bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of management status on the coral reef fish communities in Ujung Kulon National Park, Banten
Authors: Yudha F K , Fahlevy K , Andika W , Saraswati E , Hutami P R , Kamal M M , Samosir A M 
Published: May 2019

Abstract
Ujung Kulon National Park (TNUK) employs a management with the zonation system established to maintain the sustainability of resources, one of them are coral reef fish. This study aimed to identify the influence of management status on coral reef fish. Field observations were conducted on 14-22 October 2017 in Ujung Kulon using underwater visual census method, by recording the fish found in observation transects. The coral reef fish most frequently found in Core Zone was Caesionidae, while in The Marine Protection Zone is Acanthuridae. The Core Zone has higher species richness, and more abundance of coral reef fish than the Marine Protection Zone, although only species richness parameter shows a significant difference based on statistical tests. The management status that regulates the activities in each zoning has an impact on the coral reef ecosystem, including coral reef fish communities in it. Coral reef fish in the Core Zone have more diverse species than the Marine Protection Zone, because the coral reefs in the Core Zone are more preserved than the Marine Protection Zone.
Orographic effect and multiscale interactions during an extreme rainfall event
Authors: Baisya Himadri , Pattnaik Sandeep 
Published: May 2019

AbstractInteraction of multiple oscillations of different time scales may result in severe weather events. The presence of orography can modulate the intensity of these events even further. Kerala witnessed one such heavy rainfall event in August, 2018, claiming 483 lives and damages worth INR 200 billion. This study focuses on the peak rainfall duration (13–17 August) when the departure from normal was 42%. Segregating moisture transport into its mean and perturbation terms show that an anomalous moisture channel over the Arabian Sea supplied continuous moisture to the Western Ghats (WG), whereas anomalous wind due to a monsoon depression advected moisture towards the southern peninsula. It is evident in the form of Moisture Flux Convergence (MFC) towers traversing along the Eastern Ghats before merging with the semi-permanent MFC feature over the WG. The presence of positive quasi bi-weekly oscillations and of Intra Seasonal Oscillations (ISO) aggravated the event as they complemented the anomalous moisture transport, with ISO constantly providing winds of the order of 2–3 ms−1. In addition, shedding of MFC towers by the depression is accredited to the synoptic scale oscillation.
A Cross-Sectional Analysis of Telomere Length and Sleep in the Women’s Health Initiative
Authors: Grieshober Laurie , Wactawski-Wende Jean , Hageman Blair Rachael , Mu Lina , Liu Jingmin , Nie Jing , Carty Cara L , Hale Lauren , Kroenke Candyce H , LaCroix Andrea Z , Reiner Alex P , Ochs-Balcom Heather M 
Published: May 2019

Abstract
Telomere length is a heritable marker of cellular age that is associated with morbidity and mortality. Poor sleep behaviors, which are also associated with adverse health events, may be related to leukocyte telomere length (LTL). We studied a subpopulation of 3,145 postmenopausal women (1,796 European-American (EA) and 1,349 African-American (AA)) enrolled in the Women’s Health Initiative in 1993–1998 with data on Southern blot-measured LTL and self-reported usual sleep duration and sleep disturbance. LTL-sleep associations were analyzed separately for duration and disturbance using weighted and confounder-adjusted linear regression models in the entire sample (AAs + EAs; adjusted for race/ethnicity) and in racial/ethnic strata, since LTL differs by ancestry. After adjustment for covariates, each additional daily hour of sleep beyond 5 hours, approximately, was associated with a 27-base-pair (95% confidence interval (CI): 6, 48) longer LTL in the entire sample. Associations between sleep duration and LTL were strongest among AAs (adjusted β = 37, 95% CI: 4, 70); a similar, nonsignificant association was observed for EAs (adjusted β = 20, 95% CI: −7, 48). Sleep disturbance was not associated with LTL in our study. Our models did not show departure from linearity (quadratic sleep terms: P ≥ 0.55). Our results suggest that longer sleep duration is associated with longer LTL in postmenopausal women.
Deep fusion of contextual and object-based representations for delineation of multiple nuclear phenotypes
Authors: Khoshdeli Mina , Winkelmaier Garrett , Parvin Bahram 
Published: May 2019

Abstract

Motivation
Nuclear delineation and phenotypic profiling are important steps in the automated analysis of histology sections. However, these are challenging problems due to (i) technical variations (e.g. fixation, staining) that originate as a result of sample preparation; (ii) biological heterogeneity (e.g. vesicular versus high chromatin phenotypes, nuclear atypia) and (iii) overlapping nuclei. This Application-Note couples contextual information about the cellular organization with the individual signature of nuclei to improve performance. As a result, routine delineation of nuclei in H&E stained histology sections is enabled for either computer-aided pathology or integration with genome-wide molecular data.

