bluuebunny/crossref_metadata_2025_split huggingface dataset:
HemaCisDB: An Interactive Database for Analyzing Cis-Regulatory Elements Across Hematopoietic Malignancies
Authors: Cai Xinping , Zhang Qianru , Liu Bolin , Sun Lu , Liu Yuxuan 
Published: December 2024

Abstract
Noncoding cis-regulatory elements (CREs), such as transcriptional enhancers, are key regulators of gene expression programs. Accessible chromatin and H3K27ac are well-recognized markers for CREs associated with their biological function. Deregulation of CREs is commonly found in hematopoietic malignancies yet the extent to which CRE dysfunction contributes to pathophysiology remains incompletely understood. Here, we developed HemaCisDB, an interactive, comprehensive, and centralized online resource for CRE characterization across hematopoietic malignancies, serving as a useful resource for investigating the pathological roles of CREs in blood disorders. Currently, we collected 922 ATAC-seq, 190 DNase-seq, and 531 H3K27ac ChIP-seq datasets from patient samples and cell lines across different myeloid and lymphoid neoplasms. HemaCisDB provides comprehensive quality control metrics to assess ATAC-seq, DNase-seq, and H3K27ac ChIP-seq data quality. The analytic modules in HemaCisDB include transcription factor (TF) footprinting inference, super-enhancer identification, and core transcriptional regulatory circuitry analysis. Moreover, HemaCisDB also enables the study of TF binding dynamics by comparing TF footprints across different disease types or conditions via web-based interactive analysis. Together, HemaCisDB provides an interactive platform for CRE characterization to facilitate mechanistic studies of transcriptional regulation in hematopoietic malignancies. HemaCisDB is available at https://hemacisdb.chinablood.com.cn/.
Convergence and quasi-optimality of an AFEM for the Dirichlet boundary control problem
Authors: Pal Arnab , Gudi Thirupathi 
Published: December 2024

Abstract
In this article, convergence and quasi-optimal rate of convergence of an Adaptive Finite Element Method is shown for the Dirichlet boundary control problem that was proposed by Chowdhury et al. (2017, Error bounds for a Dirichlet boundary control problem based on energy spaces, Math. Comp., 86, 1103–1126). The theoretical results are illustrated by numerical experiments.
Peacemaking and the Maintenance of International Order: Alignment under Hegemony versus Multipolar Misalignment
Authors: Richmond Oliver P , Pogodda Sandra 
Published: December 2024

Abstract
With the publication of Agenda for Peace, the UN system opened its peace interventions up to critiques that allowed a tentative incorporation of critical, ethnographic, feminist, and rights-based approaches. Yet, subsequent efforts to reform the international peace architecture have been more limited, reflecting geopolitical interests rather than critical methodologies. Since the 1990s, two trends have occurred: within the liberal international order legitimate political claims from outside Western understandings of peacemaking have been marginalized, while liberal peacemaking has been undermined by competing actors, institutions, and processes in an emerging multipolar order. But has the latter developed a significant capacity for peacemaking? This article argues that the “liberal alignment” appears to have broken down but a “misaligned multipolar” order offers few if any tools that respond to critical arguments about peacemaking. This article critically evaluates the potential for peacemaking in a liberal aligned order versus that of a multipolar misaligned order.
The Serial Killer’s Religion: Religious Racism in Brazil
Authors: Vasconcelos de Castro Moreira Leonardo 
Published: December 2024

Abstract
This article analyzes the case of the serial killer Lázaro Barbosa and religious racism in Brazil. It provides a brief overview of the racialization of religion and the background behind policies and ideologies that tried to “whiten” the country, both racially and culturally. Based on data gathered from the Brazilian media, the article analyzes the case of the serial killer and the ways his religiosity is constructed in relation to Afro-Brazilian religions, leading to cases of violence against practitioners and temples due to their alleged connection with Barbosa. The objective is also to analyze the discourses of demonization that were capable of materializing this persecution. Lastly, this article argues that religious racism in Brazil is not simply about anti-Black racism but also has sui generis features, which include prejudice against African cultural origins.
Doctors’ perceptions of antimicrobial resistance in the Northern West Bank, Palestine: a qualitative study
Authors: Gustafsson Lotta , Nazzal Zaher , Wiskin Connie Mary , Belkebir Souad , Sayeed Shameq , Wood Alix 
Published: December 2024

Abstract

Objectives
In the West Bank, antimicrobial resistance (AMR) is increasingly and alarmingly common. Efforts are being made to introduce antimicrobial stewardship programmes (ASPs). This study explores doctors’ perceptions of AMR and context-specific barriers and facilitators to ASPs at a critical point in national ASP development.

