bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using visual scores and categorical data for genomic prediction of complex traits in breeding programs
Authors: Ferreira Azevedo Camila , Ferrão Luis Felipe Ventorim , Benevenuto Juliana , de Resende Marcos Deon Vilela , Nascimento Moyses , Campana Nascimento Ana Carolina , Munoz Patricio 
Published: March 2023

AbstractMost genomic prediction methods are based on assumptions of normality due to their simplicity, robustness, and ease of implementation. However, in plant and animal breeding, target traits are often collected as categorical data, thus violating the normality assumption, which could affect the prediction of breeding values and the estimation of crucial genetic parameters. In this study, we examined the main challenges of categorical phenotypes in genomic prediction and genetic parameter estimation using mixed models, Bayesian approaches, and machine learning techniques. We evaluated these approaches using simulated and real breeding data sets. Our contribution in this study is a five-fold demonstration: (i) collecting data using an intermediate number of categories (1 to 3 and 1 to 5 scores) is the best strategy, even considering errors and subjectivity associated with visual scores; (ii) in the context of genomic prediction, Linear Mixed Models and Bayesian Linear Regression Models are robust to the normality violation, but marginal gains can be achieved when using Bayesian Ordinal Regression Models (BORM) and Random Forest Classification technique; (iii) genetic parameters are better estimated using BORM; (iv) our conclusions using simulated data are also applicable to real data in autotetraploid blueberry, which can guide breeders’ decisions; and (v) a comparison of continuous and categorical phenotype testing for complex traits with low heritability, found that investing in the evaluation of 600-1000 categorical data points with low error, when it is not feasible to collect continuous phenotypes, is a strategy for improving predictive abilities. Our findings suggest the best approaches for effectively using categorical traits to explore genetic information in breeding programs, and highlight the importance of investing in the training of evaluator teams and in high-quality phenotyping.Key messageAn approach for handling categorical data with potential errors and subjectivity in scores was evaluated in simulated and blueberry recurrent selection breeding schemes to assist breeders in their decision-making.
The two-component regulator WalKR provides an essential link between cell wall homeostasis with DNA replication inStaphylococcus aureus
Authors: Sharkey Liam K. R. , Guerillot Romain , Walsh Calum , Turner Adrianna M. , Lee Jean Y. H. , Neville Stephanie L. , Klatt Stephan , Baines Sarah L. , Pidot Sacha , Rossello Fernando J. , Seemann Torsten , McWilliam Hamish , Cho Ellie , Carter Glen P. , Howden Benjamin P. , McDevitt Christopher A. , Hachani Abderrahman , Stinear Timothy P. , Monk Ian R. 
Published: March 2023

AbstractAmong the 16 two-component systems (TCSs) in the opportunistic human pathogenStaphylococcus aureus, only WalKR is essential. Like orthologous systems in other Bacillota,S. aureusWalKR controls autolysins involved in peptidoglycan remodelling and is therefore intimately involved in cell division. However, despite the importance of WalKR inS. aureus, the basis for its essentiality is not understood and the regulon poorly defined. Here, we defined a consensus WalR DNA-binding motif and the direct WalKR regulon by using functional genomics, including ChIP-seq, with a panel of isogenicwalKRmutants that had a spectrum of altered activities. Consistent with prior findings, the direct regulon includes multiple autolysin genes. However, this work also revealed that WalR directly regulates at least five essential genes involved in lipoteichoic acid synthesis (ltaS); translation(rplK); DNA compaction (hup); initiation of DNA replication (dnaA, hup); and purine nucleotide metabolism (prs). Thus, WalKR inS. aureusserves as a polyfunctional regulator that contributes to fundamental control over critical cell processes by co-ordinately linking cell wall homeostasis with purine biosynthesis, protein biosynthesis, and DNA replication. Collectively, our findings address the essentiality of this locus and highlight the importance of WalKR as abona fidetarget for novel anti-staphylococcal therapeutics.
First in family Rhabdiasidae: the reference-guided genome assembly of an invasive parasite, the cane toad lungworm (Rhabdias pseudosphaerocephala)
Authors: Eyck Harrison JF. , Edwards Richard J. , Brown Gregory P. , Shine Richard , Rollins Lee A. 
Published: March 2023

