bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential Associations of Diastolic and Systolic Pressures With Cerebral Measures in Older Individuals With Mild Cognitive Impairment
Authors: Shokouhi Mahsa , Qiu Deqiang , Samman Tahhan Ayman , Quyyumi Arshed A , Hajjar Ihab 
Published: July 2018

Abstract

BACKGROUND
Reports on the relative importance of the diastolic and systolic blood pressures (DBP and SBP) in age-related cognitive decline are mixed. Investigating the relation between DBP/SBP and functional and structural brain changes could elucidate which of the 2 measures is more critically important for brain function and, consequently, cognitive impairment.

METHODS
We investigated the association of SBP and DBP with cortical volume, cerebral blood flow (CBF), and white matter lesions (WML), in nondemented older adults with and without mild cognitive impairment (MCI; N = 265, 185 MCI, mean age = 64 years). Brachial blood pressure was measured twice while seated, and the average of the 2 measures was used. Cortical volume, gray matter (GM) CBF, and WML were estimated using T1-weighted imaging, arterial spin labeling, and fluid attenuation inversion recovery, respectively.

RESULTS
Reduced cortical volume was associated with elevated DBP (β= −0.18, P = 0.034) but not with SBP (β = −0.10, P = 0.206). GM CBF was associated with DBP (β = −0.13, P = 0.048) but not with SBP (β = −0.07, P = 0.275). Likewise, CBF within brain regions where MCI patients showed hypoperfusion were only associated with DBP (DBP: β = −0.17, P = 0.005; SBP: β = −0.09, P = 0.120). WML volume was associated with both DBP (β = 0.20, P = 0.005) and SBP (β = 0.30, P &lt; 0.001). For all measures, there was no interaction between DBP/SBP and cognitive status, indicating that these associations were independent of the cognitive status.

CONCLUSIONS
Independently of the cognitive status, DBP is more critically important for GM volume and perfusion, whereas WML is associated with both blood pressures, likely reflecting long-term effect of hypertension and autoregulation dysfunction.
Black–White Difference in the Impact of Long-Term Blood Pressure From Childhood on Adult Renal Function: The Bogalusa Heart Study
Authors: Yan Yinkun , Zhang Tao , Li Shengxu , Liu Yang , Bazzano Lydia , He Jiang , Mi Jie , Chen Wei 
Published: July 2018

Abstract

BACKGROUND
To examine racial difference in the impact of long-term burden of blood pressure (BP) from childhood on adult renal function between middle-aged blacks and whites.

METHODS
The study cohort consisted of 1,646 whites and 866 blacks aged 20–51 years at follow-up who had BP measured at least 4 times since childhood, with a mean follow-up period of 25.3 years. The area under the curve (AUC) was calculated as a measure of long-term burden of BP from childhood to adulthood. Estimated glomerular filtration rate (eGFR) was calculated based on serum creatinine to assess renal function in adulthood.

RESULTS
Black vs. white adults had significantly higher values of eGFR and long-term burden of systolic BP for both males and females. In multivariable linear regression analyses, adjusting for sex, adult age, body mass index, smoking, and alcohol use, adult eGFR was significantly and negatively associated with adult systolic BP (standardized regression coefficient [β] = −0.10, P = 0.005) and diastolic BP (β = −0.11, P = 0.003) in blacks, but not in whites. The total BP AUC values were also significantly and negatively associated with adult eGFR (β = −0.10, P = 0.005 for systolic BP and β = −0.09, P = 0.013 for diastolic BP) in blacks only. Childhood BP was not significantly associated with adult eGFR in blacks and whites.