Methods
Semi-structured interviews were conducted with 22 doctors working in primary healthcare, government and non-governmental hospitals in Nablus in 2019. Two researchers thematically analysed the data.

Results
Participants recognized antibiotic resistance as a major threat to health. Few felt that doctors were well informed about ASPs; many had not heard of them. However, there was willingness to expand and begin new education programmes. Barriers and facilitators to ASPs included: (i) doctors were perceived to ‘misuse’ antibiotics, lack awareness, favour short-term outcomes, and externalize blame; (ii) patients reportedly treat antibiotics ‘like analgesia’ with high expectations of doctors; (iii) resource limitations make ASPs and infection control difficult—a lack of drugs, laboratory services, infectious disease specialists, and research to develop local guidelines; and (iv) top-down policy is recommended to restrict access to antibiotics without a prescription, but should be coupled with support, collaboration and community action.

Conclusions
Doctors’ appreciation of the severity of the issue, and willingness for the expansion of existing programmes targeted at their own prescribing practices, provides a strong foundation for successful ASPs. A top-down approach to prevent inappropriate antibiotic prescribing is welcomed by participating doctors. If financial and resource limitations could be addressed, a continued multifaceted approach may enable physician, pharmacist and patient behaviours to change.
Total Prostate-Specific Antigen (PSA) Testing in Capillary Samples: Proof-of-Principle and Feasibility Study for Home Self-Testing for Prostate Cancer
Authors: Sodi Ravinder , Young Noel , Tetucci Alessandra , Woolley Timothy , Shah Vishal , Maund Isabella 
Published: December 2024

Abstract

Background
There is growing interest in the use of capillary blood sampling (CBS) for testing biochemical analytes owing to the advantages it offers including home surveillance of chronic conditions. In this study, we aimed to determine whether the use of CBS was a viable and feasible method for testing total prostate-specific antigen (TPSA) concentrations in men with prostate disease.

Methods
Men with known prostate disease were recruited from a urology clinic where they were being treated or followed up. Samples were collected in serum separating tubes by the finger-prick method using validated devices. Simultaneously, venous blood was collected by venipuncture. We used validated immunoassays on both the Roche (Cobas 801) and Beckman (DXi) platforms to measure TPSA.

Results
In total, 66 adult men between 26 and 64 years of age were tested. Across the concentration range of normal (0.3 µg/L) to pathological (314 µg/L), the results between CBS and venous samples were highly comparable and correlated (r = 0.997). The average bias was 0.112 µg/L or 1.07% and was not significant (P = 0.274). Overall, there was no apparent proportional or constant bias observed. Our data showed that TPSA may be stable in CBS stored at ambient temperature for up to 8 days in the samples tested using either the Roche or Beckman assays.

Conclusions
This feasibility study shows that CBS and venous samples are highly correlated and there was negligible bias. Further validation work is now required for the measurement of TPSA in CBS and determining outcomes in men with prostate disease.
A novel tank-mix formulation increases the efficacy of alphabaculoviruses on different phylloplanes
Authors: Mehrvar Ali , Ghanbari Solmaz , Söylemezoğlu Gökhan , Toprak Umut 
Published: December 2024