AbstractRhabdias pseudosphaerocephalais a well-studied invasive nematode parasite of amphibians. However, there are several outstanding questions aboutR. pseudosphaerocephalathat are best answered using genomic data. This species differs phenotypically across its invasive range. These differences are challenging to interpret because this species is part of a complex that is diverse and cryptic in its home-range, and we do not know how many species from this complex originally colonised Australia. For this reason, it is unknown whether the phenotypic differences across the introduced range are due to intraspecific differentiation between populations or due to the presence of multiple species. In addition, there is little consensus in the placement of Rhabdiasidae family within the phylum Nematoda, making it difficult to perform comparative analyses with other nematodes. Within this paper, we assemble a reference genome forR. pseudosphaerocephala, the first assembly of any Rhabdiasidae species. We then use resequencing data to address outstanding questions about this species. Specifically, we combine population genetic and phylogenetic analyses to determine that there is likely only a singleR. pseudosphaerocephalalineage within Australia, and identify that the invasive range population is closely related to home rage isolates that infect similar host species. We present compelling evidence for a genetic bottleneck following introduction to Australia and genetic differentiation occurring between invasive range populations. We then use genome-scale phylogenomic analysis to place the Rhabdiasidae family in the suborder Rhabditina. Ultimately, this paper brings the study of Rhabdiasidae into the genomic era, and sheds light on its ancient and modern evolutionary history.
SARS-CoV-2 surveillance between 2020 and 2021 of all mammalian species in two Flemish zoos (Antwerp Zoo and Planckendael Zoo)
Authors: Joffrin Léa , Cooreman Tine , Verheyen Erik , Vercammen Francis , Mariën Joachim , Leirs Herwig , Gryseels Sophie 
Published: March 2023

ABSTRACTThe COVID-19 pandemic has led to millions of human infections and deaths worldwide. Several other mammal species are also susceptible to SARS-CoV-2, and multiple instances of transmission from humans to pets, farmed mink, wildlife and zoo animals have been recorded. We conducted a systematic surveillance of SARS-CoV-2 in all mammal species in two zoos in Belgium between September and December 2020 and July 2021 in four sessions, and a targeted surveillance of selected mammal enclosures following SARS-CoV-2 infection in hippos in December 2021. A total of 1523 faecal samples were tested for SARS-CoV-2 via real-time PCR. None of the samples tested positive for SARS-CoV-2. Additional surrogate virus neutralization tests conducted on 50 routinely collected serum samples during the same period were all negative. This study is a first to our knowledge to conduct active SARS-CoV-2 surveillance for several months in all mammal species of a zoo. We conclude that at the time of our investigation, none of the screened animals were excreting SARS-CoV-2.
Mechanical Properties of DNA Double-Crossover Motif
Authors: Matoušková Eva , Růžička Michal , Réblová Kamila , Lankaš Filip 
Published: March 2023

AbstractThe double-crossover (DX) motif is a key building block of DNA nanostructures. It connects two double helices by two closely spaced Holliday junctions. Despite its prominent importance, the structure and elasticity of the DX motif is not fully understood. Here we employ extensive all-atom molecular dynamics (MD) simulations of an antiparallel DNA DX motif with two full turns between crossovers to infer its global structure and deformability. We quantitatively reproduce the experimentally known two-fold increase of bending stiffness upon incorporation of a DNA duplex into the DX motif, and find out that its stretching and twisting stiffness are only slightly influenced. To further describe the motif, we define four effective rigid bodies, each involving several base pairs flanking the Holliday junctions from the outside, and consider internal coordinates capturing relative displacement and orientation of the bodies. Time series of the coordinates from MD then yield the global structure of the DX motif and its stiffness in the harmonic approximation.
“Then someone takes my picture…” and other disrupted (drinking) stories: constructing narratives about alcohol and intoxication among young Muslim women in Denmark
Authors: Bærndt Marie Fjellerup 
Published: March 2023

Purpose
This paper aims to explore the existence of drinking stories among young Muslim women in Denmark. More specifically, the author investigates the significance of having a double audience (one Muslim, one Danish) for the construction of narratives about alcohol and intoxication.

