bluuebunny/crossref_metadata_2025_split huggingface dataset:
Agreement in Occupational Exposures Between Men and Women Using Retrospective Assessments by Expert Coders
Authors: Lacourt Aude , Labrèche France , Goldberg Mark S , Siemiatycki Jack , Lavoué Jérôme 
Published: July 2018

Abstract

Objectives
To estimate the level of agreement and identify notable differences in occupational exposures (agents) between men and women from retrospective assessments by expert coders.

Methods
Lifetime occupational histories of 1657 men and 2073 women from two case–control studies, were translated into exposure estimates to 243 agents, from data on 13882 jobs. Exposure estimates were summarized as proportions and frequency-weighted intensity of exposure for 59 occupational codes by sex. Agreement between metrics of exposure in men’s and women’s jobs was determined with intraclass correlation coefficients (ICC) and weighted Kappa coefficients, using as unit of analysis (‘cell’) a combination of occupational code and occupational agent. ‘Notable’ differences between men and women were identified for each cell, according to a Bayesian hierarchical model for both proportion and frequency-weighted intensity of exposure.

Results
For cells common to both men and women, the ICC for continuous probability of exposure was 0.84 (95% CI: 0.83–0.84) and 7.4% of cells showed notable differences with jobs held by men being more often exposed. A weighted kappa of 0.67 (95% CI: 0.61–0.73) was calculated for intensity of exposure, and an ICC of 0.67 (95% CI: 0.62–0.71) for frequency-weighted intensity of exposure, with a tendency of higher values of exposure metrics in jobs held by men.

Conclusions
Exposures were generally in agreement between men and women. Some notable differences were identified, most of them explained by differential sub-occupations or industries or dissimilar reported tasks within the studied occupations.
Machine learning meets genome assembly
Authors: Padovani de Souza Kleber , Setubal João Carlos , Ponce de Leon F. de Carvalho André Carlos , Oliveira Guilherme , Chateau Annie , Alves Ronnie 
Published: July 2018

AbstractMotivation: With the recent advances in DNA sequencing technologies, the study of the genetic composition of living organisms has become more accessible for researchers. Several advances have been achieved because of it, especially in the health sciences. However, many challenges which emerge from the complexity of sequencing projects remain unsolved. Among them is the task of assembling DNA fragments from previously unsequenced organisms, which is classified as an NP-hard (nondeterministic polynomial time hard) problem, for which no efficient computational solution with reasonable execution time exists. However, several tools that produce approximate solutions have been used with results that have facilitated scientific discoveries, although there is ample room for improvement. As with other NP-hard problems, machine learning algorithms have been one of the approaches used in recent years in an attempt to find better solutions to the DNA fragment assembly problem, although still at a low scale.Results: This paper presents a broad review of pioneering literature comprising artificial intelligence-based DNA assemblers—particularly the ones that use machine learning—to provide an overview of state-of-the-art approaches and to serve as a starting point for further study in this field.
Higher-order molecular organization as a source of biological function
Authors: Gaudelet Thomas , Malod-Dognin Noël , Pržulj Nataša 
Published: July 2018

AbstractMotivationMolecular interactions have widely been modelled as networks. The local wiring patterns around molecules in molecular networks are linked with their biological functions. However, networks model only pairwise interactions between molecules and cannot explicitly and directly capture the higher-order molecular organization, such as protein complexes and pathways. Hence, we ask if hypergraphs (hypernetworks), that directly capture entire complexes and pathways along with protein–protein interactions (PPIs), carry additional functional information beyond what can be uncovered from networks of pairwise molecular interactions. The mathematical formalism of a hypergraph has long been known, but not often used in studying molecular networks due to the lack of sophisticated algorithms for mining the underlying biological information hidden in the wiring patterns of molecular systems modelled as hypernetworks.ResultsWe propose a new, multi-scale, protein interaction hypernetwork model that utilizes hypergraphs to capture different scales of protein organization, including PPIs, protein complexes and pathways. In analogy to graphlets, we introduce hypergraphlets, small, connected, non-isomorphic, induced sub-hypergraphs of a hypergraph, to quantify the local wiring patterns of these multi-scale molecular hypergraphs and to mine them for new biological information. We apply them to model the multi-scale protein networks of bakers yeast and human and show that the higher-order molecular organization captured by these hypergraphs is strongly related to the underlying biology. Importantly, we demonstrate that our new models and data mining tools reveal different, but complementary biological information compared with classical PPI networks. We apply our hypergraphlets to successfully predict biological functions of uncharacterized proteins.Availability and implementationCode and data are available online at http://www0.cs.ucl.ac.uk/staff/natasa/hypergraphlets.
Quantifying heterogeneity of expression data based on principal components
Authors: Yang Zi , Michailidis George 
Published: July 2018

Abstract

Motivation
The diversity of biological omics data provides richness of information, but also presents an analytic challenge. While there has been much methodological and theoretical development on the statistical handling of large volumes of biological data, far less attention has been devoted to characterizing their veracity and variability.