Results
The method has been evaluated on two independent datasets. One dataset originates from our lab and includes H&E stained sections of brain and breast samples. The second dataset is publicly available through IEEE with a focus on gland-based tissue architecture. We report an approximate AJI of 0.592 and an F1-score 0.93 on both datasets.

Availability and implementation
The code-base, modified dataset and results are publicly available.

Supplementary information
Supplementary data are available at Bioinformatics online.
CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures
Authors: Jia Peilin , Pei Guangsheng , Zhao Zhongming 
Published: May 2019

Abstract

Motivation
Genome-wide multi-omics profiling of complex diseases provides valuable resources and opportunities to discover associations between various measures of genes and diseases. Currently, a pressing challenge is how to effectively detect functional genes associated with or causing phenotypic outcomes. We developed CNet to identify groups of genomic signatures whose combinatory effect is significantly associated with clinical and phenotypical outcomes.

Results
CNet builds on a generalized sequential feedforward method, augmented by a down-sampling bootstrap strategy to reduce random hitchhiking signatures. It further applies a dynamic trimming procedure to remove relatively less informative signatures at every step. CNet can manage heterogeneous genomic signature profiles simultaneously and select the best signature to represent a specific gene. To deal with various forms of clinical and phenotypical measurements, we introduced four models to deal with continuous, categorical and censored data. We tested CNet using drug-response data, multidimensional cancer genomics data and genome-wide association study data for multiple traits. Our results demonstrated that in various scenarios, CNet could effectively identify signatures that are associated with the outcomes. In addition, we applied CNet to identify likely disease-causing chains involving somatic mutations, pathway activities and patient outcomes. With appropriate setting, CNet can be applied in many biological conditions.

Availability and implementation
CNet can be downloaded at https://github.com/bsml320/CNet.

Supplementary information
Supplementary data are available at Bioinformatics online.
White matter hyperintensities: relationship to amyloid and tau burden
Authors: Graff-Radford Jonathan , Arenaza-Urquijo Eider M , Knopman David S , Schwarz Christopher G , Brown Robert D , Rabinstein Alejandro A , Gunter Jeffrey L , Senjem Matthew L , Przybelski Scott A , Lesnick Timothy , Ward Chadwick , Mielke Michelle M , Lowe Val J , Petersen Ronald C , Kremers Walter K , Kantarci Kejal , Jack Clifford R , Vemuri Prashanthi 
Published: May 2019

Abstract
Although white matter hyperintensities have traditionally been viewed as a marker of vascular disease, recent pathology studies have found an association between white matter hyperintensities and Alzheimer’s disease pathologies. The objectives of this study were to investigate the topographic patterns of white matter hyperintensities associated with Alzheimer’s disease biomarkers measured using PET. From the population-based Mayo Clinic Study of Aging, 434 participants without dementia (55% male) with FLAIR and gradient recall echo MRI, tau-PET (AV-1451) and amyloid-PET scans were identified. A subset had cerebral microbleeds detected on T2* gradient recall echo scans. White matter hyperintensities were semi-automatically segmented using FLAIR MRI in participant space and normalized to a custom template. We used statistical parametric mapping 12-based, voxel-wise, multiple-regression analyses to detect white matter hyperintense regions associated with Alzheimer’s biomarkers (global amyloid from amyloid-PET and meta-regions of interest tau uptake from tau-PET) after adjusting for age, sex and hypertension. For amyloid associations, we additionally adjusted for tau and vice versa. Topographic patterns of amyloid-associated white matter hyperintensities included periventricular white matter hyperintensities (frontal and parietal lobes). White matter hyperintense volumes in the detected topographic pattern correlated strongly with lobar cerebral microbleeds (P < 0.001, age and sex adjusted Cohen’s d = 0.703). In contrast, there were no white matter hyperintense regions significantly associated with increased tau burden using voxel-based analysis or region-specific analysis. Among non-demented elderly, amyloid load correlated with a topographic pattern of white matter hyperintensities. Further, the amyloid-associated, white matter hyperintense regions strongly correlated with lobar cerebral microbleeds suggesting that cerebral amyloid angiopathy contributes to the relationship between amyloid and white matter hyperintensities. The study did not support an association between increased tau burden and white matter hyperintense burden.
TSC22D2 identified as a candidate susceptibility gene of multi-cancer pedigree using genome-wide linkage analysis and whole-exome sequencing
Authors: Xiao Lan , Wei Fang , Liang Fang , Li Qiao , Deng Hao , Tan Shiming , Chen Shuai , Xiong Fang , Guo Can , Liao Qianjin , Li Xiayu , Zhang Wenling , Wu Minghua , Zhou Yanhong , Xiang Bo , Zhou Ming , Li Xiaoling , Xiong Wei , Zeng Zhaoyang , Li Guiyuan 
Published: May 2019

