bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trivalent immunization with metal-binding proteins confers protection against enterococci in a mouse infection model
Authors: Lam Ling Ning , Sedra Angie , Kajfasz Jessica , Berges Aym , Saengpet Irene S , Adams Grace , Fairman Jeffery , Lemos José A 
Published: October 2024

Abstract
Enterococcus faecalis is ranked among the top five bacterial pathogens responsible for catheter-associated urinary tract infections, wound infections, secondary root canal infections, and infective endocarditis. Previously, we showed that inactivation of either the manganese- and iron-binding (EfaA) or zinc-binding (AdcA and AdcAII) lipoproteins significantly reduced E. faecalis virulence. Here, we explored whether immunization using a multi-valent approach induces protective immunity against systemic enterococcal infections. We found that multi-antigen antisera raised against EfaA, AdcA, and AdcAII displayed similar capacities to initiate neutrophil-mediated opsonization, like their single-antigen counterparts. Further, these antigen-specific antibodies worked synergistically with calprotectin, a divalent host metal chelator, to inhibit the growth of E. faecalis in laboratory media as well as in human sera. Using the Galleria mellonella invertebrate model and mouse peritonitis model, we showed that passive immunization with multi-antigen antisera conferred robust protection against E. faecalis infection, while the protective effects of single antigen antisera were negligible in G. mellonella, and negligible-to-moderate in the mouse model. Lastly, active immunization with the 3-antigen (trivalent) cocktail significantly protected mice against either lethal or non-lethal E. faecalis infections, with this protection appearing to be far-reaching based on immunization results obtained with contemporary strains of E. faecalis and closely related Enterococcus faecium.
Genome-wide association studies of photosynthetic and agronomic traits in cowpea collection
Authors: Sansa Olakunle , Abberton Michael Terrance , Ariyo Johnson , Paliwal Rajneesh , Ige Adenike , Dieng Ibnou , Ayo-Vaughan Moninuola , Olowe Victor Idowu , Oyatomi Olaniyi 
Published: October 2024

Abstract
Exploring genomic regions linked with drought tolerance and photosynthesis in cowpea could accelerate breeding of climate-resilient cowpea varieties. A genome-wide association study (GWAS) was conducted to identify marker–trait associations for agronomic and photosynthetic traits measured under well-watered and water-stressed conditions. One hundred and twelve cowpea accessions from IITA were phenotyped for agronomic and photosynthetic traits across 3 locations in 2 years: Ibadan, Ikenne (2020 and 2021), and Kano (2021 and 2022). The accessions were genotyped using 19,000 Diversity Arrays Technology sequencing single-nucleotide polymorphism (SNP) markers from which 9,210 markers were utilized for GWAS analysis using BLINK and linear mixed model (LMM) in GAPIT. Results revealed significant accession × environment interactions for measured traits, while ΦPSII, ΦNO, and ΦNPQ had significant and consistent correlations with grain yield across conditions. GWAS identified 5 SNP markers having consistent associations with grain yield under well-watered and water-stressed conditions and 3 markers associated with ΦNPQ and ΦNO. Gene annotations revealed Vigun04g169000 and Vigun08g168900 genes linked with grain yield and highly expressed under water-stressed conditions have functional roles in regulating plant development and adaptive response to environmental stress. Vigun07g133400, Vigun07g132700, and Vigun07g258000 genes linked with ΦNPQ and ΦNO are involved in activities controlling photoprotection and stress-induced damage in plants. This study identified natural genetic variation in cowpea and correlations between photosynthetic traits and grain yield under real-field drought conditions. The identified SNP markers upon validation would be valuable in marker-assisted selection and useful for cowpea breeders to harness the role of photosynthesis in genetic enhancement of cowpea’s tolerance to drought.
CIEC: Cross-tissue Immune Cell Type Enrichment and Expression Map Visualization for Cancer
Authors: He Jinhua , Luo Haitao , Wang Wei , Bu Dechao , Zou Zhengkai , Wang Haolin , Tang Hongzhen , Han Zeping , Luo Wenfeng , Shen Jian , Xie Fangmei , Zhao Yi , Xiang Zhiming 
Published: October 2024

