bluuebunny/crossref_metadata_2025_split huggingface dataset:
A quantum annealer with fully programmable all-to-all coupling via Floquet engineering
Authors: Onodera Tatsuhiro , Ng Edwin , McMahon Peter L. 
Published: May 2020

AbstractQuantum annealing is a promising approach to heuristically solving difficult combinatorial optimization problems. However, the connectivity limitations in current devices lead to an exponential degradation of performance on general problems. We propose an architecture for a quantum annealer that achieves full connectivity and full programmability while using a number of physical resources only linear in the number of spins. We do so by application of carefully engineered periodic modulations of oscillator-based qubits, resulting in a Floquet Hamiltonian in which all the interactions are tunable. This flexibility comes at the cost of the coupling strengths between qubits being smaller than they would be compared with direct coupling, which increases the demand on coherence times with increasing problem size. We analyze a specific hardware proposal of our architecture based on Josephson parametric oscillators. Our results show how the minimum-coherence-time requirements imposed by our scheme scale, and we find that the requirements are not prohibitive for fully connected problems with up to at least 1000 spins. Our approach could also have impact beyond quantum annealing, since it readily extends to bosonic quantum simulators, and would allow the study of models with arbitrary connectivity between lattice sites.
A macroscopic and stereological imaging dataset of Pleuronectes platessa ovaries
Authors: Sauger Carine , Quinquis Jérôme , Kellner Kristell , Heude-Berthelin Clothilde , Lepoittevin Mélanie , Elie Nicolas , Dubroca Laurent 
Published: May 2020

AbstractThe North Sea plaice, Pleuronectes platessa (Linnaeus, 1758), is a commonly studied commercial flatfish with poorly known ovarian histology. The following dataset is a collection of female plaice gonad images and their corresponding histological slides, collected during a complete season of the plaice’s reproduction cycle. Stereology was used to determine the percentage of different structures found throughout the ovaries. Inter-agent calibrations were accomplished in order to harmonize the stereological readings, and were based on a comprehensive reading protocol and histological lexicon that were specifically written for the plaice’s ovaries. The distribution and homogeneity of the different cell types found throughout the ovaries were also evaluated. This dataset can be used to automate the stereological reading process (through statistical learning methods for example) or to objectively determine the plaice’s maturity phase, and link that information to either macroscopic measurements or through image analysis of the full ovaries.
Measuring dementia incidence within a cohort of 267,153 older Australians using routinely collected linked administrative data
Authors: Welberry Heidi J. , Brodaty Henry , Hsu Benjumin , Barbieri Sebastiano , Jorm Louisa R. 
Published: May 2020

AbstractTo estimate dementia incidence rates using Australian administrative datasets and compare the characteristics of people identified with dementia across different datasets. This data linkage study used a cohort of 267,153 from the Australian 45 and Up Study. Participants completed a survey in 2006–2009 and subsequent dementia was identified through pharmaceutical claims, hospitalisations, aged care eligibility assessments, care needs at residential aged care entry and death certificates. Age-specific, and age-standardised incidence rates, incidence rate ratios and survival from first dementia diagnosis were estimated. Estimated age-standardised dementia incidence rates using all linked datasets was 16.8 cases per 1000 person years for people aged 65+. Comparing incidence rates to the global published rates suggested 77% of cases were identified but this varied by age with highest coverage among those aged 80–84 years (92%). Incidence rate ratios were inconsistent across datasets for: sex, socio-economic disadvantage, size of support network, marital status, functional limitations and diabetes. Median survival from first dementia diagnosis ranged from 1.80 years in the care needs dataset to 3.74 years in the pharmaceutical claims dataset. Characteristics of people identified with dementia in different administrative datasets reflect the factors that drive interaction with specific services; this may introduce bias in observational studies using a single data-source to identify dementia.
Chemical and Microstructural Characterization of pH and [Ca2+] Dependent Sol-Gel Transitions in Mucin Biopolymer
Authors: Curnutt Austin , Smith Kaylee , Darrow Emily , Walters Keisha B. 
Published: May 2020

