bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms
Authors: Zyla Joanna , Marczyk Michal , Domaszewska Teresa , Kaufmann Stefan H E , Polanska Joanna , Weiner January 
Published: May 2019

AbstractMotivationAnalysis of gene set (GS) enrichment is an essential part of functional omics studies. Here, we complement the established evaluation metrics of GS enrichment algorithms with a novel approach to assess the practical reproducibility of scientific results obtained from GS enrichment tests when applied to related data from different studies.ResultsWe evaluated eight established and one novel algorithm for reproducibility, sensitivity, prioritization, false positive rate and computational time. In addition to eight established algorithms, we also included Coincident Extreme Ranks in Numerical Observations (CERNO), a flexible and fast algorithm based on modified Fisher P-value integration. Using real-world datasets, we demonstrate that CERNO is robust to ranking metrics, as well as sample and GS size. CERNO had the highest reproducibility while remaining sensitive, specific and fast. In the overall ranking Pathway Analysis with Down-weighting of Overlapping Genes, CERNO and over-representation analysis performed best, while CERNO and GeneSetTest scored high in terms of reproducibility.Availability and implementationtmod package implementing the CERNO algorithm is available from CRAN (cran.r-project.org/web/packages/tmod/index.html) and an online implementation can be found at http://tmod.online/. The datasets analyzed in this study are widely available in the KEGGdzPathwaysGEO, KEGGandMetacoreDzPathwaysGEO R package and GEO repository.Supplementary informationSupplementary data are available at Bioinformatics online.
A dynamic programing approach to integrate gene expression data and network information for pathway model generation
Authors: Jiang Yuexu , Liang Yanchun , Wang Duolin , Xu Dong , Joshi Trupti 
Published: May 2019

Abstract

Motivation
As large amounts of biological data continue to be rapidly generated, a major focus of bioinformatics research has been aimed toward integrating these data to identify active pathways or modules under certain experimental conditions or phenotypes. Although biologically significant modules can often be detected globally by many existing methods, it is often hard to interpret or make use of the results toward pathway model generation and testing.

Results
To address this gap, we have developed the IMPRes algorithm, a new step-wise active pathway detection method using a dynamic programing approach. IMPRes takes advantage of the existing pathway interaction knowledge in Kyoto Encyclopedia of Genes and Genomes. Omics data are then used to assign penalties to genes, interactions and pathways. Finally, starting from one or multiple seed genes, a shortest path algorithm is applied to detect downstream pathways that best explain the gene expression data. Since dynamic programing enables the detection one step at a time, it is easy for researchers to trace the pathways, which may lead to more accurate drug design and more effective treatment strategies. The evaluation experiments conducted on three yeast datasets have shown that IMPRes can achieve competitive or better performance than other state-of-the-art methods. Furthermore, a case study on human lung cancer dataset was performed and we provided several insights on genes and mechanisms involved in lung cancer, which had not been discovered before.

Availability and implementation
IMPRes visualization tool is available via web server at http://digbio.missouri.edu/impres.

Supplementary information
Supplementary data are available at Bioinformatics online.
Enhanced Bottom-Up and Reduced Top-Down fMRI Activity Is Related to Long-Lasting Nonreinforced Behavioral Change
Authors: Botvinik-Nezer Rotem , Salomon Tom , Schonberg Tom 
Published: May 2019

