bluuebunny/crossref_metadata_2025_split huggingface dataset:
Principles and Issues for Physical Frailty Measurement and Its Clinical Application
Authors: Bandeen-Roche Karen , Gross Alden L , Varadhan Ravi , Buta Brian , Carlson Michelle C , Huisingh-Scheetz Megan , Mcadams-Demarco Mara , Piggott Damani A , Brown Todd T , Hasan Rani K , Kalyani Rita R , Seplaki Christopher L , Walston Jeremy D , Xue Qian-Li 
Published: July 2019

Abstract

Introduction
“Frailty” has attracted attention for its promise of identifying vulnerable older adults, hence its potential use to better tailor geriatric health care. There remains substantial controversy, however, regarding its nature and ascertainment. Recent years have seen a proliferation of frailty assessment methods. We argue that the development of frailty assessments should be grounded in “validation”—the process of substantiating that a measurement accurately and precisely measures what it intends, identify unresolved measurement issues, and highlight measurement-related considerations for clinical practice.

Methods
Principles for validating frailty measures are elucidated. We follow principles—articulated, for example, by Borsboom—in which a construct must be clearly defined and then analyses undertaken to substantiate that a measurement accurately and precisely measures what it intends. Key elements are content validity, criterion validity, and construct validity, with an emphasis on the latter.

Results
We illustrate the principles for a physical frailty phenotype construct.

Conclusions
Unresolved conceptual issues include the roles of intersecting concepts such as cognition, disease severity, and disability in frailty measurement, conceptualization of frailty as a state versus a continuum, and the potential need for dynamic measures and systems concepts in furthering understanding of frailty. Clinical considerations include needs to distinguish interventions designed to address frailty “symptoms” versus underlying physiology, improve “prefrailty” measures intended to screen individuals early in their frailty progression, address feasibility demands, and further visioning followed by rigorous efficacy research to address the landscape of potential uses of frailty assessment in clinical practice.
OMMA enables population-scale analysis of complex genomic features and phylogenomic relationships from nanochannel-based optical maps
Authors: Leung Alden King-Yung , Liu Melissa Chun-Jiao , Li Le , Lai Yvonne Yuk-Yin , Chu Catherine , Kwok Pui-Yan , Ho Pak-Leung , Yip Kevin Y , Chan Ting-Fung 
Published: July 2019

Abstract

Background
Optical mapping is an emerging technology that complements sequencing-based methods in genome analysis. It is widely used in improving genome assemblies and detecting structural variations by providing information over much longer (up to 1 Mb) reads. Current standards in optical mapping analysis involve assembling optical maps into contigs and aligning them to a reference, which is limited to pairwise comparison and becomes bias-prone when analyzing multiple samples.

Findings
We present a new method, OMMA, that extends optical mapping to the study of complex genomic features by simultaneously interrogating optical maps across many samples in a reference-independent manner. OMMA captures and characterizes complex genomic features, e.g., multiple haplotypes, copy number variations, and subtelomeric structures when applied to 154 human samples across the 26 populations sequenced in the 1000 Genomes Project. For small genomes such as pathogenic bacteria, OMMA accurately reconstructs the phylogenomic relationships and identifies functional elements across 21 Acinetobacter baumannii strains.

Conclusions
With the increasing data throughput of optical mapping system, the use of this technology in comparative genome analysis across many samples will become feasible. OMMA is a timely solution that can address such computational need. The OMMA software is available at https://github.com/TF-Chan-Lab/OMTools.
A probabilistic multi-omics data matching method for detecting sample errors in integrative analysis
Authors: Lee Eunjee , Yoo Seungyeul , Wang Wenhui , Tu Zhidong , Zhu Jun 
Published: July 2019

Abstract

Background
Data errors, including sample swapping and mis-labeling, are inevitable in the process of large-scale omics data generation. Data errors need to be identified and corrected before integrative data analyses where different types of data are merged on the basis of the annotated labels. Data with labeling errors dampen true biological signals. More importantly, data analysis with sample errors could lead to wrong scientific conclusions. We developed a robust probabilistic multi-omics data matching procedure, proMODMatcher, to curate data and identify and correct data annotation and errors in large databases.

