bluuebunny/crossref_metadata_2025_split huggingface dataset:
TypeTaxonScript: sugarifying and enhancing data structures in biological systematics and biodiversity research
Authors: Jordão Lucas Sá Barreto , Morim Marli Pires , Baumgratz José Fernando A , Simon Marcelo Fragomeni , Eppinghaus André L C , Calfo Vicente A 
Published: March 2024

Abstract
Object-oriented programming (OOP) embodies a software development paradigm grounded in representing real-world entities as objects, facilitating a more efficient and structured modelling approach. In this article, we explore the synergy between OOP principles and the TypeScript (TS) programming language to create a JSON-formatted database designed for storing arrays of biological features. This fusion of technologies fosters a controlled and modular code script, streamlining the integration, manipulation, expansion, and analysis of biological data, all while enhancing syntax for improved human readability, such as through the use of dot notation. We advocate for biologists to embrace Git technology, akin to the practices of programmers and coders, for initiating versioned and collaborative projects. Leveraging the widely accessible and acclaimed IDE, Visual Studio Code, provides an additional advantage. Not only does it support running a Node.js environment, which is essential for running TS, but it also efficiently manages GitHub versioning. We provide a use case involving taxonomic data structure, focusing on angiosperm legume plants. This method is characterized by its simplicity, as the tools employed are both fully accessible and free of charge, and it is widely adopted by communities of professional programmers. Moreover, we are dedicated to facilitating practical implementation and comprehension through a comprehensive tutorial, a readily available pre-built database at GitHub, and a new package at npm.
External Quality Assessment on Molecular Tumor Profiling with Circulating Tumor DNA-Based Methodologies Routinely Used in Clinical Pathology within the COIN Consortium
Authors: van der Leest Paul , Rozendal Pim , Hinrichs John , van Noesel Carel J M , Zwaenepoel Karen , Deiman Birgit , Huijsmans Cornelis J J , van Eijk Ronald , Speel Ernst Jan M , van Haastert Rick J , Ligtenberg Marjolijn J L , van Schaik Ron H N , Jansen Maurice P H M , Dubbink Hendrikus J , de Leng Wendy W , Leers Mathie P G , Tamminga Menno , van den Broek Daan , van Kempen Léon C , Schuuring Ed 
Published: March 2024

Abstract

Background
Identification of tumor-derived variants in circulating tumor DNA (ctDNA) has potential as a sensitive and reliable surrogate for tumor tissue-based routine diagnostic testing. However, variations in pre(analytical) procedures affect the efficiency of ctDNA recovery. Here, an external quality assessment (EQA) was performed to determine the performance of ctDNA mutation detection work flows that are used in current diagnostic settings across laboratories within the Dutch COIN consortium (ctDNA on the road to implementation in The Netherlands).

Methods
Aliquots of 3 high-volume diagnostic leukapheresis (DLA) plasma samples and 3 artificial reference plasma samples with predetermined mutations were distributed among 16 Dutch laboratories. Participating laboratories were requested to perform ctDNA analysis for BRAF exon 15, EGFR exon 18–21, and KRAS exon 2–3 using their regular circulating cell-free DNA (ccfDNA) analysis work flow. Laboratories were assessed based on adherence to the study protocol, overall detection rate, and overall genotyping performance.

Results
A broad range of preanalytical conditions (e.g., plasma volume, elution volume, and extraction methods) and analytical methodologies (e.g., droplet digital PCR [ddPCR], small-panel PCR assays, and next-generation sequencing [NGS]) were used. Six laboratories (38%) had a performance score of &gt;0.90; all other laboratories scored between 0.26 and 0.80. Although 13 laboratories (81%) reached a 100% overall detection rate, the therapeutically relevant EGFR p.(S752_I759del) (69%), EGFR p.(N771_H773dup) (50%), and KRAS p.(G12C) (48%) mutations were frequently not genotyped accurately.

