028). Os estudos tiveram baixo risco de viés e alta qualidade metodológica. As estimativas de efeito mostraram que o exercício melhorou significativamente a fadiga (DMP = -3,0; IC95%: -5,21; -0,80), p < 0,0001. Efeitos semelhantes sobre o treinamento de resistência (DMP = -4,5; IC95%: -7,24; -1,82), p = 0,001 foram encontrados. O exercício físico é uma intervenção segura e eficaz contra a fadiga em pacientes submetidos ao tratamento ativoEl presente trabajo forma parte del Proyecto Práctica del autoexamen de seno y los conocimientos, factores de riesgo y estilos de vida relacionados con el cáncer de mama en mujeres jóvenes de la Universidad Santo Tomás de Bogotá: un análisis transversal (9ª Convocatoria FODEIN- Código del proyecto 4110060001 - 008)

A Novel Semi-Supervised Methodology for Extracting Tumor Type-Specific MRS Sources in Human Brain Data

BackgroundThe clinical investigation of human brain tumors often starts with a non-invasive imaging study, providing information about the tumor extent and location, but little insight into the biochemistry of the analyzed tissue. Magnetic Resonance Spectroscopy can complement imaging by supplying a metabolic fingerprint of the tissue. This study analyzes single-voxel magnetic resonance spectra, which represent signal information in the frequency domain. Given that a single voxel may contain a heterogeneous mix of tissues, signal source identification is a relevant challenge for the problem of tumor type classification from the spectroscopic signal.Methodology/Principal FindingsNon-negative matrix factorization techniques have recently shown their potential for the identification of meaningful sources from brain tissue spectroscopy data. In this study, we use a convex variant of these methods that is capable of handling negatively-valued data and generating sources that can be interpreted as tumor class prototypes. A novel approach to convex non-negative matrix factorization is proposed, in which prior knowledge about class information is utilized in model optimization. Class-specific information is integrated into this semi-supervised process by setting the metric of a latent variable space where the matrix factorization is carried out. The reported experimental study comprises 196 cases from different tumor types drawn from two international, multi-center databases. The results indicate that the proposed approach outperforms a purely unsupervised process by achieving near perfect correlation of the extracted sources with the mean spectra of the tumor types. It also improves tissue type classification.Conclusions/SignificanceWe show that source extraction by unsupervised matrix factorization benefits from the integration of the available class information, so operating in a semi-supervised learning manner, for discriminative source identification and brain tumor labeling from single-voxel spectroscopy data. We are confident that the proposed methodology has wider applicability for biomedical signal processing

Obesity Indexes and Total Mortality among Elderly Subjects at High Cardiovascular Risk: The PREDIMED Study

BackgroundDifferent indexes of regional adiposity have been proposed for identifying persons at higher risk of death. Studies specifically assessing these indexes in large cohorts are scarce. It would also be interesting to know whether a dietary intervention may counterbalance the adverse effects of adiposity on mortality.MethodsWe assessed the association of four different anthropometric indexes (waist-to-height ratio (WHtR), waist circumference (WC), body mass index (BMI) and height) with all-cause mortality in 7447 participants at high cardiovascular risk from the PREDIMED trial. Forty three percent of them were men (55 to 80 years) and 57% were women (60 to 80 years). All of them were initially free of cardiovascular disease. The recruitment took place in 11 recruiting centers between 2003 and 2009.ResultsAfter adjusting for age, sex, smoking, diabetes, hypertension, intervention group, family history of coronary heart disease, and leisure-time physical activity, WC and WHtR were found to be directly associated with a higher mortality after 4.8 years median follow-up. The multivariable-adjusted HRs for mortality of WHtR (cut-off points: 0.60, 0.65, 0.70) were 1.02 (0.78–1.34), 1.30 (0.97–1.75) and 1.55 (1.06–2.26). When we used WC (cut-off points: 100, 105 and 110 cm), the multivariable adjusted Hazard Ratios (HRs) for mortality were 1.18 (0.88–1.59), 1.02 (0.74–1.41) and 1.57 (1.19–2.08). In all analyses, BMI exhibited weaker associations with mortality than WC or WHtR. The direct association between WHtR and overall mortality was consistent within each of the three intervention arms of the trial.ConclusionsOur study adds further support to a stronger association of abdominal obesity than BMI with total mortality among elderly subjects at high risk of cardiovascular disease. We did not find evidence to support that the PREDIMED intervention was able to counterbalance the harmful effects of increased adiposity on total mortality.Trial RegistrationControlled-Trials.com ISRCTN3573963