Results
We propose a method of statistically quantifying heterogeneity among multiple groups of datasets, derived from different omics modalities over various experimental and/or disease conditions. It draws upon strategies from analysis of variance and principal component analysis in order to reduce dimensionality of the variability across multiple data groups. The resulting hypothesis-based inference procedure is demonstrated with synthetic and real data from a cell line study of growth factor responsiveness based on a factorial experimental design.

Availability and implementation
Source code and datasets are freely available at https://github.com/yangzi4/gPCA.

Supplementary information
Supplementary data are available at Bioinformatics online.
Instrumental variables estimation with competing risk data
Authors: Martinussen Torben , Vansteelandt Stijn 
Published: July 2018

Summary
Time-to-event analyses are often plagued by both—possibly unmeasured—confounding and competing risks. To deal with the former, the use of instrumental variables (IVs) for effect estimation is rapidly gaining ground. We show how to make use of such variables in competing risk analyses. In particular, we show how to infer the effect of an arbitrary exposure on cause-specific hazard functions under a semi-parametric model that imposes relatively weak restrictions on the observed data distribution. The proposed approach is flexible accommodating exposures and IVs of arbitrary type, and enabling covariate adjustment. It makes use of closed-form estimators that can be recursively calculated, and is shown to perform well in simulation studies. We also demonstrate its use in an application on the effect of mammography screening on the risk of dying from breast cancer.
On the Multiplicative Chaos of Non-Gaussian Log-Correlated Fields
Authors: Junnila Janne 
Published: July 2018

Abstract
We study non-Gaussian log-correlated multiplicative chaos, where the random field is defined as a sum of independent fields that satisfy suitable moment and regularity conditions. The convergence, existence of moments, and analyticity with respect to the inverse temperature are proven for the resulting chaos in the full subcritical range. These results are generalizations of the corresponding theorems for Gaussian multiplicative chaos. A basic example where our results apply is the non-Gaussian Fourier series $$\sum_{k=1}^\infty \frac{1}{\sqrt{k}}(A_k \cos(2\pi k x) + B_k \sin(2\pi k x)),$$where $A_k$ and $B_k$ are i.i.d. random variables.
A Venetian mystery: two paintings by Walter Osborne in the Kildare Street and University Club, Dublin
Authors: Milligan Kathryn 
Published: July 2018

Abstract
In 1916, Sir Robert Henry Woods (1865–1938), eminent surgeon and Unionist Member of Parliament, presented two large-scale paintings by Walter Osborne (1859–1903) to the University Club, Dublin, now known as the Kildare Street and University Club. Drawing on new research, this article seeks to counter the long-standing suspicions surrounding the attribution of these works to Osborne, and through hitherto unused contemporary materials, outline the circumstances of their creation, the larger group to which they once belonged, and the story they tell about an ambitious artist seeking to further his career in Victorian Dublin. Further to this, the case of Osborne’s Venetian paintings illuminates a previously unexplored area of collecting in nineteenth-century Dublin, demonstrating the networks that existed between the city’s artistic and professional élites.
Vertebrate Dynein-f depends on Wdr78 for axonemal localization and is essential for ciliary beat
Authors: Zhang Yirong , Chen Yawen , Zheng Jianqun , Wang Juan , Duan Shichao , Zhang Wei , Yan Xiumin , Zhu Xueliang 
Published: July 2018

