bluuebunny/crossref_metadata_2025_split huggingface dataset:
A genome-wide association and prediction study in grapevine deciphers the genetic architecture of multiple traits and identifies genes under many new QTLs
Authors: Flutre Timothée , Le Cunff Loïc , Fodor Agota , Launay Amandine , Romieu Charles , Berger Gilles , Bertrand Yves , Terrier Nancy , Beccavin Isabelle , Bouckenooghe Virginie , Roques Maryline , Pinasseau Lucie , Verbaere Arnaud , Sommerer Nicolas , Cheynier Véronique , Bacilieri Roberto , Boursiquot Jean-Michel , Lacombe Thierry , Laucou Valérie , This Patrice , Péros Jean-Pierre , Doligez Agnès 
Published: April 2022

AbstractTo cope with the challenges facing agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennial species such as grapevine, but requires understanding the genetic architecture of target traits. To go beyond the mapping of quantitative trait loci in bi-parental crosses, we exploited a diversity panel of 279 Vitis vinifera L. cultivars planted in 5 blocks in the vineyard. This panel was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. The panel was genotyped for 63k single nucleotide polymorphisms by combining an 18K microarray and genotyping-by-sequencing. The experimental design allowed to reliably assess the genotypic values for most traits. Marker densification via genotyping-by-sequencing markedly increased the proportion of genetic variance explained by single nucleotide polymorphisms, and 2 multi-single nucleotide polymorphism models identified quantitative trait loci not found by a single nucleotide polymorphism-by-single nucleotide polymorphism model. Overall, 489 reliable quantitative trait loci were detected for 41% more response variables than by a single nucleotide polymorphism-by-single nucleotide polymorphism model with microarray-only single nucleotide polymorphisms, many new ones compared with the results from bi-parental crosses. A prediction accuracy higher than 0.42 was obtained for 50% of the response variables. Our overall approach as well as quantitative trait locus and prediction results provide insights into the genetic architecture of target traits. New candidate genes and the application into breeding are discussed.
Coexpression of MEIOTIC-TOPOISOMERASE VIB-dCas9 with guide RNAs specific to a recombination hotspot is insufficient to increase crossover frequency in Arabidopsis
Authors: Yelina Nataliya E , Holland Daniel , Gonzalez-Jorge Sabrina , Hirsz Dominique , Yang Ziyi , Henderson Ian R 
Published: April 2022

Abstract
During meiosis, homologous chromosomes pair and recombine, which can result in reciprocal crossovers that increase genetic diversity. Crossovers are unevenly distributed along eukaryote chromosomes and show repression in heterochromatin and the centromeres. Within the chromosome arms, crossovers are often concentrated in hotspots, which are typically in the kilobase range. The uneven distribution of crossovers along chromosomes, together with their low number per meiosis, creates a limitation during crop breeding, where recombination can be beneficial. Therefore, targeting crossovers to specific genome locations has the potential to accelerate crop improvement. In plants, meiotic crossovers are initiated by DNA double-strand breaks that are catalyzed by SPO11 complexes, which consist of 2 catalytic (SPO11-1 and SPO11-2) and 2 noncatalytic subunits (MTOPVIB). We used the model plant Arabidopsis thaliana to coexpress an MTOPVIB-dCas9 fusion protein with guide RNAs specific to the 3a crossover hotspot. We observed that this was insufficient to significantly change meiotic crossover frequency or pattern within 3a. We discuss the implications of our findings for targeting meiotic recombination within plant genomes.
Seasonal terrestrial water load modulation of seismicity at the southeastern margin of the Tibetan Plateau constrained by GNSS and GRACE data
Authors: She Yawen , Fu Guangyu , Xu Changyi 
Published: April 2022