Conclusions
Divergent (pre)analytical protocols could lead to discrepant clinical outcomes when using the same plasma samples. Standardization of (pre)analytical work flows can facilitate the implementation of reproducible liquid biopsy testing in the clinical routine.
Two case reports of fulminant giant cell myocarditis treated with rabbit anti-thymocyte globulin
Authors: Bartz-Overman Colin , Li Sarah , Puligandla Balaram , Colaco Nalini , Steiner Johannes , Masha Luke 
Published: March 2024

Abstract

Background
Giant cell myocarditis (GCM) is an inflammatory form of acute heart failure with high rates of cardiac transplantation or death. Standard acute treatment includes multi-drug immunosuppressive regimens. There is a small but growing number of case reports utilizing rabbit anti-thymocyte globulin in severe cases.

Case summary
Two cases are presented with similar presentations and clinical courses. Both are middle-aged patients with no significant past medical history, who presented with new acute decompensated heart failure that quickly progressed to cardiogenic shock requiring inotropic and mechanical circulatory support. Both underwent endomyocardial biopsies that diagnosed GCM. Both were treated with a multi-agent immunosuppressive regimen, notably including rabbit anti-thymocyte globulin, with subsequent resolution of shock and recovery of left ventricular ejection fraction. Both remain transplant-free and without ventricular arrhythmias at 7 months and 26 months, respectively.

Discussion
In aggregate, these cases are typical of GCM. They add to growing observational data that upfront rabbit anti-thymocyte globulin may reduce morbidity and mortality in GCM, including potentially preventing the need for complex interventions like orthotopic heart transplantation.
Textbooks as Markers and Makers of International Law: A Brazilian Case Study
Authors: Leão Soares Pereira Luíza , Morosini Fabio Costa 
Published: March 2024

Abstract
This article challenges conventional views of international law textbooks as mere instructional tools and explores them as powerful sites for shaping knowledge and the discipline. Drawing on empirical methods and critical theory, we analyse the 10 main international law textbooks used in Brazil and conduct interviews with their authors to illuminate the textbooks’ complexities and their potential for shaping the discipline and the profession. The article delves into the tension between the structure of international law as depicted in the textbooks and the agency of their authors, investigating the authors’ identities and backgrounds. Brazil serves as a compelling case study due to its numerous international law textbooks and their widespread use. Our results indicate a predominant universalist approach in Brazilian textbooks and their connection to the French international law tradition. Moreover, the study sheds light on the Brazilian ‘invisible college’ of international lawyers, revealing gender and racial disparities and institutional centralities. It also uncovers crucial omissions in the textbooks, such as the relationship of international law to colonialism, slavery, race, gender and economic inequality. Overall, this study offers a comprehensive understanding of international law as a field in Brazil and provides a valuable methodological framework for future research on textbooks’ role in shaping the discipline.
Site-specific immobilization of the endosialidase reveals QSOX2 is a novel polysialylated protein
Authors: Hunter Carmanah , Derksen Tahlia , Makhsous Sogand , Doll Matt , Perez Samantha Rodriguez , Scott Nichollas E , Willis Lisa M 
Published: March 2024

Abstract
Polysialic acid (polySia) is a linear polymer of α2,8-linked sialic acid residues that is of fundamental biological interest due to its pivotal roles in the regulation of the nervous, immune, and reproductive systems in healthy human adults. PolySia is also dysregulated in several chronic diseases, including cancers and mental health disorders. However, the mechanisms underpinning polySia biology in health and disease remain largely unknown. The polySia-specific hydrolase, endoneuraminidase NF (EndoN), and the catalytically inactive polySia lectin EndoNDM, have been extensively used for studying polySia. However, EndoN is heat stable and remains associated with cells after washing. When studying polySia in systems with multiple polysialylated species, the residual EndoN that cannot be removed confounds data interpretation. We developed a strategy for site-specific immobilization of EndoN on streptavidin-coated magnetic beads. We showed that immobilizing EndoN allows for effective removal of the enzyme from samples, while retaining hydrolase activity. We used the same strategy to immobilize the polySia lectin EndoNDM, which enabled the enrichment of polysialylated proteins from complex mixtures such as serum for their identification via mass spectrometry. We used this methodology to identify a novel polysialylated protein, QSOX2, which is secreted from the breast cancer cell line MCF-7. This method of site-specific immobilization can be utilized for other enzymes and lectins to yield insight into glycobiology.
Novel signals and polygenic score for height are associated with pubertal growth traits in Southwestern American Indians
Authors: Ramírez-Luzuriaga Maria J , Kobes Sayuko , Hsueh Wen-Chi , Baier Leslie J , Hanson Robert L 
Published: March 2024