Abstract
Spodoptera littoralis Boisduval (Lepidoptera: Noctuidae) and Spodoptera exigua Hübner (Lepidoptera: Noctuidae) pose substantial threats to many crops, necessitating the exploration of biopesticides as potential chemical alternatives. One alternative is baculoviruses; however, their instability in the field has hindered their widespread use. Host plant phylloplane affects baculovirus activity at varying levels in different host plants. Formulation contributes significantly to optimizing the baculoviral stability on different phylloplanes against environmental conditions; however, it is expensive and difficult to make in developing or nondeveloped countries. In the current study, we developed a simple tank-mix application (MBF-Tm5) for immediate use, resembling the characteristics of a suspension concentrate formulation for Spodoptera littoralis nucleopolyhedrovirus (SpliNPV) and Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV). We examined their biological activity against 2nd instar larvae first on an artificial diet under laboratory conditions and on eggplant and pepper phylloplane in greenhouse conditions compared to plain viruses. This formulation exhibited no significant improvement in the biological activity of both viruses on an artificial diet under laboratory conditions but significantly improved the biological activity of both viruses on both plants under greenhouse conditions. The original activity remaining (OAR%) of both unformulated and formulated viruses decreased over time under greenhouse conditions; however, the OAR value of both viruses on eggplants was significantly higher than on pepper plants. Overall, the tank-mix simple formulation of baculoviruses might be a great alternative for improved stability in nature, providing better control.
Characteristics of structurally finite classes of order-preserving three-valued logic maps
Authors: Esin Anton A 
Published: December 2024

Abstract
This paper investigates structural properties of monotone function classes within the framework of three-valued logic (3VL), aiming to characterize dependencies and constraints that ensure structural finiteness and order-preserving properties. This research delves into characteristics of structurally finite classes of order-preserving 3VL map. Monotonicity plays a critical role in understanding functional behaviour, which is essential for structuring closed logical operations within $ P_{k} $. We define $ F $ as a closed class in $ P_{k} $, consisting only of mappings that comply with specified operations and are strictly confined to $ P_{k} $. The notation $ F(n) $ represents the subset of mappings in $ F $ dependent on $ n $ variables, highlighting the limited scope of inputs and their respective outputs. Further analysis through $ CR(F) $ facilitates the identification of precursor subclasses within $ F $, which have not yet achieved closure under all necessary operations—a pivotal step in constructing intermediate mapping classes. Within the framework of 3VL, the study examines order-preserving maps $ f_{D}, f_{K}, f_{M^{(2)}}, f_{DM^{(2)}}, f_{KM^{(2)}} $, deliberately excluding the sets $ D, K, M^{(2)} $, where $ DM^{(2)} $ is defined as $ D \cap M^{(2)} $ and $ KM^{(2)} $ as $ K \cap M^{(2)} $. The lattice framework in $ P_{k}(1) $ for $ k = 3 $ systematically organizes these mapping classes based on their completeness properties, with particular emphasis on classes such as $ M $, which is characterized as a comprehensive set governed by the operations of maximum and minimum.
Our theorems establish structural finiteness for classes of unary order-preserving maps, emphasizing their two-variable dependency in class construction. This study extends existing findings on single-variable monotonic functions within 3VL by integrating criteria of linear order. Key results include the classification of mapping classes $ F \subseteq M $ containing $ M^{(1)}_{3} $, categorized into distinct groups: $ M^{(1)}_{3}, KM^{(2)}, DM^{(2)}, M^{(2)}, K, D, M $. Inclusion relations are visualized diagrammatically, showing the hierarchical structure of these monotone classes, ultimately validating the structural finiteness of classes incorporating all unary order-preserving maps within the broader context of 3VL.
Probabilistic Richardson extrapolation
Authors: Oates Chris J , Karvonen Toni , Teckentrup Aretha L , Strocchi Marina , Niederer Steven A 
Published: December 2024

Abstract
For over a century, extrapolation methods have provided a powerful tool to improve the convergence order of a numerical method. However, these tools are not well-suited to modern computer codes, where multiple continua are discretized and convergence orders are not easily analysed. To address this challenge, we present a probabilistic perspective on Richardson extrapolation, a point of view that unifies classical extrapolation methods with modern multi-fidelity modelling, and handles uncertain convergence orders by allowing these to be statistically estimated. The approach is developed using Gaussian processes, leading to Gauss–Richardson Extrapolation. Conditions are established under which extrapolation using the conditional mean achieves a polynomial (or even an exponential) speed-up compared to the original numerical method. Further, the probabilistic formulation unlocks the possibility of experimental design, casting the selection of fidelities as a continuous optimization problem, which can then be (approximately) solved. A case study involving a computational cardiac model demonstrates that practical gains in accuracy can be achieved using the GRE method.
Simultaneous triple peptic perforations: a report of an extremely rare case
Authors: La Van Phu , Tong Hai Duong , La Vinh Phuc , Le Thanh Nhat Minh , Tran Quan Minh , Dang Cong Phi , Doan Anh Vu 
Published: December 2024

