bluuebunny/crossref_metadata_2025_split huggingface dataset:
De-biasing the bias: methods for improving disparity assessments with noisy group measurements
Authors: Wastvedt Solvejg , Snoke Joshua , Agniel Denis , Lai Julie , Elliott Marc N , Martino Steven C 
Published: December 2024

ABSTRACT
Health care decisions are increasingly informed by clinical decision support algorithms, but these algorithms may perpetuate or increase racial and ethnic disparities in access to and quality of health care. Further complicating the problem, clinical data often have missing or poor quality racial and ethnic information, which can lead to misleading assessments of algorithmic bias. We present novel statistical methods that allow for the use of probabilities of racial/ethnic group membership in assessments of algorithm performance and quantify the statistical bias that results from error in these imputed group probabilities. We propose a sensitivity analysis approach to estimating the statistical bias that allows practitioners to assess disparities in algorithm performance under a range of assumed levels of group probability error. We also prove theoretical bounds on the statistical bias for a set of commonly used fairness metrics and describe real-world scenarios where our theoretical results are likely to apply. We present a case study using imputed race and ethnicity from the modified Bayesian Improved First and Surname Geocoding algorithm for estimation of disparities in a clinical decision support algorithm used to inform osteoporosis treatment. Our novel methods allow policymakers to understand the range of potential disparities under a given algorithm even when race and ethnicity information is missing and to make informed decisions regarding the implementation of machine learning for clinical decision support.
The benefits and harms of oral iron supplementation in non-anaemic pregnant women: a systematic review and meta-analysis
Authors: Watt Archie , Eaton Holden , Eastwick-Jones Kate , Thomas Elizabeth T , Plüddemann Annette 
Published: December 2024

Abstract

Background
Iron deficiency during pregnancy poses a significant risk to both maternal and foetal health. Current international guidelines provide discrepant advice on antenatal iron supplementation for non-anaemic women.

Objective
We aimed to quantify the benefits and harms of routine antenatal supplementation in non-anaemic women.

Methods
The Cochrane Library, MEDLINE, Embase, and clinical trial registries were searched for randomized controlled trials and observational studies comparing oral iron supplementation with placebo or no supplement in non-anaemic pregnant women. Risk of bias was assessed for each study and the results were synthesized via meta-analysis.

Results
Twenty-three eligible studies were identified with 4492 non-anaemic pregnant women. Supplemented groups had higher haemoglobin [mean difference = 6.95 g/l, 95% confidence interval (CI): 4.81–9.09, P &lt; .001, moderate certainty, I2 = 91%] and ferritin (mean difference = 12.22 ng/ml, 95% CI: 6.92–17.52, P &lt; .001, moderate certainty, I2 = 87%) and were at lower risk of anaemia (relative risk = 0.50, 95% CI: 0.34–0.74, P &lt; .001, high certainty, I2 = 42%, number needed to treat (NNT) = 10). There was no difference in birth weight, preterm birth, and rate of caesarean section. Reporting on harms was inconsistent and there was insufficient evidence to determine an association between iron supplements and any negative outcome.

Discussion
Prophylactic iron supplementation likely results in a large reduction in maternal anaemia during pregnancy. Future research should qualify the impact of this benefit on women’s quality of life and determine which subpopulations benefit most. Evidence surrounding the harms of iron supplementation in the non-anaemic population is poor quality and inconsistent. Randomized controlled trials quantifying the risk of gastrointestinal (GI) disturbance and iron overload are essential to inform iron supplement use and reduce unwarranted variations in international guidelines.
Can Policy Succeed through Inactivity? A Case Study of UK Foreign Policy after the Gulf War
Authors: Kettle Louise 
Published: December 2024