AbstractBehavioral change studies and interventions focus on self-control and external reinforcements to influence preferences. Cue-approach training (CAT) has been shown to induce preference changes lasting months by merely associating items with neutral cues and speeded responses. We utilized this paradigm to study neural representation of preferences and their modification without external reinforcements. We scanned 36 participants with fMRI during a novel passive viewing task before, after and 30 days following CAT. We preregistered the predictions that activity in memory, top-down attention, and value-processing regions will underlie preference modification. While most theories associate preferences with prefrontal regions, we found that “bottom-up” perceptual mechanisms were associated with immediate change, whereas reduced “top-down” parietal activity was related to long-term change. Activity in value-related prefrontal regions was enhanced immediately after CAT for trained items and 1 month after for all items. Our findings suggest a novel neural mechanism of preference representation and modification. We suggest that nonreinforced change of preferences occurs initially in perceptual representation of items, putatively leading to long-term changes in “top-down” processes. These findings offer implementation of bottom-up instead of top-down targeted interventions for long-lasting behavioral change.
The Emperor’s New Clothes: PRospective Observational Evaluation of the Association Between Initial VancomycIn Exposure and Failure Rates Among ADult HospitalizEd Patients With Methicillin-resistant Staphylococcus aureus Bloodstream Infections (PROVIDE)
Authors: Lodise Thomas P , Rosenkranz Susan L , Finnemeyer Matthew , Evans Scott , Sims Matthew , Zervos Marcus J , Creech C Buddy , Patel Pratish C , Keefer Michael , Riska Paul , Silveira Fernanda P , Scheetz Marc , Wunderink Richard G , Rodriguez Martin , Schrank John , Bleasdale Susan C , Schultz Sara , Barron Michelle , Stapleton Ann , Wray Dannah , Chambers Henry , Fowler Vance G , Holland Thomas L 
Published: May 2019

AbstractBackgroundVancomycin is the most commonly administered antibiotic in hospitalized patients, but optimal exposure targets remain controversial. To clarify the therapeutic exposure range, this study evaluated the association between vancomycin exposure and outcomes in patients with methicillin-resistant Staphylococcus aureus (MRSA) bacteremia.MethodsThis was a prospective, multicenter (n = 14), observational study of 265 hospitalized adults with MRSA bacteremia treated with vancomycin. The primary outcome was treatment failure (TF), defined as 30-day mortality or persistent bacteremia ≥7 days. Secondary outcomes included acute kidney injury (AKI). The study was powered to compare TF between patients who achieved or did not achieve day 2 area under the curve to minimum inhibitory concentration (AUC/MIC) thresholds previously found to be associated with lower incidences of TF. The thresholds, analyzed separately as co-primary endpoints, were AUC/MIC by broth microdilution ≥650 and AUC/MIC by Etest ≥320.ResultsTreatment failure and AKI occurred in 18% and 26% of patients, respectively. Achievement of the prespecified day 2 AUC/MIC thresholds was not associated with less TF. Alternative day 2 AUC/MIC thresholds associated with lower TF risks were not identified. A relationship between the day 2 AUC and AKI was observed. Patients with day 2 AUC ≤515 experienced the best global outcomes (no TF and no AKI).ConclusionsHigher vancomycin exposures did not confer a lower TF risk but were associated with more AKI. The findings suggest that vancomycin dosing should be guided by the AUC and day 2 AUCs should be ≤515. As few patients had day 2 AUCs &lt;400, further study is needed to define the lower bound of the therapeutic range.
Community-acquired Invasive Bacterial Disease in Urban Gambia, 2005–2015: A Hospital-based Surveillance
Authors: Darboe Saffiatou , Okomo Uduak , Muhammad Abdul-Khalie , Ceesay Buntung , Jallow Mamadou , Usuf Effua , Tweed Sam , Akpalu Edem , Kwambana-Adams Brenda , Kariuki Samuel , Antonio Martin , Bradbury Richard S , Forrest Karen , de Silva Thushan I , Lawal Bolarinde Joseph , Nwakanma Davis , Secka Ousman , Roca Anna 
Published: May 2019

