bluuebunny/crossref_metadata_2025_split huggingface dataset:
The 100 most-cited articles in COVID-19: a bibliometric analysis
Authors: Liew Yong Y , Dong Qiming , Lakshman Nivan , Khajuria Ankur 
Published: July 2024

Abstract
Corona virus disease 2019 (COVID-19) pandemic, sparked by the emergence of a novel coronavirus in early 2020, has prompted a surge in published articles. This study aims to systematically analyse the characteristics and trends of impactful research in the field. The 100 most-cited publications associated with COVID-19 were identified by two independent reviewers using the ‘Web of Science’ database across all available journals up to the year 2023. Data collected include country, citation count, subject, level of evidence (using Oxford Centre for Evidence-Based Medicine System 2011), impact factor, funding, and study design. We identified 394 038 publications, and the 100 most-cited publications were ranked. These were cited by a total of 283 034 articles (median citation = 767), median impact factor of 66.9 and 72 articles with fundings. China (n = 44), USA (n = 19), and UK (n = 13) were the three highest contributors (n = 220 505). Most articles were level 5 evidence (n = 48), followed by level 3 (n = 28), 4 (n = 14), 2 (n = 7), and 1 (n = 3). The main subjects were mechanism of action and structures of SARS-CoV-2 virus (n = 18) and impact of COVID-19 on public health (n = 18). Publications in 2022 and 2023 predominantly focused on the impact of COVID-19. Majority of the highly cited studies were of low-to-moderate quality, with only 10 consisting of randomized controlled trials or systematic reviews with or without meta-analysis. These findings reflect a growing interest in understanding the impact of COVID-19 pandemic on public and mental health. This analysis found the potential for future double-blinded randomized controlled trials to validate existing findings.
The effectiveness of endolysin ENDO-1252 from Salmonella bacteriophage-1252 against nontyphoidal Salmonella enterica
Authors: Tung Chuan-Wei , Julianingsih Dita , Canagarajah Christa , Sellers George , Scriba Aaron , Alvarado-Martínez Zabdiel , Tabashsum Zajeba , Biswas Debabrata 
Published: July 2024

Abstract
Salmonella enterica (S. enterica) is the most common food and waterborne pathogen worldwide. The growing trend of antibiotic-resistant S. enterica poses severe healthcare threats. As an alternative antimicrobial agent, bacteriophage-encoded endolysins (endolysins) are a potential agent in controlling S. enterica infection. Endolysins are enzymes that particularly target the peptidoglycan layer of bacterial cells, leading to their rupture and destruction. However, the application of endolysins against Gram-negative bacteria is limited due to the presence of the outer membrane in the cell wall, which hinders the permeation of externally applied endolysins. This study aimed the prokaryotic expression system to produce the recombinant endolysin ENDO-1252, encoded by the Salmonella bacteriophage-1252 associated with S. Enteritidis. Subsequently, ENDO-1252 had strong lytic activity not only against S. Enteritidis but also against S. Typhimurium. In addition, ENDO-1252 showed optimal thermostability and lytic activity at 25°C with a pH of 7.0. In combination with 0.1 mM EDTA, the effect of 120 µg of ENDO-1252 for 6 hours exhibited the highest lytic activity, resulting in a reduction of 1.15 log or 92.87% on S. Enteritidis. These findings suggest that ENDO-1252 can be used as a potential and innovative antibacterial agent for controlling the growth of S. Enteritidis.
Beauty with an Explanation and the Poetics of Acculturation: How, and Why, Michael Ondaatje’s Poetic Novels Work
Authors: Whetter Darryl 
Published: July 2024

Abstract
Michael Ondaatje’s first three novels, those which cemented his international fiction career, each use a pattern in which metaphors which begin as isolated comparisons of A to B are also sequentially repackaged into the lesser known (but equally substitutive) trope of metonymy. In sequence, this metonymic use of metaphor fuses the self-evident comparison of metaphor with the more acculturated substitution of metonymy – a substitution taught within a culture, not self-evident like a metaphor – ultimately enacting a poetics of acculturation. Loading a novel’s metaphorical terms with sequential meaning was crucial to an Ondaatje who was not only transitioning from poet to novelist, but doing so in an aesthetic fusion of the postmodern and the postcolonial also found in other late-twentieth-century postcolonial novels.
Nomogram for predicting pathologic complete response following preoperative chemoradiotherapy in patients with esophageal squamous cell carcinoma
Authors: Shin Young Seob , Jang Jeong Yun , Yoo Ye Jin , Yu Jesang , Song Kye Jin , Jo Yoon Young , Kim Sung-Bae , Park Sook Ryun , Song Ho June , Kim Yong-Hee , Kim Hyeong Ryul , Kim Jong Hoon 
Published: July 2024