Design/methodology/approach
The paper draws on qualitative data from semi-structured in-depth interviews with 32 young Muslim women (average age 23 years) and uses the analytical concept of storytelling.

Findings
Firstly, the narratives are qualitatively different from majority narratives, revealing distinct Muslim minority experiences. Secondly, the stories are disrupted in more serious ways than majority drinking stories. Lastly, for some young women, there is no wriggle room, and rather than being part of stories of intoxication, they subvert the drinking story into sober narratives to uphold respectable norms around alcohol while being both Muslim and Danish.

Originality/value
This research is unique in its focus on alcohol and parties among Muslim minority youth in a white-majority country. The narratives would usually be overlooked in a drinking story context because of the association between Muslims and abstinence and because the drinking story literature originates from a narrower focus on young white men’s experiences. Including more ethnic, religious and gender-diverse minorities in future research on drinking stories will challenge our knowledge in the field and add much-needed nuances.
From affective polarization to fruitful politics: a new public leadership inspired by the UN's 2030 Agenda
Authors: Romero-Martín Gonzalo , Caraballo-Pou María Ángeles , Merchán-Hernández Carmen 
Published: March 2023

PurposeWho leads and the purpose of public leadership matter. The aim of this viewpoint essay is to examine the fundamentals of public policy design and implementation as well as contemporary public leadership from a new approach inspired by the 2030 Agenda. This work provides a more humanistic and fruitful approach to public leadership, which is crucial in the current context of social division, turbulent politics and weak and infertile leadership.Design/methodology/approachThis viewpoint essay is based on academic literature as well as on institutional reports to explore the 2030 Agenda's potential when it comes to outlining a new style of public leadership.FindingsThe 2030 potential has always been analyzed from the different synergies that can be established from the 17 Sustainable Development Goals (SDGs). Nevertheless, this essay proposes to separate from the mainstream discourse by outlining six core properties of the 2030 Agenda as key elements that implicate a new roadmap in the design and evaluation of public policies and contribute in a disruptive way to conceive public leadership.Originality/valueThis essay offers an innovative leadership framework that integrates key elements from the 2030 Agenda perspective with theoretical and practical notions of policy-making and public leadership to overcome the main challenges of the present and future days.
Transcriptome profiles and chromatin states in mouse androgenetic haploid embryonic stem cells
Authors: Zheng Weisheng , Wang Liping , He Wenteng , Hu Xinjie , Zhu Qianshu , Gu Liang , Jiang Cizhong 
Published: March 2023

AbstractHaploid embryonic stem cells (haESCs) are derived from the inner cell mass of the haploid blastocyst, containing only one set of chromosomes. Extensive and accurate chromatin remodelling occurs during haESC derivation, but the intrinsic transcriptome profiles and chromatin structure of haESCs have not been fully explored. We profiled the transcriptomes, nucleosome positioning, and key histone modifications of four mouse haESC lines, and compared these profiles with those of other closely‐related stem cell lines, MII oocytes, round spermatids, sperm, and mouse embryonic fibroblasts. haESCs had transcriptome profiles closer to those of naïve pluripotent stem cells. Consistent with the one X chromosome in haESCs, Xist was repressed, indicating no X chromosome inactivation. haESCs and ESCs shared a similar global chromatin structure. However, a nucleosome depletion region was identified in 2056 promoters in ESCs, which was absent in haESCs. Furthermore, three characteristic spatial relationships were formed between transcription factor motifs and nucleosomes in both haESCs and ESCs, specifically in the linker region, on the nucleosome central surface, and nucleosome borders. Furthermore, the chromatin state of 4259 enhancers was off in haESCs but active in ESCs. Functional annotation of these enhancers revealed enrichment in regulation of the cell cycle, a predominantly reported mechanism of haESC self‐diploidization. Notably, the transcriptome profiles and chromatin structure of haESCs were highly preserved during passaging but different from those of differentiated cell types.
Progress of metabolomics in atopic dermatitis: a systematic review
Authors: Zhang Lishan , Zeng Yueping , Sun Jinlyu 
Published: March 2023