Abstract
Motile cilia and flagella are microtubule-based organelles important for cell locomotion and extracellular liquid flow through beating. Although axonenal dyneins that drive ciliary beat have been extensively studied in unicellular Chlamydomonas, to what extent such knowledge can be applied to vertebrate is poorly known. In Chlamydomonas, Dynein-f controls flagellar waveforms but is dispensable for beating. The flagellar assembly of its heavy chains (HCs) requires its intermediate chain (IC) IC140 but not IC138. Here we show that, unlike its Chlamydomonas counterpart, vertebrate Dynein-f is essential for ciliary beat. We confirmed that Wdr78 is the vertebrate orthologue of IC138. Wdr78 associated with Dynein-f subunits such as Dnah2 (a HC) and Wdr63 (IC140 orthologue). It was expressed as a motile cilium-specific protein in mammalian cells. Depletion of Wdr78 or Dnah2 by RNAi paralyzed mouse ependymal cilia. Zebrafish Wdr78 morphants displayed ciliopathy-related phenotypes, such as curved bodies, hydrocephalus, abnormal otolith, randomized left–right asymmetry, and pronephric cysts, accompanied with paralyzed pronephric cilia. Furthermore, all the HCs and ICs of Dynein-f failed to localize in the Wdr78-depleted mouse ependymal cilia. Therefore, both the functions and subunit dependency of Dynein-f are altered in evolution, probably to comply with ciliary roles in higher organisms.
Inpatient and Postdischarge Outcomes Following Elective Craniotomy for Mass Lesions
Authors: Fry Donald E , Nedza Susan M , Pine Michael , Reband Agnes M , Huang Chun-Jung , Pine Gregory 
Published: July 2018

Abstract

BACKGROUND
Interpretation of hospital quality requires objective evaluation of both inpatient and postdischarge adverse outcomes (AOs).

OBJECTIVE
To develop risk-adjusted predictive models for inpatient and 90-d postdischarge AOs in elective craniotomy and apply those models to individual hospital performance to provide benchmarks to improve care.

METHODS
The Medicare Limited Dataset (2012-2014) was used to define all elective craniotomy procedures for mass lesions in patients ≥65 yr. Predictive logistic models were designed for inpatient mortality, inpatient prolonged length of stay, 90-d postdischarge deaths without readmission, and 90-d readmissions after exclusions. The total observed patients with one or more AOs were then compared to predicted AO values, and z-scores were computed for each hospital that met minimum volume requirements. Risk-adjusted AO rates allowed stratification of eligible hospitals into deciles of performance.

RESULTS
The hospital evaluation was performed for 223 facilities with 7624 patients that met criteria. A total of 849 patients (11.1%) died inclusive of 90 d postdischarge; 635 (8.3%) were 3σ length-of-stay outliers; and 1928 patients (25.3%) with one or more 90-d readmissions; 2716 patients experienced one or more AOs (35.6%). Six hospitals were 2 z-scores better than average, and 8 were 2 z-scores poorer. The median risk-adjusted AO rate was 18% for the first decile and 53.4% for the 10th decile.

CONCLUSION
There was a 35% difference between best and suboptimal performing hospitals for this operation. Hospitals must know their risk-adjusted AO rates and benchmark their results to inform processes of care redesign.
Impact of a Multidisciplinary Infection Prevention Initiative on Central Line and Urinary Catheter Utilization in a Long-term Acute Care Hospital
Authors: Chandramohan Suganya , Navalkele Bhagyashri , Mushtaq Ammara , Krishna Amar , Kacir John , Chopra Teena 
Published: July 2018

Abstract

Background
Prolonged central line (CL) and urinary catheter (UC) use can increase risk of central line–associated bloodstream infection (CLABSI) and catheter-associated urinary tract infection (CAUTI).

Methods
This interventional study conducted in a 76-bed long-term acute care hospital (LTACH) in Southeast Michigan was divided into 3 periods: pre-intervention (January 2015–June 2015), intervention (July–November 2015), and postintervention (December 2015–March 2017). During the intervention period, a multidisciplinary infection prevention team (MIPT) made weekly recommendations to remove unnecessary CL/UC or switch to alternate urinary/intravenous access. Device utilization ratios (DURs) and infection rates were compared between the study periods. Interrupted time series (ITS) and 0-inflated poisson (ZIP) regression were used to analyze DUR and CLABSI/CAUTI data, respectively.

Results
UC-DUR was 31% in the pre- and postintervention periods and 21% in the intervention period. CL-DUR decreased from 46% (pre-intervention) to 39% (intervention) to 37% (postintervention). The results of ITS analysis indicated nonsignificant decrease and increase in level/trend in DURs coinciding with our intervention. The CAUTI rate per catheter-days did not decrease during intervention (4.36) compared with pre- (2.49) and postintervention (1.93). The CLABSI rate per catheter-days decreased by 73% during intervention (0.39) compared with pre-intervention (1.45). Rates again quadrupled postintervention (1.58). ZIP analysis indicated a beneficial effect of intervention on infection rates without reaching statistical significance.

