bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surrogate minimal depth as an importance measure for variables in random forests
Authors: Seifert Stephan , Gundlach Sven , Szymczak Silke 
Published: February 2019

AbstractMotivationIt has been shown that the machine learning approach random forest can be successfully applied to omics data, such as gene expression data, for classification or regression and to select variables that are important for prediction. However, the complex relationships between predictor variables, in particular between causal predictor variables, make the interpretation of currently applied variable selection techniques difficult.ResultsHere we propose a new variable selection approach called surrogate minimal depth (SMD) that incorporates surrogate variables into the concept of minimal depth (MD) variable importance. Applying SMD, we show that simulated correlation patterns can be reconstructed and that the increased consideration of variable relationships improves variable selection. When compared with existing state-of-the-art methods and MD, SMD has higher empirical power to identify causal variables while the resulting variable lists are equally stable. In conclusion, SMD is a promising approach to get more insight into the complex interplay of predictor variables and outcome in a high-dimensional data setting.Availability and implementationhttps://github.com/StephanSeifert/SurrogateMinimalDepth.Supplementary informationSupplementary data are available at Bioinformatics online.
AutoDock Bias: improving binding mode prediction and virtual screening using known protein–ligand interactions
Authors: Arcon Juan Pablo , Modenutti Carlos P , Avendaño Demian , Lopez Elias D , Defelipe Lucas A , Ambrosio Francesca Alessandra , Turjanski Adrian G , Forli Stefano , Marti Marcelo A 
Published: February 2019

Abstract

Summary
The performance of docking calculations can be improved by tuning parameters for the system of interest, e.g. biasing the results towards the formation of relevant protein–ligand interactions, such as known ligand pharmacophore or interaction sites derived from cosolvent molecular dynamics. AutoDock Bias is a straightforward and easy to use script-based method that allows the introduction of different types of user-defined biases for fine-tuning AutoDock4 docking calculations.

Availability and implementation
AutoDock Bias is distributed with MGLTools (since version 1.5.7), and freely available on the web at http://ccsb.scripps.edu/mgltools/ or http://autodockbias.wordpress.com.

Supplementary information
Supplementary data are available at Bioinformatics online.
Epicardial fat, cardiovascular risk factors and calcifications in patients with chronic kidney disease
Authors: Saritas Turgay , Reinartz Sebastian Daniel , Nadal Jennifer , Schmoee Jonas , Schmid Matthias , Marwan Mohamed , Achenbach Stephan , Störk Stefan , Wanner Christoph , Eckardt Kai-Uwe , Floege Jürgen , Peter Schneider Markus , Schlieper Georg 
Published: February 2019

Abstract

Background
Epicardial adipose tissue (EAT) exerts cardiopathogenic effects, but the independent association between EAT and cardiovascular (CV) calcification in patients with chronic kidney disease (CKD) remains controversial. We therefore assessed the association between EAT, CV risk factors and CV calcifications.

Methods
257 patients with CKD Stage 3 and/or overt proteinuria underwent quantification of EAT, coronary artery calcification and aortic valve calcification by computed tomography. Framingham and American College of Cardiology and American Heart Association (ACC-AHA) 10-year CV event risk scores were calculated for each patient.

Results
Using multivariable regression analysis, higher EAT was significantly associated with the majority of investigated risk factors {higher age: odds ratio [OR] 1.05/year [95% confidence interval (CI) 1.02–1.08]; male sex: OR 4.03 [95% CI 2.22–7.31]; higher BMI: OR 1.28/kg/m2 [95% CI 1.20–1.37]; former smoking: OR 1.84 [95% CI 1.07–3.17]; lower high-density lipoprotein cholesterol: OR 0.98/mg/dL [95% CI 0.96–1.00] and lower estimated glomerular filtration rate: OR 0.98/mL/min/1.73 m2 [95% CI 0.97–0.99]; all P &lt; 0.05} and was not associated with diabetes mellitus, hypertensive nephropathy, total cholesterol and albuminuria. EAT was positively associated with higher ACC-AHA and Framingham risk scores. EAT correlated with coronary artery calcification and aortic valve calcification [Spearman ρ = 0.388 (95% CI 0.287–0.532) and rrb = 0.409 (95% CI 0.310–0.556), respectively], but these correlations were dependent on CV risk factors.