AbstractMucus is responsible for controlling transport and barrier function in biological systems, and its properties can be significantly affected by compositional and environmental changes. In this study, the impacts of pH and CaCl2were examined on the solution-to-gel transition of mucin, the primary structural component of mucus. Microscale structural changes were correlated with macroscale viscoelastic behavior as a function of pH and calcium addition using rheology, dynamic light scattering, zeta potential, surface tension, and FTIR spectroscopic characterization. Mucin solutions transitioned from solution to gel behavior between pH 4–5 and correspondingly displayed a more than ten-fold increase in viscoelastic moduli. Addition of CaCl2increased the sol-gel transition pH value to ca. 6, with a twofold increase in loss moduli at low frequencies and ten-fold increase in storage modulus. Changing the ionic conditions—specifically [H+] and [Ca2+] —modulated the sol-gel transition pH, isoelectric point, and viscoelastic properties due to reversible conformational changes with mucin forming a network structure via non-covalent cross-links between mucin chains.
Uncovering Sub-Structure and Genomic Profiles in Across-Countries Subpopulations of Angus Cattle
Authors: Cardoso Diercles Francisco , Fernandes Júnior Gerardo Alves , Scalez Daiane Cristina Becker , Alves Anderson Antonio Carvalho , Magalhães Ana Fabrícia Braga , Bresolin Tiago , Ventura Ricardo Vieira , Li Changxi , de Sena Oliveira Márcia Cristina , Porto-Neto Laercio Ribeiro , Carvalheiro Roberto , de Oliveira Henrique Nunes , Tonhati Humberto , Albuquerque Lucia Galvão 
Published: May 2020

AbstractHighlighting genomic profiles for geographically distinct subpopulations of the same breed may provide insights into adaptation mechanisms to different environments, reveal genomic regions divergently selected, and offer initial guidance to joint genomic analysis. Here, we characterized similarities and differences between the genomic patterns of Angus subpopulations, born and raised in Canada (N = 382) and Brazil (N = 566). Furthermore, we systematically scanned for selection signatures based on the detection of autozygosity islands common between the two subpopulations, and signals of divergent selection, via FSTand varLD tests. The principal component analysis revealed a sub-structure with a close connection between the two subpopulations. The averages of genomic relationships, inbreeding coefficients, and linkage disequilibrium at varying genomic distances were rather similar across them, suggesting non-accentuated differences in overall genomic diversity. Autozygosity islands revealed selection signatures common to both subpopulations at chromosomes 13 (63.77–65.25 Mb) and 14 (22.81–23.57 Mb), which are notably known regions affecting growth traits. Nevertheless, further autozygosity islands along with FSTand varLD tests unravel particular sites with accentuated population subdivision at BTAs 7 and 18 overlapping with known QTL and candidate genes of reproductive performance, thermoregulation, and resistance to infectious diseases. Our findings indicate overall genomic similarity between Angus subpopulations, with noticeable signals of divergent selection in genomic regions associated with the adaptation in different environments.
CYP17A1 deficient XY mice display susceptibility to atherosclerosis, altered lipidomic profile and atypical sex development
Authors: Aherrahrou Redouane , Kulle Alexandra E. , Alenina Natalia , Werner Ralf , Vens-Cappell Simeon , Bader Michael , Schunkert Heribert , Erdmann Jeanette , Aherrahrou Zouhair 
Published: May 2020