CONCLUSIONS
These findings suggest that black–white disparities in the influence of elevated BP on the development of renal dysfunction occur in middle adulthood, which underscores the importance of BP control in the black population.
Review and comparative assessment of similarity-based methods for prediction of drug–protein interactions in the druggable human proteome
Authors: Wang Chen , Kurgan Lukasz 
Published: July 2018

AbstractDrug–protein interactions (DPIs) underlie the desired therapeutic actions and the adverse side effects of a significant majority of drugs. Computational prediction of DPIs facilitates research in drug discovery, characterization and repurposing. Similarity-based methods that do not require knowledge of protein structures are particularly suitable for druggable genome-wide predictions of DPIs. We review 35 high-impact similarity-based predictors that were published in the past decade. We group them based on three types of similarities and their combinations that they use. We discuss and compare key aspects of these methods including source databases, internal databases and their predictive models. Using our novel benchmark database, we perform comparative empirical analysis of predictive performance of seven types of representative predictors that utilize each type of similarity individually and all possible combinations of similarities. We assess predictive quality at the database-wide DPI level and we are the first to also include evaluation over individual drugs. Our comprehensive analysis shows that predictors that use more similarity types outperform methods that employ fewer similarities, and that the model combining all three types of similarities secures area under the receiver operating characteristic curve of 0.93. We offer a comprehensive analysis of sensitivity of predictive performance to intrinsic and extrinsic characteristics of the considered predictors. We find that predictive performance is sensitive to low levels of similarities between sequences of the drug targets and several extrinsic properties of the input drug structures, drug profiles and drug targets. The benchmark database and a webserver for the seven predictors are freely available at http://biomine.cs.vcu.edu/servers/CONNECTOR/.
Comprehensive comparative analysis of methods and software for identifying viral integrations
Authors: Chen Xun , Kost Jason , Li Dawei 
Published: July 2018

Abstract
Many viruses are capable of integrating in the human genome, particularly viruses involved in tumorigenesis. Viral integrations can be considered genetic markers for discovering virus-caused cancers and inferring cancer cell development. Next-generation sequencing (NGS) technologies have been widely used to screen for viral integrations in cancer genomes, and a number of bioinformatics tools have been developed to detect viral integrations using NGS data. However, there has been no systematic comparison of the methods or software. In this study, we performed a comprehensive comparative analysis of the designs, performance, functionality and limitations among the existing methods and software for detecting viral integrations. We further compared the sensitivity, precision and runtime of integration detection of four representative tools. Our analyses showed that each of the existing software had its own merits; however, none of them were sufficient for parallel or accurate virome-wide detection. After carefully evaluating the limitations shared by the existing methods, we proposed strategies and directions for developing virome-wide integration detection.
Insights on the alteration of functionality of a tyrosine kinase 2 variant: a molecular dynamics study
Authors: Lesgidou Nastazia , Eliopoulos Elias , Goulielmos George N , Vlassi Metaxia 
Published: July 2018

Abstract

Motivation
The tyrosine kinase 2 protein (Tyk2), encoded by the TYK2 gene, has a crucial role in signal transduction and the pathogenesis of many diseases. A single nucleotide polymorphism of the TYK2 gene, SNP rs34536443, is of major importance, since it has been shown to confer protection against various, mainly, autoimmune diseases. This polymorphism results in a Pro to Ala change at amino acid position 1104 of the encoded Tyk2 protein that affects its enzymatic activity. However, the details of the underlined mechanism are unknown. To address this issue, in this study, we used molecular dynamics simulations on the kinase domains of both wild type and variant Tyk2 protein.

Results
Our MD results provided information, at atomic level, on the consequences of the Pro1104 to Ala substitution on the structure and dynamics of the kinase domain of Tyk2 and suggested reduced enzymatic activity of the resulting protein variant due to stabilization of inactive conformations, thus adding to knowledge towards the elucidation of the protection mechanism against autoimmune diseases associated with this point mutation.
MAVIS: merging, annotation, validation, and illustration of structural variants
Authors: Reisle Caralyn , Mungall Karen L , Choo Caleb , Paulino Daniel , Bleile Dustin W , Muhammadzadeh Amir , Mungall Andrew J , Moore Richard A , Shlafman Inna , Coope Robin , Pleasance Stephen , Ma Yussanne , Jones Steven J M 
Published: July 2018

Abstract

Summary
Reliably identifying genomic rearrangements and interpreting their impact is a key step in understanding their role in human cancers and inherited genetic diseases. Many short read algorithmic approaches exist but all have appreciable false negative rates. A common approach is to evaluate the union of multiple tools increasing sensitivity, followed by filtering to retain specificity. Here we describe an application framework for the rapid generation of structural variant consensus, unique in its ability to visualize the genetic impact and context as well as process both genome and transcriptome data.