Abstract
Can policy succeed through inactivity? Why does some inactivity lead to policy success, whilst others lead to policy failure? Whilst traditional approaches to policy success and failure have focused upon the impact of active policy interventions, this article draws together literature on policy failure and inactivity to develop hypotheses and a new conceptual framework to engage with the problem of inactivity in foreign policy. These are then applied to the case study of UK foreign policy in the Middle East after the 1990–1991 Gulf War. During this time the British government established four key policies; two would succeed, whilst two would fail. Using the new framework, extensive archival research, and documents received under the Freedom of Information Act, conditions for policy success and failure are revealed. As a result, this article argues that inactivity can be highly consequential and deserves much greater attention within foreign policy scholarship.
A virulent milRNA of Fusarium oxysporum f. sp. cubense impairs plant resistance by targeting banana AP2 transcription factor coding gene MaPTI6L
Authors: Zhong Jiaqi , Situ Junjian , He Chengcheng , He Jiahui , Kong Guanghui , Li Huaping , Jiang Zide , Li Minhui 
Published: December 2024

Abstract
Fungi produce microRNA-like RNAs (milRNAs) with functional importance in various biological processes. Our previous research identified a new milRNA Foc-milR87 from Fusarium oxysporum f. sp. cubense, which contributes to fungal virulence by targeting the pathogen glycosyl hydrolase encoding gene. However, the potential roles of fungal milRNAs in interactions with hosts are not well understood. This study demonstrated that Foc-milR87 specifically suppressed the expression of MaPTI6L, a pathogenesis-related gene that encodes a transcriptional activator in the banana (Musa acuminata Cavendish group cv. ‘Baxi Jiao’) genome, by targeting the 3'untranslated region (UTR) of MaPTI6L. Transient overexpression of MaPTI6L activated plant defense responses that depend on its nuclear localization, yet co-expression with Foc-milR87 attenuated these responses. MaPTI6L enhanced plant resistance by promoting transcription of the salicylic acid (SA) signaling pathway marker gene MaEDS1. Sequence analysis of the MaPTI6L gene in 19 banana varieties, particularly those resistant to Fusarium wilt, uncovered single nucleotide polymorphisms (SNPs) at Foc-milR87 target sites. Experimental validation showed that these SNPs significantly reduce the microRNA's ability to suppress target gene expression. Our findings reveal that Foc-milR87 plays an important role in impairing plant resistance by targeting MaPTI6L mRNA and reducing MaEDS1 transcription during the early infection stage, suggesting the 3'UTR of MaPTI6L as a promising target for genome editing in generation of disease-resistant banana cultivars.
Development of an efficient and heritable virus-induced genome editing system in Solanum lycopersicum
Authors: Lee HuiJun , Baik Ji Eun , Kim Kyung-Nam 
Published: December 2024

Abstract
The CRISPR-Cas9 system can be used to introduce site-specific mutations into the genome of tomato (Solanum lycopersicum) plants. However, the direct application of this revolutionary technology to desirable tomato cultivars has been hindered by the challenges of generating transgenic plants. To address this issue, we developed an efficient and heritable genome editing system using tobacco rattle virus (TRV) for an elite tomato cultivar (the paternal line of Saladette). Notably, this virus-induced genome editing (VIGE) system enables the rapid production of various mutant seeds without the need for additional plant transformation and tissue culture, once a Cas9-expressing tomato line is established. This VIGE system consists of transgenic tomato plants that express Cas9 under the control of the tomato ubiquitin 10 (SlUbi10) gene promoter and a mobile guide RNA scaffold (gRNA:SlmFT) generated using the sequence of the tomato Flowering Locus T (SlFT) gene. We determined its editing efficiency by targeting the tomato phytoene desaturase (SlPDS) gene, which causes photobleaching symptoms when disrupted. Most transgenic seedlings infected with the TRV vectors carrying the SlPDS-targeting sgRNA developed chimeric albino leaves associated with a high frequency of indel mutations in the SlPDS gene. Remarkably, fruits from these plants yielded homozygous SlPDS knockout seeds at rates ranging from 15% to 100%. These results demonstrate the exceptional effectiveness of our VIGE system in rapidly generating heritable genome edits in tomato.
Does methylene blue improve outcomes in patients with post-cardiac surgery vasoplegic syndrome?
Authors: Zhu Michael Z L , Scullion Jackson , Stroebel Andrie , He Cheng 
Published: December 2024

Abstract

OBJECTIVES
A best evidence topic was written according to a structured protocol described in ICVTS. The question addressed was ‘In patients with vasoplegic syndrome following cardiac surgery with cardiopulmonary bypass, does adjunctive methylene blue improve outcomes including reduced mortality, morbidity and vasopressor requirements?’