Abstract
Single-cell transcriptome sequencing technology has been applied to decode the cell types and functional states of immune cells, revealing their tissue-specific gene expression patterns and functions in cancer immunity. Comprehensive assessments of immune cells within and across tissues will provide us with a deeper understanding of the tumor immune system in general. Here, we present Cross-tissue Immune cell type or state Enrichment analysis of gene lists for Cancer (CIEC), the first web-based application that integrates database and enrichment analysis to estimate the cross-tissue immune cell type or state. CIEC version 1.0 consists of 480 samples covering primary tumor, adjacent normal tissue, lymph node, metastasis tissue, and peripheral blood from 323 cancer patients. By applying integrative analysis, we constructed an immune cell-type/state map for each context and adopted our previously developed Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology Based Annotation System (KOBAS) algorithm to estimate the enrichment for context-specific immune cell type/state. In addition, CIEC also provides an easy-to-use online interface for users to comprehensively analyze the immune cell characteristics mapped across multiple tissues, including expression map, correlation, similar genes detection, signature score, and expression comparison. We believe that CIEC will be a valuable resource for exploring the intrinsic characteristics of immune cells in cancer patients and for potentially guiding novel cancer–immune biomarker development and immunotherapy strategies. CIEC is freely accessible at http://ciec.gene.ac/.
A liberal defense of no-platforming
Authors: Adenitire John Olusegun 
Published: October 2024

Abstract
This article defends a definition of no-platforming as the practice by private actors of obstructing, or attempting to obstruct, a speaker on the ground that the speech or speaker is deeply objectionable, typically for moral reasons. A liberal defense of no-platforming is presented, asserting that it is a form of free speech protected by liberal principles, provided it is not violent. The core implication is that advocates of free speech should also support non-violent no-platforming. However, the free speech rights of no-platformers must be carefully balanced against those of the individuals being no-platformed, which may require ensuring that obstructed speakers still have an opportunity to be heard. Ultimately, the moral conflict is not merely between free speech and nondiscrimination, or between free speech and academic freedom, but rather a conflict within the realm of free speech itself.
Still Engaging, Not Avoiding, Contradictions: Conceptualizing Cooperative Research in Practical, Structural and Epistemic Terms
Authors: Lottholz Philipp , Kluczewska Karolina 
Published: October 2024

Abstract
Critical methodologies in International Political Sociology (IPS) and its intersecting fields and research traditions have increasingly coalesced around the idea that research should be done in dialogue, and possibly cooperation, with people rather than only about them. Drawing together research under this theme and wider debates on participatory, activist, and action research, alongside our own research experience, this article proposes the notion of cooperative research to capture and further develop this research agenda. In the context of neoliberal academia and its narrow insurance-based conception of research ethics and safety, we argue that cooperative and ethical research can be done and developed further both in the cracks and margins of the system, and in a gradual reform process within it. Starting with a survey of existing traditions and recent advances towards cooperative research, we proceed to unpack what cooperative research looks like in practice and how it benefits the involved parties. The article then explores structural and epistemic obstacles that cooperative research faces within the current institutional, body, and geo-politics of knowledge production. It also reflects on future avenues to productively deal with the inherent contradictions of cooperative research, not only by embracing the “ethos of critique”, but also by trying to make (even small) changes within the Western knowledge production system by promoting, and rendering more legitimate, alternative forms of knowledge and storytelling.
More Women, Fewer Nukes?
Authors: Wattenberg Jana 
Published: October 2024