Results
Application to simulated datasets suggests that proMODMatcher achieved robust statistical power even when the number of cis-associations was small and/or the number of samples was large. Application of our proMODMatcher to multi-omics datasets in The Cancer Genome Atlas and International Cancer Genome Consortium identified sample errors in multiple cancer datasets. Our procedure was not only able to identify sample-labeling errors but also to unambiguously identify the source of the errors. Our results demonstrate that these errors should be identified and corrected before integrative analysis.

Conclusions
Our results indicate that sample-labeling errors were common in large multi-omics datasets. These errors should be corrected before integrative analysis.
The Evolution of Color Pattern in Butterflyfishes (Chaetodontidae)
Authors: Alfaro Michael E , Karan Elizabeth A , Schwartz Shawn T , Shultz Allison J 
Published: July 2019

Abstract
Coral reef fishes constitute one of the most diverse assemblages of vertebrates on the planet. Color patterns are known to serve a number of functions including intra- and inter-specific signaling, camouflage, mimicry, and defense. However, the relative importance of these and other factors in shaping color pattern evolution is poorly understood. Here we conduct a comparative phylogenetic analysis of color pattern evolution in the butterflyfishes (Chaetodontidae). Using recently developed tools for quantifying color pattern geometry as well as machine learning approaches, we investigate the tempo of evolution of color pattern elements and test whether ecological variables relating to defense, depth, and social behavior predict color pattern evolution. Butterflyfishes exhibit high diversity in measures of chromatic conspicuousness and the degrees of fine versus gross scale color patterning. Surprisingly, most diversity in color pattern was not predicted by any of the measures of ecology in our study, although we did find a significant but weak relationship between the level of fine scale patterning and some aspects of defensive morphology. We find that the tempo of color pattern diversification in butterflyfishes has increased toward the present and suggest that rapid evolution, presumably in response to evolutionary pressures surrounding speciation and lineage divergence, has effectively decoupled color pattern geometry from some aspects of ecology. Machine learning classification of color pattern appears to rely on a set of features that are weakly correlated with current color pattern geometry descriptors, but that may be better suited for the detection of discrete components of color pattern. A key challenge for future studies lies in determining whether rapid evolution has generally decoupled color patterns from ecology, or whether convergence in function produces convergence in color pattern at phylogenetic scales.
The enigmatic Cyclida (Pancrustacea): morphological terminology and family-level classification
Authors: Feldmann Rodney M , Schweitzer Carrie E 
Published: July 2019

Abstract
The Cyclida comprise six families embracing 55 species in 17 genera. Diagnoses for each family based upon examination of type and referred material as well as photographs of specimens previously known only from drawings has confirmed that four of the families, Cyclidae Packard, 1885; Americlidae Dzik, 2008; Halicynidae Gall & Grauvogel, 1967; and Schraminidae Dzik, 2008, form a unified group morphologically whereas Alsasuacaridae van Bakel, Jagt, Fraaije & Artal, 2011, and Hemitrochiscidae Trauth, 1918 are morphological outliers. Each of the families is documented by illustrations of type or representative genera and species. To assure accurate and uniform comparisons of taxa, a morphological terminology is presented, recognizing synonymous terms that could potentially obscure evaluation of relationships. This provides a framework for future analysis of membership within each family and for phylogenetic analyses.
The Corn–Cotton Agroecosystem in the Mid-Southern United States: What Insecticidal Event Pyramids Should be Used in Each Crop to Extend Vip3A Durability
Authors: Caprio Michael A , Kurtz Ryan , Catchot Angus , Kerns David , Reisig Dominic , Gore Jeff , Reay-Jones Francis P F 
Published: July 2019