AbstractCancer is a complex disease, which may involve multiple tumor susceptibility genes that mediate the occurrence and development of tumor molecular events. This study aimed to identify new genetic loci using genome-wide linkage analysis and whole-exome sequencing in a rare, large multi-cancer pedigree recently found in China. We performed high-throughput single-nucleotide polymorphism (SNP) array and linkage analyses of 24 core members of this pedigree and found that the disease susceptibility locus in the multi-cancer pedigree was mapped to chromosome 3q24-26. We also used microsatellites to further validate the results of the SNP locus linkage analysis. Furthermore, we sequenced the whole exome of three members in this pedigree and identified a novel mutant of transforming growth factor β stimulated clone 22 domain family, member 2 (TSC22D2, c.-91T-C) cosegregated with the cancer phenotype. This change was at a highly conserved position, and the exome results were validated using linkage analysis. Moreover, we found the histone H4 transcription factor (HINFP) binds to the promoter region of TSC22D2 and may regulate its transcription. In conclusion, our findings are of great significance to the early pathogenesis of tumors and contribute to the search for molecular targets for the early prevention and treatment of tumors.
Reduced Segregation Between Cognitive and Emotional Processes in Cannabis Dependence
Authors: Manza Peter , Shokri-Kojori Ehsan , Volkow Nora D 
Published: May 2019

Abstract
Addiction is characterized by an erosion of cognitive control toward drug taking that is accentuated by negative emotional states. Here we tested the hypothesis that enhanced interference on cognitive control reflects a loss of segregation between cognition and emotion in addiction. We analyzed Human Connectome Project data from 1206 young adults, including 89 with cannabis dependence (CD). Two composite factors, one for cognition and one for emotion, were derived using principal component (PC) analyses. Component scores for these PCs were significantly associated in the CD group, such that negative emotionality correlated with poor cognition. However, the corresponding component scores were uncorrelated in matched controls and nondependent recreational cannabis users (n = 87). In CD, but not controls or recreational users, functional magnetic resonance imaging activations to emotional stimuli (angry/fearful faces &gt; shapes) correlated with activations to cognitive demand (working memory; 2-back &gt; 0-back). Canonical correlation analyses linked individual differences in cognitive and emotional component scores with brain activations. In CD, there was substantial overlap between cognitive and emotional brain–behavior associations, but in controls, associations were more restricted to the cognitive domain. These findings support our hypothesis of impaired segregation between cognitive and emotional processes in CD that might contribute to poor cognitive control under conditions of increased emotional demand.
Predicting Hemolytic Uremic Syndrome and Renal Replacement Therapy in Shiga Toxin–producing Escherichia coli–infected Children
Authors: McKee Ryan S , Schnadower David , Tarr Phillip I , Xie Jianling , Finkelstein Yaron , Desai Neil , Lane Roni D , Bergmann Kelly R , Kaplan Ron L , Hariharan Selena , Cruz Andrea T , Cohen Daniel M , Dixon Andrew , Ramgopal Sriram , Rominger Annie , Powell Elizabeth C , Kilgar Jennifer , Michelson Kenneth A , Beer Darcy , Bitzan Martin , Pruitt Christopher M , Yen Kenneth , Meckler Garth D , Plint Amy C , Bradin Stuart , Abramo Thomas J , Gouin Serge , Kam April J , Schuh Abigail , Balamuth Fran , Hunley Tracy E , Kanegaye John T , Jones Nicholas E , Avva Usha , Porter Robert , Fein Daniel M , Louie Jeffrey P , Freedman Stephen B 
Published: May 2019