Abstract
Most genetic variants associated with adult height have been identified through large genome-wide association studies (GWASs) in European-ancestry cohorts. However, it is unclear how these variants influence linear growth during adolescence. This study uses anthropometric and genotypic data from a longitudinal study conducted in an American Indian community in Arizona between 1965–2007. Growth parameters (i.e. height, velocity, and timing of growth spurt) were derived from the Preece-Baines growth model, a parametric growth curve fitted to longitudinal height data, in 787 participants with height measurements spanning the whole period of growth. Heritability estimates suggested that genetic factors could explain 25% to 71% of the variance of pubertal growth traits. We performed a GWAS of growth parameters, testing their associations with 5 077 595 imputed or directly genotyped variants. Six variants associated with height at peak velocity (P &lt; 5 × 10-8, adjusted for sex, birth year and principal components). Implicated genes include NUDT3, previously associated with adult height, and PACSIN1. Two novel variants associated with duration of growth spurt (P &lt; 5 × 10-8) in LOC105375344, an uncharacterized gene with unknown function. We finally examined the association of growth parameters with a polygenic score for height derived from 9557 single nucleotide polymorphisms (SNPs) identified in the GIANT meta-analysis for which genotypic data were available for the American Indian study population. Height polygenic score was correlated with the magnitude and velocity of height growth that occurred before and at the peak of the adolescent growth spurt, indicating overlapping genetic architecture, with no influence on the timing of adolescent growth.
To Arrest or Not Arrest? South Africa, the International Criminal Court, and New Frameworks for Assessing Noncompliance
Authors: Jay Zoë , Killingsworth Matt 
Published: March 2024

AbstractWhat are the consequences of prioritizing one obligation over another in a norm conflict on the norm that “loses”? How do these difficult choices affect how we understand the intent behind noncompliance with international law? This article examines South Africa’s decision not to arrest the then-President of Sudan, Omar al-Bashir, in the face of conflicting pressures from multiple international and domestic actors. South Africa’s conundrum over whether to arrest al-Bashir resulted in what we call “collateral noncompliance”: noncompliance with one obligation as a product of compliance with another. Understanding noncompliance like this highlights how seemingly bad-faith noncompliance can be a consequence of weighing competing obligations, rather than a deliberate attempt to shirk or undermine the nonchosen norm. It offers an alternative to perspectives that frame African states’ noncompliance with the International Criminal Court as inherently problematic, contributing instead to more critical, reflexive understandings of noncompliance and contestation as a natural part of norm development.
Do Threats or Shaming Increase Public Support for Policy Concessions? Alliance Coercion and Burden-Sharing in NATO
Authors: Blankenship Brian 
Published: March 2024

AbstractExisting literature suggests that alliance members can use their partners’ abandonment fears to obtain favorable concessions for themselves. However, evidence on the effectiveness of threats of abandonment as motivation for defense burden-sharing remains limited. This article uses a survey experiment conducted in Poland and Germany to assess how American signals of support and threats of abandonment shape public support for increasing their countries’ military spending. The findings suggest that threats of abandonment increase public support for higher defense spending, whereas approaches like “naming and shaming” under-contributing partners do not. However, assurances of protection did not decrease support for defense spending, and combining threats with assurances if anything increased those threats’ effects. Threats are thus most effective when they do not fundamentally undermine targets’ confidence in US protection. The findings have implications for understanding alliance politics and the utility of public pressure, and for policy debates about encouraging defense burden-sharing.
A qualitative analysis of the unwritten rules influencing antibiotic prescribing practices among French poultry veterinarians
Authors: Moya Sebastián , Coviglio Alexandra , Belloc Catherine , Comer Clementine , Eberhart Josephine , Fortané Nicolas , Paul Mathilde C 
Published: March 2024

