bluuebunny/crossref_metadata_2025_split huggingface dataset:
Consensus genomic regions for grain quality traits in wheat revealed by Meta‐QTL analysis and in silico transcriptome integration
Authors: Li Na , Miao Yongping , Ma Jingfu , Zhang Peipei , Chen Tao , Liu Yuan , Che Zhuo , Shahinnia Fahimeh , Yang Delong 
Published: May 2023

AbstractGrain quality traits are the key factors that determine the economic value of wheat and are largely influenced by genetics and the environment. In this study, using a meta‐analysis of quantitative trait loci (QTLs) and a comprehensive in silico transcriptome assessment, we identified key genomic regions and putative candidate genes for the grain quality traits protein content, gluten content, and test weight. A total of 508 original QTLs were collected from 41 articles on QTL mapping for the three quality traits in wheat published from 2003 to 2021. When these original QTLs were projected onto a high‐density consensus map consisting of 14,548 markers, 313 QTLs resulted in the identification of 64 MQTLs distributed across 17 of the 21 chromosomes. Most of the meta‐QTLs (MQTLs) were distributed on sub‐genomes A and B. Compared with the original QTLs, the confidence interval (CI) of the MQTLs was smaller, with an average CI of 4.47 cM, while the projected QTLs CI was 11.13 cM (2.49‐fold lower). The corresponding physical length of the MQTL ranged from 0.45 to 239.01 Mb. Thirty‐one of these 64 MQTLs were validated in at least one genome‐wide association study. In addition, five of the 64 MQTLs were selected and designated as core MQTLs. The 211 quality‐related genes from rice were used to identify wheat homologs in MQTLs. In combination with transcriptional and omics analyses, 135 putative candidate genes were identified from 64 MQTL regions. The findings should contribute to a better understanding of the molecular genetic mechanisms underlying grain quality and the improvement of these traits in wheat breeding.
Anicteric gall bladder rupture secondary to necrotising cholecystitis in a dog
Authors: Travail Victoria , Motta Claudio , Moreno‐Aguado Beatriz , Torres‐Canto Lucia , Juvet Florence 
Published: May 2023

AbstractA 4‐year‐old, female cocker spaniel was presented for investigation of acute onset of vomiting and lethargy. Pyrexia, abdominal discomfort and marked abdominal distension were detected during clinical examination. Clinicopathological findings revealed mild neutrophilia with band neutrophils. Biochemistry showed a mild hyperalbuminemia (40 g/L; reference: 23–35) and mild elevation of alanine aminotransferase (165 U/L; reference: 0–110). A computed tomography scan of the abdomen raised suspicion of gall bladder wall rupture secondary to necrotising cholecystitis, associated with marked peritoneal effusion and cholangitis with duodenitis. An exploratory laparotomy and cholecystectomy were performed, with intraoperative abdominal lavage. Histopathology revealed a necrotic gall bladder wall, and analysis and culture of the abdominal free fluid confirmed the presence of a septic exudate with growth of Escherichia coli. The dog was treated with potentiated amoxicillin and clinical signs resolved. Cases presenting with biliary tract rupture could occur without suggestive serum biochemistry findings.
A spectrum of explainable and interpretable machine learning approaches for genomic studies
Authors: Conard Ashley Mae , DenAdel Alan , Crawford Lorin 
Published: May 2023

AbstractThe advancement of high‐throughput genomic assays has led to enormous growth in the availability of large‐scale biological datasets. Over the last two decades, these increasingly complex data have required statistical approaches that are more sophisticated than traditional linear models. Machine learning methodologies such as neural networks have yielded state‐of‐the‐art performance for prediction‐based tasks in many biomedical applications. However, a notable downside of these machine learning models is that they typically do not reveal how or why accurate predictions are made. In many areas of biomedicine, this “black box” property can be less than desirable—particularly when there is a need to perform in silico hypothesis testing about a biological system, in addition to justifying model findings for downstream decision‐making, such as determining the best next experiment or treatment strategy. Explainable and interpretable machine learning approaches have emerged to overcome this issue. While explainable methods attempt to derive post hoc understanding of what a model has learned, interpretable models are designed to inherently provide an intelligible definition of their parameters and architecture. Here, we review the model transparency spectrum moving from black box and explainable, to interpretable machine learning methodology. Motivated by applications in genomics, we provide background on the advances across this spectrum, detailing specific approaches in both supervised and unsupervised learning. Importantly, we focus on the promise of incorporating existing biological knowledge when constructing interpretable machine learning methods for biomedical applications. We then close with considerations and opportunities for new development in this space.This article is categorized under:
Statistical Models > Nonlinear Models
Applications of Computational Statistics > Genomics/Proteomics/Genetics
Applications of Computational Statistics > Computational and Molecular Biology
A Broken National Consensus? EU Issue Voting and the Radical Right in Spain
Authors: Marcos-Marne Hugo 
Published: May 2023