Conclusions
The increase of EAT can be explained by individual CV risk factors and kidney function and correlates with 10-year risk for CV event scores, suggesting that EAT is a modifiable risk factor in patients with CKD. Although EAT correlates with CV calcifications, these relations depend on CV risk factors.
Fruit Consumption is Associated with Alterations in Microbial Composition and Lower Rates of Pouchitis
Authors: Godny L , Maharshak N , Reshef L , Goren I , Yahav L , Fliss-Isakov N , Gophna U , Tulchinsky H , Dotan I 
Published: February 2019

AbstractBackgroundPatients with ulcerative colitis [UC] who undergo proctocolectomy with an ileal pouch–anal anastomosis commonly develop pouch inflammation [pouchitis]. Pouchitis develops in a previously normal small intestine and may involve environmental factors. We explored whether diet and microbiota alterations contributed to the pathogenesis of pouchitis.MethodsPatients were recruited and prospectively followed at a comprehensive pouch clinic. Pouch behaviour was clinically defined as a normal pouch [NP] or pouchitis. Patients completed Food Frequency Questionnaires [FFQs]. Faecal samples were analysed for microbial composition [16S rRNA gene pyrosequencing].ResultsNutritional evaluation was performed in 172 patients [59% females], and of these, faecal microbial analysis was performed in 75 patients (microbiota cohort: NP [n = 22], pouchitis [n = 53]). Of the entire cohort, a subgroup of 39 [22.6%] patients had NP at recruitment [NP cohort]. Of these, 5 [12.8%] developed pouchitis within a year. Patients at the lowest tertile of fruit consumption [<1.45 servings/day] had higher rates of pouchitis compared with those with higher consumption [30.8% vs 3.8%, log rank, p = 0.03]. Fruit consumption was correlated with microbial diversity [r = 0.35, p = 0.002] and with the abundance of several microbial genera, including Faecalibacterium [r = 0.29, p = 0.01], Lachnospira [r = 0.38, p = 0.001], and a previously uncharacterized genus from the Ruminococcaceae family [r = 0.25, p = 0.05]. Reduction in fruit consumption over time was associated with disease recurrence and with reduced microbial diversity [Δ = –0.8 ± 0.3, p = 0.008].ConclusionsFruit consumption is associated with modification of microbial composition, and lower consumption was correlated with the development of pouchitis. Thus, fruit consumption may protect against intestinal inflammation via alteration of microbial composition.
Aprotinin versus tranexamic acid in children undergoing cardiac surgery: an observational study
Authors: Willems Ariane , De Groote Françoise , Dumoulin Melanie , Fils Jean-François , Van der Linden Philippe 
Published: February 2019

Abstract

OBJECTIVES:
The upcoming release of aprotinin in paediatric cardiac surgery prompted a re-evaluation of its use in comparison to tranexamic acid (TXA) focusing on their effect on exposure to blood transfusions as well as severe postoperative morbidity or mortality.

METHODS:
This retrospective study was conducted in a tertiary children hospital from 2002 to 2015. Patients receiving aprotinin (Aprotinin group: 2002–2007) were compared with those receiving TXA group (2008–2015) using propensity score analysis. Primary outcome measures were ‘exposure to blood products’ and ‘severe postoperative morbidity or mortality’. High-risk subgroups that included neonates, complex (Risk Adjusted Classification for Congenital Heart Surgery-1 ≥ 3) and redo surgery were also analysed.