SUMMARY
The seasonal terrestrial water load modulation of seismicity is an important phenomenon to understand the mechanism behind earthquake triggering and nucleation. The presence of high-level seismicity and large seasonal water load amplitudes at the southeastern margin of the Tibetan Plateau provides a natural experimental environment for studying the modulation mechanism. The spatiotemporal distribution of the water load was inverted using Global Navigation Satellite System (GNSS) and Gravity Recovery and Climate Experiment (GRACE) data, and an earthquake catalogue (M ≥ 2.5) was declustered to obtain the background seismicity using the Epidemic Type Aftershock Sequences (ETAS) model. The Multichannel Singular-Spectrum Analysis (M-SSA) is adopted to the time-series of monthly averaged terrestrial water load and background seismicity rates, and the results show 1- and 2-yr periodicities in the seismicity rates and water load. The 1-yr periodicity in the seismicity rate is correlated with the rate of change of the monthly averaged water load. To evaluate the seasonal principal stress perturbations on the tectonic background stress orientations, the stress changes caused by the seasonal water load changes are projected onto the tectonic background stress field orientations constraining by 8 yr of earthquake focal mechanism solutions. The results show that the largest change of the seasonal principal stress perturbations is about 16 kPa. The number of excess earthquakes is evaluated with the background seismicity rates for discrete stress intervals. The results indicate a ∼10 per cent increase in the seismicity rates that correlate with the rates of the minimum and mean principal stress perturbations. The results above can be explained by the model of harmonic stress perturbations on rate-and-state fault. Based on this model, the nucleation period of the seasonal seismicity should be less than 1 yr at the southeastern margin of the Tibetan Plateau.
Linear array analysis of passive surface waves combined with mini-Sosie technique
Authors: Guan Jianbo , Li Yu , Yan Yingwei , Yang Zhi , Liu Guohua 
Published: April 2022

SUMMARY
Mini-Sosie, which is convenient and environmentally friendly with high energy output, is gaining increasing attention as a seismic exploration source. Passive surface wave survey using ambient noise have become a powerful tool for exploration in urban areas due to the advantages of being efficient and non-destructive. A 2-D or pseudo-1D array that can attenuate phase velocity overestimation due to directional noise are the optimal choice, but such arrays are limited by the complex environment of the experimental site on the one hand and the need to ensure that the medium beneath the array meets the assumption of lateral isotropy on the other. However, the fully 1-D linear array as an alternative lacks the ability to suppress the directional effect of the noise source. In this study, we develop a novel approach for linear array analysis of passive surface waves combined with mini-Sosie technique, called LAPSS. We use the mini-Sosie technique with fixed-frequency impact in the in-line direction to provide the theoretical phase velocity values at several frequency points as a reference for the biased dispersion image obtained from the linear array analysis, so as to estimate the azimuth of the noise source and to perform the correction of the biased dispersion image. We present the detailed workflow of LAPSS and compare the performance of LAPSS with PLAS (which has proven to be superior to the frequency–wavenumber method, spatial autocorrelation method, refraction microtremor and multichannel analysis of passive surface waves) in achieving unbiased dispersion image with different noise source distributions through synthetic tests. The results show that the accuracy of the two methods is comparable, but LAPSS greatly improves the computational efficiency, has stronger generalizability and depends on weaker assumptions. Finally, a field experiment is conducted to verify the feasibility and effectiveness of LAPSS in obtaining unbiased dispersion images using a fully linear array.
Marine Life 2030: building global knowledge of marine life for local action in the Ocean Decade
Authors: Muller-Karger Frank E , Canonico Gabrielle , Aguilar Claudia Baron , Bax Nicholas J , Appeltans Ward , Yarincik Kristen , Leopardas Venus , Sousa-Pinto Isabel , Nakaoka Masahiro , Aikappu Akkeshi , Giddens Jonatha , Heslop Emma , Montes Enrique , Duffy J Emmett 
Published: April 2022

AbstractMarine Life 2030 is a programme endorsed by the United Nations Decade of Ocean Science for Sustainable Development (the Ocean Decade) to establish a globally coordinated system that delivers knowledge of ocean life to those who need it, promoting human well-being, sustainable development, and ocean conservation. It is an open network to unite existing and new programmes into a co-designed, global framework to share information on methods, standards, observations, and applications. Goals include realizing interoperable information and transforming the observation and forecasting of marine life for the benefit of all people. Co-design, sharing local capacity, and coordination between users of ocean resources across regions is fundamental to enable sustainable use and conservation. A novel, bottom-up networking structure is now engaging members of the ocean community to address local issues, with Marine Life 2030 facilitating the linkage between groups across different regions to meet the challenges of the Ocean Decade. A variety of metrics, including those proposed by the Group on Earth Observations, will be used to track the success of the co-design process.
Professionalism development and assessment in the pre-registration pharmacist placement in England: transformative moments and maturation periods
Authors: Ireland Helen , Sowter Julie , O’Rourke Rebecca 
Published: April 2022