Abstract

Background
It is now recognized that a better understanding of prescriber behaviour is needed to improve antimicrobial stewardship programmes. Most studies conducted in the livestock sector have focused on farmers’ perspectives, while the prescribing habits of veterinarians have remained overlooked.

Objective
Our study explored the psychosocial determinants associated with antibiotic prescribing practices in the French poultry sector by analysing the informal norms and unwritten rules that influence veterinarians’ prescribing decisions.

Methods
A qualitative study was conducted in four French regions in February 2021. Using the biographical narrative interpretive method, semi-structured interviews were conducted with 16 poultry veterinarians with varying professional experience. Three main themes were retained for data analysis: (i) compliance with and deviations from prescribing recommendations, (ii) the influence of fellow veterinarians on antibiotic decisions and (iii) the key role of veterinary corporate groups.

Results
When prescribing antibiotics, junior veterinarians were strongly influenced by senior veterinarians who acted as role models driving clinical practices. Prescribing habits were shared through peer networks in which veterinarians participated throughout their careers. Finally, veterinary corporate groups helped to shape veterinarians’ prescribing habits by promoting existing guidelines and even producing in-house recommendations.

Conclusions
We show that, in parallel with official guidelines, prescribing habits circulate among veterinarians and are shared in professional circles. Therefore, antimicrobial stewardship interventions should focus not only on official guidelines and communication channels, but also unwritten professional rules and organizations influencing veterinarians’ prescribing practices.
Disparities in seizure outcomes revealed by large language models
Authors: Xie Kevin , Ojemann William K S , Gallagher Ryan S , Shinohara Russell T , Lucas Alfredo , Hill Chloé E , Hamilton Roy H , Johnson Kevin B , Roth Dan , Litt Brian , Ellis Colin A 
Published: March 2024

Abstract

Objective
Large-language models (LLMs) can potentially revolutionize health care delivery and research, but risk propagating existing biases or introducing new ones. In epilepsy, social determinants of health are associated with disparities in care access, but their impact on seizure outcomes among those with access remains unclear. Here we (1) evaluated our validated, epilepsy-specific LLM for intrinsic bias, and (2) used LLM-extracted seizure outcomes to determine if different demographic groups have different seizure outcomes.

Materials and Methods
We tested our LLM for differences and equivalences in prediction accuracy and confidence across demographic groups defined by race, ethnicity, sex, income, and health insurance, using manually annotated notes. Next, we used LLM-classified seizure freedom at each office visit to test for demographic outcome disparities, using univariable and multivariable analyses.

Results
We analyzed 84 675 clinic visits from 25 612 unique patients seen at our epilepsy center. We found little evidence of bias in the prediction accuracy or confidence of outcome classifications across demographic groups. Multivariable analysis indicated worse seizure outcomes for female patients (OR 1.33, P ≤ .001), those with public insurance (OR 1.53, P ≤ .001), and those from lower-income zip codes (OR ≥1.22, P  ≤ .007). Black patients had worse outcomes than White patients in univariable but not multivariable analysis (OR 1.03, P = .66).