Abstract

Background
Shiga toxin–producing Escherichia coli (STEC) infections are leading causes of pediatric acute renal failure. Identifying hemolytic uremic syndrome (HUS) risk factors is needed to guide care.

Methods
We conducted a multicenter, historical cohort study to identify features associated with development of HUS (primary outcome) and need for renal replacement therapy (RRT) (secondary outcome) in STEC-infected children without HUS at initial presentation. Children aged &lt;18 years who submitted STEC-positive specimens between January 2011 and December 2015 at a participating study institution were eligible.

Results
Of 927 STEC-infected children, 41 (4.4%) had HUS at presentation; of the remaining 886, 126 (14.2%) developed HUS. Predictors (all shown as odds ratio [OR] with 95% confidence interval [CI]) of HUS included younger age (0.77 [.69–.85] per year), leukocyte count ≥13.0 × 103/μL (2.54 [1.42–4.54]), higher hematocrit (1.83 [1.21–2.77] per 5% increase) and serum creatinine (10.82 [1.49–78.69] per 1 mg/dL increase), platelet count &lt;250 × 103/μL (1.92 [1.02–3.60]), lower serum sodium (1.12 [1.02–1.23 per 1 mmol/L decrease), and intravenous fluid administration initiated ≥4 days following diarrhea onset (2.50 [1.14–5.46]). A longer interval from diarrhea onset to index visit was associated with reduced HUS risk (OR, 0.70 [95% CI, .54–.90]). RRT predictors (all shown as OR [95% CI]) included female sex (2.27 [1.14–4.50]), younger age (0.83 [.74–.92] per year), lower serum sodium (1.15 [1.04–1.27] per mmol/L decrease), higher leukocyte count ≥13.0 × 103/μL (2.35 [1.17–4.72]) and creatinine (7.75 [1.20–50.16] per 1 mg/dL increase) concentrations, and initial intravenous fluid administration ≥4 days following diarrhea onset (2.71 [1.18–6.21]).

Conclusions
The complex nature of STEC infection renders predicting its course a challenge. Risk factors we identified highlight the importance of avoiding dehydration and performing close clinical and laboratory monitoring.
A novel therapeutic peptide targeting myocardial reperfusion injury
Authors: Boisguérin Prisca , Covinhes Aurélie , Gallot Laura , Barrère Christian , Vincent Anne , Busson Muriel , Piot Christophe , Nargeot Joël , Lebleu Bernard , Barrère-Lemaire Stéphanie 
Published: May 2019

Abstract

Aims
Regulated cell death is a main contributor of myocardial ischaemia-reperfusion (IR) injury during acute myocardial infarction. In this context, targeting apoptosis could be a potent therapeutical strategy. In a previous study, we showed that DAXX (death-associated protein) was essential for transducing the FAS-dependent apoptotic signal during IR injury. The present study aims at evaluating the cardioprotective effects of a synthetic peptide inhibiting FAS:DAXX interaction.

Methods and results
An interfering peptide was engineered and then coupled to the Tat cell penetrating peptide (Tat-DAXXp). Its internalization and anti-apoptotic properties were demonstrated in primary cardiomyocytes. Importantly, an intravenous bolus injection of Tat-DAXXp (1 mg/kg) 5 min before reperfusion in a murine myocardial IR model decreased infarct size by 48% after 24 h of reperfusion. In addition, Tat-DAXXp was still efficient after a 30-min delayed administration, and was completely degraded and eliminated within 24 h thereby reducing risks of potential side effects. Importantly, Tat-DAXXp reduced mouse early post-infarction mortality by 67%. Mechanistically, cardioprotection was supported by both anti-apoptotic and pro-survival effects, and an improvement of myocardial functional recovery as evidenced in ex vivo experiments.