AbstractBackground. Invasive bacterial diseases cause significant disease and death in sub-Saharan Africa. Several are vaccine preventable, although the impact of new vaccines and vaccine policies on disease patterns in these communities is poorly understood owing to limited surveillance data.Methods. We conducted a hospital-based surveillance of invasive bacterial diseases in The Gambia where blood and cerebrospinal fluid (CSF) samples of hospitalized participants were processed. Three surveillance periods were defined in relation to the introduction of pneumococcal conjugate vaccines (PCVs), before (2005- 2009), during (2010–2011) and after (2012–2015) PCV introduction. We determined the prevalences of commonly isolated bacteria and compared them between the different surveillance periods.Results. A total of 14 715 blood and 1103 CSF samples were collected over 11 years; overall, 1045 clinically significant organisms were isolated from 957 patients (972 organisms [6.6%] from blood and 73 [6.6%] from CSF). The most common blood culture isolates were Streptococcus pneumoniae (24.9%), Staphylococcus aureus (22.0%), Escherichia coli (10.9%), and nontyphoidal Salmonella (10.0%). Between the pre-PCV and post-PCV eras, the prevalence of S. pneumoniae bacteremia dropped across all age groups (from 32.4% to 16.5%; odds ratio, 0.41; 95% confidence interval, .29–.58) while S. aureus increased in prevalence, becoming the most prevalent bacteria (from 16.9% to 27.2%; 1.75; 1.26–2.44). Overall, S. pneumoniae (53.4%), Neisseria meningitidis (13.7%), and Haemophilus influenzae (12.3%) were the predominant isolates from CSF. Antimicrobial resistance to common antibiotics was low.Conclusions. Our findings demonstrate that surveillance data on the predominant pathogens associated with invasive disease is necessary to inform vaccine priorities and appropriate management of patients.
The Costs of Economic Nationalism: Evidence from the Brexit Experiment*
Authors: Born Benjamin , Müller Gernot J , Schularick Moritz , Sedláček Petr 
Published: May 2019

AbstractEconomic nationalism is on the rise, but at what cost? We study this question using the unexpected outcome of the Brexit referendum vote as a natural macroeconomic experiment. Employing synthetic control methods, we first show that the Brexit vote has caused a UK output loss of 1.7% to 2.5% by year-end 2018. An expectations-augmented VAR suggests that these costs are, to a large extent, driven by a downward revision of growth expectations in response to the vote. Linking quasi-experimental identification to structural time-series estimation allows us not only to quantify the aggregate costs but also to understand the channels through which expected economic disintegration impacts the macroeconomy.
Medication-taking after stroke: a qualitative meta-synthesis of the perspectives of stroke survivors, informal carers and health professionals
Authors: Gibson Josephine M E , Miller Colette , Coupe Jacqueline , Jones Stephanie P 
Published: May 2019

Abstract

Background
Lifelong secondary prevention medication is recommended after stroke or transient ischaemic attack. However, poor medication adherence and persistence, which lead to suboptimal health outcomes, are common, but the reasons for this are not well understood, mainly because there have been few studies reporting adherence barriers in stroke survivors.

Objective
The aim of this review was to undertake a meta-synthesis of qualitative studies of medication-taking after stroke. Outcomes of interest were: lived experiences, views and beliefs, and strategies and solutions used by community-dwelling stroke and transient ischaemic attack survivors, informal carers and health care professionals in relation to medication-taking.

Method
The review protocol was registered on PROSPERO (CRD42018086792). A search of online bibliographic databases was performed using key search terms of stroke, persistence, adherence and medication for years 1980–2018. Citation tracking was also carried out. Studies using qualitative or mixed methods were included. Systematic data extraction and synthesis were conducted using a meta-ethnographic approach.

Results
Twelve studies were eligible for inclusion, with a total of 412 participants, two-thirds of whom were stroke survivors, ranging from 1 month to over 20 years post-stroke. Third-order themes identified were ‘Medicines Work’—Information Work; Health Care Work; Carer Work; Emotional Work; Practical Work and an underpinning theme of Trust. However, many studies had significant methodological weaknesses.

Conclusions
This synthesis suggests that the burden of ‘medicines work’ after stroke is substantial and multifaceted. Its successful undertaking depends on mutual trust between stroke survivors, carers and health care professionals and trust in the benefits of medicines themselves.
An Ecologist’s Guide to Mitochondrial DNA Mutations and Senescence
Authors: Hood Wendy R , Williams Ashley S , Hill Geoffrey E 
Published: May 2019