Abstract

Objectives
Development of new patient-facing roles for pharmacists and reports of poor patient care in the UK has led to questions concerning how pharmacists develop professionalism. This study explored how professionalism is developed and assessed during the post-graduation year in practice or pre-registration placement. The perspectives of two staff at the professional regulator UK (General Pharmaceutical Council), eight service users, seven pre-registration trainees, and 12 pre-registration tutors were recruited.

Methods
An interpretative paradigm was adopted. Data collection involved a semi-structured group interview, focus groups and a qualitative e-questionnaire. An inductive reasoning approach informed data analysis and interpretation.

Key findings
All groups provided insights into examples of transformative moments which potentiated professionalism development, the first being awarding the ‘pre-registration trainee’ title. All groups reported that contact with patients and trainee reflection aided professionalism maturation from a ‘self-centred student’ to becoming a ‘responsible professional’ where more than ‘doing’ is demanded. Furthermore, tutors stated the rate of professionalism development was affected by the sector of training and its opportunities for patient contact. Tutors felt they alone, not the registration exam, assessed professionalism using a variety of assessment approaches. Importantly, no tutors reported patient involvement in the assessment of trainees’ professionalism, yet service users expected to be involved.

Conclusions
Transformative moments and maturation periods during pre-registration training develop professionalism and enable trainees to ‘become’ a pharmacist. Careful planning of placements to optimise professionalism development across pharmacy sectors and consistent patient involvement in assessing trainee professionalism is recommended.
Bootstrap prediction intervals with asymptotic conditional validity and unconditional guarantees
Authors: Zhang Yunyi , Politis Dimitris N 
Published: April 2022

AbstractIt can be argued that optimal prediction should take into account all available data. Therefore, to evaluate a prediction interval’s performance one should employ conditional coverage probability, conditioning on all available observations. Focusing on a linear model, we derive the asymptotic distribution of the difference between the conditional coverage probability of a nominal prediction interval and the conditional coverage probability of a prediction interval obtained via a residual-based bootstrap. Applying this result, we show that a prediction interval generated by the residual-based bootstrap has approximately $50\%$ probability to yield conditional under-coverage. We then develop a new bootstrap algorithm that generates a prediction interval that asymptotically controls both the conditional coverage probability as well as the possibility of conditional under-coverage. We complement the asymptotic results with several finite-sample simulations.
Preserved Mucosal-Associated Invariant T Cells in the Cervical Mucosa of HIV-Infected Women with Dominant Expression of the TRAV1-2–TRAJ20 T Cell Receptor α-Chain
Authors: Gibbs Anna , Healy Katie , Kaldhusdal Vilde , Sundling Christopher , Franzén-Boger Mathias , Edfeldt Gabriella , Buggert Marcus , Lajoie Julie , Fowke Keith R , Kimani Joshua , Kwon Douglas S , Andersson Sonia , Sandberg Johan K , Broliden Kristina , Davanian Haleh , Chen Margaret Sällberg , Tjernlund Annelie 
Published: April 2022

Abstract

Background
Mucosa-associated invariant T (MAIT) cells are innate-like T cells with specialized antimicrobial functions. Circulating MAIT cells are depleted in chronic human immunodeficiency virus (HIV) infection, but studies examining this effect in peripheral tissues, such as the female genital tract, are lacking.

Methods
Flow cytometry was used to investigate circulating MAIT cells in a cohort of HIV-seropositive (HIV+) and HIV-seronegative (HIV−) female sex workers (FSWs), and HIV− lower-risk women (LRW). In situ staining and quantitative polymerase chain reaction were performed to explore the phenotype of MAIT cells residing in paired cervicovaginal tissue. The cervicovaginal microbiome was assessed by means of 16S ribosomal RNA gene sequencing.