AbstractThis chapter examines the extent to which European Union (EU) politicization exists in diverse media and is fostered by different political parties in Spain. It also delves into the dynamics of EU issue voting in national elections. To deal with the first issue, the chapter considers news published by two main newspapers in Spain, El País and El Mundo, and parliamentary discourses from all political parties with representation. As for the presence of EU issue voting, it utilizes survey data gathered online in May 2019. Results evidence an increase in the salience of EU issues after 2008 that declines again after 2012, and a not-so-clear pattern regarding negative mentions of the EU. However, it is evident that Euroscepticism never dominated public debates in Spain (more salience without more contestation). They also show that preferring less EU integration is associated with having voted for the radical-right VOX both in general and within-ideological-blocks comparisons. Implications and limitations of these results are considered in the conclusion section.
News vs. Opinion Articles on the European Union: The Politicisation of the EU in the Mainstream Press
Authors: Silva Tiago , Kartalis Yani 
Published: May 2023

AbstractThis chapter assesses the politicisation of the EU in six European countries, by looking at the media coverage of 29 legislative elections held between 2002 and 2017. Using a combination of automated and manual methods of content analysis, this chapter goes beyond the existing studies to examine how the Eurozone crises impacted the traditional media coverage of the EU not only in terms of magnitude but also in terms of framing and content. Using a unique dataset of 165,341 news items, from 12 mainstream newspapers, this study answers three questions relevant to the main goal of this book: (1) does EU politicisation vary between left- and right-leaning newspapers; (2) is there a difference between news and opinion articles in terms of EU salience and tone; (3) what dimensions of EU debates are more prevalent in the media. Our analysis shows that, after the crisis, the countries’ politicisation of the EU diverged more in terms of content than magnitude. However, when we only consider opinion articles, the differences within mainstream media, from the left and right, become more salient. These results confirm the role and importance of the media for EU politicisation and its potential impact on national politics.
Parties Acting Strategically: National Parliaments’ Role in Holding the EU Accountable
Authors: Kartalis Yani , Silva Tiago 
Published: May 2023

AbstractThe existing assessments of EU politicization have predominantly focused on the media and in the actors that are reported in that arena. This chapter offers a novel approach to the study of EU politicization by focusing, instead, on the institutional arena of six EU countries. Using the MAPLE dataset of parliamentary debates, with a total of 724,963 speeches covering a period of 20 years, this chapter offers a comparative and longitudinal analysis of EU politicization at the institutional level, assessing the impact that the Eurozone crisis had in the parliamentary debates of the EU. Automated and manual content analysis methods are used to answer three main questions: Has the EU been politicized at the institutional level? Did the Eurozone crisis affect the politicization of the EU in parliaments? What characteristics of political parties have determined the salience and contestation of the EU topic? Our results suggest that the EU has not been, in the past 20 years, a very salient nor contested topic at the institutional level. However, we find that the parties’ contribution to the democratic legitimacy of the European integration varies significantly, with the parties’ position on the EU topic being the strongest determinant of EU politicization.
Detection of Listeria monocytogenes in foods with a textile organic electrochemical transistor biosensor
Authors: Vizzini Priya , Beltrame Elena , Coppedè Nicola , Vurro Filippo , Andreatta Francesco , Torelli Emanuela , Manzano Marisa 
Published: May 2023