Availability and implementation
http://mavis.bcgsc.ca

Supplementary information
Supplementary data are available at Bioinformatics online.
Reproducible and replicable comparisons using SummarizedBenchmark
Authors: Kimes Patrick K , Reyes Alejandro 
Published: July 2018

Abstract

Summary
Benchmark studies are widely used to compare and evaluate tools developed for answering various biological questions. Despite the popularity of these comparisons, the implementation is often ad hoc, with little consistency across studies. To address this problem, we developed SummarizedBenchmark, an R package and framework for organizing and structuring benchmark comparisons. SummarizedBenchmark defines a general grammar for benchmarking and allows for easier setup and execution of benchmark comparisons, while improving the reproducibility and replicability of such comparisons. We demonstrate the wide applicability of our framework using four examples from different applications.

Availability and implementation
SummarizedBenchmark is an R package available through Bioconductor (http://bioconductor.org/packages/SummarizedBenchmark).

Supplementary information
Supplementary data are available at Bioinformatics online.
Simulating Illumina metagenomic data with InSilicoSeq
Authors: Gourlé Hadrien , Karlsson-Lindsjö Oskar , Hayer Juliette , Bongcam-Rudloff Erik 
Published: July 2018

Abstract

Motivation
The accurate in silico simulation of metagenomic datasets is of great importance for benchmarking bioinformatics tools as well as for experimental design. Users are dependant on large-scale simulation to not only design experiments and new projects but also for accurate estimation of computational needs within a project. Unfortunately, most current read simulators are either not suited for metagenomics, out of date or relatively poorly documented. In this article, we describe InSilicoSeq, a software package to simulate metagenomic Illumina sequencing data. InsilicoSeq has a simple command-line interface and extensive documentation.

Results
InSilicoSeq is implemented in Python and capable of simulating realistic Illumina (meta) genomic data in a parallel fashion with sensible default parameters.

Availability and implementation
Source code and documentation are available under the MIT license at https://github.com/HadrienG/InSilicoSeq and https://insilicoseq.readthedocs.io/.

Supplementary information
Supplementary data are available at Bioinformatics online.
SonicParanoid: fast, accurate and easy orthology inference
Authors: Cosentino Salvatore , Iwasaki Wataru 
Published: July 2018

AbstractMotivationOrthology inference constitutes a common base of many genome-based studies, as a pre-requisite for annotating new genomes, finding target genes for biotechnological applications and revealing the evolutionary history of life. Although its importance keeps rising with the ever-growing number of sequenced genomes, existing tools are computationally demanding and difficult to employ.ResultsHere, we present SonicParanoid, which is faster than, but comparably accurate to, the well-established tools with a balanced precision-recall trade-off. Furthermore, SonicParanoid substantially relieves the difficulties of orthology inference for those who need to construct and maintain their own genomic datasets.Availability and implementationSonicParanoid is available with a GNU GPLv3 license on the Python Package Index and BitBucket. Documentation is available at http://iwasakilab.bs.s.u-tokyo.ac.jp/sonicparanoid.Supplementary informationSupplementary data are available at Bioinformatics online.
Being a good egg in the 21st century
Authors: Anderson Richard A , Telfer Evelyn E 
Published: July 2018

Abstract

Introduction
Women are increasingly having children at a later age, but this can conflict with declining fertility in the later 30′s and thereafter.

Areas of agreement
Declining egg quality and quantity with age are well-established, although egg quality can only be surmised from reproductive success or failure.

