bluuebunny/crossref_metadata_2025_split huggingface dataset:
A predictive language model for SARS-CoV-2 evolution
Authors: Ma Enhao , Guo Xuan , Hu Mingda , Wang Penghua , Wang Xin , Wei Congwen , Cheng Gong 
Published: December 2024

AbstractModeling and predicting mutations are critical for COVID-19 and similar pandemic preparedness. However, existing predictive models have yet to integrate the regularity and randomness of viral mutations with minimal data requirements. Here, we develop a non-demanding language model utilizing both regularity and randomness to predict candidate SARS-CoV-2 variants and mutations that might prevail. We constructed the “grammatical frameworks” of the available S1 sequences for dimension reduction and semantic representation to grasp the model’s latent regularity. The mutational profile, defined as the frequency of mutations, was introduced into the model to incorporate randomness. With this model, we successfully identified and validated several variants with significantly enhanced viral infectivity and immune evasion by wet-lab experiments. By inputting the sequence data from three different time points, we detected circulating strains or vital mutations for XBB.1.16, EG.5, JN.1, and BA.2.86 strains before their emergence. In addition, our results also predicted the previously unknown variants that may cause future epidemics. With both the data validation and experiment evidence, our study represents a fast-responding, concise, and promising language model, potentially generalizable to other viral pathogens, to forecast viral evolution and detect crucial hot mutation spots, thus warning the emerging variants that might raise public health concern.
Designing and implementation of a mobile application for teaching population oral health needs assessment for dental students; a non-randomized trial
Authors: Ghasemi Hadi , Habibi Amin , Ahmady Soleiman 
Published: December 2024

Abstract
Objective
This study investigates the effectiveness of a newly developed smartphone-based application for teaching population oral health needs assessment to undergraduate dental students.

Methods
Target population in this study consisted of all students of Shahid Beheshti School of dentistry in the 7th and 8th semesters in the year 2023. The intervention group (7th semester) received teaching about population oral health needs assessment based on the book “Oral health surveys; basic methods”, by means of an application, while the control group (8th semester) received the same content through self-learning activity. A questionnaire inquiring about the students’ general aspects of smartphone usage, attitude towards learning based on mobile devices (m-learning), and level of knowledge about the content of the book was used for data collection.

Results
Most dental students used smartphones extensively and expressed positive attitudes toward mobile learning with no significant statistical difference between intervention and control groups. However, both groups demonstrated limited knowledge gain from the book content, with the mobile application showing no superiority to self-learning education.

Conclusion
The present study did not demonstrate superior effectiveness of a smartphone app compared to traditional teacher-centered instruction, but the students’ significant mobile usage and positive attitude towards m-learning suggest potential for further investigation in dental education.
A laboratory-scale simulation framework for analysing wildfire hydrologic and water quality effects
Authors: Brucker Carli P. , Livneh Ben , Butler Claire E. , Rosario-Ortiz Fernando L. 
Published: December 2024

Background Wildfires can significantly impact water quality and supply. However logistical difficulties and high variability in in situ data collection have limited previous analyses. Aims We simulated wildfire and rainfall effects at varying terrain slopes in a controlled setting to isolate driver-response relationships. Methods Custom-designed laboratory-scale burn and rainfall simulators were applied to 154 soil samples, measuring subsequent runoff and constituent responses. Simulated conditions included low, moderate, and high burn intensities (~100–600°C); 10-, 200-, and 1000-year storm events (~14–51 mm/h); and 10–29° terrain slopes. Key results Simulators can control key drivers, with burn intensities highly correlated (R2 = 0.64) with heat treatment durations. Increasing burn intensity treatments generally saw significant (α = 0.05) increases in responses, with runoff and sedimentation increasing by ~30–70% with each intensity increment. Carbon and nitrogen peaked at moderate intensities (~250°C), however, with concentrations ~200–250% of unburned samples. Conclusions Distinct responses at each burn intensity indicate nuanced changes in soil physical and chemical composition with increased heating, exacerbating driving mechanisms of runoff and sedimentation while reducing carbon and nitrogen through volatilisation. Implications This work furthers our understanding of interactions between complex geographic features and the mosaic of burn intensities which exist in wildfire-affected landscapes.
Case Reports in the Integration of Technology with Cognitive Rehabilitation for Individuals with Memory Concerns and Their Care Partners
Authors: Grewal Karl S , Grewal Eric S , Cammer Allison , McWilliams Lachlan A , Spiteri Raymond J , O’Connell Megan E 
Published: December 2024

Abstract

Objective
Technology can be combined with psychological interventions to support older adults with memory concerns. Using a bi-phasic design, cognitive rehabilitation (CR) was integrated with off-the-shelf technology and delivered to two people with cognitive impairment, and one care partner.

Method
Pre- and post-intervention assessments were completed for all participants. Individuals with memory problems received pre- and post-intervention remote neuropsychological assessment (i.e., Rey auditory verbal learning test; mental alternations test; animal fluency), and the hospital anxiety and depression scale (HADS). The care partner completed the HADS, Zarit burden interview, and neuropsychiatric inventory questionnaire. Change metrics incorporated reliable change indices where possible. Goals were tracked using the Canadian occupation performance measure; these data were analyzed through visual inspection. A research journal (used to document intervention process) was analyzed thematically.