SummaryAtopic dermatitis (AD), a chronic inflammatory skin disorder characterized by recurrent eczema and intense pruritus, is a major skin‐related burden worldwide. The diagnosis and treatment of AD is often challenging due to the high heterogeneity of AD, and its exact etiology is unknown. Metabolomics offers the opportunity to follow continuous physiological and pathological changes in individuals, which allows accurate diagnosis and management as well as providing deep insights into the etiopathogenesis of AD. Several metabolomic studies of AD have been published over the past few years. The aim of this review is to summarize these findings and help researchers to understand the rapid development of metabolomics for AD.A comprehensive and systematic search was performed using the PubMed, Embase, Cochrane Library and Web of Science databases. Twenty‐six papers were finally included in the review after quality assessment. Significant differences in metabolite profiles were found between patients with AD and healthy individuals.This study provides a comprehensive overview of metabolomic research in AD. A better understanding of the metabolomics of AD may offer novel diagnostic, prognostic, and therapeutic approaches.
First record in Europe of the Asian gobiid, shimofuri (marbled) goby Tridentiger bifasciatus Steindachner, 1881
Authors: Verhelst Pieterjan , Verreycken Hugo 
Published: March 2023

AbstractIn November 2022, two shimofuri (marbled) gobies Tridentiger bifasciatus Steindachner, 1881 were caught in the Gent–Terneuzen shipping canal, Belgium. It is the first record of the species in Europe. Outside its native distribution area in Japan, China and South Korea, thus far the shimofuri goby has been observed only on the West Coast of the USA, where established populations exist. The introduction vector potentially was ballast water exchange.
Pediatric hidradenitis suppurativa: Describing care patterns in the emergency department
Authors: Lambert Raphaella A. , Stein Sarah L. 
Published: March 2023

AbstractBackground/ObjectivesThe emergency department (ED) is a common point of care for many pediatric hidradenitis suppurativa (HS) patients; however, ED care may not align with recommended treatment standards. The objective of this study is to describe the care pediatric HS patients receive in the ED compared to both HS management guidelines and the management of pediatric skin and soft tissue abscess (SSTA) patients.MethodsWe performed a retrospective chart review of pediatric HS and SSTA patients who presented to a single pediatric ED. Demographic and ED encounter data including medications, procedures, recommendations, consults, and referrals were collected.Results58 HS and 175 SSTA charts were reviewed. 69.5% of patients were female and 93.6% were African American/Black. 29.3% of HS and 61.7% of SSTA encounters involved incision and drainage (I&D); 62.1% of HS and 70.1% of SSTA encounters involved the prescription or administration of oral clindamycin; 3.4% of HS and 0.6% of SSTA encounters involved dermatology consultation in the ED; and 22.4% of HS and 5.1% of SSTA encounters involved outpatient referrals to dermatology.ConclusionsOur data reveal a pediatric HS and SSTA population that is predominantly female and African American/Black. Significant differences were found in the average ages and number of lesions between HS and SSTA patients. I&D and oral clindamycin were the most common treatments across groups; however, I&D was performed significantly more frequently among SSTA encounters than HS encounters. Our results suggest that subtle knowledge gaps may exist in ED provider management of pediatric HS.
Evaluation of finger weeder safety and efficacy for intra‐row weed removal in irrigated field crops
Authors: Asaf Evyatar , Rozenberg Gal , Shulner Itai , Eizenberg Hanan , Lati Ran Nisim 
Published: March 2023

