bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence of local adaptation and stabilizing selection on quantitative traits in populations of the multipurpose American species Acacia aroma (Fabaceae)
Authors: Pometti Carolina L , Bessega Cecilia F , Cialdella Ana M , Ewens Mauricio , Saidman Beatriz O , Vilardi Juan C 
Published: May 2019

Abstract
Economically and ecologically important quantitative traits of Acacia aroma are related to life history and the size and shape of fruits and leaves. Substantial variation is observed for these traits in natural populations, suggesting a possible genetic basis that could be useful for selection programmes. Our objective was to detect signals of selection on 12 phenotypic traits in 170 individuals belonging to seven populations of A. aroma in the Chaco Region of Argentina. Phenotypic traits were compared with molecular markers assessed in the same populations. Here, we search for signatures of natural selection by comparing quantitative trait variation to neutral genetic variation through the PST–FST test. We further test for differences among populations for the 12 phenotypic traits, an association of phenotypic variation with environmental variables and geographical distance, and we compare the power of discrimination between the phenotypic and AFLP datasets. The PST–FST test suggested directional selection for tree height and stabilizing selection for the remaining traits. Analyses of variance showed significant differentiation for eight phenotypic traits. These results suggest selecting among provenances as a management strategy to improve tree height (which showed divergent selection), whereas significant genetic gain for the other traits might be obtained by selection within provenances.
Institutional barriers and enablers to implementing and complying with internationally accepted quality standards in the local pharmaceutical industry of Pakistan: a qualitative study
Authors: Tauqeer Fatima , Myhr Kirsten , Gopinathan Unni 
Published: May 2019

Abstract
Complying with good manufacturing practices (GMP) and ensuring a quality system is integral to production and supply of quality medicines and achieving universal health coverage. This study focus on the local production of medicines in Pakistan, a lower middle-income country that has observed considerable growth in the number of pharmaceutical companies over the past two decades. Against this background, we investigated: (1) How is quality assurance (QA) and GMP compliance understood and acted upon by local pharmaceutical manufacturers?; (2) What are the institutional barriers and enablers for QA and GMP compliance in the local pharmaceutical sector from the perspective of key stakeholders?; and (3) What are the institutional barriers and enablers for strengthening local regulatory capacity to improve QA in the industry in the long term? We used a qualitative study design involving 22 interviews of the drug regulatory bodies (n = 9), academia (n = 3) and local manufacturers (n = 10), identifying key themes in data by thematic analysis. Document analysis was used to collect additional information and supplement the interview data. We identified that manufacturing facilities operated under different GMP standards and interpretations, pointing towards an absence of harmonization in quality standards across the industry. Views diverged about the status of GMP compliance, with interviewees from academia presenting a more critical view compared with regulators who promoted a more positive story. Among the barriers explaining why companies struggled with quality standards, the lack of a mindset promoting quality and safety among profit-oriented manufacturers was prominent. At the federal level, DRAP’s establishment represented an institutional improvement aiming to promote QA through inspections and guidance. While some positive measures to promote quality have been observed, the need for DRAP to strengthen its technical and regulatory capacity, enhance its engagement in international collaboration and learning, and improve transparency and accountability were highlighted. Overall, since the challenges in Pakistan are shared with other low- and middle-income countries with local production, there is a need to commit to international collaborative mechanisms, such as those lead by WHO, on this issue.
Not As Clear As It May Appear: Challenges Associated with Transparent Camouflage in the Ocean
Authors: Bagge Laura E 
Published: May 2019

Abstract
The “superpower” of invisibility is a reality and a necessity for many animals that live in featureless environments like the open ocean, where there is nowhere to hide. How do animals achieve invisibility? Many animals match their color patterns to their background, but this strategy is limited when the background scene is dynamic. Transparency allows organisms to match any background all the time. However, it is challenging for an organism to maintain transparency across its entire body volume. To be transparent, tissues must minimize light scattering, both at the surface and within. Until recently, it has been unclear how clear animals with complex bodies (such as many crustaceans with hard cuticles, thick muscles, and other internal organs) minimize such light scattering. This is especially challenging in an environment where light can come from many directions: reflections from downwelling sunlight and bioluminescent searchlights from predators. This review summarizes several recent discoveries of multiple unique adaptations for minimizing light scattering both on the exterior cuticle surface and throughout the body volume of transparent crustaceans, as well as the potential tradeoffs and challenges associated with transparent camouflage.
Words Matter: How WTO Rulings Handle Controversy
Authors: Busch Marc L , Pelc Krzysztof J 
Published: May 2019

