bluuebunny/crossref_metadata_2025_split huggingface dataset:
Poor Awareness of Hypertension in France: The CONSTANCES Population-Based Study
Authors: Fenech Goël , Vallée Alexandre , Cherfan Michelle , Kab Sofiane , Goldberg Marcel , Zins Marie , Blacher Jacques 
Published: March 2020

Abstract

OBJECTIVES
We aimed to assess the hypertension (HTN) awareness and associated factors in France.

METHODS
We conducted a cross-sectional analysis using data from the CONSTANCES population-based cohort involving 87,808 volunteer participants included between 2012 and 2018. HTN was defined as average blood pressure (BP) over 140/90 or use of BP medication, awareness as self-reported HTN. Multivariable logistic regression models were used to identify the associated factors.

RESULTS
Overall, 27,160 hypertensive participants (men = 16,569) above 18 years old were analyzed. Hypertension awareness rate was 37.5%. In the multivariable regression model, awareness was predicted by female gender, age, prior cardiovascular disease (CVD), presence of diabetes mellitus (DM), presence of chronic kidney disease (CKD), level of education, and obesity or overweight. Older participants (P &lt; 0.001), females (P &lt; 0.001), participants with comorbidities (P &lt; 0.001), were more likely to be aware when compared with younger participants, males and participants without comorbidities, respectively. The unawareness among participants without cardiometabolic factors (CMF, i.e., CVD, DM, CKD) was higher than participants with CMF (67% vs. 41%, respectively, P &lt; 0.001). Moreover, some differences appeared in both genders in the association between awareness of HTN and health and lifestyle factors.

CONCLUSION
Our findings show that HTN awareness is low. Particular attention should be given to young men without comorbidities as these characteristics were predictors of poor awareness. Immediate action is required to improve HTN awareness in France.
Alcohol Consumption by Older New York City Residents: The Need for New Policies to Address Misuse
Authors: Weisz Daniel , Gusmano Michael Kelley 
Published: March 2020

Abstract

Aims
The aim of this study is to assess risk factors for alcohol misuse among older New York City residents and examine the effect of local public health efforts to address alcohol misuse.

Methods
The Community Health Survey, a cross-sectional telephone survey of 8500 randomly selected adult New Yorkers, records the frequency of alcohol use. We examine these results among 65 and older subjects by sociodemographic status using logistic regression modeling and compare trends in smoking and alcohol consumption between 2002 and 2016.

Results
Those with unhealthy drinking habits, combining binge drinking and excessive consumption, constituted 5.7% of 65 plus population and were more likely to be White, US born, healthy, better educated and wealthier. The percentage of older smokers in New York City has decreased while unhealthy drinking is nearly flat since 2002.

Conclusions
Our findings reinforce the importance of screening geriatric populations for alcohol use disorders and support the development of new public health efforts to address alcohol misuse if the city is to achieve results similar to those obtained in decreasing tobacco consumption.
Unified methods for feature selection in large-scale genomic studies with censored survival outcomes
Authors: Spirko-Burns Lauren , Devarajan Karthik 
Published: March 2020

AbstractMotivationOne of the major goals in large-scale genomic studies is to identify genes with a prognostic impact on time-to-event outcomes which provide insight into the disease process. With rapid developments in high-throughput genomic technologies in the past two decades, the scientific community is able to monitor the expression levels of tens of thousands of genes and proteins resulting in enormous datasets where the number of genomic features is far greater than the number of subjects. Methods based on univariate Cox regression are often used to select genomic features related to survival outcome; however, the Cox model assumes proportional hazards (PH), which is unlikely to hold for each feature. When applied to genomic features exhibiting some form of non-proportional hazards (NPH), these methods could lead to an under- or over-estimation of the effects. We propose a broad array of marginal screening techniques that aid in feature ranking and selection by accommodating various forms of NPH. First, we develop an approach based on Kullback–Leibler information divergence and the Yang–Prentice model that includes methods for the PH and proportional odds (PO) models as special cases. Next, we propose R2 measures for the PH and PO models that can be interpreted in terms of explained randomness. Lastly, we propose a generalized pseudo-R2 index that includes PH, PO, crossing hazards and crossing odds models as special cases and can be interpreted as the percentage of separability between subjects experiencing the event and not experiencing the event according to feature measurements.ResultsWe evaluate the performance of our measures using extensive simulation studies and publicly available datasets in cancer genomics. We demonstrate that the proposed methods successfully address the issue of NPH in genomic feature selection and outperform existing methods.Availability and implementationR code for the proposed methods is available at github.com/lburns27/Feature-Selection.Contactkarthik.devarajan@fccc.eduSupplementary informationSupplementary data are available at Bioinformatics online.
iATC-FRAKEL: a simple multi-label web server for recognizing anatomical therapeutic chemical classes of drugs with their fingerprints only
Authors: Zhou Jian-Peng , Chen Lei , Wang Tianyun , Liu Min 
Published: March 2020