AbstractIncreased demand for pesticide‐free food and the development of herbicide‐resistant weed populations have created a need for non‐chemical weed‐control tools. A candidate mechanical tool for controlling weeds in the seeding line (intra‐row zone) is the finger weeder. This study thus aimed to evaluate the safety and weed‐control efficacy of the finger weeder in various irrigated field crops. Eight field trials were conducted in processing tomato, sweet corn, sunflower, cotton, and beetroot over 2 years. The finger weeder treatments were applied as the sole weed‐control method (single or double treatments) and in combination with herbicides. A mini meta‐analysis was used to evaluate the overall effect of the finger weeder treatments on crop stand and yield and on weed control efficacy. Weed density in the control not treated with herbicides nor a finger weeder ranged between 2 and 62 weeds m−2. The finger weeder treatments resulted in a significant reduction in weed density, which ranged between 40% and 90%. The weed density following the double finger weeder treatment was not significantly different from that for the conventional herbicide‐based treatment (p = 0.32) and could therefore be considered as an effective environmentally friendly alternative. Furthermore, a single FW treatment integrated with herbicide application gave better weed control than the conventional herbicide treatment (p = 0.04). This treatment was safe for the crops with no significant stand (p = 0.19) or yield (p = 0.29) reductions compared to commercial treatment. The results of this study demonstrate the promise of the finger weeder as an effective tool within integrated weed management systems for conventional agro‐systems. The tool offers a rational weed‐control solution for sustainable systems under irrigation.
Supplemental Material: Reconstructing the erosional and tectonic record of Laramide contraction to Rio Grande rift extension, southern Indio Mountains, western Texas, USA
Authors: Conley A. , Ricketts J.W. , al. et 
Published: March 2023

<p>Text File S1: Description of all map units that are shown on Plates 1 and 2 and are described in the text and figures; <sup>40</sup>Ar/<sup>39</sup>Ar methods and fault measurements and locations. Dataset S1 and Table S1: <sup>40</sup>Ar/<sup>39</sup>Ar data tables and thermochronology modeling parameters. </p>
The Dualistic Trends of Sinophobia and Sinophilia: Impact on Foreign Policy Towards China
Authors: Jain Shree , Chakrabarti Sukalpa 
Published: March 2023

The People’s Republic of China has invited both fascination and fear, admiration and contempt in the last few years. Various public opinion surveys’ data findings reveal a nuanced and conflicted phenomenon of ‘Sinophobia’ and ‘Sinophillia’ across the world nations. One view of China is that of an ‘autocratic,’ ‘anti-democratic’ regime provoking anxiety and suspicion reflected in a trending wave of anti-China sentiments evolving into ‘Sinophobia,’ with its prevalence and intensity highlighted in increasing cases of racism and violence towards immigrant Chinese after the novel coronavirus outbreak. The growing intensity of Sinophobia is noticed in countries witnessing a barging influx of Chinese investment with Chinese land grabs and the loss of native jobs. However, another view is of a nation that inspires vast admiration for its economic ascent and traditional culture. Today, China has an increasing appeal and attraction not just for its economic engagement but also for its culture, language and tourism.  Public perceptions and opinions are critical factors in determining a state’s foreign policy preferences and choices. This qualitative study utilises various global surveys and public opinion polls to gauge the dualistic trends of public opinion on China and examines the salience of public opinion in foreign relations, underlining a pluralist approach. The article illustrates multiple cases highlighting how negative or positive public opinion of China is correlated with an aggressive or friendly foreign policy posture towards China.
Comply while keeping your autonomy, or the art of managing paradox through dialogue
Authors: Ragaigne Aurélien 
Published: March 2023

Our paper analyses the role of dialogue in managing the autonomy and compliance paradox within a public authority. The literature on paradoxes presents management as being characterised by the coexistence of contradictory elements. We propose to build on this work by drawing on the literature on the concept of ‘dialogue’. By focusing on the case of a French Departmental Council that set up a procedure to manage travel authorisations for its staff, we study the way in which the dialogue between stakeholders ensured both the application of the framework prescribed by the procedure and the autonomy of the management teams when it came to managing these rules on the ground. Using a longitudinal analysis methodology combining semi-directive interviews and observations of working group meetings, we show that this space for dialogue provides an important opportunity for a face-off between the demands for compliance and autonomy and their further evolution. Points for practitioners The research raises awareness among public managers of the importance of establishing forums as a way of managing the complementarity of the logics of autonomy and compliance. Discussion offers opportunities to explore together the different possibility of management. Our paper thus underlines the importance of the art of interaction and discussion between the stakeholders, by creating opportunities for brainstorming and convergence.