AbstractRecent studies suggest that resistance in Helicoverpa zea (Boddie) (Lepidoptera, Noctuidae) to Cry1A(b/c) and Cry2Ab2 toxins from the bacterium Bacillus thuringiensis Berliner (Bacillales: Bacillaceae) has increased and field efficacy is impacted in transgenic corn and cotton expressing these toxins. A third toxin, Vip3A, is available in pyramids expressing two or more Bt toxins in corn hybrids and cotton varieties, but uncertainty exists regarding deployment strategies. During a growing season, H. zea infests corn and cotton, and debate arises over use of Vip3A toxin in corn where H. zea is not an economic pest. We used a three-locus, spatially explicit simulation model to evaluate when using Vip3A in corn might hasten evolution of resistance to Vip3A, with implications in cotton where H. zea is a key pest. When using a conventional refuge in corn and initial resistance allele frequencies of Cry1A and Cry2A were 10%, transforming corn with Vip3A slowed resistance to these toxins and delayed resistance evolution to the three-toxin pyramid as a whole. When Cry resistance allele frequencies exceeded 30%, transforming corn with Vip3A hastened the evolution of resistance to the three-toxin pyramid in cotton. When using a seed blend refuge strategy, resistance was delayed longest when Vip3A was not incorporated into corn and used only in cotton. Simulations of conventional refuges were generally more durable than seed blends, even when 75% of the required refuge was not planted. Extended durability of conventional refuges compared to other models of resistance evolution are discussed as well as causes for unusual survivorship in seed blends.
The Practitioner’s Bookshelf: Tenth Anniversary Recommendations
Authors: Loeffler James , Weisbord Noah , Phillips Brian 
Published: July 2019

Abstract
With this tenth anniversary issue of the Journal of Human Rights Practice, we are launching ‘The Practitioner’s Bookshelf’—a new feature of the JHRP Review section containing brief reviews of recent publications of particular interest to human rights practitioners. In this instalment, James Loeffler (University of Virginia), Noah Weisbord (Queen’s University, Canada), and Brian Phillips (JHRP) discuss three books they consider to be among the most significant contributions to the literature of human rights practice to have appeared during the JHRP’s first decade.
Are We Living in an Era of Nihilism? Jean-Luc Marion and Reading the Signs of the Times
Authors: Benjamins Jacob 
Published: July 2019

Abstract
This article critiques Jean-Luc Marion’s understanding of nihilism based on its inconsistency with his own theological convictions. It contextualises Marion’s account of nihilism within his relatively precise theological and philosophical critique of the modern subject. Then, it identifies how he broadens his philosophical account by relating it to an interpretation of culture. Finally, the article argues that Marion overextends the applicability of the concept in a way that is inconsistent with his overall theological position and further nuance is needed in order to read the signs of the times.
OGLE-2017-BLG-1186: first application of asteroseismology and Gaussian processes to microlensing
Authors: Li S-S , Zang W , Udalski A , Shvartzvald Y , Huber D , Lee C-U , Sumi T , Gould A , Mao S , Fouqué P , Wang T , Dong S , Jørgensen U G , Cole A , Mróz P , Szymański M K , Skowron J , Poleski R , Soszyński I , Pietrukowicz P , Kozłowski S , Ulaczyk K , Rybicki K A , Iwanek P , Yee J C , Calchi Novati S , Beichman C A , Bryden G , Carey S , Gaudi B S , Henderson C B , Zhu W , Albrow M D , Chung S-J , Han C , Hwang K-H , Jung Y K , Ryu Y-H , Shin I-G , Cha S-M , Kim D-J , Kim H-W , Kim S-L , Lee D-J , Lee Y , Park B-G , Pogge R W , Bond I A , Abe F , Barry R , Bennett D P , Bhattacharya A , Donachie M , Fukui A , Hirao Y , Itow Y , Kondo I , Koshimoto N , Li M C A , Matsubara Y , Muraki Y , Miyazaki S , Nagakane M , Ranc C , Rattenbury N J , Suematsu H , Sullivan D J , Suzuki D , Tristram P J , Yonehara A , Christie G , Drummond J , Green J , Hennerley S , Natusch T , Porritt I , Bachelet E , Maoz D , Street R A , Tsapras Y , Bozza V , Dominik M , Hundertmark M , Peixinho N , Sajadian S , Burgdorf M J , Evans D F , Figuera Jaimes R , Fujii Y I , Haikala L K , Helling C , Henning T , Hinse T C , Mancini L , Longa-Peña P , Rahvar S , Rabus M , Skottfelt J , Snodgrass C , Southworth J , Unda-Sanzana E , von Essen C , Beaulieu J-P , Blackman J , Hill K 
Published: July 2019

