bluuebunny/crossref_metadata_2025_split huggingface dataset:
DASH Diet and Blood Pressure Among Black Americans With and Without CKD: The Jackson Heart Study
Authors: Tyson Crystal C , Davenport Clemontina A , Lin Pao-Hwa , Scialla Julia J , Hall Rasheeda , Diamantidis Clarissa J , Lunyera Joseph , Bhavsar Nrupen , Rebholz Casey M , Pendergast Jane , Boulware L Ebony , Svetkey Laura P 
Published: June 2019

Abstract

BACKGROUND
The Dietary Approaches to Stop Hypertension (DASH) diet lowers blood pressure (BP) more effectively in blacks compared to other US racial subgroups. Considering chronic kidney disease (CKD) raises BP through complex mechanisms, DASH may affect BP differently among blacks with and without CKD. We compared the association of DASH accordance to BP and prevalent hypertension among blacks with and without CKD.

METHODS
Our study involved 3,135 black Americans enrolled in the Jackson Heart Study (2000–2004) with diet and office BP data. Using linear models adjusted for demographics, health behaviors, and clinical factors, we determined the association of a modified DASH score (excluding sodium intake, ranging from 0 to 8 with increasing DASH accordance) with BP. We performed tests for interaction between DASH score and CKD status.

RESULTS
Among participants (mean age: 55 years; hypertension: 60%; CKD: 19%), the median DASH score was similar among participants with and without CKD (1.0 [interquartile range (IQR): 0.5–2] and 1.0 [IQR: 0.5–1.5]). CKD status modified the association of the DASH score with systolic BP (SBP) and diastolic BP (DBP; P interactions were 0.06 and &lt;0.01). Among participants without CKD, SBP and DBP were not associated with the DASH score (−0.4 [95% confidence interval: −1.0, 0.1] mm Hg and −0.1 [−0.4, 0.2] mm Hg per one unit higher DASH score). Among participants with CKD, one unit higher DASH score was associated with lower SBP by 1.6 (0.5, 2.6) mm Hg and lower DBP by 0.9 (0.3, 1.5) mm Hg.

CONCLUSIONS
Despite low DASH scores overall, better DASH accordance was associated with lower BP among Black Americans with CKD.
VI—Should We Believe Philosophical Claims on Testimony?
Authors: Allen Keith 
Published: June 2019

AbstractThis paper considers whether we should believe philosophical claims on the basis of testimony in light of related debates about aesthetic and moral testimony. It is argued that we should not believe philosophical claims on testimony, and different explanations of why we should not are considered. It is suggested that the reason why we should not believe philosophical claims on testimony might be that philosophy is not truth-directed.
VIII—Propositions and Cognitive Relations
Authors: Jones Nicholas K 
Published: June 2019

AbstractThere are two broad approaches to theorizing about ontological categories. Quineans use first-order quantifiers to generalize over entities of each category, whereas type theorists use quantification on variables of different semantic types to generalize over different categories. Does anything of import turn on the difference between these approaches? If so, are there good reasons to go type-theoretic? I argue for positive answers to both questions concerning the category of propositions. I also discuss two prominent arguments for a Quinean conception of propositions, concerning their role in natural language semantics and apparent quantification over propositions within natural language. It will emerge that even if these arguments are sound, there need be no deep question about Quinean propositions’ true nature, contrary to much recent work on the metaphysics of propositions.
SCANVIS: a tool for SCoring, ANnotating and VISualizing splice junctions
Authors: Agius Phaedra , Geiger Heather , Robine Nicolas 
Published: June 2019

Abstract

Motivation
The association of splicing signatures with disease is a leading area of study for prognosis, diagnosis and therapy. We present a novel fast-performing annotation-dependent tool called SCANVIS for scoring and annotating splice junctions (SJs), with an efficient visualization tool that highlights SJ details such as frame-shifts and annotation support for individual samples or a sample cohort.

Results
Using publicly available samples, we show that the tissue specificity inherent in splicing signatures is maintained with the Relative Read Support scoring method in SCANVIS, and we showcase some visualizations to demonstrate the usefulness of incorporating annotation details into sashimi plots.