Abstract
Longevity plays a key role in the fitness of organisms, so understanding the processes that underlie variance in senescence has long been a focus of ecologists and evolutionary biologists. For decades, the performance and ultimate decline of mitochondria have been implicated in the demise of somatic tissue, but exactly why mitochondrial function declines as individual’s age has remained elusive. A possible source of decline that has been of intense debate is mutations to the mitochondrial DNA. There are two primary sources of such mutations: oxidative damage, which is widely discussed by ecologists interested in aging, and mitochondrial replication error, which is less familiar to most ecologists. The goal of this review is to introduce ecologists and evolutionary biologists to the concept of mitochondrial replication error and to review the current status of research on the relative importance of replication error in senescence. We conclude by detailing some of the gaps in our knowledge that currently make it difficult to deduce the relative importance of replication error in wild populations and encourage organismal biologists to consider this variable both when interpreting their results and as viable measure to include in their studies.
Genes coding for LysM domains in the dermatophyte Trichophyton rubrum: A transcription analysis
Authors: Lopes Lúcia , Bitencourt Tamires A , Lang Elza A S , Sanches Pablo R , Peres Nalu T A , Rossi Antonio , Martinez-Rossi Nilce M 
Published: May 2019

Abstract
The filamentous fungus Trichophyton rubrum is a pathogen that causes superficial mycoses in humans, predominantly in keratinized tissues. The occurrence of dermatophytoses has increased in the last decades, mainly in immunocompromised patients, warranting research on the mechanisms involved in dermatophyte virulence. The genomes of dermatophytes are known to be enriched in genes coding for proteins containing the LysM domain, a carbohydrate-binding module, indicating the possible involvement of these genes in virulence. Although the LysM domains have already been described in other fungi, their biological functions in dermatophytes are unknown. Here we assessed the transcription of genes encoding proteins containing the LysM domains in T. rubrum grown on different substrates using quantitative real-time polymerase chain reaction. Some of these genes showed changes in transcription levels when T. rubrum was grown on keratin. In silico analyses suggest that some of these proteins share features, namely, they are anchored in the plasma membrane and contain the catalytic domain chitinase II and signal peptide domains. Here we show a detailed study of genes encoding the proteins with LysM-containing domains in T. rubrum, aiming to contribute to the understanding of their functions in dermatophytes.
Weak lensing measurements of the APEX-SZ galaxy cluster sample
Authors: Klein Matthias , Israel Holger , Nagarajan Aarti , Bertoldi Frank , Pacaud Florian , Lee Adrian T , Sommer Martin , Basu Kaustuv 
Published: May 2019

ABSTRACT
We present a weak lensing analysis for galaxy clusters from the APEX-SZ survey. For 39 massive galaxy clusters that were observed via the Sunyaev–Zel’dovich effect (SZE) with the APEX telescope, we analyse deep optical imaging data from WFI(@2.2mMPG/ESO) and Suprime-Cam(@SUBARU) in three bands. The masses obtained in this study, including an X-ray selected sub-sample of 27 clusters, are optimized for and used in studies constraining the mass to observable scaling relations at fixed cosmology. A novel focus of our weak lensing analysis is the multicolour background selection to suppress effects of cosmic variance on the redshift distribution of source galaxies. We investigate the effects of cluster member contamination through galaxy density, shear profile, and recovered concentrations. We quantify the impact of variance in source redshift distribution on the mass estimate by studying nine sub-fields of the COSMOS survey for different cluster redshift and magnitude limits. We measure a standard deviation of ∼6 per cent on the mean angular diameter distance ratio for a cluster at z = 0.45 and shallow imaging data of R ≈ 23 mag. It falls to ∼1 per cent for deep, R = 26 mag, observations. This corresponds to 8.4 per cent and 1.4 per cent scatter in M200. Our background selection reduces this scatter by 20−40 per cent, depending on cluster redshift and imaging depth. We derived cluster masses with and without using a mass concentration relation and find consistent results, and concentrations consistent with the used mass–concentration relation.
Inelastic processes in oxygen–hydrogen collisions
Authors: Belyaev A K , Voronov Ya V , Mitrushchenkov A , Guitou M , Feautrier N 
Published: May 2019