Abstract
Peptic ulcer perforations are common in surgical emergencies, whereas double perforations are rare, and triple peptic perforations are even exceedingly rare, with only a few cases documented. While undetected perforation during surgery can be fatal, the absence of standardized procedures for managing multiple perforations remains an ongoing challenge for surgeons. Herein, we describe a rare case of simultaneous triple peptic perforations in an elderly man with a prolonged history of analgesic and corticosteroid use. This case underscores the importance of screening multiple peptic perforations intraoperatively. Subtotal gastrectomy is suggested as an effective option when simple closure of perforations is infeasible.
Perforation of sigmoid colon by a migrated intrauterine contraceptive device (IUCD), diagnosis and surgical management: a case report
Authors: Khan Muhammad E A , Kelly Elaine , Haidaran Ahmed I D 
Published: December 2024

Abstract
We describe the case of a 43-year-old woman presented with an 8-month history of intermittent non-specific abdominal pain. She had an Intrauterine Contraceptive Device (IUCD) inserted 4-years ago and the device was still in-situ. After initial gynaecological assessment, further clinical radiological investigations, computerized tomography imaging showed that the intraluminal part of the radiological foreign body was seen to be possibly perforating the sigmoid colon after having migrated. Diagnostic laparoscopy confirmed this and a laparotomy was performed to remove the foreign body (IUCD) followed by primary closure of the defect in the sigmoid colon.
Clinical outcomes and complications of retained biliary stents during the COVID-19 pandemic: a case series
Authors: Kandel Bishnu P , Luitel Prajjwol , Shrestha Asim , Sharma Deepak , Manandhar Narendra , Maskey Sumita P , Bhandari Ramesh S , Lakhey Paleswan J 
Published: December 2024

Abstract
Biliary stents are widely used following endoscopic management of choledocholithiasis. Removal is recommended within 3–6 months to prevent complications. This study analyzed cases of retained biliary stents managed at our institution. Data on patient demographics, duration of stent retention, complications, and management outcomes were collected and analyzed. The mean age of the patients was 60 years (range: 50–82), and the mean stent retention duration was 29.5 months (range: 12–52 months). Acute cholangitis (83.3%) was the most frequent clinical presentation. Endoscopic stone removal was successful in two cases (33.3%), while the remaining four required open bile duct exploration due to technical challenges. Retained biliary stents are associated with severe complications such as recurrent choledocholithiasis and acute cholangitis, often necessitating invasive interventions. These findings underscore the critical importance of timely stent retrieval to minimize morbidity.
A pipeline for validation of Serendipita indica effector-like sRNA suggests cross-kingdom communication in the symbiosis with Arabidopsis
Authors: Nasfi Sabrine , Shahbazi Saba , Bitterlich Katharina , Šečić Ena , Kogel Karl-Heinz , Steinbrenner Jens 
Published: December 2024

Abstract
Bidirectional communication between pathogenic microbes and their plant hosts via small RNA (sRNA)-mediated cross-kingdom RNAi (ckRNAi) is a key element for successful host colonization. Whether mutualistic fungi of the Serendipitaceae family, known for their extremely broad host range, use sRNAs to colonize plant roots is still under debate. To address this question, we developed a pipeline to validate the accumulation, translocation, and activity of fungal sRNAs in post-transcriptional silencing of Arabidopsis thaliana genes. Using stem–loop quantitative reverse transcription–PCR, we detected the expression of a specific set of Serendipita indica (Si) sRNAs, targeting host genes involved in cell wall organization, hormonal signalling regulation, immunity, and gene regulation. To confirm the gene silencing activity of these sRNAs in plant cells, SisRNAs were transiently expressed in protoplasts. Stem–loop PCR confirmed sRNA expression and accumulation, while qPCR validated post-transcriptional gene silencing of their predicted target genes. Furthermore, Arabidopsis ARGONAUTE 1 immunoprecipitation revealed the loading of fungal SisRNAs into the plant RNAi machinery, suggesting the translocation of SisRNA from the fungus into root cells. In conclusion, this study provides a blueprint for rapid selection and analysis of sRNA effectors and further supports the model of cross-kingdom communication in the Sebacinoid symbiosis.
Detection and Successful Treatment of Gunshot Wound to the Femoral Artery and Vein Four Days Post-incident: A Case Study
Authors: Yatsun Vladyslav , Yatsun Oleksandr 
Published: December 2024