Availability and implementation
https://github.com/nygenome/SCANVIS and https://bioconductor.org/packages/SCANVIS.

Supplementary information
Supplementary data are available at Bioinformatics online.
Cloud bursting galaxy: federated identity and access management
Authors: Jalili Vahid , Afgan Enis , Taylor James , Goecks Jeremy 
Published: June 2019

Abstract

Motivation
Large biomedical datasets, such as those from genomics and imaging, are increasingly being stored on commercial and institutional cloud computing platforms. This is because cloud-scale computing resources, from robust backup to high-speed data transfer to scalable compute and storage, are needed to make these large datasets usable. However, one challenge for large-scale biomedical data on the cloud is providing secure access, especially when datasets are distributed across platforms. While there are open Web protocols for secure authentication and authorization, these protocols are not in wide use in bioinformatics and are difficult to use for even technologically sophisticated users.

Results
We have developed a generic and extensible approach for securely accessing biomedical datasets distributed across cloud computing platforms. Our approach combines OpenID Connect and OAuth2, best-practice Web protocols for authentication and authorization, together with Galaxy (https://galaxyproject.org), a web-based computational workbench used by thousands of scientists across the world. With our enhanced version of Galaxy, users can access and analyze data distributed across multiple cloud computing providers without any special knowledge of access/authorization protocols. Our approach does not require users to share permanent credentials (e.g. username, password, API key), instead relying on automatically generated temporary tokens that refresh as needed. Our approach is generalizable to most identity providers and cloud computing platforms. To the best of our knowledge, Galaxy is the only computational workbench where users can access biomedical datasets across multiple cloud computing platforms using best-practice Web security approaches and thereby minimize risks of unauthorized data access and credential use.

Availability and implementation
Freely available for academic and commercial use under the open-source Academic Free License (https://opensource.org/licenses/AFL-3.0) from the following Github repositories: https://github.com/galaxyproject/galaxy and https://github.com/galaxyproject/cloudauthz.
Mycorrhiza: genotype assignment using phylogenetic networks
Authors: Georges-Filteau Jeremy , Hamelin Richard C , Blanchette Mathieu 
Published: June 2019

Abstract

Motivation
The genotype assignment problem consists of predicting, from the genotype of an individual, which of a known set of populations it originated from. The problem arises in a variety of contexts, including wildlife forensics, invasive species detection and biodiversity monitoring. Existing approaches perform well under ideal conditions but are sensitive to a variety of common violations of the assumptions they rely on.

Results
In this article, we introduce Mycorrhiza, a machine learning approach for the genotype assignment problem. Our algorithm makes use of phylogenetic networks to engineer features that encode the evolutionary relationships among samples. Those features are then used as input to a Random Forests classifier. The classification accuracy was assessed on multiple published empirical SNP, microsatellite or consensus sequence datasets with wide ranges of size, geographical distribution and population structure and on simulated datasets. It compared favorably against widely used assessment tests or mixture analysis methods such as STRUCTURE and Admixture, and against another machine-learning based approach using principal component analysis for dimensionality reduction. Mycorrhiza yields particularly significant gains on datasets with a large average fixation index (FST) or deviation from the Hardy-Weinberg equilibrium. Moreover, the phylogenetic network approach estimates mixture proportions with good accuracy.

Availability and implementation
Mycorrhiza is released as an easy to use open-source python package at github.com/jgeofil/mycorrhiza.

Supplementary information
Supplementary data are available at Bioinformatics online.
Immunologic Alterations Associated With Oral Delivery of Anti-CD3 (OKT3) Monoclonal Antibodies in Patients With Moderate-to-Severe Ulcerative Colitis
Authors: Boden Elisa K , Canavan James B , Moran Christopher J , McCann Katelyn , Dunn William A , Farraye Francis A , Ananthakrishnan Ashwin N , Yajnik Vijay , Gandhi Roopali , Nguyen Deanna D , Bhan Atul K , Weiner Howard L , Korzenik Joshua R , Snapper Scott B 
Published: June 2019

Abstract

Aim
The aim of this study was to determine the immunologic effects and safety of oral anti-CD3 in patients with ulcerative colitis (UC).