AbstractCYP17A1 is a cytochrome P450 enzyme with 17-alpha-hydroxylase and C17,20-lyase activities. CYP17A1 genetic variants are associated with coronary artery disease, myocardial infarction and visceral and subcutaneous fat distribution; however, the underlying pathological mechanisms remain unknown. We aimed to investigate the function of CYP17A1 and its impact on atherosclerosis in mice. At 4–6 months, CYP17A1-deficient mice were viable, with a KO:Het:WT ratio approximating the expected Mendelian ratio of 1:2:1. All Cyp17a1 knockout (KO) mice were phenotypically female; however, 58% were Y chromosome-positive, resembling the phenotype of human CYP17A1 deficiency, leading to 46,XY differences/disorders of sex development (DSD). Both male and female homozygous KO mice were infertile, due to abnormal genital organs. Plasma steroid analyses revealed a complete lack of testosterone in XY-KO mice and marked accumulation of progesterone in XX-KO mice. Elevated corticosterone levels were observed in both XY and XX KO mice. In addition, Cyp17a1 heterozygous mice were also backcrossed onto an Apoe KO atherogenic background and fed a western-type diet (WTD) to study the effects of CYP17A1 on atherosclerosis. Cyp17a1 x Apoe double KO XY mice developed more atherosclerotic lesions than Apoe KO male controls, regardless of diet (standard or WTD). Increased atherosclerosis in CYP17A1 XY KO mice lacking testosterone was associated with altered lipid profiles. In mice, CYP17A1 deficiency interferes with sex differentiation. Our data also demonstrate its key role in lipidomic profile, and as a risk factor in the pathogenesis of atherosclerosis.
The effectiveness of quick starting oral contraception containing nomegestrol acetate and 17-β estradiol on ovulation inhibition: A randomized controlled trial
Authors: Jirakittidul Preeyaporn , Angsuwathana Surasak , Rattanachaiyanont Manee , Thiampong Thunyada , Neungton Chanon , Chotrungrote Benjaphorn 
Published: May 2020

AbstractTo determine the effectiveness of quick starting combined oral contraception (COC) contain 2.5 mg nomegestrol acetate and 1.5 mg estradiol (NOMAC/E2) comparing with 0.075 mg gestodene and 0.02 mg ethinyl estradiol (GS/EE) on ovarian ovulation inhibition rate, we conducted a non-inferiority randomized controlled trial involving 69 healthy female volunteers aged 18–40 years who had normal menstrual history and were randomized at a 2:1 ratio to take one pack of COC containing either NOMAC/E2 (study group) or GS/EE (control group) starting on menstrual cycle Day7–9. The ovarian activity was assessed by using Hoogland and Skouby grading. Forty-six and 23 participants were randomized to NOMAC/E2 and GS/EE groups, respectively. Baseline characteristics were similar between groups. No significant difference was observed between the study and control groups for ovulation inhibition rate (93.4% vs. 95.6%, risk difference: –2.2%, 95% CI: –13.1, 8.8), ovarian quiescence rate (91.2% vs. 91.2%, P = 1.000), persistent cyst rate (2.2% vs. 4.4%, P = 1.000), and ovulation rate (6.6% vs. 4.4%, P = 1.000). Quick starting COC during day7–9 of menstrual cycle can inhibit ovulation for more than 90%. The quick starting NOMAC/E2 is non-inferior to GS/EE for preventing ovulation and suppressing follicular growth.
Station and train surface microbiomes of Mexico City’s metro (subway/underground)
Authors: Hernández Apolinar Misael , Vargas-Robles Daniela , Alcaraz Luis David , Peimbert Mariana 
Published: May 2020

AbstractThe metro is one of the more representative urban transportation systems of Mexico City, and it transports approximately 4.5 million commuters every day. Large crowds promote the exchange of microbes between humans. In this study, we determined the bacterial diversity profile of the Mexico City metro by massive sequencing of the 16S rRNA gene. We identified a total of 50,174 operational taxonomic units (OTUs) and 1058 genera. The metro microbiome was dominated by the phylum Actinobacteria and by the genera Cutibacterium (15%) (C. acnes 13%), Corynebacterium (13%), Streptococcus (9%), and Staphylococcus (5%) (S. epidermidis; 4%), reflecting the microbe composition of healthy human skin. The metro likely microbial sources were skin, dust, saliva, and vaginal, with no fecal contribution detected. A total of 420 bacterial genera were universal to the twelve metro lines tested, and those genera contributed to 99.10% of the abundance. The annual 1.6 billion ridership makes this public transport a main hub for microbe-host-environment interactions. Finally, this study shows that the microbial composition of the Mexico City metro comes from a mixture of environmental and human sources and that commuters are exposed to healthy composition of the human microbiota.
Anti-Adhesion Behavior from Ring-Strain Amine Cyclic Monolayers Grafted on Silicon (111) Surfaces
Authors: Ching Jing Yuan , Huang Brian. J. , Hsu Yu-Ting , Khung Yit Lung 
Published: May 2020