Abstract

Motivation
Anatomical therapeutic chemical (ATC) classification system is very important for drug utilization and studies. Correct prediction of the 14 classes in the first level for given drugs is an essential problem for the study on such system. Several multi-label classifiers have been proposed in this regard. However, only two of them provided the web servers and their performance was not very high. On the other hand, although some rest classifiers can provide better performance, they were built based on some prior knowledge on drugs, such as information of chemical–chemical interaction and chemical ontology, leading to limited applications. Furthermore, provided codes of these classifiers are almost inaccessible for pharmacologists.

Results
In this study, we built a simple web server, namely iATC-FRAKEL. This web server only required the SMILES format of drugs as input and extracted their fingerprints for making prediction. The performance of the iATC-FRAKEL was much higher than all existing web servers and was comparable to the best multi-label classifier but had much wider applications. Such web server can be visited at http://cie.shmtu.edu.cn/iatc/index.

Availability and implementation
The web server is available at http://cie.shmtu.edu.cn/iatc/index.

Contact
chen_lei1@163.com

Supplementary information
Supplementary data are available at Bioinformatics online.
More efficient approximation of smoothing splines via space-filling basis selection
Authors: Meng Cheng , Zhang Xinlian , Zhang Jingyi , Zhong Wenxuan , Ma Ping 
Published: March 2020

SummaryWe consider the problem of approximating smoothing spline estimators in a nonparametric regression model. When applied to a sample of size $n$, the smoothing spline estimator can be expressed as a linear combination of $n$ basis functions, requiring $O(n^3)$ computational time when the number $d$ of predictors is two or more. Such a sizeable computational cost hinders the broad applicability of smoothing splines. In practice, the full-sample smoothing spline estimator can be approximated by an estimator based on $q$ randomly selected basis functions, resulting in a computational cost of $O(nq^2)$. It is known that these two estimators converge at the same rate when $q$ is of order $O\{n^{2/(pr+1)}\}$, where $p\in [1,2]$ depends on the true function and $r &gt; 1$ depends on the type of spline. Such a $q$ is called the essential number of basis functions. In this article, we develop a more efficient basis selection method. By selecting basis functions corresponding to approximately equally spaced observations, the proposed method chooses a set of basis functions with great diversity. The asymptotic analysis shows that the proposed smoothing spline estimator can decrease $q$ to around $O\{n^{1/(pr+1)}\}$ when $d\leq pr+1$. Applications to synthetic and real-world datasets show that the proposed method leads to a smaller prediction error than other basis selection methods.
Robust estimation of causal effects via a high-dimensional covariate balancing propensity score
Authors: Ning Yang , Sida Peng , Imai Kosuke 
Published: March 2020