Methods
An open-label pilot study of orally delivered anti-CD3 was performed in patients with moderate-to-severe UC. The primary end points were changes in immunologic parameters and evaluation for safety.

Results
Six subjects received oral OKT3. Biologic effects of oral anti-CD3 included significantly increased proliferation in response to anti-CD3 and anti-inflammatory gene expression profile in peripheral blood mononuclear cells. No serious treatment-related adverse events occurred.

Conclusion
Orally delivered anti-CD3 resulted in immunologic changes in patients with UC.
Foraging Economics of the Hunt Bumble Bee, a Viable Pollinator for Commercial Agriculture
Authors: Baur Abby , Strange James P , Koch Jonathan B 
Published: June 2019

AbstractGlobally, there are only five bumble bee (Hymenoptera: Apidae, Bombus) species that have been successfully commercialized for agriculture. The Hunt bumble bee, Bombus huntii Green, 1860, has been recognized as a suitable pollinator of crops and has a broad distribution in western North America, making it a viable candidate for commercialization. In this study, our goal was to characterize the foraging dynamics of B. huntii female workers under open field conditions. To accomplish this goal, we monitored three B. huntii colonies over an 8-wk period in the summer of 2012 in northern Utah. Using marked bees, we studied the relationship between foraging duration/offloading and pollen/nonvisible pollen collection. In total, we observed 921 foraging events across all three colonies. Of our observations, 82% (n = 756) were foraging events that included both a departure and arrival time observation. Average duration of pollen and nonpollen (i.e., nectar) trips across foragers is 41.86 ± 5.65 min (±SE) and 32.18 ± 5.89 min, respectively. Workers spent a significantly longer time offloading pollen in the nest after a foraging trip relative to workers without pollen present on their corbicula. Pollen foraging rate increases over the course of the day, likely due to the time it takes to learn how to forage on a diverse array of flower morphologies. Our study provides data on how long it takes for B. huntii to forage in open field conditions and will be useful when comparing foraging rates in controlled crop systems.
Machine learning in agricultural and applied economics
Authors: Storm Hugo , Baylis Kathy , Heckelei Thomas 
Published: June 2019

AbstractThis review presents machine learning (ML) approaches from an applied economist’s perspective. We first introduce the key ML methods drawing connections to econometric practice. We then identify current limitations of the econometric and simulation model toolbox in applied economics and explore potential solutions afforded by ML. We dive into cases such as inflexible functional forms, unstructured data sources and large numbers of explanatory variables in both prediction and causal analysis, and highlight the challenges of complex simulation models. Finally, we argue that economists have a vital role in addressing the shortcomings of ML when used for quantitative economic analysis.
Productivity and Cost of Processors in Whole-Tree Harvesting Systems in Southern Pine Stands
Authors: Conrad Joseph L , Dahlen Joseph 
Published: June 2019

AbstractLogging businesses in the US South have not adopted cut-to-length harvesting systems. Adding dangle head processors on the landing of whole-tree harvesting systems may allow southern loggers to achieve some of the advantages of cut-to-length systems (i.e., precise length and diameter measurements) while maintaining high productivity and low costs per ton characteristic of current whole-tree systems. We conducted a designed study of conventional (i.e., feller-buncher, grapple skidder, loader) and processor (i.e., feller-buncher, grapple skidder, processor, loader) systems. Four harvest sites were split, with half of each site harvested by a conventional system and the other half by a processor system. Harvesting productivity was estimated using time-and-motion studies, and costs were estimated using the machine rate method. Cut-and-load costs averaged US$13.57 and US$14.67 ton–1 on the processor and conventional harvests, respectively (P > .10). Cost per ton was elevated on several conventional harvest tracts because of long skidding distances, indicating harvest planning is more important than harvesting system in determining harvesting costs. Processing and loading costs were US$1.70 ton–1 higher on processor harvests, which, combined with restrictive mill quotas being more problematic for processor crews, suggests loggers will require a logging rate premium in order to invest in processors.
The Effects of Neighborhood Built Environment on Walking for Leisure and for Purpose Among Older People
Authors: Christman Zachary J , Wilson-Genderson Maureen , Heid Allison , Pruchno Rachel 
Published: June 2019

Abstract

Background and Objectives
Characteristics of a neighborhood’s built environment affect the walking behavior of older people, yet studies typically rely on small nonrepresentative samples that use either subjective reports or aggregate indicators from administrative sources to represent neighborhood characteristics. Our analyses examine the usefulness of a novel method for observing neighborhoods—virtual observations—and assess the extent to which virtual-based observations predict walking among older adults.