Abstract
Women increasingly feature in nuclear diplomacy, both as participants and as subject matter. Research institutes report a steady increase in women's representation in large multilateral disarmament forums. Diplomats emphasize the importance of women in statements and working papers. The recent conversation on women in nuclear diplomacy forms part of a wider discourse on women in the nuclear weapons field. This article studies portrayals of women in the discourse. It identifies three narratives as prominent themes: women are missing, women are change-makers and women are victims. The narratives can generate support for political projects for gender equality and nuclear disarmament. However, they also create an ideal image of women as peaceful that bears negative connotations for perceptions of women's political agency. The article makes three contributions to feminist literature in International Relations. First, it brings the debate on the value of strategic essentialism to the nuclear case. Second, it proposes a new research agenda on women in the nuclear field to complexify the image of women as peaceful. Lastly, the article identifies tensions between feminisms in the nuclear field and suggests viewing these tensions as an indication that feminism is an ongoing conversation shaped by contention and solidarity. The practical significance of the article concerns the way in which the use of narratives about women can reinforce gender stereotypes. Practitioners might want to consider this implication when drawing on the narratives in their advocacy for women's inclusion and nuclear disarmament.
The quantification of bone mineral density using photon counting computed tomography and its implications for detecting bone remodeling
Authors: Quintiens Jilmen , Coudyzer Walter , Bevers Melissa , Vereecke Evie , van den Bergh Joop P , Manske Sarah L , van Lenthe G Harry 
Published: October 2024

Abstract
HR-pQCT has become standard practice when quantifying volumetric BMD (vBMD) in vivo. Yet, it is only accessible to peripheral sites, with small fields of view and lengthy scanning times. This limits general applicability in clinical workflows. The goal of this study was to assess the potential of photon counting CT (PCCT) in quantitative bone imaging. Using the European Forearm Phantom, PCCT was calibrated to hydroxyapatite (HA) density. Eight cadaveric forearms were scanned twice with PCCT and once with HR-pQCT. The dominant forearm of two volunteers was scanned twice with PCCT. In each scan, the carpals were delineated. At bone level, accuracy was assessed with a paired measurement of total vBMD (Tt.vBMD) calculated with PCCT and HR-pQCT. At voxel-level, repeatability was assessed by image registration and voxel-wise subtraction of the ex vivo PCCT scans. In an ideal scenario, this difference would be zero; any deviation was interpreted as falsely detected remodeling. For clinical usage, the least detectable remodeling was determined by finding a threshold in the PCCT difference image that resulted in a classification of bone formation and resorption below acceptable noise levels (&lt;0.5%). The paired measurement of Tt.vBMD had a Pearson correlation of 0.986. Compared to HR-pQCT, PCCT showed a bias of 7.46 mgHA/cm3. At voxel-level, the repeated PCCT scans showed a bias of 17.66 mgHA/cm3 and a standard error of 96.23 mgHA/cm3. Least detectable remodeling was found to be 250 mgHA/cm3, for which 0.37% of the voxels was incorrectly classified as newly added or resorbed bone. In vivo, this volume increased to 0.97%. Based on the cadaver data, we conclude that PCCT can be used to quantify vBMD and bone turnover. We provided proof of principle that this technique is also accurate in vivo, hence, that it has high potential for clinical applications.
Automatic cable routing based on improved pathfinding algorithm and B-spline optimization for collision avoidance
Authors: Kim Kunchan , Yoon Yeongjun , Kim Byung Chul , Kim Jongguk , Han Soonhung , Kwon Soonjo 
Published: October 2024

Abstract
With the recent growth of electrical and electronic systems such as electric vehicles, the demand for automatic cable routing for electrical wiring design is increasing. However, real industry use cases of automatic cable routing are still rare especially in three-dimensional design. In this study, we propose a new pathfinding algorithm, JPS–Theta*, which combines the existing pathfinding algorithms, Jump Point Search and Theta*, that is better suited for cable routing. In addition, we propose a B-spline optimization algorithm to create natural cable shapes while avoiding collisions. In the experiments, it was found that the proposed pathfinding algorithm complements the existing algorithms and is thought to be more suitable for the purpose of automatic cable routing. Additionally, ant colony optimization for continuous domains, a meta-heuristic algorithm, was successfully used for optimizing the B-spline to obtain cable shapes without collision. Lastly, as a case study, the proposed method was directly applied to the electrical panel design to show its effectiveness. We expect that the proposed method will be able to improve the efficiency and quality of electrical wiring design.
Numerical simulation of three-phase mud invasion using an epidermal effect model and adaptive time-stepping
Authors: Xiao Jiaqi , Chen Xinliang , Wang Peisheng , Gao Meixiang 
Published: October 2024