AbstractThe rulings of internationals courts are often reduced to “who won?,” but much more is at stake. Like other institutions, the World Trade Organization (WTO) offers rulings that balance legal discipline against political constraints. We argue that one way in which the WTO handles politically sensitive issues is by increasing the amount of affect in their rulings. In doing so, judges provide national governments with discursive resources to persuade their domestic audiences of the legitimacy of compliance. To test our expectations, we conduct a text analysis of all rulings rendered by the institution since 1995. Specifically, we find that more politically charged decisions, such as the ones concerning nonfiscal rather than fiscal aspects of national treatment claims, are explained in qualitatively different terms. We also find that, as an issue gets ruled on repeatedly, the amount of affect deployed progressively decreases. In sum, the WTO chooses its words strategically to persuade litigants, and their domestic audiences, of the legitimacy of compliance in politically fraught disputes.
Identifying current and emerging resources and tools utilized for detection, prediction, and visualization of viral zoonotic disease clusters: a Delphi study
Authors: Beard Rachel , Scotch Matthew 
Published: May 2019

Abstract
Zoonotic disease surveillance presents a substantial problem in the management of public health. Globally, zoonoses have the potential to spread and negatively impact population health economic growth, and security. This research was conducted to investigate the current data sources, analytical methods, and limitations for cluster detection and prediction with particular interest in emerging bioinformatics tools and resources to inform the development of zoonotic surveillance spatial decision support systems. We recruited 10 local health personnel to participate in a Delphi study. Participants agreed cluster detection is a priority, though mathematical modeling methods and bioinformatics resources are not commonly used toward this endeavor. However, participants indicated a desire to utilize preventative measures. We identified many limitations for identifying clusters including software availability, appropriateness, training, and usage of emerging genetic data. Future decision support system development should focus on state health personnel priorities and tasks to better utilize emerging developments and available data.
Substituting corn silage with reconstituted forage or nonforage fiber sources in the starter diets of Holstein calves: effects on performance, ruminal fermentation, and blood metabolites
Authors: Kargar Shahryar , Kanani Meysam , Albenzio Marzia , Caroprese Mariangela 
Published: May 2019

Abstract
We examined the effects of replacing corn silage (CS) with reconstituted alfalfa hay (AH) or beet pulp (BP) in the starter diet on the nutrient intake and digestibility, growth performance, rumen fermentation characteristics, selected blood metabolites, and health status in Holstein dairy calves. Newborn female calves (n = 54; 3 d of age; 39.8 ± 1.36 kg BW) were assigned randomly to 3 groups receiving starter diets containing CS [10% dry matter (DM) basis; CS diet) and reconstituted AH (10% DM, RAH diet) or BP (10% DM; RBP diet). The starter diets had the same nutrient composition and DM content. The calves were weaned on day 50 and the study continued until day 70. Nutrient intake, body weight (at weaning and at the end of the study), daily weight gain, feed efficiency, and body measurements (including heart girth, withers height, body length, body barrel, hip height, and hip width) were not affected by the diet (P > 0.05). Health-related variables including rectal temperature, fecal score, and general appearance score were not influenced by the diets (P > 0.05). During the postweaning period, apparent total tract digestibility of DM, organic matter, and crude protein were higher for RBP (P = 0.001); however, digestibility of neutral detergent fiber was lower in RAH compared with CS or RBP (P = 0.001). Daily amount of nutrient digestibility did not change across the diets (P > 0.05). Rumen fluid pH and total volatile fatty acid concentration and profile were not different across the diets after weaning (P > 0.05). Calves fed RAH or RBP had higher blood concentration of β-hydroxy butyric acid compared with CS only before weaning (P = 0.03). Blood albumin concentration was higher for RBP compared with CS or RAH during the preweaning (P = 0.006) and overall (P = 0.005) periods; however, it was lower for CS compared with RBP after weaning (P = 0.03). Concentration of other blood variables including glucose, blood urea N, total protein, and globulin did not change across the diets (P > 0.05). Calves, in general, were healthy, and replacing CS with RAH or RBP in the starter diet had no beneficial effect on their feed intake or growth performance indicating that CS and reconstituted AH or BP can be used interchangeably in dairy calf starter diets until 70 d of age, allowing dairy producers more choices in selecting the feed ingredients.
Lipid peroxidation impairs growth and viability of nursery pigs reared under commercial conditions1
Authors: Chang Petra L , Boyd R Dean , Zier-Rush Cate , Rosero David S , van Heugten Eric 
Published: May 2019