Conclusions
Our study demonstrates that a single dose of Tat-DAXXp injected intravenously at the onset of reperfusion leads to a strong cardioprotection in vivo by inhibiting IR injury validating Tat-DAXXp as a promising candidate for therapeutic application.
Supplementary Nutrition of Eucryptorrhynchus brandti (Coleoptera: Curculionidae: Cryptorrhychinae): Effect of Ailanthus altissima Host Tissues on Ovary Maturation and Oviposition
Authors: Guo Wenjuan , Yang Kailang , Zhang Ganyu , Wen Junbao 
Published: May 2019

Abstract
Eucryptorrhynchus brandti is a trunk-boring pest that causes severe damage to its single host, Ailanthus altissima in China. Eucryptorrhynchus brandti adults require supplementary nutrition to achieve sexual maturity. Adults feed on petioles, shoots, 2- to 3-yr-old branches, and stems of A. altissima, but prefer to feed on stems. The effects of different host plant tissues on ovary development and oviposition in E. brandti are unclear. Thus, we examined the effects of the consumption of A. altissima petioles, shoots, branches, and stems on ovary development of E. brandti. Using ovaries of different ages, we also evaluated the differentiation of ovarioles, presence and appearance of follicular relics, number of eggs, cuticle hardness, and fat body quantity over time. We found the reproductive system was composed of two ovaries, lateral oviducts, a common oviduct, and spermatheca. The physiological age of ovaries was divided into three nulliparous and three parous stages. Females fed on stems had mature ovaries and successfully oviposited; females fed on other tree tissues or water had no functional ovaries and did not lay eggs. We found virgin females must obtain sufficient nutrition, as evidenced by the immature ovaries in females fed the water. We also found that only stems of A. altissima contribute to egg development; however, the other tree tissues do not contribute to egg development. These findings improve our understanding of the feeding preference of E. brandti from the perspective of ovary development as well as optimal host tissues for ovary development.
Minimally invasive surgical approaches to left main and left anterior descending coronary artery revascularization are superior compared to first- and second-generation drug-eluting stents: a network meta-analysis
Authors: Indja Ben , Woldendorp Kei , Black Deborah , Bannon Paul G , Wilson Michael K , Vallely Michael P 
Published: May 2019

Abstract

OBJECTIVES
There are a number of minimally invasive approaches to revascularization of coronary artery disease that involve the left main or proximal left anterior descending artery; however, studies to date provide mixed results.

METHODS
A Bayesian network meta-analysis was performed to compare early and late postoperative outcomes between percutaneous coronary intervention with first- and second-generation drug-eluting stents (DESs), off-pump coronary artery bypass and minimally invasive direct coronary artery bypass (MIDCAB) in patients with involvement of left main or left anterior descending disease.

RESULTS
A total of 37 studies with 31 728 patients were included in the analysis. There were no significant differences in early mortality rates, strokes or myocardial infarctions (MIs). The long-term all-cause mortality rate was equivalent between the groups. Patients who had off-pump coronary artery bypass had fewer late MI compared with those who had first-generation DES (DES1) [odds ratio (OR) 0.38, 95% confidence interval (CI) 0.20–0.72] and MIDCAB (OR 0.41, 95% CI 0.17–0.97) and reduced late target vessel revascularization compared with DES1 (OR 0.17, 95% CI 0.09–0.32) and second-generation DES (DES2) (OR 0.32, 95% CI 0.14–0.72). The rate of late major adverse cardiac events was lower with off-pump coronary artery bypass compared with that with DES1 (OR 0.33, 95% CI 0.26–0.43) and DES2 (OR 0.62, 95% CI 0.45–0.90). The rate of late major adverse cardiac events with MIDCAB was lower than that with DES1 (OR 0.43, 95% CI 0.31–0.62) as was that with DES2 compared with DES1 (OR 0.53, 95% CI 0.39–0.70).

CONCLUSIONS
Surgical approaches to left main or proximal left anterior descending disease remain superior to first- or second-generation DES in terms of long-term freedom from MI and target vessel revascularization as well as improved overall long-term survival. Conflicting rates of late MI and target vessel revascularization in patients who underwent MIDCAB suggest disease in alternate vessels that may best be approached via hybrid techniques.