Abstract

Foods contaminated by pathogens are responsible for foodborne diseases which have socioeconomic impacts. Many approaches have been extensively investigated to obtain specific and sensitive methods to detect pathogens in food, but they are often not easy to perform and require trained personnel. This work aims to propose a textile organic electrochemical transistor-based (OECT) biosensor to detect L. monocytogenes in food samples. The analyses were performed with culture-based methods, Listeria Precis™ method, PCR, and our textile OECT biosensor which used poly(3,4-ethylenedioxythiophene) (PEDOT):polystyrene sulfonate (PSS) (PEDOT:PSS) for doping the organic channel. Atomic force microscopy (AFM) was used to obtain topographic maps of the gold gate. The electrochemical activity on gate electrodes was measured and related to the concentration of DNA extracted from samples and hybridized to the specific capture probe immobilized onto the gold surface of the gate. This assay reached a limit of detection of 1.05 ng/μL, corresponding to 0.56 pM of L. monocytogenes ATCC 7644, and allowed the specific and rapid detection of L. monocytogenes in the analyzed samples.

Keypoints
• Textile organic electrochemical transistors functionalized with a specific DNA probe
• AFM topographic and surface potential maps of a functionalized gold gate surface
• Comparison between the Listeria monocytogenes Precis™ method and an OECT biosensor
PET imaging of PARP expression using 68Ga-labelled inhibitors
Authors: Wang Xiangwei , Liu Wei , Li Ke , Chen Kaiwen , He Simin , Zhang Jianping , Gu Bingxin , Xu Xiaoping , Song Shaoli 
Published: May 2023

Abstract
Purpose
Imaging the PARP expression using 18F probes
has been approved in clinical trials. Nevertheless, hepatobiliary clearance of both 18F probes hindered their application in monitoring abdominal lesions. Our novel 68Ga-labelled probes aim for fewer abdominal signals while ensuring PARP targeting by optimizing the pharmacokinetic properties of radioactive probes.

Methods
Three radioactive probes targeted PARP were designed, synthesized, and evaluated based on the PARP inhibitor Olaparib. These 68Ga-labelled radiotracers were assessed in vitro and in vivo.

Results
Precursors that did not lose binding affinity for PARP were designed, synthesized, and then labelled with 68Ga in high radiochemical purity (> 97%). The 68Ga-labelled radiotracers were stable. Due to the increased expression of PARP-1 in SK-OV-3 cells, the uptake of the three radiotracers by SK-OV-3 cells was significantly greater than that by A549 cells. PET/CT imaging of the SK-OV-3 models indicated that the tumor uptake of 68Ga-DOTA-Olaparib (0.5 h: 2.83 ± 0.55%ID/g; 1 h: 2.37 ± 0.64%ID/g) was significantly higher than that of the other 68Ga-labelled radiotracers. There was a significant difference in the T/M (tumor-to-muscle) ratios between the unblocked and blocked groups as calculated from the PET/CT images (4.07 ± 1.01 vs. 1.79 ± 0.45, P = 0.0238 < 0.05). Tumor autoradiography revealed high accumulation in tumor tissues, further confirming the above data. PARP-1 expression in the tumor was confirmed by immunochemistry.

Conclusion
As the first 68Ga-labelled PARP inhibitor, 68Ga-DOTA-Olaparib displayed high stability and quick PARP imaging in a tumor model. This compound is thus a promising imaging agent that can be used in a personalized PARP inhibitor treatment regimen.
Nd:YAG/Er:YAG dual laser vs. topical steroid to treat vulvar lichen sclerosus: study protocol of a randomized controlled trial
Authors: Viereck Volker , Gamper Marianne , Regauer Sigrid , Walser Claudia , Zivanovic Irena 
Published: May 2023

Abstract
Purpose
Vulvar lichen sclerosus (LS) is a chronic debilitating inflammatory skin disease. Today, the gold standard is a life-long topical steroid treatment. Alternative options are highly desired. We present a study protocol of a prospective, randomized, active-controlled, investigator-initiated clinical trial comparing a novel non-invasive dual Nd:YAG/Er:YAG laser therapy with the gold standard for the management of LS.