Abstract

Background
In patients with esophageal squamous cell carcinoma (ESCC), accurately predicting a pathologic complete response (pCR) to preoperative chemoradiotherapy (PCRT) has the potential to enable an active surveillance strategy without esophagectomy. We aimed to establish a reliable multiparameter nomogram model that combines tumor characteristics, imaging modalities, and hematologic markers to predict pCR in patients with ESCC who underwent PCRT and esophagectomy.

Methods
We retrospectively reviewed the medical records of 457 patients with ESCC who received PCRT followed by esophagectomy between January 2005 and October 2020. The nomogram model was developed using logistic regression analysis with a training cohort and externally validated with a validation cohort.

Results
In the training and validation cohorts, 44.2% (126/285) and 48.3% (83/172) of patients, respectively, achieved pCR after PCRT. The 5-year rates of overall survival, progression-free survival, and freedom from local progression in the training cohort were 51.6%, 48.5%, and 77.6%, respectively. The parameters included in the nomogram were histologic grade, clinical N stage, maximum standardized uptake value on positron emission tomography, and post-PCRT biopsy. Hematologic markers were significantly associated with survival outcomes but not with pCR. The area under the receiver operating characteristic curve of the nomogram was 0.717, 0.704, and 0.707 for the training cohort, internal validation cohort, and external validation cohort, respectively.

Conclusion
Our nomogram model based on four parameters obtained from standard clinical practice demonstrated good performance in both the training and validation cohorts and could be useful to aid clinical decision-making to determine whether surgery or active surveillance strategy should be pursued.
Pan-cancer Analysis Reveals m6A Variation and Cell-specific Regulatory Network in Different Cancer Types
Authors: Lin Yao , Li Jingyi , Liang Shuaiyi , Chen Yaxin , Li Yueqi , Cun Yixian , Tian Lei , Zhou Yuanli , Chen Yitong , Chu Jiemei , Chen Hubin , Luo Qiang , Zheng Ruili , Wang Gang , Liang Hao , Cui Ping , An Sanqi 
Published: July 2024

Abstract
As the most abundant messenger RNA (mRNA) modification, N6-methyladenosine (m6A) plays a crucial role in RNA fate, impacting cellular and physiological processes in various tumor types. However, our understanding of the role of the m6A methylome in tumor heterogeneity remains limited. Herein, we collected and analyzed m6A methylomes across nine human tissues from 97 m6A sequencing (m6A-seq) and RNA sequencing (RNA-seq) samples. Our findings demonstrate that m6A exhibits different heterogeneity in most tumor tissues compared to normal tissues, which contributes to the diverse clinical outcomes in different cancer types. We also found that the cancer type-specific m6A level regulated the expression of different cancer-related genes in distinct cancer types. Utilizing a novel and reliable method called “m6A-express”, we predicted m6A-regulated genes and revealed that cancer type-specific m6A-regulated genes contributed to the prognosis, tumor origin, and infiltration level of immune cells in diverse patient populations. Furthermore, we identified cell-specific m6A regulators that regulate cancer-specific m6A and constructed a regulatory network. Experimental validation was performed, confirming that the cell-specific m6A regulator CAPRIN1 controls the m6A level of TP53. Overall, our work reveals the clinical relevance of m6A in various tumor tissues and explains how such heterogeneity is established. These results further suggest the potential of m6A in cancer precision medicine for patients with different cancer types.
Exploring the complexity of systemic sclerosis etiology by trio whole genome sequencing
Authors: Dai Hongzheng , Ketkar Shamika , Tan Taotao , Atkinson Elizabeth G , Burrage Lindsay , Worley Kim C , Christopher Brian , Lyons Marka A , Assassi Shervin , Mayes Maureen D , Lee Brendan 
Published: July 2024