Results
MAIT cells in the HIV+ FSW group were low in frequency in the circulation but preserved in the ectocervix. MAIT cell T-cell receptor gene segment usage differed between the HIV+ and HIV− FSW groups. The TRAV1-2–TRAJ20 transcript was the most highly expressed MAIT TRAJ gene detected in the ectocervix in the HIV+ FSW group. MAIT TRAVJ usage was not associated with specific genera in the vaginal microbiome.

Conclusions
MAIT cells residing in the ectocervix are numerically preserved irrespective of HIV infection status and displayed dominant expression of TRAV1-2–TRAJ20. These findings have implications for understanding the role of cervical MAIT cells in health and disease.
Genomic surveillance and antimicrobial resistance in Neisseria gonorrhoeae isolates in Bangkok, Thailand in 2018
Authors: Golparian Daniel , Kittiyaowamarn Rossaphorn , Paopang Porntip , Sangprasert Pongsathorn , Sirivongrangson Pachara , Franceschi Francois , Jacobsson Susanne , Wi Teodora , Unemo Magnus 
Published: April 2022

Abstract

Objectives
Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a substantial global public health problem. Gonococcal infections acquired in or from Asia represent most verified ceftriaxone treatment failures, and several ceftriaxone-resistant strains have emerged in Asia and subsequently spread globally. Additionally, in Thailand the gonorrhoea incidence remains high. Herein, we investigate the genomic diversity, AMR and AMR determinants in gonococcal isolates cultured in 2018 in Bangkok, Thailand.

Methods
Gonococcal isolates from males (n = 37) and females (n = 62) were examined by Etest and WGS. AMR determinants and molecular epidemiological STs were characterized. For phylogenomic comparison, raw sequence data were included from China (432 isolates), Japan (n = 270), Vietnam (n = 229), Thailand (n = 3), a global dataset (n = 12 440) and the 2016 WHO reference strains plus WHO Q (n = 15).

Results
In total, 88, 66 and 41 different NG-MAST, NG-STAR and MLST STs, respectively, and 31 different NG-STAR clonal complexes were found. A remarkably high frequency (88%) of β-lactamase TEM genes was detected and two novel TEM alleles were found. The phylogenomic analysis divided the isolates into the previously described lineages A and B, with a large proportion of Thai isolates belonging to the novel sublineage A3.

Conclusions
We describe the first molecular epidemiological study using WGS on gonococcal isolates from Thailand. The high prevalence of AMR and AMR determinants for ciprofloxacin, tetracycline and benzylpenicillin, and some strains belonging to clones/clades especially in sublineage A2 that are prone to develop resistance to extended-spectrum cephalosporins (ESCs) and azithromycin, should prompt continued and strengthened AMR surveillance, including WGS, of N. gonorrhoeae in Thailand.
Supporting Micro-enterprise in Humanitarian Programming: Impact Evaluation of Business Grants versus Unconditional Cash Transfer
Authors: Abdullahi Arays , Ali Mohamed , Kipchumba Elijah , Sulaiman Munshi 
Published: April 2022

Abstract
Humanitarian programming in fragile economies often use unconditional cash transfers (UCTs) to offset food insecurity. However, there is an increasing focus on using cash transfers to boost household incomes beyond the short-term through micro-enterprise start-up and growth. This paper conducts a randomised control trial to measure the impact of three different sizes of business grants against UCT in Somalia. We find that giving the same amount of money as a lump sum business grant results in higher likelihood of business ownership and income compared with UCT in the short run (3–4 months after the transfers). However, the impacts are larger and persist 3 years later only for those who received larger amount of grants. The results indicate our ‘medium’-sized grant being more cost-effective.
The effects of competition law on inequality—an incidental by-product or a path for societal change?
Authors: Ezrachi Ariel , Zac Amit , Decker Christopher 
Published: April 2022

ABSTRACT
Rising economic inequality presents society with unprecedented challenges. Direct instruments designed to address these worrying trends have often under performed. As a result, we find ourselves on a potentially dangerous and downward path. In this article we explore whether, in parallel to other efforts to mitigate the rise of inequality, there can be a role for competition law in the quest to reduce the widening inequality gap. We begin by outlining the possible relationship between competition law enforcement, market power, and economic inequality. We supplement the theoretical discussion with a review of empirical analysis of these linkages. We look at macro and micro data and emphasize the role of labour compensation as a key mechanism which links competition law enforcement, competition dynamics, and economic inequality. We then reflect on the policy implications and possible means to utilize competition enforcement in a manner that could reduce economic inequality.
Electronic blood glucose monitoring impacts on provider and patient behavior
Authors: Root Allyson , Connolly Christopher , Majors Season , Ahmed Hassan , Toma Mattie 
Published: April 2022