AbstractIn this manuscript, a series of amine tagged short cyclic molecules (cyclopropylamine, cyclobutylamine, cyclopentylamine and cyclohexylamine) were thermally grafted onto p-type silicon (111) hydride surfaces via nucleophilic addition. The chemistries of these grafting were verified via XPS, AFM and sessile droplet measurements. Confocal microscopy and cell viability assay was performed on these surfaces incubated for 24 hours with triple negative breast cancer cells (MDA-MB 231), gastric adenocarcinoma cells (AGS) endometrial adenocarcinoma (Hec1A). All cell types had shown a significant reduction when incubated on these ring-strain cyclic monolayer surfaces than compared to standard controls. The expression level of focal adhesion proteins (vinculin, paxilin, talin and zyxin) were subsequently quantified for all three cell types via qPCR analysis. Cells incubate on these surface grafting were observed to have reduced levels of adhesion protein expression than compared to positive controls (collagen coating and APTES). A potential application of these anti-adhesive surfaces is the maintenance of the chondrocyte phenotype during in-vitro cell expansion. Articular chondrocytes cultured for 6 days on ring strained cyclopropane-modified surfaces was able to proliferate but had maintained a spheroid/aggregated phenotype with higher COL2A1 and ACAN gene expression. Herein, these findings had help promote grafting of cyclic monolayers as an viable alternative for producing antifouling surfaces.
High-content fluorescence imaging with the metabolic flux assay reveals insights into mitochondrial properties and functions
Authors: Little Andrew Charles , Kovalenko Ilya , Goo Laura Elaine , Hong Hanna Sungok , Kerk Samuel Andrew , Yates Joel Anthony , Purohit Vinee , Lombard David Benner , Merajver Sofia Diana , Lyssiotis Costas Andreas 
Published: May 2020

AbstractMetabolic flux technology with the Seahorse bioanalyzer has emerged as a standard technique in cellular metabolism studies, allowing for simultaneous kinetic measurements of respiration and glycolysis. Methods to extend the utility and versatility of the metabolic flux assay would undoubtedly have immediate and wide-reaching impacts. Herein, we describe a platform that couples the metabolic flux assay with high-content fluorescence imaging to simultaneously provide means for normalization of respiration data with cell number; analyze cell cycle distribution; and quantify mitochondrial content, fragmentation state, membrane potential, and mitochondrial reactive oxygen species. Integration of fluorescent dyes directly into the metabolic flux assay generates a more complete data set of mitochondrial features in a single assay. Moreover, application of this integrated strategy revealed insights into mitochondrial function following PGC1a and PRC1 inhibition in pancreatic cancer and demonstrated how the Rho-GTPases impact mitochondrial dynamics in breast cancer.
Key words when text forms the unit of study
Authors: Jeaco Stephen 
Published: May 2020

Abstract
Throughout the social sciences, there has been growing pressure to present effect sizes when publishing empirical data (see American Psychological Association, 2001; Parsons & Nelson, 2004). While it seems indisputable that for the majority of quantitative research foci, effect size is an essential element of statistical analysis, this paper argues that specifically for key word analysis in corpus linguistics, the means of reporting effect size must depend on the level of the unit of study of each investigation (single text, collection or large corpus). After exploring some main criticisms of the log-likelihood measure, this paper unpacks the parameters of different measures for keyness and how they might address underlying concerns. It maintains that for the exploration of foregrounded/deviant/salient/marked features in text, the use of log-likelihood scores to rank the results is still fit for purpose and coupled with Bayes Factors is a solid approach for key word analyses.
Turn structure and inserts
Authors: Rühlemann Christoph 
Published: May 2020