Abstract
Systemic sclerosis (SSc) is a heterogeneous rare autoimmune fibrosing disorder affecting connective tissue. The etiology of systemic sclerosis is largely unknown and many genes have been suggested as susceptibility loci of modest impact by genome-wide association study (GWAS). Multiple factors can contribute to the pathological process of the disease, which makes it more difficult to identify possible disease-causing genetic alterations. In this study, we have applied whole genome sequencing (WGS) in 101 indexed family trios, supplemented with transcriptome sequencing on cultured fibroblast cells of four patients and five family controls where available. Single nucleotide variants (SNVs) and copy number variants (CNVs) were examined, with emphasis on de novo variants. We also performed enrichment test for rare variants in candidate genes previously proposed in association with systemic sclerosis. We identified 42 exonic and 34 ncRNA de novo SNV changes in 101 trios, from a total of over 6000 de novo variants genome wide. We observed higher than expected de novo variants in PRKXP1 gene. We also observed such phenomenon along with increased expression in patient group in NEK7 gene. Additionally, we also observed significant enrichment of rare variants in candidate genes in the patient cohort, further supporting the complexity/multi-factorial etiology of systemic sclerosis. Our findings identify new candidate genes including PRKXP1 and NEK7 for future studies in SSc. We observed rare variant enrichment in candidate genes previously proposed in association with SSc, which suggest more efforts should be pursued to further investigate possible pathogenetic mechanisms associated with those candidate genes.
Following Through: The Impact of Culinary Medicine on Mediterranean Diet Uptake in Inflammatory Bowel Disease
Authors: Ryan Kelsey , Salozzo Caroline , Schwartz Sally , Hart Micquel , Tuo Ya , Wenzel Amanda , Saul Samantha , Strople Jennifer , Brown Jeffrey , Runde Joseph 
Published: July 2024

Abstract

Background
The Mediterranean diet (MD) is recommended for all patients with inflammatory bowel disease (IBD) unless there is a specific contraindication. Culinary medicine has emerged as a method for improving dietary education. Patients and caregivers are often invested in making dietary changes to improve disease control. Here, we examine the dietary preferences of a group of young people with IBD and apply culinary medicine techniques with an in-person MD-focused cooking class.

Methods
A survey evaluating dietary attitudes was sent to an IBD email listserv at our tertiary care center (n = 779). A validated questionnaire, the Mediterranean Diet Quality Index for Children and Adolescents was used to assess MD adherence. IBD dietitians customized 2 in-person MD-focused cooking classes, one for children 6 to 12 years of age (arm 1) and one for adolescents 13 to 17 years of age (arm 2). Baseline, 1-month follow-up, and 3-month follow-up surveys were completed.

Results
There were 112 survey responses. Participants were 67.0% male with diagnosis of Crohn’s disease (50.0%), ulcerative colitis (42.0%), or IBD unclassified (8.0%). Most were managed on advanced therapies (82.0%). Most reported making decisions about diet (82.0%) in order to help with IBD, had met with a dietitian (69.0%), and were interested in learning more about the MD (55.3%). MD scores were primarily in the average (49.5%) and poor (41.1%) diet categories. Only those eating together as a family 3 or more times per week or those who had met with a dietitian scored in the optimal diet category. The median MD score at baseline was 4.5, increasing to 6.0 at 1 month and 7.0 at 3 months postintervention. Almost all (90%) would recommend cooking classes to others. Common barriers to MD uptake included lack of knowledge about which foods to prepare, concern about taste, and time to prepare food.

Conclusions
This study showcases high patient and caregiver interest in dietary management of IBD and demonstrates efficacy of education via application of culinary medicine. Classes were well received by families and MD adherence scores increased postintervention. As patients with IBD and their families are often motivated to incorporate dietary therapy into their care, this work highlights the role of culinary medicine and value of future study.
Gender and Transitional Justice: Explaining Global Trends
Authors: Sikkink Kathryn , Clapp Helen , Marín-López Daniel , Schmidt Averell 
Published: July 2024