Research Design and Methods
Using Google Street View, we observed the neighborhoods of 2,224 older people and examined how characteristics of the neighborhood built environments are associated with the amount of time older people spend walking for leisure and purpose.

Results
Multilevel model analyses revealed that sidewalk characteristics had significant associations with both walking for purpose and leisure. Land use, including the presence of multifamily dwellings, commercial businesses, and parking lots were positively associated with walking for purpose and single-family detached homes were negatively associated with walking for purpose, but none of these characteristics were associated with leisure walking. Gardens/flowers were associated with walking for leisure but not purpose. Garbage/litter was not associated with either type of walking behavior.

Discussion and Implications
Virtual observations are a useful method that provides meaningful information about neighborhoods. Findings demonstrate how neighborhood characteristics assessed virtually differentially impact walking for leisure and purpose among older adults and are interpreted within a social-ecological model.
Damage-Fitness Model: Evaluation and synthesis
Authors: Wada Haruka , Heidinger Britt 
Published: June 2019

AbstractDecades of research into stress responses have highlighted large variation among individuals, populations, and species, and the sources of this variation have been a center of research across disciplines. The most common measure of the vertebrate stress response is glucocorticoids. However, the predictive power of glucocorticoid responses to fitness is surprisingly low. This is partly because the hormone levels rapidly change in response to stressor exposure and elevated levels at one time point can indicate either that glucocorticoids are helping the organism cope with the stressor or that dysregulation of hormone release is harming the organism. Meaning, the fitness consequences of the stressor depends on how efficient the stress responses are at negating the harmful impacts of stressors to cells and tissues. To encompass the idea of the efficiency of stress responses and to integrate cellular and organismal stress responses, a new theoretical model called the Damage-Fitness Model was developed. The model focuses on the downstream effects of stress responses and predicts that the accumulation of damage in cells and tissues (e.g., persistent damage to proteins, lipids, and DNA) negatively impacts fitness components. In this mini-review, we examine evidence supporting the Damage-Fitness Model and explore new directions forward.
The Structure of the Grothendieck Rings of Wreath Product Deligne Categories and their Generalisations
Authors: Ryba Christopher 
Published: June 2019

AbstractGiven a tensor category $\mathcal{C}$ over an algebraically closed field of characteristic zero, we may form the wreath product category $\mathcal{W}_n(\mathcal{C})$. It was shown in [10] that the Grothendieck rings of these wreath product categories stabilise in some sense as $n \to \infty $. The resulting “limit” ring, $\mathcal{G}_\infty ^{\mathbb{Z}}(\mathcal{C})$, is isomorphic to the Grothendieck ring of the wreath product Deligne category $S_t(\mathcal{C})$ as defined by [9] (although it is also related to $FI_G$-modules). This ring only depends on the Grothendieck ring $\mathcal{G}(\mathcal{C})$. Given a ring $R$ that is free as a $\mathbb{Z}$-module, we construct a ring $\mathcal{G}_\infty ^{\mathbb{Z}}(R)$ that specialises to $\mathcal{G}_\infty ^{\mathbb{Z}}(\mathcal{C})$ when $R = \mathcal{G}(\mathcal{C})$. We give a description of $\mathcal{G}_\infty ^{\mathbb{Z}}(R)$ using generators very similar to the basic hooks of [5]. We also show that $\mathcal{G}_\infty ^{\mathbb{Z}}(R)$ is a $\lambda $-ring wherever $R$ is and that $\mathcal{G}_\infty ^{\mathbb{Z}}(R)$ is (unconditionally) a Hopf algebra. Finally, we show that $\mathcal{G}_\infty ^{\mathbb{Z}}(R)$ is isomorphic to the Hopf algebra of distributions on the formal neighbourhood of the identity in $(W\otimes _{\mathbb{Z}} R)^\times $, where $W$ is the ring of Big Witt Vectors.
Production and characterization of monoclonal antibodies against the DNA binding domain of the RE1-silencing transcription factor
Authors: Cortés-Sarabia Karen , Medina-Flores Yolanda , Alarcón-Romero Luz Del Carmen , Mata-Ruíz Olga , Vences-Velázquez Amalia , Rodríguez-Ruíz Hugo Alberto , Valdés Jesús , Ortuño-Pineda Carlos 
Published: June 2019