AbstractTurns-at-talk often do not start with their main business but rather with a pre-start (Sacks et al., 1974). This paper investigates the correlation of pre-starts with inserts, one of three major word classes (Biber et al., 1999). Based on the BNC’s mark-up, I investigate how inserts are positionally distributed in large amounts of turns of varied lengths. The analysis shows that inserts are overwhelmingly attracted to turn-first positions, the likely location of pre-starts. Further, in a subsample of 1,000 ten-word turns manually coded for pre-starts, 86% of all inserts serve a pre-start function. The findings call into question current speech processing models that fail to factor in turn structure. Further, pre-starts have crucial sequential and interactional implications as early indicators whether the new turn “agrees” with the prior turn and are likely key signals aiding listeners’ action ascription.
Decision support system based on database system of genetic resources for Central Kalimantan local crops to develop ex situ and in situ conservation
Authors: Bhermana A , Susilawati  
Published: May 2020

Abstract
The results of exploration and inventory of local crop genetic resources from Central Kalimantan have been compiled into a genetic resource database system. The data and other information that have been integrated into a database system can be further developed systematically to become a decision support system so that it can be utilized as a useful tool in decision making. This system can be built by combining data, models and analytical tools in an application system with a user-friendly interface. This system can be utilized in the preparation of genetic resources development planning, such as for the determination of location for in situ and ex situ conservation areas in Central Kalimantan. The objective of this study was to develop such system, through the application of MS Access database as the Database Management System (DBMS) for storage (repository) and accessing database system applications that have been prepared interactively. The System is systematically designed to include geographic information system and based on the spatial analysis which can provide guidance and recommendation for zoning areas based on the suitability of plant commodities, both inside and outside of their natural habitat environment.
Simulation of QTL by sequencing for agronomic quantitative trait loci detection in small to medium population size in soybean
Authors: Satyawan D , Rijzaani H , Tasma I M 
Published: May 2020

Abstract
Quantitative Trait Loci by sequencing (QTL-seq) is a QTL detection method that utilizes the principles of Bulked Segregants Analysis. It detects alleles with extreme frequencies in whole-genome sequence data from two bulked populations with contrasting phenotypes. This approach is less laborious than QTL detection using linkage mapping, and the result had been shown to be comparable in the same mapping population. However, since the genomes of the two bulked populations are completely sequenced, it can facilitate further characterization of the QTL segment and the genes underlying the QTLs. In this study, QTL-seq was simulated using high-density SNP genotyping data from a recombinant inbred population consisting of 188 individuals. The genomes of both parents had been sequenced, and the SNP genotyping identified 2,207 SNP markers that were polymorphic and segregating in the population. Since the markers are dense enough and well distributed across the genome, they can be used to represent the alleles that can be obtained from whole genome resequencing of bulked individuals. The availability of genotype data for each individual in the mapping population also enabled the detection of QTL via linkage mapping. Using data generated from both approaches, various simulations were conducted to compare the results that could be obtained under ideal conditions, as well as less ideal ones such as when the QTL effects are small, the presence of skewed phenotype distribution, and a small number of bulked samples.
Studies on heritability and genetic variability for grain physical properties in Malaysian rice germplasm
Authors: Saidon S A , Kamaruzaman R , Razak M S F A , Ramli A , Sarif H M , Zuki Z M , Rahman S N A , Devarajan T , Sunian E 
Published: May 2020

Abstract
Genetic based information of different traits plays important role in varietal improvement of rice. Twenty rice accessions (Oryza sativa L.) obtained from National Rice Gene Bank were evaluated during main season 2015/2016 to estimate heritability, genetic variability and genetic advance for seven grain physical properties. Among the traits, milled grain length/width ratio, milled grain length, milled grain length after cooking and grain length exhibited high estimates of phenotypic coefficient of variation (PCV), and genotypic coefficient of variation (GCV). Highest broad sense heritability and genetic advance was obtained for grain length (98.66% and 62.25%), milled grain length (98.95% and 67.31%), milled grain length/width ratio (98.50% and 80.41%) and milled grain length after cooking (98.93% and 65.44%) which suggest these traits are most probably controlled by additive gene action and hence they can be fixed by selection. However, kernel elongation ratio showed lowest value of broad sense heritability and genetic advance (11.76% and 1.38%, respectively) and may suggest non-additive gene action in their inheritance and selection of this trait may difficult due to high environmental influences. Therefore, improvement of high quality rice with kernel elongation ability may require molecular marker application as it is highly affected by environment for precise selection.