Abstract
The numerical simulation of reservoir mud invasion is widely used for studying the dynamic invasion process. To investigate the saturation changes of the three phases (water, oil, and mud filtrate) during mud infiltration into intact formations, this study presents a mathematical model for three-phase invasion in cylindrical coordinates. The principle of mud intrusion into the reservoir allows the derivation of the basic equation of three-phase mud seepage from Darcy's law and the law of mass conservation. This is followed by the derivation of the differential equations of pressure and three-phase saturation during mud intrusion. A numerical simulation program for the three-phase seepage flow of mud intrusion is written using the finite-difference method. An adaptive time-step algorithm is developed to address the inadaptability of the intrusion algorithm in the case of mud surges. Additionally, an epithermal effect algorithm is developed to address the problem of mud particles entering the stratum and affecting the absolute permeability. The results show that, as the porosity increases, the radial depth of intrusion decreases, along with a reduction in the invaded annulus range. It can be demonstrated that, when the reservoir pressure is maintained at a constant level, the size of the borehole pressure leads to an increase in the depth of radial intrusion and the extent of the intrusion annulus, under different differential pressure conditions.
The interaction of Galectin-8 C-terminal domain with cell surface glycoconjugates modulates membrane elasticity to stimulate antigen uptake and presentation to CD4 T cells
Authors: Prato Cecilia A , Borbolla Laura V , Lizarraga Leonardo , Campetella Oscar , Tribulatti María V 
Published: October 2024

Abstract
Galectins constitute a family of soluble lectins with unique capacity to induce macroscale rearrangements upon interacting with cell membrane glycoconjugates. Galectin-8 is acknowledged for its role in facilitating antigen uptake and processing upon engaging with cell surface glycoconjugates on antigen-presenting cells. Galectin-8 consists of two covalently fused N- and C-terminal carbohydrate recognition domains, each exhibiting distinct glycan specificity. In this study, we utilized single N- and C-carbohydrate recognition domains recombinant proteins to dissect the nature of Galectin-8-glycan interactions during antigen internalization enhancement. Single C-carbohydrate recognition domain was able to replicate the effect of full-length Galectin-8 on antigen internalization in bone marrow-derived dendritic cells. Antigen uptake enhancement was diminished in the presence of lactose or when N-glycosylation-deficient macrophages served as antigen-presenting cells, underscoring the significance of glycan recognition. Measurement of the elastic modulus using Atomic Force Microscopy unveiled that full-length Galectin-8- and C-carbohydrate recognition domain-stimulated macrophages exhibited heightened membrane stiffness compared to untreated cells, providing a plausible mechanism for their involvement in endocytosis. C-carbohydrate recognition domain proved to be as efficient as full-length Galectin-8 in promoting antigen degradation, suggesting its implication in antigen-processing induction. Lastly, C-carbohydrate recognition domain was able to replicate full-length Galectin-8-induced antigen presentation in the major histocompatibility complex class II (MHC-II) context both in vitro and in vivo. Our findings support the notion that Galectin-8 binds through its C-carbohydrate recognition domain to cell surface N-glycans, thereby altering membrane mechanical forces conducive to soluble antigen endocytosis, processing, and presentation to cognate CD4 T cells. These findings contribute to a deeper comprehension of Galectin-8 and its mechanisms of action, paving the way for the development of more efficacious immunotherapies.
Germline reflex BRCA1/2 testing following tumor-only comprehensive genomic profiling: why, when, and how
Authors: Maneri Giulia , Nero Camilla , Giacò Luciano , Scambia Giovanni , Minucci Angelo 
Published: October 2024