Abstract
The objective of this study was to investigate the impact of lipid peroxidation in a dose-dependent manner on growth, health, and oxidative stress status of nursery pigs. A total of 2,200 weaned pigs (5.95 ± 0.20 kg BW) were housed in 100 pens (22 pigs per pen) in a randomized complete block design based on initial BW and sex. Pigs were randomly assigned within blocks to 5 dietary treatments, consisting of a corn–soybean meal-based diet supplemented with 5% of either control corn oil (iodine value = 118, FFA = 0.06%, anisidine value = 3, peroxide value = 3 mEq/kg oil) or peroxidized corn oil (iodine value = 120, FFA = 0.35%, anisidine value = 30, peroxide value = 163 mEq/kg oil). These 2 diets were blended to obtain 5 levels of peroxidation with final treatments designated as 0 (diet with 5% control oil), 25%, 50%, 75%, and 100% (diet with peroxidized corn oil) peroxidation. Diets were fed ad libitum for 43 d. Blood samples were collected on d 33 from 20 pigs per treatment to determine serum oxidative stress markers and vitamin E concentrations and again on d 43 (14 d after vaccination) to determine immune response to porcine circovirus type 2 (PCV2) and Mycoplasma hyopneumoniae (Mhyo). Gain:feed ratio decreased linearly (P = 0.023) with increasing peroxidation, but pen ADG and ADFI were not affected. Number of pigs removed for medical treatment, total number medically treated, pigs culled for low end weight, and mortality increased, and full-value pigs linearly decreased (P < 0.04) with increasing peroxidation. Consequently, total pen gain (weight of viable pigs that remained in test pens at the end of the study minus weight of pigs placed) decreased linearly (P < 0.01) with increasing peroxidation. Antibody titers to Mhyo and PCV2 increased postvaccination (P < 0.001), but did not differ due to dietary treatment. Serum concentrations of malondialdehyde, 8-hydroxy-2′-deoxyguanosine, and protein carbonyl were not affected by peroxidation. Total antioxidant capacity and serum vitamin E concentrations decreased (P = 0.01) linearly with increasing peroxidation. Data show a dose-dependent negative impact of lipid peroxidation on pig productivity when determined under field population conditions, being primarily manifested by increased mortality, number of pigs medically treated, and number of culled pigs (≤13.6 kg BW). Results underscore the importance of proper assessment of lipid peroxidation as part of quality control to prevent oxidative stress and performance losses in weaned pigs.
Compositional Hierarchical Structure Evolves through Cultural Transmission: An Experimental Study
Authors: Saldana Carmen , Kirby Simon , Truswell Robert , Smith Kenny 
Published: May 2019

AbstractCompositional hierarchical structure is a prerequisite for productive languages; it allows language learners to express and understand an infinity of meanings from finite sources (i.e., a lexicon and a grammar). Understanding how such structure evolved is central to evolutionary linguistics. Previous work combining artificial language learning and iterated learning techniques has shown how basic compositional structure can evolve from the trade-off between learnability and expressivity pressures at play in language transmission. In the present study we show, across two experiments, how the same mechanisms involved in the evolution of basic compositionality can also lead to the evolution of compositional hierarchical structure. We thus provide experimental evidence showing that cultural transmission allows advantages of compositional hierarchical structure in language learning and use to permeate language as a system of behaviour.
Long-Term Outcomes of Refractive Surgery Performed During the Military
Authors: Godiwalla Roxana Y , Magone M Teresa , Kaupp Sandor B , Jung Hoon , Cason John B 
Published: May 2019

Abstract

Introduction
To evaluate the long-term refractive results of laser in situ keratomileusis (LASIK) and photorefractive keratectomy (PRK) performed by the military in a veteran population.