AbstractThe use of monoclonal antibodies for the detection of cellular biomarkers during carcinogenesis provides new strategies for cancer diagnosis or prognosis in patients. Loss of the Restrictive Element 1-Silencing Transcription (REST) factor has been observed in previous molecular and immunological approaches in aggressive breast cancer, small cell lung cancer, liver carcinoma, and colo-rectal cancer; however, for clinic diagnosis, monoclonal antibodies for REST recognition are unavailable. The goal of this work was to design, produce and characterize monoclonal antibodies against the REST DNA binding damain (DBD) that would be suitable for immunoassays. We searched for conserved domains, and immunogenic and antigenic sites in the REST structure via in silico analysis. For mice immunization, we used a recombinant REST DBD purified by affinity chromatography, and then Hybridomas were generated by mouse spleen fusion with myeloma cells. Finally, for monoclonal antibody characterization, we performed enzyme-linked immunosorbent (ELISA), western blot, dot blot, immunocytochemistry (ICC) and immunoprecipitation assays. Results showed that the DBD is conserved in REST isoforms and contains immunogenic and antigenic sites. We generated three clones producing monoclonal antibodies against REST DBD, one of them specifically recognized native REST and was suitable for ICC in samples from patients.
Recent Developments in the Case-Law of the ECtHR on the Right to a Fair Trial in Competition Proceedings
Authors: Berghe Pascal 
Published: June 2019

Abstract
Judgment of 23 October 2018, Produkcija Plus Storitveno Podjetje v Slovenia, Application No 47072/15
Judgment of 14 February 2019, SA-Capital v Finland, Application No 5556/10
Dynamics of Apis cerana Sacbrood Virus (AcSBV) Prevalence in Apis cerana (Hymenoptera: Apidae) in Northern Taiwan and Demonstration of its Infection in Apis mellifera (Hymenoptera: Apidae)
Authors: Ko Chong-Yu , Chiang Zong-Lin , Liao Ruo-Jyun , Chang Zih-Ting , Chang Ju-Chun , Kuo Tsun-Yung , Chen Yue-Wen , Nai Yu-Shin 
Published: June 2019

AbstractSince 2016, Apis cerana sacbrood virus (AcSBV) has been recorded in Taiwan. It is epizootic in Apis cerana (Hymenoptera: Apidae) and causing serious loss of A. cerana. Herein, we performed a long-term survey of AcSBV prevalence in the populations of A. cerana in Northern Taiwan from January 2017 to July 2018. The surveillance of AcSBV prevalence in A. mellifera (Hymenoptera: Apidae) populations was starting and further confirmed by sequencing since April 2017; thus, these data were also included in this survey. In our survey, the average prevalence rates of AcSBV were 72 and 53% in A. cerana and A. mellifera, respectively, in 2017, which decreased to 45 and 27% in 2018. For the spatial analysis of AcSBV in two honey bee populations, Hsinchu showed the highest prevalence, followed by New Taipei, Yilan, Taipei, and Keelung, suggesting that AcSBV might have come from the southern part of Taiwan. Interestingly, the AcSBV prevalence rates from A. cerana and A. mellifera cocultured apiaries gradually synchronized. The result of phylogenetic analysis and comparison of the annual AcSBV prevalence in A. cerana-only, A. mellifera-only, and A. cerana/A. mellifera cocultured sample sites indicate cross-infection between A. cerana and A. mellifera; however, AcSBV may lose the advantage of virulence in A. mellifera. The evidence suggested that the transmission of AcSBV might occur among these two honey bee species in the field. Therefore, A. mellifera may serve as a guard species to monitor AcSBV in A. cerana, but the cross-infection still needs to be surveyed.