Abstract

Objective
Recent technological development along with the constraints imposed by the coronavirus disease 2019 (COVID-19) pandemic have led to increased availability of patient-generated health data. However, it is not well understood how to effectively integrate this new technology into large health systems. This article seeks to identify interventions to increase utilization of electronic blood glucose monitoring for patients with diabetes.

Materials and Methods
A large randomized controlled trial tested the impact of multiple interventions to promote use of electronic blood glucose tracking. The total study sample consisted of 7052 patients with diabetes across 68 providers at 20 selected primary care offices. The design included 2 stages: First, primary care practices were randomly assigned to have their providers receive education regarding blood glucose flowsheet orders. Then, patients in the treated practices were assigned to 1 of 4 reminder interventions.

Results
Provider education successfully increased provider take-up of an online blood glucose monitoring tool by 64 percentage points, while a comparison of reminder interventions revealed that emphasizing accountability to the provider encouraged patients to track their blood glucose online. An assessment of downstream outcomes revealed impacts of the interventions on prescribing behavior and A1c testing frequency.

Discussion
It is important to understand how health systems can practically promote take-up and awareness of emerging digital health alternatives or those with persistently low utilization in clinical settings.

Conclusion
These results indicate that provider training and support are critical first steps to promote utilization of patient-generated health data, and that patient communications can provide further motivation.
The Pursuit of Meaning and the Preference for Less Expensive Options
Authors: Mead Nicole L , Williams Lawrence E 
Published: April 2022

AbstractFinding meaning in life is a fundamental human motivation. Along with pleasure, meaning is a pillar of happiness and well-being. Yet, despite the centrality of this motive, and despite firms’ attempts to appeal to this motive, scant research has investigated how the pursuit of meaning influences consumer choice, especially in comparison to the study of pleasure. While previous perspectives would suggest that the pursuit of meaning tilts consumers toward high-quality products, we predicted and found the opposite. As compared to a pleasure or (no goal) baseline condition, six studies demonstrate that the pursuit of meaning causes people to consider how they can otherwise use their money (opportunity costs) which in turn leads to a preference for less expensive goods. This effect is robust across multiple product categories and usage situations, including both experiential and material purchases, and is obtained even when the more expensive product is perceived to deliver greater meaning. For participants pursuing meaning, making opportunity costs salient has no effect on their choices, and encouraging opportunity cost neglect increases their willingness to pay for a more expensive item. This research thus provides an initial answer as to how the pursuit of meaning shapes consumer choice processes and preferences.
A De Novo Chromosome-Level Genome Assembly of the White-Tailed Deer, Odocoileus Virginianus
Authors: London Evan W , Roca Alfred L , Novakofski Jan E , Mateus-Pinilla Nohra E 
Published: April 2022

Abstract
Cervids are distinguished by the shedding and regrowth of antlers. Furthermore, they provide insights into prion and other diseases. Genomic resources can facilitate studies of the genetic underpinnings of deer phenotypes, behavior, and disease resistance. Widely distributed in North America, the white-tailed deer (Odocoileus virginianus) has recreational, commercial, and food source value for many households. We present a genome generated using DNA from a single Illinois white-tailed sequenced on the PacBio Sequel II platform and assembled using Wtdbg2. Omni-C chromatin conformation capture sequencing was used to scaffold the genome contigs. The final assembly was 2.42 Gb, consisting of 508 scaffolds with a contig N50 of 21.7 Mb, a scaffold N50 of 52.4 Mb, and a BUSCO complete score of 93.1%. Thirty-six chromosome pseudomolecules comprised 93% of the entire sequenced genome length. A total of 20 651 predicted genes using the BRAKER pipeline were validated using InterProScan. Chromosome length assembly sequences were aligned to the genomes of related species to reveal corresponding chromosomes.