ABSTRACT∞
In this article, we explore historical trends in gender-attentive transitional justice policies using a new global dataset of truth commissions, prosecutions and reparations policies. We find that gender was largely absent from these policies from 1970 through 1990 but that more attention to gender began in the 1990s and has been sustained since that time. Initial attention to gender focused primarily on violence against women; more recently, some limited attention to broader understandings of gender that include men, boys and LGBTQI+ individuals has started to appear. We argue that the early efforts of feminist activists in countries both in the Global North and the Global South to frame and set the global agenda on violence against women shaped when transitional justice policies became gender attentive and how these policies have diffused across countries. We argue that attention to female victims and physical gender violence is associated with a positive spillover, leading to broader attention to gender issues rather than crowding out attention to other gender harms.
First-Order Perturbation Theory of Trust-Region Subproblem
Authors: Feng Bo , Wu Gang 
Published: July 2024

Abstract
Trust-region subproblem (TRS) is an important problem arising in many applications such as numerical optimization, Tikhonov regularization of ill-posed problems and constrained eigenvalue problems. In recent decades, extensive works focus on how to solve the trust-region subproblem efficiently. To the best of our knowledge, there are few results on perturbation analysis of the trust-region subproblem. In order to fill in this gap, we focus on first-order perturbation theory of the trust-region subproblem. The main contributions of this paper are three-fold. First, suppose that the TRS is in easy case, we give a sufficient condition under which the perturbed TRS is still in easy case. Secondly, with the help of the structure of the TRS and the classical eigenproblem perturbation theory, we perform first-order perturbation analysis on the Lagrange multiplier and the solution of the TRS, and define their condition numbers. Thirdly, we point out that the solution and the Lagrange multiplier could be well-conditioned even if TRS is in nearly hard case. The established results are computable, and are helpful to evaluate ill-conditioning of the large-scale TRS problem beforehand. Numerical experiments show the sharpness of the established bounds and the effectiveness of the proposed strategies.
Soviet Active Measures and the Second Cold War: Security, Truth, and the Politics of Self
Authors: Whyte Jeffrey 
Published: July 2024

Abstract
This paper explores the emergence of “Soviet active measures” in US political discourse during the “Second Cold War” of the early 1980s. It follows the efforts of the Active Measures Working Group, a little-known interagency organization led by Reagan administration appointees that constructed an image of Soviet active measures as a threat to national security. I detail, especially, how the Working Group framed the US anti-war movement as both a target of and vehicle for active measures. In so doing, I show how the active measure was constructed in US political discourse through a dramaturgy of secrecy and revelation that placed it within a broader “covert imaginary.” This paper concludes with a theorization of these efforts in relation to Foucault’s concept of “alethurgy,” considering how the construction of the active measure produced a “politics of truth” in which the anti-war protestor appeared as a dangerous, disinformed subject.
Divergent marine anaerobic ciliates harbor closely related Methanocorpusculum endosymbionts
Authors: Schrecengost Anna , Rotterová Johana , Poláková Kateřina , Čepička Ivan , Beinart Roxanne A 
Published: July 2024

Abstract
Ciliates are a diverse group of protists known for their ability to establish various partnerships and thrive in a wide variety of oxygen-depleted environments. Most anaerobic ciliates harbor methanogens, one of the few known archaea living intracellularly. These methanogens increase the metabolic efficiency of host fermentation via syntrophic use of host end-product in methanogenesis. Despite the ubiquity of these symbioses in anoxic habitats, patterns of symbiont specificity and fidelity are not well known. We surveyed two unrelated, commonly found groups of anaerobic ciliates, the Plagiopylea and Metopida, isolated from anoxic marine sediments. We sequenced host 18S rRNA and symbiont 16S rRNA marker genes as well as the symbiont internal transcribed spacer region from our cultured ciliates to identify hosts and their associated methanogenic symbionts. We found that marine ciliates from both of these co-occurring, divergent groups harbor closely related yet distinct intracellular archaea within the Methanocorpusculum genus. The symbionts appear to be stable at the host species level, but at higher taxonomic levels, there is evidence that symbiont replacements have occurred. Gaining insight into this unique association will deepen our understanding of the complex transmission modes of marine microbial symbionts, and the mutualistic microbial interactions occurring across domains of life.
Ideology, Local-Level Policymaking, and International Governmental Organizations
Authors: Bayram A Burcu , Sledge Daniel , Thomas Herschel F 
Published: July 2024