ABSTRACT
This case study presents the successful treatment of a 26-year-old male who experienced profuse bleeding from a gunshot wound to his thigh 4 days after the initial injury. The patient underwent surgery performed by a military vascular surgeon, during which previously undetected injuries to the femoral artery and vein were identified. The surgeon conducted a femoral artery alloprosthesis and sutured the damaged femoral vein. Following the surgery, the patient received post-operative conservative treatment and vacuum-assisted closure therapy, resulting in no complications or development of irreversible ischemic manifestation. The clinical case demonstrates the possible positive effects of placing an endovascular balloon in the main artery (more proximal lesion) for prolonged bleeding control without the use of a tourniquet. In this case, the role of the endovascular balloon was played by a hematoma. As a result, the lower extremity survived 4 days before the arterial blood flow reconstruction was done. Although such a model of bleeding control is absolutely unacceptable for planned specialized surgery or even military surgery at a medical assistance level of II-III, it may be considered as a lifesaving measure when surgical intervention is not immediately available.
A general strategy for engineering GU base pairs to facilitate RNA crystallization
Authors: Ren Yangyi , Lin Xiaowei , Liao Wenjian , Peng Xuemei , Deng Jie , Zhang Zhe , Zhan Jian , Zhou Yaoqi , Westhof Eric , Lilley David M J , Wang Jia , Huang Lin 
Published: December 2024

Abstract
X-ray crystallography is a fundamental technique that provides atomic-level insights into RNA structures. However, obtaining crystals of RNA structures diffracting to high resolution is challenging. We introduce a simple strategy to enhance the resolution limit of RNA crystals by the selective substitution of Watson–Crick pairs by GU pairs within RNA sequences. Our approach has successfully yielded high-resolution structures for eight unique RNA crystals. Notably, six instances showed marked resolution enhancement upon GC/AU to GU base pair substitution, with two cases achieving high-resolution structures from initially poor data. In one case, reverting GU to GC base pairs also improved resolution. Our method facilitated the first structural determinations of the Long Interspersed Nuclear Element-1 and Olfactory Receptor family 4 subfamily K member 15 ribozymes, the 2′-deoxyguanosine-III riboswitch and the Broccoli RNA aptamer. The placement of GU base pairs within the first 5′ helical stem of any given RNA species, or in one peripheral stem, is shown to be sufficient. These results offer a simple and effective approach for designing sequences or selecting sequences from homologous sequences, for high-resolution RNA structure determination.
The impact of traumatic brain injury on visual processing: a neuro-ophthalmological perspective
Authors: Tukur Hajar Nasir , Uwishema Olivier , Sheikhah Dalal , Akbay Hatice , Chehab Tarek Emir , Wellington Jack 
Published: December 2024

Abstract

Introduction
Traumatic brain injury (TBI) is a critical global health issue characterized by perturbance in cerebral function attributed to mechanical force. TBI often precipitates significant visual impairment that negatively impacts the patients’ quality of life. This review examines the effects of TBI on visual function from a neuro-ophthalmological perspective, focusing on the assessment, diagnostics, and management of associated sequelae.

Methods
A comprehensive literature review was conducted using PubMed/MEDLINE, ScienceDirect, and Google Scholar to garner and collate relevant data.

Results
TBI may result in visual field defects, ocular motor dysfunction, insufficiency of accommodation, and photosensitivity. Early detection remains a profound challenge, partly due to a dearth of standardized protocols for evaluating visual impairment. Diagnostic methodologies include visual field testing, ocular motility assessments, and fundus photography, while rehabilitation approaches encompass vision therapy and low-vision rehabilitation.

Conclusion
Establishing hospital-based multidisciplinary teams is essential for effectively addressing TBI-related visual impairment. Future research should prioritize evidence-based treatment protocols and explore diverse vision rehabilitation strategies through large-scale studies.