Methods
We recruited 66 patients, 44 in the laser arm and 22 in the steroid arm. Patients with a physician-administered clinical LS score ≥ 4 were included. Participants received either four laser treatments 1–2 months apart, or 6 months of topical steroid application. Follow-ups were planned at 6, 12, and 24 months. The primary outcome looks at the efficacy of the laser treatment at the 6-month follow-up. Secondary outcomes look at comparisons between baseline and follow-ups within the laser or the steroid arm, and comparisons between laser vs. steroid arm. Objective (LS score, histopathology, photo documentation) and subjective (Vulvovaginal Symptoms Questionnaire, symptom VAS score, patient satisfaction) measurements, tolerability, and adverse events are evaluated.

Conclusion
The findings of this trial have the potential to offer a novel treatment option for LS. The standardized Nd:YAG/Er:YAG laser settings and the treatment regime are presented in this paper.

Clinical trial identification number
NCT03926299.
Drivers of Batrachochytrium dendrobatidis infection load, with evidence of infection tolerance in adult male toads (Bufo spinosus)
Authors: Bosch Jaime , Thumsová Barbora , Puschendorf Robert , Bielby Jon 
Published: May 2023

AbstractChytridiomycosis is affecting hundreds of amphibian species worldwide, but while in tropical areas, adult individuals have been the focus of most investigations, the exact role played by infection intensity of breeding adults is not well understood in temperate areas. We conducted mark–recapture–capture surveys during spiny common toad breeding seasons from 2006 to 2018 at the site of the first recorded outbreak of chytridiomycosis in Europe, the Peñalara Massif (Sierra de Guadarrama National Park, central Spain), and collected infection samples and several variables related to the reproductive effort of male individuals. We used general linear mixed models to evaluate the contribution of study variables on the infection loads of adult male toads exhibited at their capturing date. We also analysed the differences on several male characteristics between the pond with the largest breeding population against the rest of the ponds. We found that the duration of time spent in the waterbody and the condition of the host predicted infection loads. Animals of good physical condition, that spent longer in water, have higher infection levels than individuals with the opposite set of traits. The pond supporting the largest breeding population housed smaller male toads and in poorer condition. Our results are consistent with a shift in reproductive strategy in response to infection and potentially a strategy of tolerance, rather than resistance to infection. These findings have applications for disease mitigation and theoretical implications related to the trade-offs made and the evolution of traits in response to the disease.
Ensuring privacy protection in the era of big laparoscopic video data: development and validation of an inside outside discrimination algorithm (IODA)
Authors: Schulze A. , Tran D. , Daum M. T. J. , Kisilenko A. , Maier-Hein L. , Speidel S. , Distler M. , Weitz J. , Müller-Stich B. P. , Bodenstedt S. , Wagner M. 
Published: May 2023

Abstract
Background
Laparoscopic videos are increasingly being used for surgical artificial intelligence (AI) and big data analysis. The purpose of this study was to ensure data privacy in video recordings of laparoscopic surgery by censoring extraabdominal parts. An inside-outside-discrimination algorithm (IODA) was developed to ensure privacy protection while maximizing the remaining video data.

Methods
IODAs neural network architecture was based on a pretrained AlexNet augmented with a long-short-term-memory. The data set for algorithm training and testing contained a total of 100 laparoscopic surgery videos of 23 different operations with a total video length of 207 h (124 min ± 100 min per video) resulting in 18,507,217 frames (185,965 ± 149,718 frames per video). Each video frame was tagged either as abdominal cavity, trocar, operation site, outside for cleaning, or translucent trocar. For algorithm testing, a stratified fivefold cross-validation was used.

Results
The distribution of annotated classes were abdominal cavity 81.39%, trocar 1.39%, outside operation site 16.07%, outside for cleaning 1.08%, and translucent trocar 0.07%. Algorithm training on binary or all five classes showed similar excellent results for classifying outside frames with a mean F1-score of 0.96 ± 0.01 and 0.97 ± 0.01, sensitivity of 0.97 ± 0.02 and 0.0.97 ± 0.01, and a false positive rate of 0.99 ± 0.01 and 0.99 ± 0.01, respectively.