Areas of controversy
Whether increasing the number of eggs that can be obtained from ovarian stimulation is of value, and whether there are precursor cells within the adult ovary that could become mature eggs.

Growing points
There is increasing use of donated eggs by older women to enhance their chances of conception. The storage of frozen eggs for potential use later in life is also becoming more common.

Areas timely for developing research
Understanding of growth initiation of follicles and development of an artificial ovary may lead to the ability to affect fertility and reproductive lifespan.
Legitimating Media: Shakespeare’s Awkward Travels Through Video Games and Twitter
Authors: Cornfeld Li , Simon Victoria , Sterne Jonathan 
Published: July 2018

AbstractSince the 19th century, Shakespeare references have recurred with surprising consistency in experimental forms of media. This article considers the role of references to and adaptations of Shakespeare texts when a media form takes on a new valence for a set of users in a particular time and place. We consider two different moments at length: a commercial interactive game from 1984 that made novel use of cassettes and sound, and the production and reception of early Twitter adaptations of Shakespeare in 2010. By standing in for the aesthetic possibilities and limits of a changing media space, Shakespearean references and deviations from them serve a key role for artists and critics in debates over the legitimacy and significance of creative work in emergent media. Thus, cultural producers, critics and audiences thus use these sometimes-awkward appearances of Shakespeare as a means of describing their aesthetic potentials and limits.
Maintained Frontal Activity Underlies High Memory Function Over 8 Years in Aging
Authors: Vidal-Piñeiro Didac , Sneve Markus H , Nyberg Lars H , Mowinckel Athanasia M , Sederevicius Donatas , Walhovd Kristine B , Fjell Anders M 
Published: July 2018

AbstractAging is characterized by substantial average decline in memory performance. Yet contradictory explanations have been given for how the brains of high-performing older adults work: either by engagement of compensatory processes such as recruitment of additional networks or by maintaining young adults’ patterns of activity. Distinguishing these components requires large experimental samples and longitudinal follow-up. Here, we investigate which features are key to high memory in aging, directly testing these hypotheses by studying a large sample of adult participants (n > 300) with fMRI during an episodic memory experiment where item-context relationships were implicitly encoded. The analyses revealed that low levels of activity in frontal networks—known to be involved in memory encoding—were associated with low memory performance in the older adults only. Importantly, older participants with low memory performance and low frontal activity exhibited a strong longitudinal memory decline in an independent verbal episodic memory task spanning 8 years back (n = 52). These participants were also characterized by lower hippocampal volumes and steeper rates of cortical atrophy. Altogether, maintenance of frontal brain function during encoding seems to be a primary characteristic of preservation of memory function in aging, likely reflecting intact ability to integrate information.
Adolescent Nicotine Exposure Induces Dysregulation of Mesocorticolimbic Activity States and Depressive and Anxiety-like Prefrontal Cortical Molecular Phenotypes Persisting into Adulthood
Authors: Jobson Christina L M , Renard Justine , Szkudlarek Hanna , Rosen Laura G , Pereira Brian , Wright Daniel J , Rushlow Walter , Laviolette Steven R 
Published: July 2018