Materials and Methods
Three Department of Veterans Affairs (VA) hospital sites (Puget Sound, Buffalo, and Washington D.C.) obtained IRB approval for this multi-center study. Comprehensive ophthalmologic assessment including refraction and keratometry were obtained at the time of the long-term VA examination and compared to the patients’ postoperative military records.

Results
Eighty patients (160 eyes) enrolled in this study. At the time of treatment, patients were 21–52 years of age. Long-term post-operative data was available from 4 to 17 years post-operatively. Fifteen percent of the treatment types were LASIK and 85% PRK. At the time of their military post-operative exam (range 3–14 months, mean 4 months), 82% of patients had uncorrected visual acuity (UCVA) of 20/20 or better, and their average manifest refraction was −0.08 D (SD ± 0.48 D). At the time of the long-term ophthalmological exam at the VA medical centers (range 4–11 years, mean of 8.2 years), 49% of patients had an UCVA of 20/20 or better and an average manifest refraction was −0.64 D (SD ± 0.69 D).

Conclusion
This is the first long-term study evaluating refractive surgery outcomes up to 17 years in a military population. Our study demonstrates safety after refractive surgery in the military with less than 0.1D increase in myopia per year and strong keratometric stability. Other changes in the eye may be the likely cause for this observed mild refractive shift.
A new RASS galaxy cluster catalogue with low contamination extending to z ∼ 1 in the DES overlap region
Authors: Klein M , Grandis S , Mohr J J , Paulus M , Abbott T M C , Annis J , Avila S , Bertin E , Brooks D , Buckley-Geer E , Rosell A Carnero , Kind M Carrasco , Carretero J , Castander F J , Cunha C E , D’Andrea C B , da Costa L N , De Vicente J , Desai S , Diehl H T , Dietrich J P , Doel P , Evrard A E , Flaugher B , Fosalba P , Frieman J , García-Bellido J , Gaztanaga E , Giles P A , Gruen D , Gruendl R A , Gschwend J , Gutierrez G , Hartley W G , Hollowood D L , Honscheid K , Hoyle B , James D J , Jeltema T , Kuehn K , Kuropatkin N , Lima M , Maia M A G , March M , Marshall J L , Menanteau F , Miquel R , Ogando R L C , Plazas A A , Romer A K , Roodman A , Sanchez E , Scarpine V , Schindler R , Serrano S , Sevilla-Noarbe I , Smith M , Smith R C , Soares-Santos M , Sobreira F , Suchyta E , Swanson M E C , Tarle G , Thomas D , Vikram V ,   the DES Collaboration
Published: May 2019

ABSTRACT
We present the MARD-Y3 catalogue of between 1086 and 2171 galaxy clusters (52 per cent and 65 per cent new) produced using multicomponent matched filter (MCMF) follow-up in 5000 deg2 of DES-Y3 optical data of the ∼20 000 overlapping ROSAT All-Sky Survey source catalogue (2RXS) X-ray sources. Optical counterparts are identified as peaks in galaxy richness as a function of redshift along the line of sight towards each 2RXS source within a search region informed by an X-ray prior. All peaks are assigned a probability fcont of being a random superposition. The clusters lie at 0.02 &lt; z &lt; 1.1 with more than 100 clusters at z &gt; 0.5. Residual contamination is 2.6 per cent and 9.6 per cent for the cuts adopted here. For each cluster we present the optical centre, redshift, rest frame X-ray luminosity, M500 mass, coincidence with NWAY infrared sources, and estimators of dynamical state. About 2 per cent of MARD-Y3 clusters have multiple possible counterparts, the photo-z’s are high quality with σΔz/(1 + z) = 0.0046, and ∼1 per cent of clusters exhibit evidence of X-ray luminosity boosting from emission by cluster active galactic nuclei. Comparison with other catalogues (MCXC, RM, SPT-SZ, Planck) is performed to test consistency of richness, luminosity, and mass estimates. We measure the MARD-Y3 X-ray luminosity function and compare it to the expectation from a fiducial cosmology and externally calibrated luminosity- and richness–mass relations. Agreement is good, providing evidence that MARD-Y3 has low contamination and can be understood as a simple two step selection – X-ray and then optical – of an underlying cluster population described by the halo mass function.
Highly efficient silencing of microRNA by heteroduplex oligonucleotides
Authors: Yoshioka Kotaro , Kunieda Taiki , Asami Yutaro , Guo Huijia , Miyata Haruka , Yoshida-Tanaka Kie , Sujino Yumiko , Piao Wenying , Kuwahara Hiroya , Nishina Kazutaka , Hara Rintaro Iwata , Nagata Tetsuya , Wada Takeshi , Obika Satoshi , Yokota Takanori 
Published: May 2019