RESULTS:
The study included 2157 patients, 1136 in the Aprotinin group and 1021 in the TXA group. Exposure to blood products was significantly higher in the Aprotinin group (78% vs 60%; P < 0.001) as well as in the complex and redo surgery subgroups. Incidence of mortality and/or severe morbidity was higher in the Aprotinin group (33% vs 28%; P = 0.007), as well as in the neonate group. However, cardiopulmonary bypass priming volume and intraoperative fluid balance were significantly decreased, and the use of modified ultrafiltration significantly increased in the TXA group.

CONCLUSIONS:
In our population, children receiving aprotinin were more frequently transfused and were at a higher risk of developing severe postoperative morbidity or mortality than those receiving TXA. Subgroups at high risk of bleeding or inflammation did not seem to benefit from aprotinin. These differences might be explained by a safer profile of TXA, but also attributed to major changes in our patient blood management strategies over years.
The hypoxic transcription factor KlMga2 mediates the response to oxidative stress and influences longevity in the yeast Kluyveromyces lactis
Authors: Santomartino Rosa , Camponeschi Ilaria , Polo Germano , Immesi Alessio , Rinaldi Teresa , Mazzoni Cristina , Brambilla Luca , Bianchi Michele M 
Published: February 2019

ABSTRACT
Hypoxia is defined as the decline of oxygen availability, depending on environmental supply and cellular consumption rate. The decrease in O2 results in reduction of available energy in facultative aerobes. The response and/or adaptation to hypoxia and other changing environmental conditions can influence the properties and functions of membranes by modifying lipid composition. In the yeast Kluyveromyces lactis, the KlMga2 gene is a hypoxic regulatory factor for lipid biosynthesis—fatty acids and sterols—and is also involved in glucose signaling, glucose catabolism and is generally important for cellular fitness.
In this work we show that, in addition to the above defects, the absence of the KlMGA2 gene caused increased resistance to oxidative stress and extended lifespan of the yeast, associated with increased expression levels of catalase and SOD genes. We propose that KlMga2 might also act as a mediator of the oxidative stress response/adaptation, thus revealing connections among hypoxia, glucose signaling, fatty acid biosynthesis and ROS metabolism in K. lactis.
Nonpharmacological Interventions for Anxiety and Dementia in Nursing Homes: A Systematic Review
Authors: Brown Wilson Christine , Arendt Lars , Nguyen Mynhi , Scott Theresa L , Neville Christine C , Pachana Nancy A 
Published: February 2019

AbstractAnxiety is a major mental disorder in later life that impacts on activities of daily living and quality of life for adults living with dementia in nursing homes. The aim of this article was to systematically review nonpharmacological interventions for older adults living in nursing homes who experience comorbid anxiety and dementia.MethodA systematic literature search was conducted across key databases (Cinahl, ASSIA, Cochrane reviews and trials, psycARTICLES, psycINFO, and PubMed) to identify studies measuring anxiety as an outcome for an intervention for older adults living with dementia in nursing homes, up to December 31, 2017.ResultsThe search yielded a total of 1,925 articles with 45 articles accessed for full article review. A total of 13 articles were included in this review following quality appraisal based on Cochrane methodology with six different anxiety measures used. The studies included were moderate to high-quality randomized control trials although heterogeneity precluded a combined meta-analysis.Clinical implicationsThe most common interventions used to address anxiety in this population were music therapy and activity-based interventions although there was limited evidence for the efficacy of either intervention. Little is known about effective nonpharmacological treatment for anxiety for people living with dementia in nursing homes. Further research using consistent measurement tools and time points is required to identify effective interventions to improve the quality of life for people living with both dementia and anxiety in nursing homes.
Ambient noise tomography across the Cascadia subduction zone using dense linear seismic arrays and double beamforming
Authors: Wang Yadong , Lin Fan-Chi , Ward Kevin M 
Published: February 2019