SummaryWe propose a robust method to estimate the average treatment effects in observational studies when the number of potential confounders is possibly much greater than the sample size. Our method consists of three steps. We first use a class of penalized $M$-estimators for the propensity score and outcome models. We then calibrate the initial estimate of the propensity score by balancing a carefully selected subset of covariates that are predictive of the outcome. Finally, the estimated propensity score is used to construct the inverse probability weighting estimator. We prove that the proposed estimator, which we call the high-dimensional covariate balancing propensity score, has the sample boundedness property, is root-$n$ consistent, asymptotically normal, and semiparametrically efficient when the propensity score model is correctly specified and the outcome model is linear in covariates. More importantly, we show that our estimator remains root-$n$ consistent and asymptotically normal so long as either the propensity score model or the outcome model is correctly specified. We provide valid confidence intervals in both cases and further extend these results to the case where the outcome model is a generalized linear model. In simulation studies, we find that the proposed methodology often estimates the average treatment effect more accurately than existing methods. We also present an empirical application, in which we estimate the average causal effect of college attendance on adulthood political participation. An open-source software package is available for implementing the proposed methodology.
Transplanted Embryonic Neurons Improve Functional Recovery by Increasing Activity in Injured Cortical Circuits
Authors: Andreoli Evgenia , Petrenko Volodymyr , Constanthin Paul Eugène , Contestabile Alessandro , Bocchi Riccardo , Egervari Kristof , Quairiaux Charles , Salmon Patrick , Kiss Jozsef Zoltan 
Published: March 2020

AbstractTransplantation of appropriate neuronal precursors after injury is a promising strategy to reconstruct cortical circuits, but the efficiency of these approaches remains limited. Here, we applied targeted apoptosis to selectively ablate layer II/III pyramidal neurons in the rat juvenile cerebral cortex and attempted to replace lost neurons with their appropriate embryonic precursors by transplantation. We demonstrate that grafted precursors do not migrate to replace lost neurons but form vascularized clusters establishing reciprocal synaptic contacts with host networks and show functional integration. These heterotopic neuronal clusters significantly enhance the activity of the host circuits without causing epileptic seizures and attenuate the apoptotic injury-induced functional deficits in electrophysiological and behavioral tests. Chemogenetic activation of grafted neurons further improved functional recovery, and the persistence of the graft was necessary for maintaining restored functions in adult animals. Thus, implanting neuronal precursors capable to form synaptically integrated neuronal clusters combined with activation-based approaches represents a useful strategy for helping long-term functional recovery following brain injury.
ENaC-Dependent Sodium Chloride Taste Responses in the Regenerated Rat Chorda Tympani Nerve After Lingual Gustatory Deafferentation Depend on the Taste Bud Field Reinnervated
Authors: Jiang Enshe , Blonde Ginger D , Garcea Mircea , Spector Alan C 
Published: March 2020

Abstract
The chorda tympani (CT) nerve is exceptionally responsive to NaCl. Amiloride, an epithelial Na+ channel (ENaC) blocker, consistently and significantly decreases the NaCl responsiveness of the CT but not the glossopharyngeal (GL) nerve in the rat. Here, we examined whether amiloride would suppress the NaCl responsiveness of the CT when it cross-reinnervated the posterior tongue (PT). Whole-nerve electrophysiological recording was performed to investigate the response properties of the intact (CTsham), regenerated (CTr), and cross-regenerated (CT-PT) CT in male rats to NaCl mixed with and without amiloride and common taste stimuli. The intact (GLsham) and regenerated (GLr) GL were also examined. The CT responses of the CT-PT group did not differ from those of the GLr and GLsham groups, but did differ from those of the CTr and CTsham groups for some stimuli. Importantly, the responsiveness of the cross-regenerated CT to a series of NaCl concentrations was not suppressed by amiloride treatment, which significantly decreased the response to NaCl in the CTr and CTsham groups and had no effect in the GLr and GLsham groups. This suggests that the cross-regenerated CT adopts the taste response properties of the GL as opposed to those of the regenerated CT or intact CT. This work replicates the 5 decade-old findings of Oakley and importantly extends them by providing compelling evidence that the presence of functional ENaCs, essential for sodium taste recognition in regenerated taste receptor cells, depends on the reinnervated lingual region and not on the reinnervating gustatory nerve, at least in the rat.
First Case of Invasive Stachybotrys Sinusitis
Authors: Semis Margarita , Dadwal Sanjeet S , Tegtmeier Bernard R , Wilczynski Sharon P , Ito James I , Kalkum Markus 
Published: March 2020

Abstract

Background
The toxigenic mold Stachybotrys has controversially been linked to idiopathic pulmonary hemorrhage and “sick building syndrome.” However, there are no previous clinical records of invasive stachybotryosis.