METHODS
Ovid Medline was searched using a reported search algorithm. Articles that represented the best evidence to answer the clinical question were selected, tabulated and discussed.

RESULTS
Seven articles were selected: 4 randomized controlled trials and 3 observational studies. Studies were single centre with sample sizes ranging from 30 to 120 patients. Two studies reported a significant reduction in mortality among patients who received adjunctive methylene blue for post-cardiopulmonary bypass (CPB) vasoplegic syndrome compared with placebo or standard therapy. Four studies reported improved haemodynamic stability and reduced vasopressor requirements following methylene blue. No studies reported methylene blue-related adverse events or worse outcomes compared to controls or standard therapy. There was significant heterogeneity among the included studies in terms of the timing and dosage of methylene blue therapy as well as the definition of vasoplegic syndrome.

CONCLUSIONS
The summation of the best available evidence, which was limited to small clinical trials and observational studies, suggests that the adjunctive administration of methylene blue for refractory post-CPB vasoplegic syndrome is safe and may provide benefits in terms of improved haemodynamic stability, reduction in vasopressor requirements and reduced mortality. Questions surrounding the optimal timing of methylene blue administration, as prophylactic, adjunctive, or rescue therapy for vasoplegic syndrome, require further investigation.
The Design of Autocratic Trade Agreements: Economic Integration and Political Survival
Authors: Postnikov Evgeny , Gamso Jonas 
Published: December 2024

Abstracts
The number of preferential trade agreements signed among non-democratic states (autocratic PTAs) has grown significantly over the last decades. Trade policy scholarship remains silent on the institutional design of these autocratic economic arrangements. In this paper, we explore the core institutional characteristic of autocratic PTAs—their depth. It has been shown that many North–South and, increasingly, South–South PTAs tend to be deep, yet the depth of PTAs comprised of autocratic members remains puzzling, as government elites are faced with competing pressures for economic integration and political survival. We argue that autocratic PTAs tend to have considerable depth when it comes to the coverage of certain trade-plus issues, such as investment and trade-in services, due to the desire of government elites to attract trade and investment and enhance the ruling regime's legitimacy and political survival. However, dispute settlement provisions that could breach domestic political autonomy are carefully eschewed. We also expect to see higher levels of agreement flexibility in deep autocratic PTAs, reflecting autocrats’ dual interests in economic openness and political control. We test these expectations using data from the Design of Trade Agreements Database and we carry out interviews with trade officials to clarify the mechanisms at work.
SmartChart Suite: a Fast Healthcare Interoperability Resources-based framework for longitudinal syphilis surveillance using structured and unstructured data
Authors: Stevens Andrew , Karki Saugat , Shivers Elizabeth , Pérez Alejandro , Choi Myung , Berro Andre , Riley Michael , Yang Jane , Tassev Plamen , Jackson David Alexander , Kim Inho , Duke Jon D 
Published: December 2024

Abstract

Objective
The resurgence of syphilis in the United States presents a significant public health challenge. Much of the information needed for syphilis surveillance resides in electronic health records (EHRs). In this manuscript, we describe a surveillance platform for automating the extraction of EHR data, known as SmartChart Suite, and the results from a pilot.

Materials and Methods
The SmartChart Suite framework has been developed in compliance with the HHS Health IT Alignment Policy. The platform’s major functionalities are (1) data retrieval; (2) logical evaluation; (3) standardized data storage; and (4) results display. The SmartChart Suite was deployed in September 2023 at the Grady Health System in Atlanta, Georgia. We established a cohort of likely syphilis patients, randomly selected 50 medical records for manual and automated chart review, and analyzed the results.