Abstract
Considerable evidence demonstrates strong comorbidity between nicotine dependence and mood and anxiety disorders. Nevertheless, the neurobiological mechanisms linking adolescent nicotine exposure to mood and anxiety disorders are not known. Disturbances in the mesocorticolimbic dopamine (DA) system, comprising the prefrontal cortex (PFC), ventral tegmental area (VTA), and nucleus accumbens (NAc), are correlates of mood and anxiety-related symptoms and this circuitry is strongly influenced by acute or chronic nicotine exposure. Using a combination of behavioral pharmacology, in vivo neuronal electrophysiology and molecular analyses, we examined and compared the effects of chronic nicotine exposure in rats during adolescence versus adulthood to characterize the mechanisms by which adolescent nicotine may selectively confer increased risk of developing mood and anxiety-related symptoms in later life. We report that exposure to nicotine, selectively during adolescence, induces profound and long-lasting neuronal, molecular and behavioral disturbances involving PFC DA D1R and downstream extracellular-signal-related kinase 1-2 (ERK 1-2) signaling. Remarkably, adolescent nicotine induced a persistent state of hyperactive DA activity in the ventral tegmental area (VTA) concomitant with hyperactive neuronal activity states in the PFC. Our findings identify several unique neuronal and molecular biomarkers that may serve as functional risk mechanisms for the long-lasting neuropsychiatric effects of adolescent smoking behaviors.
Reappraisal of Interpersonal Criticism in Social Anxiety Disorder: A Brain Network Hierarchy Perspective
Authors: Jacob Y , Shany O , Goldin P R , Gross J J , Hendler T 
Published: July 2018

AbstractEmotion regulation is thought to involve communication between and within large-scale brain networks that underlie emotion reactivity and cognitive control. Aberrant network interaction might therefore be a key neural feature of mental disorders that involve emotion dysregulation. Here we tested whether connectivity hierarchies within and between emotion reactivity and cognitive reappraisal networks distinguishes social anxiety disorder (SAD) patients (n = 70) from healthy controls (HC) (n = 25). To investigate network organization, we implemented a graph-theory method called Dependency Network Analysis. Participants underwent fMRI while watching or reappraising video clips involving interpersonal verbal criticism. During reappraisal, the reappraisal network exerted less influence on the reactivity network in SAD participants. Specifically, the influence of the right inferior frontal gyrus on both reappraisal and reactivity networks was significantly reduced in SAD compared with HC, and correlated negatively with negative emotion ratings among SAD participants. Surprisingly, the amygdala exhibited reduced influence on the reappraisal network in SAD relative to HC. Yet, during the watch condition, the left amygdala’s influence on the reactivity network increased with greater social anxiety symptoms among SAD participants. These findings refine our understanding of network organization that contributes to efficient reappraisal or to disturbances in applying this strategy in SAD.
Longer-term Direct and Indirect Effects of Infant Rotavirus Vaccination Across All Ages in the United States in 2000–2013: Analysis of a Large Hospital Discharge Data Set
Authors: Baker Julia M , Tate Jacqueline E , Steiner Claudia A , Haber Michael J , Parashar Umesh D , Lopman Benjamin A 
Published: July 2018

AbstractBackgroundRotavirus disease rates dramatically declined among children &lt;5 years of age since the rotavirus vaccine was introduced in 2006; population-level impacts remain to be fully elucidated.MethodsData from the Healthcare Cost and Utilization Project State Inpatient Databases were used to conduct a time-series analysis of monthly hospital discharges across age groups for acute gastroenteritis and rotavirus from 2000 to 2013. Rate ratios were calculated comparing prevaccine and postvaccine eras.ResultsFollowing vaccine introduction, a decrease in rotavirus hospitalizations occurred with a shift toward biennial patterns across all ages. The 0–4-year age group experienced the largest decrease in rotavirus hospitalizations (rate ratio, 0.14; 95% confidence interval, .09–.23). The 5–19-year and 20–59-year age groups experienced significant declines in rotavirus hospitalization rates overall; the even postvaccine calendar years were characterized by progressively lower rates, and the odd postvaccine years were associated with reductions in rates that diminished over time. Those aged ≥60 years experienced the smallest change in rotavirus hospitalization rates overall, with significant reductions in even postvaccine years compared with prevaccine years (rate ratio, 0.51; 95% confidence interval, .39–.66).ConclusionsIndirect impacts of infant rotavirus vaccination are apparent in the emergence of biennial patterns in rotavirus hospitalizations that extend to all age groups ineligible for vaccination. These observations are consistent with the notion that young children are of primary importance in disease transmission and that the initial postvaccine period of dramatic population-wide impacts will be followed by more complex incidence patterns across the age range in the long term.