Conclusion
We found little evidence that our LLM was intrinsically biased against any demographic group. Seizure freedom extracted by LLM revealed disparities in seizure outcomes across several demographic groups. These findings quantify the critical need to reduce disparities in the care of people with epilepsy.
Is the Preoperative Wound Culture Necessary Before Skin Grafting Minor Burns? A Pilot Study in a Low Resource Setting Burn Service
Authors: Holm Sebastian , Smith Michelle T D , Huss Fredrik , Allorto Nikki 
Published: March 2024

Abstract
The most common cited cause of split-thickness skin graft failure is infection and due to the association between bacterial findings in wound beds an attempt to decrease the bacterial burden before skin-grafting evolved. Thus, preoperative microbiology swabs of the wound bed became routine at some institutions prior to grafting. This is not standard practice in the Pietermaritzburg Burn Service. Emphasis is instead placed on a strict protocol of intraoperative wound bed preparation to promote adequate graft take. This pilot study aims to evaluate whether preoperative wound swabs are appropriate. We performed a prospective observational study to determine if positive wound cultures were associated with graft failure. All patients with a burn surface area of less than 10%, where delayed grafting (later than 28 days from the time of burn injury) was performed, from March to December 2021 were analyzed. Patient demographics, days from burn to graft, %TBSA burn, %TBSA grafted, whether sharp debridement prior to grafting in the same procedure was performed or not, use of topical gentamicin intraoperatively, graft outcome (% graft loss), need for regraft, and organism grown were recorded into an excel spreadsheet for analysis. The sample included 52 patients. Of these, 17 (31.5%) were female. The median %TBSA grafted was 8% (IQR 4%-13%) and similar in both groups. The median days from burn to grafting were 35 days. Thirty-nine patients (75%) had graft Take and 13 (25%) had graft Failure. In the failed group, the median % graft failure was 50% (30%-70%). Of the group with successful graft take, 90% were noted to have had a positive wound culture prior to grafting. A positive wound culture was not found to be a risk factor for graft failure (P = .993). Despite the positive wound cultures graft take was more than 90% in 75% of grafts performed and only 2/52 patients required supplementary grafting. We believe that this demonstrates that our local protocol is reasonable in this setting and that waiting for negative wound swabs prior to grafting should not be a reason to delay grafting.
Analysis of potential volatile organic compounds in Sitophilus zeamais (Coleoptera: Curculionidae)-infested wheat based on lipid oxidation—a reference to early and rapid detection method
Authors: Tian Qisheng , Wu Qiong , Li Tianming , Zhang Menglong , Zhang Dongdong , Qian Ranran , Zhang Yurong 
Published: March 2024

Abstract
The maize weevil, Sitophilus zeamais Motschulsky, is a hidden pest that presents serious risk to grain quality during postharvest storage. Lipid-derived volatile detection is considered a key reference for early prediction of S. zeamais infestation. However, the exact compositions of fatty acids and volatile organic compounds (VOCs) in S. zeamais-infested wheat are yet to be determined. In this study, we aimed to explore the effect of S. zeamais infestation on lipid metabolism in wheat infested with S. zeamais eggs (4 days), larvae (20 days), pupae (35 days), and adults (45 days). Compared to those in the control group, the activities of lipid oxidation enzymes, such as lipase, lipoxygenase, and alcohol dehydrogenase, increased by 82.73%, 105.12%, and 487.86%, respectively, during the storage period of 1 life cycle of S. zeamais. Additionally, the fatty acid composition of S. zeamais-infested wheat was significantly altered (palmitic acid [1.10-fold], oleic acid [1.07-fold], and linoleic acid [0.95-fold]). Furthermore, 91 VOCs were identified in all wheat samples; then, multivariate statistical analyses categorized these samples into 4 groups: uninfested, longer storage, lightly infested, and heavily infested. Moreover, 31, 26, and 45 potential VOCs were identified to distinguish uninfested wheat from those in the other 3 groups. These results demonstrated that S. zeamais infestation induces an elevation in lipid-related enzymatic activities, which potentially leads to a decrease in lipid content alongside the production of specific VOCs (undecan-4-olide, heptaldehyde, and 2-nonenal). These findings provide novel insights for rapidly identifying grains infested by hidden pests and effectively managing these pests during grain storage.