Abstract
The majority of tumor comprehensive genomic profiling (CGP) currently does not include a matched normal control. The use of a tumor-only CGP approach needs the development of a strategy to refine germline pathogenic/likely pathogenic variants (gP/LPVs) calls, so as to limit the performance of unnecessary germline reflex tests and instead successfully identify patients who are carriers of likely gP/LPVs. Guidelines have been developed for the identification of gP/LPVs in BRCA1/2 genes on the basis of tumor-only CGP results and for the evaluation of the appropriateness of performing germline reflex BRCA1/2 testing. In this study, an algorithm to assist decision-making for germline reflex testing of BRCA1/2 variants following tumor-only CGP is proposed.
A simulation study of MR-guided proton therapy system using iron-yoked superconducting open MRI: a conceptual study
Authors: Fujii Yusuke , Ueda Hideaki , Takayanagi Taisuke , Nishioka Kentaro , Mori Takashi , Hashimoto Takayuki , Aoyama Hidefumi , Umegaki Kikuo , Matsuura Taeko 
Published: October 2024

Abstract
Radiotherapy platforms integrated with magnetic resonance imaging (MRI) have been significantly successful and widely used in X-ray therapy over the previous decade. MRI provides greater soft-tissue contrast than conventional X-ray techniques, which enables more precise radiotherapy with on-couch adaptive treatment planning and direct tracking of moving tumors. The integration of MRI into a proton beam irradiation system (PBS) is still in the research stage. However, this could be beneficial as proton therapy is more sensitive to anatomical changes and organ motion. In this simulation study, we considered the integration of PBS into the 0.3-T superconducting open MRI system. Our proposed design involves proton beams traversing a hole at the center of the iron yoke, which allows for a reduced fringe field in the irradiation nozzle while maintaining a large proton scan field of the current PBS. The shape of the bipolar MRI magnets was derived to achieve a large MRI field-of-view. To monitor the beam position and size accurately while maintaining a small beam size, the beam monitor installation was redesigned from the current system. The feasibility of this system was then demonstrated by the treatment plan quality, which showed that the magnetic field did not deteriorate the plan quality from that without the magnetic field for both a rectangular target and a prostate case. Although numerous challenges remain before the proposed simulation model can be implemented in a clinical setting, the presented conceptual design could assist in the initial design for the realization of the MR-guided proton therapy.
A case of idiopathic superior lumbar hernia repaired using a transabdominal laparoscopic approach
Authors: Kawakami Koki , Moriwaki Yoshihiro , Otani Jun 
Published: October 2024

Abstract
The patient is a 78-year-old woman who presented to our hospital with left lumbar back pain as her chief complaint. She was diagnosed with superior lumbar hernia. There was no history of abdominal or lumbar surgery, or trauma, so the condition was considered idiopathic. Mesh was placed laparoscopically to repair the hernia. She was discharged on the second postoperative day. One year has passed since the surgery, and there has been no recurrence of the hernia, nor have there been any complications such as neuropathic pain. Superior lumbar hernia is a type of abdominal wall hernia that protrudes through the superior lumbar triangle and is a relatively rare condition. Due to the lack of an established standard surgical procedure, various surgical techniques have been employed depending on the facility. Laparoscopic surgery was considered a minimally invasive and reliable method for hernia repair, providing good visualization in cases without intra-abdominal adhesions.
Successful surgical repair of isolated supra-cardiac total anomalous pulmonary venous connection (TAPVC) with venous confluence stenosis using dual anastomosis: a case report from Syria
Authors: Hasan Ghaith , Almjersah Abdulrahman , Younes Mohamed 
Published: October 2024

Abstract
We present the case of a 7-month-old female infant with a history of recurrent respiratory infections and symptoms of respiratory distress during feeding. Echocardiography isolated revealed supracardiac-type total anomalous pulmonary venous connection with a large ostium secundum atrial septal defect and severe pulmonary hypertension. Computed tomographic angiography confirmed the diagnosis and identified stenosis at the level of the venous confluence. The surgical intervention involved a novel approach using dual anastomoses between the pulmonary venous confluence and the left atrium, alongside atrial septal defect repair with a bovine pericardial patch. Postoperative recovery was uneventful, with successful weaning from mechanical ventilation on Day 9 and discharge on Day 12. The patient showed optimal venous drainage and hemodynamic stability, indicating a successful surgical outcome. This case highlights the importance of early surgical intervention in total anomalous pulmonary venous connection with complex anatomical presentations.