Results
The SmartChart Suite was successfully deployed and integrated with the Epic EHR system at Grady. The overall performance results were precision of 97.6%, recall of 100.0%, and F-Score of 98.8%

Discussion
Automated abstraction of EHR data has significant potential to improve public health surveillance and case investigation processes while reducing the resource burden on health departments and reporters. The SmartChart Suite comprises a flexible open-source solution for registry development and maintenance across a wide spectrum of conditions and use cases.

Conclusion
SmartChart Suite demonstrates the potential of automated chart abstraction to support disease surveillance. HHS-compliant open-source tools such as SmartChart Suite can support more efficient human review by providing accurate and relevant data for critical public health activities.
Using Minimally Invasive Tissue Sampling and Determination of Cause of Death to Establish Etiologies of Community Respiratory Deaths Among Zambian Infants and Children
Authors: Wheelock Alyse , Chasaya Mwelwa , Namuziya Natasha , Jumbe Marsden Emilia , Kapasa Monica , Mumba Chibamba , Mulenga Bwalya , Nkole Lisa , Pieciak Rachel , Mudenda Victor , Chikoti Chilufya , Ngoma Benard , Chimoga Charles , Chirwa Sarah , Pemba Lilian , Nzara Diana , Lungu James , Forman Leah , MacLeod William , Moyo Crispin , Wa Somwe Somwe , Gill Christopher 
Published: December 2024

Abstract
In low-to-middle-income countries, acute lower respiratory infection (ALRI) remains the leading infectious cause of death among infants and children under 5 years old. Case-control studies based on upper respiratory sampling have informed current understandings of ALRI etiologies; in contrast, minimally invasive tissue sampling (MITS) offers a method of directly interrogating lower respiratory tract pathogens to establish etiologic distributions. This study performed in the postmortem setting used MITS and a Determination of Cause of Death (DeCoDe) panel to elucidate the causes of fatal pneumonia in the community in Lusaka, Zambia. For deceased infants and children under age 5 years whose next-of-kin provided consent, a verbal autopsy was obtained and 6 lung tissue biopsies from each case were sent for histopathology and multiplex polymerase chain reaction testing. Subsequently, a multi-disciplinary DeCoDe panel met to review each case, determine if the child died of respiratory causes, construct a causal chain of diagnoses directly leading to the death, and determine if the death was preventable (i.e., if an identifiable intervention would have averted the death). Among 106 deaths, 49 were adjudicated as respiratory deaths, with etiologic causes including Klebsiella pneumoniae (13), Streptococcus pneumoniae (5), and Pneumocystis jirovecii (4), among others. Of note, for 21 respiratory deaths, a causative pathogen could not be identified despite clinical and histopathologic evidence of ALRI. A large majority of all deaths were considered preventable (90/106 or 85%). This study demonstrates the impact of certain respiratory pathogens through direct in situ tissue sampling with supportive pathologic data and presents a useful method of studying the etiologic distribution of fatal ALRIs in settings where many deaths occur in the community.
The Victorian Royal Family and the Body of Princess Elizabeth Stuart: Historical Culture and Heritage, Collection and Display
Authors: Betts Sarah 
Published: December 2024

ABSTRACT
This essay explores the afterlife of Princess Elizabeth Stuart, daughter of the seventeenth-century civil war King, Charles I, and how her untimely death reverberated in Victorian culture. Drawing on a wide range of sources, from newspaper and diaries to details of memorials and history genre paintings, it argues that the interest of the Royal Family, and Queen Victoria in particular, in memorializing this tragic story should not be siloed off as is often the case with royal histories, but instead be read as part of a wider cultural movement around the romantic past which the Royal Family both passively consumed, and were actively involved in shaping. Investigating this participation and the influence of Victoria and her family in marking and representing the life of Elizabeth Stuart offers fresh perspective on currents of historicism, visual culture, and traditions around mourning and commemoration in Victorian culture and society.
Single-cell RNA sequencing reveals the intercellular crosstalk and the regulatory landscape of stromal cells during the whole life of the mouse ovary
Authors: Jiang Wan , Sun Wenya , Peng Yue , Xu Hao , Fan Haonan , Jin Xin , Xiao Yue , Wang Yuxiang , Yang Pin , Shu Wenjie , Li Jing 
Published: December 2024