AbstractAntimiR is an antisense oligonucleotide that has been developed to silence microRNA (miRNA) for the treatment of intractable diseases. Enhancement of its in vivo efficacy and improvement of its toxicity are highly desirable but remain challenging. We here design heteroduplex oligonucleotide (HDO)-antimiR as a new technology comprising an antimiR and its complementary RNA. HDO-antimiR binds targeted miRNA in vivo more efficiently by 12-fold than the parent single-stranded antimiR. HDO-antimiR also produced enhanced phenotypic effects in mice with upregulated expression of miRNA-targeting messenger RNAs. In addition, we demonstrated that the enhanced potency of HDO-antimiR was not explained by its bio-stability or delivery to the targeted cell, but reflected an improved intracellular potency. Our findings provide new insights into biology of miRNA silencing by double-stranded oligonucleotides and support the in vivo potential of this technology based on a new class of for the treatment of miRNA-related diseases.
To randomize, or not to randomize, that is the question: using data from prior clinical trials to guide future designs
Authors: Vanderbeek Alyssa M , Ventz Steffen , Rahman Rifaquat , Fell Geoffrey , Cloughesy Timothy F , Wen Patrick Y , Trippa Lorenzo , Alexander Brian M 
Published: May 2019

AbstractBackgroundUnderstanding the value of randomization is critical in designing clinical trials. Here, we introduce a simple and interpretable quantitative method to compare randomized designs versus single-arm designs using indication-specific parameters derived from the literature. We demonstrate the approach through application to phase II trials in newly diagnosed glioblastoma (ndGBM).MethodsWe abstracted data from prior ndGBM trials and derived relevant parameters to compare phase II randomized controlled trials (RCTs) and single-arm designs within a quantitative framework. Parameters included in our model were (i) the variability of the primary endpoint distributions across studies, (ii) potential for incorrectly specifying the single-arm trial’s benchmark, and (iii) the hypothesized effect size. Strengths and weaknesses of RCT and single-arm designs were quantified by various metrics, including power and false positive error rates.ResultsWe applied our method to show that RCTs should be preferred to single-arm trials for evaluating overall survival in ndGBM patients based on parameters estimated from prior trials. More generally, for a given effect size, the utility of randomization compared with single-arm designs is highly dependent on (i) interstudy variability of the outcome distributions and (ii) potential errors in selecting standard of care efficacy estimates for single-arm studies.ConclusionsA quantitative framework using historical data is useful in understanding the utility of randomization in designing prospective trials. For typical phase II ndGBM trials using overall survival as the primary endpoint, randomization should be preferred over single-arm designs.
Pseudo-chromosome length genome assembly of a double haploid ‘Bartlett’ pear (Pyrus communis L.)
Authors: Linsmith Gareth , Rombauts Stephane , Montanari Sara , Deng Cecilia H. , Celton Jean-Marc , Guérif Philippe , Liu Chang , Lohaus Rolf , Zurn Jason D. , Cestaro Alessandro , Bassil Nahla V. , Bakker Linda V. , Schijlen Elio , Gardiner Susan E. , Lespinasse Yves , Durel Charles-Eric , Velasco Riccardo , Neale David , Chagné David , Van de Peer Yves , Troggio Michela , Bianco Luca 
Published: May 2019

AbstractWe report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII Long read sequencing (PacBio), Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. A total of 496.9 million bases (Mb) corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 chromosomes of the pear genome. About 50% (247 Mb) of the genome consists of repetitive sequences. Comparison with previous assemblies of Pyrus communis and Pyrus x bretschneideri confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.