AbstractWe present the analysis of the event OGLE-2017-BLG-1186 from the 2017 Spitzer microlensing campaign. This is a remarkable microlensing event because its source is photometrically bright and variable, which makes it possible to perform an asteroseismic analysis using ground-based data. We find that the source star is an oscillating red giant with average time-scale of ∼9 d. The asteroseismic analysis also provides us source properties including the source angular size (∼27 $\mu$as) and distance (∼11.5 kpc), which are essential for inferring the properties of the lens. When fitting the light curve, we test the feasibility of Gaussian processes (GPs) in handling the correlated noise caused by the variable source. We find that the parameters from the GP model are generally more loosely constrained than those from the traditional χ2 minimization method. We note that this event is the first microlensing system for which asteroseismology and GPs have been used to account for the variable source. With both finite-source effect and microlens parallax measured, we find that the lens is likely a ∼0.045 M⊙ brown dwarf at distance ∼9.0 kpc, or a ∼0.073 M⊙ ultracool dwarf at distance ∼9.8 kpc. Combining the estimated lens properties with a Bayesian analysis using a Galactic model, we find a $\sim 35{{\ \rm per\ cent}}$ probability for the lens to be a bulge object and $\sim 65{{\ \rm per\ cent}}$ to be a background disc object.
Constraints on the formation of brown dwarfs by turbulent compression
Authors: Stamer Torsten , Inutsuka Shu-ichiro 
Published: July 2019

ABSTRACT
We perform radiation hydrodynamical simulations in spherical symmetry in order to investigate the formation of very low mass objects, i.e. brown dwarfs, by external compression. According to the Jeans stability criterion, a very low mass molecular cloud core must reach a very high density in order to become gravitationally unstable. One possibility to create such a high density is the compression by turbulent flows within the larger molecular cloud. Using our self-developed radiation hydrodynamics code, we aim to test the validity of this scenario, and to constrain the strength of the turbulence that is needed. We find that the probability for sufficiently strong and long-lived turbulence is very low under typical conditions even when using very optimistic assumptions, and therefore conclude that turbulent compression is unlikely to be the dominant mechanism for creating brown dwarfs. We also investigate the properties of objects formed by this turbulent compression process. Specifically, we compare the lifetime of the first core stage for the cases with and without external compression. We confirm our previous findings that the first core lifetime increases by about an order of magnitude at the extremely low-mass end, but this increase is somewhat less dramatic and occurs at even lower masses than in our previous work, in which no external compression was present.
Revisiting the Fanaroff–Riley dichotomy and radio-galaxy morphology with the LOFAR Two-Metre Sky Survey (LoTSS)
Authors: Mingo B , Croston J H , Hardcastle M J , Best P N , Duncan K J , Morganti R , Rottgering H J A , Sabater J , Shimwell T W , Williams W L , Brienza M , Gurkan G , Mahatma V H , Morabito L K , Prandoni I , Bondi M , Ineson J , Mooney S 
Published: July 2019

Abstract
The relative positions of the high and low surface brightness regions of radio-loud active galaxies in the 3CR sample were found by Fanaroff and Riley to be correlated with their luminosity. We revisit this canonical relationship with a sample of 5805 extended radio-loud active galactic nuclei (AGN) from the LOFAR Two-Metre Sky Survey (LoTSS), compiling the most complete data set of radio-galaxy morphological information obtained to date. We demonstrate that, for this sample, radio luminosity does not reliably predict whether a source is edge-brightened (FRII) or centre-brightened (FRI). We highlight a large population of low-luminosity FRIIs, extending three orders of magnitude below the traditional FR break, and demonstrate that their host galaxies are on average systematically fainter than those of high-luminosity FRIIs and of FRIs matched in luminosity. This result supports the jet power/environment paradigm for the FR break: low-power jets may remain undisrupted and form hotspots in lower mass hosts. We also find substantial populations that appear physically distinct from the traditional FR classes, including candidate restarting sources and ‘hybrids’. We identify 459 bent-tailed sources, which we find to have a significantly higher SDSS cluster association fraction (at z &lt; 0.4) than the general radio-galaxy population, similar to the results of previous work. The complexity of the LoTSS faint, extended radio sources not only demonstrates the need for caution in the automated classification and interpretation of extended sources in modern radio surveys, but also reveals the wealth of morphological information such surveys will provide and its value for advancing our physical understanding of radio-loud AGN.
Testing general relativity with the Doppler magnification effect
Authors: Andrianomena Sambatra , Bonvin Camille , Bacon David , Bull Philip , Clarkson Chris , Maartens Roy , Moloi Teboho 
Published: July 2019