SUMMARYIn the summer of 2017, we deployed 174 three-component nodal geophones along a 130 km west–east line across the central Oregon forearc lasting about 40 d. Our goal was to evaluate the possibility of imaging the lithospheric structure in detail with a dense but short-duration sampling of passive seismic signals. In this study, we used passive recordings from the nodal array and the previous CASC93 broad-band array along the same line to calculate noise cross-correlations. Fundamental Rayleigh wave signals were observed in the cross-correlations between 3 and 15 s period. To enhance the signal and simultaneously measure the phase velocity, we employed a double beamforming method. At each period and location, a source beam and a receiver beam were selected and the cross-correlations between the two were shifted and stacked based on the presumed local velocities. A 2-D grid search was then used to find the best velocities at the source and receiver location. Multiple velocity measurements were obtained at each location by using different source and receiver pairs, and the final velocity and uncertainty at each location were determined using the mean and the standard deviation of the mean. All available phase velocities across the profile were then used to invert for a 2-D shear wave crustal velocity model. Well resolved shallow slow velocity anomalies are observed corresponding to the sediments within the Willamette Valley, and fast velocity anomalies are observed in the mid-to-lower crust likely associated with the Siletzia terrane. We demonstrate that the ambient noise double beamforming method is an effective tool to image detailed lithospheric structures across a dense and large-scale (&gt;100 km) temporary seismic array.
Reported outcomes after aortic valve resuspension for acute type A aortic dissection: a systematic review and meta-analysis
Authors: Chen Shuang-Kun , Qiu Zhi-Huang , Fang Guan-Hua , Wu Xi-Jie , Chen Liang-Wan 
Published: February 2019

AbstractIn the majority of patients presenting with acute type A aortic dissection (AAD) complicated by aortic valve insufficiency, the aortic valve (AV) can be preserved by AV resuspension. A meta-analysis was performed to investigate the outcomes following AV resuspension for AAD. A systematic literature search for publications reporting outcomes after AV resuspension in AAD published between January 1998 and June 2018 was conducted. Early outcome events and linearized occurrence rates for late outcome events were derived. The retrieval process yielded 18 unique studies involving 3295 patients with a total of 17 532 patient-years (pt-yrs). Pooled early mortality was 15.5% [95% confidence interval (95% CI) 11.5–19.4%, I2 = 91.9%], and the linearized late mortality rate was 3.21%/pt-yrs (95% CI 2.49–3.77, I2 = 29%). The linearized occurrence rates for aortic root reintervention was 1.4%/pt-yrs (95% CI 0.88–1.79, I2 = 48%); for recurrent significant aortic valve insufficiency (>2+), it was 1.12%/pt-yrs (95% CI 0.79–1.45, I2 = 68%); and for endocarditis, it was 0.01%/pt-yrs (95% CI 0–0.04, I2 = 7%). The composite rate of thromboembolism and bleeding was 1.41%/pt-yrs (95% CI 0.18–2.63, I2 = 82%). A more recent surgical period was associated with a decreased hazard of reoperation on the aortic root (P < 0.001). Requirement of AV resuspension alone in AAD is a risk factor for mortality. The long-term durability of AV resuspension is excellent, with low rates of endocarditis and thromboembolism and bleeding. Root reoperation hazard has become acceptable in recent years. Preoperative aortic valve insufficiency grade exceeding 2+ is a predictor for root reoperation.
A Contingent Perspective on Pluralistic Ignorance: When the Attitudinal Object Matters
Authors: Eisner Léïla , Spini Dario , Sommet Nicolas 
Published: February 2019

Abstract
Although past research has suggested that pluralistic ignorance—a mismatch between perceptions of others’ opinions and actual personal opinions—does not occur in every circumstance, no studies have directly investigated variations among different attitude objects. Drawing upon theoretical and analytical approaches based on social representations, this study examines differences between personal opinions and perceived opinions of different groups toward same-sex female parenting (a newly debated attitude object) and working mothers (an older debated attitude object). Using data from a study (N = 743) conducted in Switzerland, the findings indicate that pluralistic ignorance occurs in opinions toward same-sex female parenting. Furthermore, the findings show that pluralistic ignorance arises from false consensus among conservatives and from false uniqueness among liberals.
A Markov decision process approach to optimizing cancer therapy using multiple modalities
Authors: Maass Kelsey , Kim Minsun 
Published: February 2019