Conclusion
IODA is able to discriminate between inside and outside with a high certainty. In particular, only a few outside frames are misclassified as inside and therefore at risk for privacy breach. The anonymized videos can be used for multi-centric development of surgical AI, quality management or educational purposes. In contrast to expensive commercial solutions, IODA is made open source and can be improved by the scientific community.
Taking Developmental Education Reform to Scale: How Texas Institutions Responded to Statewide Corequisite Implementation
Authors: Mokher Christine G. , Park-Gaghan Toby J. 
Published: May 2023

AbstractIn response to concerns about the additional costs and time-to-degree associated with traditional developmental education programs, several states and postsecondary systems have implemented corequisite reform where academically underprepared students take both a developmental education course and college-level course in the same subject area within a single semester. Texas is one of the first and most diverse states to require all public institutions to scale-up corequisite developmental education. In this study, we use longitudinal survey data from the population of public two-year and four-year colleges and universities in Texas to examine heterogeneity in institutional responses to implementation of a statewide corequisite developmental education reform throughout the 4-year scale-up timeline. We provide insight into how challenges, costs, and data-informed efforts differ for postsecondary institutions that were compliant versus non-compliant with the annual statewide targeted participation rates for corequisite enrollment. We conclude with implications for policy and practice to better support statewide corequisite developmental education reform.
Advice that resonates: explaining the variability in consultants’ policy influence
Authors: Bortz Martin 
Published: May 2023

AbstractThe increased presence of management consultants in public policy has resulted in concerns from practitioners and policymakers that consultants are too influential. At the same time, there are genuine reasons to downplay consultant influence on policy processes and to instead see consultants as ‘servants of power’. This tension raises questions about how much influence consultants have and the ways in which their influence might vary. Previous studies have shown how two concepts—openness and trust—are useful in understanding variability of consultant influence. As part of this, public decision-makers must be open to the involvement of consultants in a reform process and must also trust the specific consultants involved. At the same time, limited consideration has, to date, been given to discursive explanations of variability. Focusing its analysis on the influence of coalitions on education policy, this paper’s main contribution is to show that consultants will be more influential when their discursive repertoire demonstrates resonance with the narratives of the coalitions they are trying to influence. As part of this, consultants should deploy concepts and language that are recognisable to those coalitions, but which also align with the coalitions’ underlying narratives about the problem being faced and appropriate solutions.
What’s the Matter with Sound? - How Primary School Students Perceive the Nature of Sound
Authors: Veith Sonja Isabel 
Published: May 2023

AbstractSound is a very omnipresent physical phenomenon that plays a crucial role in our daily lives. It is essential for verbal communication and helps us orient ourselves. Children are especially affected by sound and its presence in their daily lives. This circumstance, and the subject-specific interesting facets of the topic of sound, make this particularly interesting for the classroom. In order to provide effective sound education, it’s important to understand how children perceive sound. This research aims to explore the ways in which primary school children experience sound. The inquiry conducted of 24 interviews with primary school children, with a focus on the propagation of sound. Various experiments were integrated into these interviews in order to provide a child-friendly approach to this rather abstract topic. The interviews were analysed phenomenographically. The focus on sound propagation allowed the children to express their understanding of the nature of sound. The various experiments that addressed different levels of awareness (black box, Schlieren setup) were also beneficial in this regard. The results showed that primary school children already have a wide range of ways of experiencing the nature of sound.
Norms, epistemic norms, context, and counterfactuals
Authors: Kroedel Thomas 
Published: May 2023

AbstractThe paper defends an account of the context-sensitivity of norms that draws on the resources of counterfactual conditionals. The account combines two assumptions: the assumption that permission is rule-abiding performance in some contextually relevant situations; and the assumption that the contextually relevant situations are picked out by the mechanism that selects the possible worlds relevant for the evaluation of counterfactual conditionals. The account explains the non-monotonicity of permissions and solves a puzzle, raised by Timothy Williamson, about the seeming failure of permissions to distribute over conjunction. In the domain of epistemic norms, the account solves an analogous puzzle and deals successfully with so-called blindspot propositions.