ABSTRACT
New accurate theoretical rate coefficients for (de)-excitation and charge transfer in low-energy O + H, O+ + H− and O− + H+ collisions are reported. The calculations of cross-sections and rate coefficients are performed by means of the quantum probability current method, using full configuration interaction ab initio electronic structure calculations that provide a global description of all 43 lowest molecular states from short to asymptotic internuclear distances. Thus, both long- and short-range non-adiabatic regions are taken into account for the first time. All the doublet, quartet and sextet OH molecular states, with excitation energy asymptotes up to 12.07 eV, as well as the two lowest ionic states with the asymptotes O−H+ and O+H− are treated. Calculations are performed for the collision energy range 0.01–100eV and the temperature range 1 000–10 000 K. The mechanisms underlying the processes are analysed: it is shown that the largest rate coefficients, with values exceeding 10−8 cm3 s−1, are due to ionic–covalent interactions present at large internuclear distances, while short-range interactions play an important role for rates with moderate values involved in (de)-excitation processes. As a consequence, a comparison of the present data with previously published results shows that differences of up to several orders of magnitude exist for rate coefficients with moderate values. It is worth pointing out the relatively large rate coefficients for triplet–quintuplet oxygen transitions, as well as for transitions between the O$(\rm 2p^{3}3s\, ^{5}$So) and O$(\rm 2p^{3}3p\, ^{5}$P) levels of the oxygen triplet and H(n = 2) levels. The calculated data are important for modelling stellar spectra, leading to accurate oxygen abundances.
Dark Energy Survey Year 1 results: measurement of the galaxy angular power spectrum
Authors: Camacho H , Kokron N , Andrade-Oliveira F , Rosenfeld R , Lima M , Lacasa F , Sobreira F , da Costa L N , Avila S , Chan K C , Crocce M , Ross A J , Troja A , García-Bellido J , Abbott T M C , Abdalla F B , Allam S , Annis J , Bernstein R A , Bertin E , Bridle S L , Brooks D , Buckley-Geer E , Burke D L , Carnero Rosell A , Carrasco Kind M , Carretero J , Castander F J , Cawthon R , Cunha C E , D’Andrea C B , De Vicente J , Desai S , Diehl H T , Doel P , Estrada J , Evrard A E , Flaugher B , Fosalba P , Frieman J , Gerdes D W , Giannantonio T , Gruendl R A , Gschwend J , Gutierrez G , Hollowood D L , Honscheid K , Hoyle B , James D J , Johnson M W G , Johnson M D , Kent S , Kirk D , Krause E , Kuehn K , Kuropatkin N , Lin H , Marshall J L , Miquel R , Percival W J , Plazas A A , Romer A K , Roodman A , Sanchez E , Schubnell M , Sevilla-Noarbe I , Smith M , Smith R C , Soares-Santos M , Suchyta E , Swanson M E C , Tarle G , Thomas D , Tucker D L , Walker A R , Zuntz J ,   (DES Collaboration)
Published: May 2019

ABSTRACTWe use data from the first-year observations of the DES collaboration to measure the galaxy angular power spectrum (APS), and search for its BAO feature. We test our methodology in a sample of 1800 DES Y1-like mock catalogues. We use the pseudo-Cℓ method to estimate the APS and the mock catalogues to estimate its covariance matrix. We use templates to model the measured spectra and estimate template parameters firstly from the Cℓ’s of the mocks using two different methods, a maximum likelihood estimator and a Markov Chain Monte Carlo, finding consistent results with a good reduced χ2. Robustness tests are performed to estimate the impact of different choices of settings used in our analysis. Finally, we apply our method to a galaxy sample constructed from DES Y1 data specifically for LSS studies. This catalogue comprises galaxies within an effective area of 1318 deg2 and 0.6 &lt; z &lt; 1.0. We find that the DES Y1 data favour a model with BAO at the $2.6 \sigma$ C.L. However, the goodness of fit is somewhat poor, with χ2/(d.o.f.) = 1.49. We identify a possible cause showing that using a theoretical covariance matrix obtained from Cℓ’s that are better adjusted to data results in an improved value of χ2/(dof) = 1.36 which is similar to the value obtained with the real-space analysis. Our results correspond to a distance measurement of DA(zeff = 0.81)/rd = 10.65 ± 0.49, consistent with the main DES BAO findings. This is a companion paper to the main DES BAO article showing the details of the harmonic space analysis.