Methods
Sinus biopsy specimens from a 23-year-old male with refractory acute lymphocytic leukemia were obtained at 3 different time points during the patient’s hospitalization (139 days) and examined by histopathology and immunohistochemistry (IHC). Antifungal susceptibility testing and fungal speciation using multilocus sequence typing were performed.

Results
Hemorrhage, fungal germination, and hyphal growth were observed in the first sinus biopsy tissues. Areas with fungal growth tested positive for Stachybotrys by IHC. Fungal isolates were genotyped and identified as Stachybotrys chlorohalonata. The patient was cured from Stachybotrys sinusitis following sinus surgery and antifungal treatment. While a subsequent second sinus biopsy and a bronchoscopy showed no signs of fungal infection, a later, third sinus biopsy tested positive for Aspergillus calidoustus, a rare human pathogen.

Conclusions
Here, we report the first case of invasive S. chlorohalonata sinusitis that was surgically and medically cured but followed by invasive A. calidoustus sinusitis in the setting of refractory leukemia. Our findings emphasize the risk for unusual fungal infections in severely immunocompromised patients.
Management of Rectal Stump During Laparoscopic Subtotal Colectomy for Inflammatory Bowel Disease: A Comparative Cohort Study from Six Referral Centres
Authors: Mege Diane , Stellingwerf Merel E , Germain Adeline , Colombo Francesco , Pellino Gianluca , Di Candido Francesca , Maggiori Léon , Foschi Diego , Buskens Christianne J , Adegbola Samuel , Spinelli Antonino , Warusavitarne Janindra , Bemelman Willem A , Sampietro Gianluca , D’Hoore André , Panis Yves 
Published: March 2020

AbstractBackground and AimsThere is no consensus on the best management of the rectum after subtotal colectomy for refractory colitis complicating inflammatory bowel disease [IBD]. The objective was to evaluate the impact of rectal stump management during laparoscopic subtotal colectomy [LSTC] for IBD.MethodsPatients who underwent LSTC with double-end ileo-sigmoidostomy [Gr.A] or end ileostomy with closed rectal stump [Gr.B] for IBD were included from a retrospective database of six European referral centres.ResultsIn total, 314 patients underwent LSTC and were allocated to Gr.A [n = 102] and B [n = 212]. After LSTC, stoma-related complications occurred more frequently in Gr.A [12%] than in Gr.B [4%, p = 0.01]. Completion proctectomy with ileal pouch-anal anastomosis [IPAA] was performed as a three-stage procedure in all patients from Gr.A, and in 88 patients from Gr.B [42%; Gr.B1]. The other 124 patients from Gr.B underwent a modified two-stage procedure [58%; Gr.B2]. The second stage was performed laparoscopically in all patients from Gr.A compared with 73% of Gr.B1 [p &lt; 0.0001] and 65% of Gr.B2 patients [p &lt; 0.0001]. When laparoscopy was intended for 2nd stage IPAA, conversion to laparotomy occurred less frequently in Gr.A when compared with B1 [0 vs 5%, p = 0.06] or B2 [10%, p = 0.001]. When all surgical stages were included [LSCT and IPAA], cumulative stoma-related complications occurred more frequently in Gr.A [n = 19] than in Gr.B1 [n = 6, p = 0.02] and Gr.B2 [n = 6, p = 0.001].ConclusionThis study suggests that both techniques of double-end ileosigmoidostomy and end ileostomy with closed rectal stump are safe and effective for rectal stump management after laparoscopic subtotal colectomy.
Discovering and genotyping genomic structural variations by yeast genome synthesis and inducible evolution
Authors: Chen Si , Xie Ze-Xiong , Yuan Ying-Jin 
Published: March 2020