ABSTRACT
The apparent sizes and brightnesses of galaxies are correlated in a dipolar pattern around matter overdensities in redshift space, appearing larger on their near side and smaller on their far side. The opposite effect occurs for galaxies around an underdense region. These patterns of apparent magnification induce dipole and higher multipole terms in the cross-correlation of galaxy number density fluctuations with galaxy size/brightness (which is sensitive to the convergence field). This provides a means of directly measuring peculiar velocity statistics at low and intermediate redshift, with several advantages for performing cosmological tests of general relativity (GR). In particular, it does not depend on empirically calibrated scaling relations like the Tully–Fisher and Fundamental Plane methods. We show that the next generation of spectroscopic galaxy redshift surveys will be able to measure the Doppler magnification effect with sufficient signal-to-noise ratio to test GR on large scales. We illustrate this with forecasts for the constraints that can be achieved on parametrized deviations from GR for forthcoming low-redshift galaxy surveys with DESI and SKA2. Although the cross-correlation statistic considered has a lower signal-to-noise ratio than RSD, it will be a useful probe of GR since it is sensitive to different systematics.
Perceived Pain and Smoking Interrelations and Expectancies Are Associated With Pain and Smoking Cessation in Individuals With Mobility Impairments
Authors: Endrighi Romano , Rueras Nicolle , Dunsiger Shira I , Borrelli Belinda 
Published: July 2019

Abstract

Introduction
Smoking and pain are highly prevalent among individuals with mobility impairments (MIs; use assistive devices to ambulate). The role of pain-related smoking motives and expectancies in smoking cessation is unknown. We examined cross-sectional and prospective associations between a novel measure of pain-related smoking motives (how smokers with pain perceive their pain and smoking to be interrelated) and pain and smoking behavior in smokers with MI.

Methods
This is a secondary data analysis of a smoking cessation induction trial (N = 263; 55% female) in smokers with MI. Participants did not have to want to quit to enroll. Pain-related smoking motives and expectancies were assessed at baseline with the pain and smoking inventory (PSI) which measures perceived pain and smoking interrelations in three distinct but related domains (smoking to cope with pain, pain as a motivator of smoking and as a barrier to cessation). Other measures included pain occurrence and interference, nicotine dependence, motivation and self-efficacy to quit smoking, and number of cigarettes per day. Biochemically verified smoking abstinence was assessed at 6 months.

Results
PSI scores were significantly higher among smokers with chronic pain occurrence compared to occasional and to no occurrence (p &lt; .002) and were associated with greater pain interference (ps &lt; .01) and lower self-efficacy to quit smoking (ps &lt; .01). In prospective analyses adjusted for age, treatment group, and chronic pain, only expectancies of smoking to help cope with pain predicted lower odds of abstinence.

Conclusions
Targeting expectancies of smoking as a mechanism to cope with pain may be useful in increasing smoking cessation in pain populations.

Implications
Individuals with MI have a high prevalence of smoking and pain, yet the extent to which this population perceives pain and smoking to be interrelated is unknown. This is the first article to examine prospective associations between a novel measure of perceived pain and smoking interrelations (PSI) and smoking outcomes. The PSI was associated with greater pain and lower self-efficacy for quitting. Prospectively, the PSI subscale tapping into expectancies that smoking help coping with pain predicted a lower probability of smoking abstinence. In smokers with MI, expectancies of smoking as pain-coping mechanism may be an important clinical target.