Abstract
There are several different modalities, e.g. surgery, chemotherapy and radiotherapy, that are currently used to treat cancer. It is common practice to use a combination of these modalities to maximize clinical outcomes, which are often measured by a balance between maximizing tumor damage and minimizing normal tissue side effects due to treatment. However, multi-modality treatment policies are mostly empirical in current practice and are therefore subject to individual clinicians’ experiences and intuition. We present a novel formulation of optimal multi-modality cancer management using a finite-horizon Markov decision process approach. Specifically, at each decision epoch, the clinician chooses an optimal treatment modality based on the patient’s observed state, which we define as a combination of tumor progression and normal tissue side effect. Treatment modalities are categorized as (1) type 1, which has a high risk and high reward, but is restricted in the frequency of administration during a treatment course; (2) type 2, which has a lower risk and lower reward than type 1, but may be repeated without restriction; and (3) type 3, no treatment (surveillance), which has the possibility of reducing normal tissue side effect at the risk of worsening tumor progression. Numerical simulations using various intuitive, concave reward functions show the structural insights of optimal policies and demonstrate the potential applications of using a rigorous approach to optimizing multi-modality cancer management.
Sparse tensor product finite element method for nonlinear multiscale variational inequalities of monotone type
Authors: Tan Wee Chin , Hoang Viet Ha 
Published: February 2019

AbstractWe study an essentially optimal finite element (FE) method for locally periodic nonlinear multiscale variational inequalities of monotone type in a domain $D\subset{\mathbb{R}}^d$ that depend on a macroscopic and $n$ microscopic scales. The scales are separable. Using multiscale convergence we deduce a multiscale homogenized variational inequality in a tensorized domain in the high-dimensional space ${\mathbb R}^{(n+1)d}$. Given sufficient regularity on the solution the sparse tensor product FE method is developed for this problem, which attains an essentially equal (i.e., it differs by only a logarithmic factor) level of accuracy to that of the full tensor product FE method, but requires an essentially optimal number of degrees of freedom which is equal to that for solving a problem in ${{\mathbb{R}}}^d$ apart from a logarithmic factor. For two-scale problems we deduce a new homogenization error for the nonlinear monotone variational inequality. A numerical corrector is then constructed with an explicit error in terms of the homogenization and the FE errors. For general multiscale problems we deduce a numerical corrector from the FE solution of the multiscale homogenized problem, but without an explicit error as such a homogenization error is not available.
A new approach and gold standard toward author disambiguation in MEDLINE
Authors: Vishnyakova Dina , Rodriguez-Esteban Raul , Rinaldi Fabio 
Published: February 2019

Abstract

Objective
Author-centric analyses of fast-growing biomedical reference databases are challenging due to author ambiguity. This problem has been mainly addressed through author disambiguation using supervised machine-learning algorithms. Such algorithms, however, require adequately designed gold standards that reflect the reference database properly. In this study we used MEDLINE to build the first unbiased gold standard in a reference database and improve over the existing state of the art in author disambiguation.

Materials and Methods
Following a new corpus design method, publication pairs randomly picked from MEDLINE were evaluated by both crowdsourcing and expert curators. Because the latter showed higher accuracy than crowdsourcing, expert curators were tasked to create a full corpus. The corpus was then used to explore new features that could improve state-of-the-art author disambiguation algorithms that would not have been discoverable with previously existing gold standards.

Results
We created a gold standard based on 1900 publication pairs that shows close similarity to MEDLINE in terms of chronological distribution and information completeness. A machine-learning algorithm that includes new features related to the ethnic origin of authors showed significant improvements over the current state of the art and demonstrates the necessity of realistic gold standards to further develop effective author disambiguation algorithms.

Discussion and Conclusion
An unbiased gold standard can give a more accurate picture of the status of author disambiguation research and help in the discovery of new features for machine learning. The principles and methods shown here can be applied to other reference databases beyond MEDLINE. The gold standard and code used for this study are available at the following repository: https://github.com/amorgani/AND/