ABSTRACT
Genomic structural variations (SVs) promote the evolution of Saccharomyces cerevisiae, and play an important role in phenotypic diversities. Yeast genomic structures can be remodeled by design and bottom-up synthesis. The synthesis of yeast genome creates novel copy number variations (CNVs) and SVs and develops new strategies to discover gene functions. Further, an inducible evolution system SCRaMbLE, consisted of 3,932 loxPsym sites, was incorporated on synthetic yeast genome. SCRaMbLE enables genomic rearrangements at will and rapidly generates chromosomal number variations, and massive SVs under customized conditions. The impacts of genetic variations on phenotypes can be revealed by genome analysis and chromosome restructuring. Yeast genome synthesis and SCRaMbLE provide a new research paradigm to explore the genotypic mechanisms of phenotype diversities, and can be used to improve biological traits and optimize industrial chassis.
Secondary Evolve and Resequencing: An Experimental Confirmation of Putative Selection Targets without Phenotyping
Authors: Burny Claire , Nolte Viola , Nouhaud Pierre , Dolezal Marlies , Schlötterer Christian 
Published: March 2020

AbstractEvolve and resequencing (E&R) studies investigate the genomic responses of adaptation during experimental evolution. Because replicate populations evolve in the same controlled environment, consistent responses to selection across replicates are frequently used to identify reliable candidate regions that underlie adaptation to a new environment. However, recent work demonstrated that selection signatures can be restricted to one or a few replicate(s) only. These selection signatures frequently have weak statistical support, and given the difficulties of functional validation, additional evidence is needed before considering them as candidates for functional analysis. Here, we introduce an experimental procedure to validate candidate loci with weak or replicate-specific selection signature(s). Crossing an evolved population from a primary E&R experiment to the ancestral founder population reduces the frequency of candidate alleles that have reached a high frequency. We hypothesize that genuine selection targets will experience a repeatable frequency increase after the mixing with the ancestral founders if they are exposed to the same environment (secondary E&R experiment). Using this approach, we successfully validate two overlapping selection targets, which showed a mutually exclusive selection signature in a primary E&R experiment of Drosophila simulans adapting to a novel temperature regime. We conclude that secondary E&R experiments provide a reliable confirmation of selection signatures that either are not replicated or show only a low statistical significance in a primary E&R experiment unless epistatic interactions predominate. Such experiments are particularly helpful to prioritize candidate loci for time-consuming functional follow-up investigations.
A least-squares method for estimating the correlated error of GRACE models
Authors: Crowley John W , Huang Jianliang 
Published: March 2020

SUMMARY
A new least-squares method is developed for estimating and removing the correlated errors (stripes) from the Gravity Recovery and Climate Experiment (GRACE) and GRACE Follow-On (GRACE-FO) mission data. This method is based on a joint parametric model of the correlated errors and temporal trends in the spherical harmonic coefficients of GRACE models. Three sets of simulation data are created from the Global Land Data Assimilation System (GLDAS), the Regional Atmospheric Climate Model 2.3 (RACMO2.3) and GRACE models and used to test it. The results show that the new method improves the decorrelation method by Swenson & Wahr significantly. Its application to the release 5 (RL05) and new release 6 (RL06) spherical harmonic solutions from the Center for Space Research (CSR) at The University of Texas at Austin demonstrates its effectiveness and provides a relative assessment of the two releases. A comparison to the Swenson & Wahr and Kusche et al. methods highlights the deficiencies in past destriping methods and shows how the inclusion and decoupling of temporal trends helps to overcome them. A comparison to the CSR mascon and JPL mascon solutions demonstrates that the new method yields global trends that have greater amplitude than those produced by the CSR RL05 mascon solution and are of comparable quality to the JPL RL06 mascon solution. Furthermore, these results are obtained without the need for a priori information, scale factors or complex regularization methods and the solutions remain in the standard form of spherical harmonics rather than discrete mascons. The latter could introduce additional discretization error when converting to the spherical harmonic model, upon which many post-processing methods and applications are built.