Abstract
A growing literature at the intersection of international relations, public policy, and comparative politics has explored the role that International Governmental Organizations (IGOs) play in influencing domestic policymaking. This literature is grounded in a commonly shared theoretical expectation that policymakers will perceive IGOs as neutral and technocratic purveyors of expert information. Based on this expectation, scholars have assumed that policymakers are likely to employ recommendations from IGOs when making decisions. In this research note, we examine this assumption through an analysis of original survey data on U.S. mayors’ responses to COVID-19-related guidance from the World Health Organization (WHO). In contrast to dominant theoretical expectations, we find that mayoral likelihood of considering WHO recommendations in policymaking and of trusting WHO-provided information was largely a function of ideology, an effect that remains after incorporating the interactive effect of Trump vote share.
A practice-based approach to teaching antimicrobial therapy using artificial intelligence and gamified learning
Authors: Driesnack Sebastian , Rücker Fabian , Dietze-Jergus Nadine , Bondarenko Alexander , Pletz Mathias W , Viehweger Adrian 
Published: July 2024

Abstract

Objectives
Scalable teaching through apps and artificial intelligence (AI) is of rising interest in academic practice. We focused on how medical students could benefit from this trend in learning antibiotic stewardship (ABS). Our study evaluated the impact of gamified learning on factual knowledge and uncertainty in antibiotic prescription. We also assessed an opportunity for AI-empowered evaluation of freeform answers.

Methods
We offered four short courses focusing on ABS, with 46 participating medical students who self-selected themselves into the elective course. Course size was limited by the faculty. At the start of the course, students were given a questionnaire about microbiology, infectious diseases, pharmacy and qualitative questions regarding their proficiency of selecting antibiotics for therapy. Students were followed up with the same questionnaire for up to 12 months. We selected popular game mechanics with commonly known rules for teaching and an AI for evaluating freeform questions.

Results
The number of correctly answered questions improved significantly for three topics asked in the introductory examination, as did the self-assessed safety of prescribing antibiotics. The AI-based review of freeform answers was found to be capable of revealing students’ learning gaps and identifying topics in which students needed further teaching.

Conclusions
We showed how an interdisciplinary short course on ABS featuring gamified learning and AI could substantially improve learning. Even though large language models are a relatively new technology that sometimes fails to produce the anticipated results, they are a possible first step in scaling a tutor-based teaching approach in ABS.
Fluoroquinolone-resistant Campylobacter in backyard and commercial broiler production systems in the United States
Authors: Parzygnat Jessica L , Dunn Robert R , Koci Matthew D , Crespo Rocio , Harden Lyndy , Thakur Siddhartha 
Published: July 2024

Abstract

Objectives
Campylobacter spp. are one of the leading foodborne pathogens in the world, and chickens are a known reservoir. This is significant considering broiler chicken is the top consumed meat worldwide. In the USA, backyard poultry production is increasing, but little research has been done to investigate prevalence and antimicrobial resistance associated with Campylobacter in these environments.

Methods
Our study encompasses a farm-to-genome approach to identify Campylobacter and investigate its antimicrobial resistance phenotypically and genotypically. We travelled to 10 backyard and 10 integrated commercial broiler farms to follow a flock throughout production. We sampled at days 10, 31 and 52 for backyard and 10, 24 and 38 for commercial farms. Bird faecal (n = 10) and various environmental samples (soil n = 5, litter/compost n = 5, and feeder and waterer swabs n = 6) were collected at each visit and processed for Campylobacter.

Results
Our results show a higher prevalence of Campylobacter in samples from backyard farms (21.9%) compared to commercial (12.2%). Most of our isolates were identified as C. jejuni (70.8%) and the remainder as C. coli (29.2%). Antimicrobial susceptibility testing reveals phenotypic resistance to ciprofloxacin (40.2%), an important treatment drug for Campylobacter infection, and tetracycline (46.6%). A higher proportion of resistance was found in C. jejuni isolates and commercial farms. Whole-genome sequencing revealed resistance genes, such as tet(O) and gyrA_T86I point mutation, that may confer resistance.

Conclusion
Overall, our research emphasizes the need for interventions to curb prevalence of resistant Campylobacter spp. on broiler production systems.