Conclusions
We demonstrated that a workable MIPT initiative focusing on removal of unnecessary CL and UC can be easily implemented in an LTACH requiring minimal time and resources. A rebound increase in UC-DURs to pre-intervention levels after intervention end indicates that continued vigilance is required to maintain performance.
Twenty-Year Secular Trends in Infective Endocarditis in a Teaching Hospital
Authors: Cuervo Guillermo , Rombauts Alexander , Caballero Queralt , Grau Immaculada , Pujol Miquel , Ardanuy Carmen , Berbel Dámaris , Gudiol Carlota , Sánchez-Salado Jose Carlos , Ruiz-Majoral Alejandro , Sbraga Fabrizio , Gracia-Sánchez Laura , Peña Carmen , Carratalà Jordi 
Published: July 2018

Abstract

Background
The purpose of this study was to analyze the secular trends of infective endocarditis in a teaching hospital between January 1996 and December 2015.

Methods
We report on a single-center retrospective study of patients with left-side valve infective endocarditis. We performed an analysis of secular trends in the main epidemiological and etiological aspects, as well as clinical outcomes, in 5 successive 4-year periods (P1 to P5).

Results
In total, 595 episodes of infective endocarditis were included, of which 76% were community-acquired and 31.3% involved prosthetic valves. Among the cases, 70% occurred in men, and the mean age (SD) was 64.1 (14.3) years. A significant increase in older patients (age ≥70 years) between P1 (15.332%) and P5 (51.9%; P &lt; .001) was observed. The rate of infective endocarditis on biological prostheses also increased in the prosthetic group, accounting for 30% in P1 and 67.3% in P5 (P &lt; .001). By contrast, there were significant decreases in vascular and immunological phenomena over the study period, with decreases in the presence of moderate to severe valvular insufficiency (75.9% in P1 to 52.6% in P5; P &lt; .001) and valvular surgery (43% in P1 vs 29.6% in P5; P = .006). Finally, overall mortality was 23.9%, and although it was highest in P1, it subsequently remained stable through P2 to P5 (38% in P1 to 20% in P5; P = .004).

Conclusions
There has been a significant increase in infective endocarditis in older patients. The decrease in moderate to severe valve regurgitation at diagnosis could explain the stable mortality despite the increase in the mean age of patients over time.
The Shadows of Sunlight: Why Disclosure Should Not Be a Priority in Addressing Conflicts of Interest
Authors: Goldberg Daniel S 
Published: July 2018

Abstract
This article argues that positioning disclosure as a primary remedy in addressing the ethical problems posed by conflicts of interest (‘COIs’) in medicine and health is an error. Instead, bioethical resources should be devoted to the problems associated with sequestration, defined as the elimination of relationships between commercial industries and health professionals in all cases where it is remotely feasible. The argument begins by arguing that adopting Andrew Stark’s conceptual framework for COIs leads to advantages in understanding COIs and in ordering priorities for intervention. The article then draws on prior work establishing that COIs are, under ordinary epidemiologic standards, properly regarded as population health hazards. This justifies attention to possible remedies, of which disclosure generates by far the most analysis. Such primacy is unwarranted given the extensive evidence suggesting that disclosure as a remedy for COIs is at best ineffective. ‘At best’ is justified because the evidence also shows that disclosure may have a perverse effect, intensifying biased behaviors. Expending significant attention on an ineffective or even deleterious intervention is unjustified and also crowds out devotion of resources to the real problems that attend sequestration. Therefore, disclosure ought to be regarded as a lower priority among possible COI interventions.
Growth-inhibiting Fungicides Affect Detection of Phytophthora ramorum from Infected Foliage and Roots
Authors: Shishkoff Nina 
Published: July 2018