Abstract
The heterogeneity of ovarian mesenchymal/stromal cells has just been revealed in both mice and humans. However, it remains unclear about the cellular development trace and the intercellular communication network in the whole life of the ovary. In the study, we integrated ours and published single-cell RNA sequencing data from E11.5 (embryonic day 11.5) until M12 (12-month-old) ovaries to show the dynamics of somatic cells along the developmental timeline. The intercellular crosstalk among somatic cell types was depicted with collagen signaling pathway as the most outgoing signals from stromal cells. We identified mesenchymal progenitor cells (CD24+) as the origin of stromal cells. Although their numbers decreased significantly in adults, the cells served as the major signal sender until ovarian senescence. Moreover, the ovarian injury could activate these stem cells and induce stroma remodeling in the aged ovary. Thus, mesenchymal progenitor cells may represent a new strategy to delay ovarian aging in the future.
Cell cycle progression of under-replicated cells
Authors: Huang Min , Yang Chang , Nie Litong , Zhang Huimin , Zhu Dandan , Wang Chao , Park Jeong-Min , Srivastava Mrinal , Mosa Elina , Li Siting , Tang Mengfan , Feng Xu , Keast Sarah J , Stossi Fabio , Chen Junjie 
Published: December 2024

Abstract
Cell cycle checkpoints are the regulatory mechanisms that secure the strict order of cellular events for cell division that ensure genome integrity. It has been proposed that mitosis initiation depends on the completion of DNA replication, which must be tightly controlled to guarantee genome duplication. Contrary to these conventional hypotheses, we showed here that cells were able to enter mitosis without completion of DNA replication. Although DNA replication was not completed in cells upon depletion of MCM2, CDC45 or GINS4, these under-replicated cells progressed into mitosis, which led to cell death. These unexpected results challenge current model and suggest the absence of a cell cycle checkpoint that monitors the completion of DNA replication.
Transcriptomic analysis of EGFR co-expression and activation in glioblastoma reveals associations with its ligands
Authors: Ghisai Santoesha A , Barin Nastaran , van Hijfte Levi , Verhagen Kim , de Wit Maurice , van den Bent Martin J , Hoogstrate Youri , French Pim J 
Published: December 2024

Abstract

Background
Approximately half of the isocitrate dehydrogenase (IDH)-wildtype glioblastomas (GBMs) exhibit EGFR amplification. Additionally, genomic changes that occur in the extracellular domain of EGFR can lead to ligand-hypersensitivity (R108K/A289V/G598V) or ligand-independence (EGFRvIII). Unlike in lung adenocarcinoma (LUAD), clinical trials with epidermal growth factor receptor (EGFR) inhibitors showed no survival benefit for GBM and it remains unclear why. We aimed to elucidate differences in molecular mechanisms of EGFR activation and regulation between GBM and LUAD.

Methods
We used RNA-sequencing (RNA-seq) data to find EGFR co-regulated genes and pathways in GBM and compare EGFR signaling patterns between GBM and LUAD. Cellular origins of expression signals were determined by analyzing single-cell RNA-seq data.

Results
We identified 2 ligands (BTC/EREG) among the significant EGFR predictor genes (TCGA-GBM: n = 169, Intellance-2: n = 166). Their expression was inversely correlated with EGFR amplification and incidence of ligand-sensitive mutations. Ligands were expressed by nonmalignant cells and differed in their primary source of expression (BTC: neurons, EREG: myeloid). High expression of MDM2 and CDK4 was less common in EGFR-amplified GBMs with ligand-sensitive mutations compared with those without these mutations. Our analyses revealed distinct transcriptional profiles between GBM and LUAD when comparing tumors carrying activating mutations.

Conclusions
BTC and EREG are negatively associated with EGFR expression in GBM. These findings emphasize the role of ligands in regulating EGFR, where EGFR activation seems to be modulated by the highly varying levels of EGFR amplification, the sensitivity of the receptor toward ligands, and ligand expression levels. Ligand expression levels and EGFR mutations could refine patient stratification for EGFR-targeted therapies in GBM.