Growth-inhibiting fungicides are used routinely to control common and regulated Oomycete pathogens. This study investigated whether such fungicides could affect detection of Phytophthora ramorum from plant tissue, both foliage and roots. Whole plants of Rhododendron × ‘Cunningham's White’ were inoculated with P. ramorum and treated 3 days later with fosetyl-Al, mefenoxam, or propamocarb. The foliage was sampled over time to see if fungicides prevented successful culturing of the pathogen from infected leaf tissue or interfered with detection using real-time PCR or ELISA. Mefenoxam significantly reduced the ability to culture the pathogen from leaves for the first 6 weeks while recovery from leaves treated with other fungicides did not differ from water-treated controls; detection using PCR or ELISA was not affected by fungicide application. The roots of Viburnum cuttings were inoculated with P. ramorum and then treated 4 days later with fosetyl-Al, mefenoxam, or propamocarb. The amount of inoculum in flow through water samples taken weekly for 5 weeks was quantified and percent root colonization determined at the end of the experiment. Propamocarb had no effect on inoculum production or root infection, while viable inoculum production was significantly decreased in fosetyl-Al- or mefenoxam-treated plants over 5 weeks, and root colonization was significantly decreased. Accepted for publication 23 January 2014. Published 18 March 2014.
Getting a Notch closer to renal dysfunction: activated Notch suppresses expression of the adaptor protein Disabled‐2 in tubular epithelial cells
Authors: Schütte-Nütgen Katharina , Edeling Maria , Mendl Gudrun , Krahn Michael P. , Edemir Bayram , Weide Thomas , Kremerskothen Joachim , Michgehl Ulf , Pavenstädt Hermann 
Published: July 2018

ABSTRACTReactivation of Notch signaling in kidneys of animal models and patients with chronic kidney disease (CKD) has been shown to contribute to epithelial injury and fibrosis development. Here, we investigated the mechanisms of Notch‐induced injury in renal epithelial cells. We performed genome‐wide transcriptome analysis to identify Notch target genes using an in vitro system of cultured tubular epithelial cells expressing the intracellular domain of Notch1. One of the top downregulated genes was Disabled‐2 (Dabi). With the use of Drosophila nephrocytes as a model system, we found that Dab (the Drosophila homolog of Dab2) knockdown resulted in a significant filtration defect, indicating that loss of Dab2 plays a functional role in kidney disease development. We showed that Dab2 expression in cultured tubular epithelial cells is involved in endocytic regulation and that it also protects cells from TGF‐β‐induced epithelial‐to‐mesenchymal transition. In vivo correlation studies indicated its additional role in renal ischemia‐induced injury. Together, these data suggest that Dab2 plays a versatile role in the kidney and may impact on acute and CKDs.—Schütte‐Nütgen, K., Edeling, M., Mendl, G., Krahn, M. P., Edemir, B., Weide, T., Kremerskothen, J., Michgehl, U., Pavenstädt, H., Getting a Notch closer to renal dysfunction: activated Notch suppresses expression of the adaptor protein Disabled‐2 in tubular epithelial cells. FASEB J. 33, 821–832 (2019). www.fasebj.org
Transient p53 inhibition sensitizes aged white adipose tissue for beige adipocyte recruitment by blocking mitophagy
Authors: Fu Wenyan , Liu Yang , Sun Christina , Yin Hang 
Published: July 2018

ABSTRACTAging of white adipose tissue (WAT) is associated with reduced insulin sensitivity, which contributes to whole‐body glucose intolerance. WAT aging in mice impairs cold‐induced beige adipocyte recruitment (beiging), which has been attributed to the senescence of adipose progenitor cells. Tumor suppressor p53 has also been implicated in WAT aging. However, whether p53‐related cellular aging in mature white adipocytes is causative of age‐impaired WAT beiging remains unknown. It is also unclear whether transient p53 inhibition can rescue WAT beiging. Herein, we report that p53 increased in adipose tissues of 28‐wk‐old (aged) mice with impaired beiging capability. Cold exposure decreased p53 in beiging WAT of young mice but not in aged mice. In aged mice, inducible p53 ablation in differentiated adipocytes restored cold‐induced WAT beiging and augmented whole‐body energy expenditure and insulin sensitivity. Transient pharmacological inhibition of p53 led to the same beneficial effects. Mechanistically, cold exposure repressed autophagy in beiging WAT of young mice yet increased autophagy in aged WAT. p53‐ablation reduced microtubule‐associated protein light chain 3‐mediated mitochondria clearance (mitophagy) and hence facilitated the increase of mitochondria during beiging. These findings suggest that p53‐induced mitophagy in aged white adipocytes impedes WAT beiging and may be therapeutically targeted to improve insulin sensitivity in aged WAT.—Fu, W., Liu, Y., Sun, C., Yin, H. Transient p53 inhibition sensitizes aged white adipose tissue for beige adipocyte recruitment by blocking mitophagy. FASEB J. 33, 844–856 (2019). www.fasebj.org