Results
Results cautiously suggested our integration was feasible and acceptable across several technologies and varying goals. Across participants, significant changes in goal progress suggested the integration of technology with CR successfully facilitated goal performance and satisfaction. The research journal underscored the importance of a visual component, intervention flexibility, and a strong therapeutic alliance in integrating technology and CR.

Conclusions
CR and technology present a promising avenue for supporting people living with cognitive impairment. Further exploration of technology and CR with a range of etiologies and target goals is warranted.
Diagnosis of Alzheimer’s disease using FusionNet with improved secretary bird optimization algorithm for optimal MK-SVM based on imaging genetic data
Authors: Wang Luyun , Sheng Jinhua , Zhang Qiao , Song Yan , Zhang Qian , Wang Binbing , Zhang Rong 
Published: December 2024

Abstract
Alzheimer’s disease is an irreversible central neurodegenerative disease, and early diagnosis of Alzheimer’s disease is beneficial for its prevention and early intervention treatment. In this study, we propose a novel framework, FusionNet-ISBOA-MK-SVM, which integrates a fusion network (FusionNet) and improved secretary bird optimization algorithm to optimize multikernel support vector machine for Alzheimer’s disease diagnosis. The model leverages multimodality data, including functional magnetic resonance imaging and genetic information (single-nucleotide polymorphisms). Specifically, FusionNet employs U-shaped hierarchical graph convolutional networks and sparse graph attention networks to select feature effectively. Extensive validation using the Alzheimer’s Disease Neuroimaging Initiative dataset demonstrates the model’s superior interpretability and classification performance. Compared to other state-of-the-art machine learning methods, FusionNet-ISBOA-MK-SVM achieves classification accuracies of 98.6%, 95.7%, 93.0%, 91.8%, 93.1%, and 95.4% for HC vs. AD, EMCI vs. AD, LMCI vs. AD, EMCI vs. AD, HC vs. EMCI, and HC vs. LMCI, respectively. Moreover, the proposed model identifies affected brain regions and pathogenic genes, offering deeper insights into the mechanisms and progression of Alzheimer’s disease. These findings provide valuable scientific evidence to support early diagnosis and preventive strategies for Alzheimer’s disease.
Borderline Sovereignty Disorder: China and the Law and Politics of the China-India Territorial Disputes
Authors: deLisle Jacques 
Published: December 2024

Abstract
International law is usually conducive to stability and peace. In the context of the China-India border and territorial disputes, however, international law exacerbates tensions and increases risks, as the incidents at the border in 2020 illustrate. Factors that explain this pattern include: the impossibility of ‘thick’ exercises of sovereignty in marginal, uninhabitable territory, the ambiguities of the human rights to self-determination of minority peoples and the dilemmas they pose for States’ central governments, China’s distinctive views on the invalidity of ‘unequal treaties,’ the relevance of various history-based claims to sovereignty, and the special place of the Five Principles of Peaceful Coexistence in international law. These law-related problems are compounded by political aspects of the border and territorial disputes and China-India relations, including: rising nationalism in both States, concentrations in and near disputed territory of minority populations with cross-border ties, China’s and India’s status as rising or renascent powers, and alignments with third-party States.
Offset attention with seed generation for point cloud completion
Authors: Li Yuke , Wang Yong , Jiang Bin 
Published: December 2024

Abstract
Point cloud data acquired through 3D scanning is frequently subject to fragmentation due to the constraints of the scanner’s field of view and occlusions within the scanned object. The ensuing incompleteness in the data can significantly degrade the accuracy of subsequent computational tasks. Traditional methods for predicting complete point clouds from these fragments often fail to capture the fine-grained local details, leading to inaccurate reconstructions. In this work, we introduce a novel neural network architecture designed for point cloud completion that addresses these limitations.Our network accepts an incomplete point cloud and employs a multi-scale feature extraction module, which integrates an offset attention mechanism alongside a feature aggregation module operating across various scales. This dual approach significantly bolsters the network’s capacity to discern both local and global features inherent in the point cloud data. Furthermore, we incorporate a seed generation module within our missing point cloud generator, harnessing a hierarchical feature pyramid network to forecast the entirety of the point cloud. This innovative strategy allows our network to accurately predict the structure of missing regions.Empirical evaluations conducted on the Shapenet-Part and ModelNet10 datasets substantiate the efficacy of our proposed methodology. Our approach outperforms the state-of-the-art PF-Net algorithm, achieving a remarkable reduction in chamfer distance by 16.15$\%$ and 41.87$\%$ on the respective datasets. Visual inspection of the results underscores the robust generalization capabilities of our algorithm, which is particularly evident in scenarios with limited dataset sizes. It adeptly predicts the contours of the missing regions and synthesizes a more comprehensive point cloud shape.
A near-complete telomere-to-telomere genome assembly for Batrachochytrium dendrobatidis GPL JEL423 reveals a larger CBM18 gene family and a smaller M36 metalloprotease gene family than previously recognized
Authors: Helmstetter Nicolas , Harrison Keith , Gregory Jack , Harrison Jamie , Ballou Elizabeth , Farrer Rhys A 
Published: December 2024

Abstract
Batrachochytrium dendrobatidis is responsible for mass extinctions and extirpations of amphibians, mainly driven by the Global Panzootic Lineage (BdGPL). BdGPL isolate JEL423 is a commonly used reference strain in studies exploring the evolution, epidemiology, and pathogenicity of chytrid pathogens. These studies have been hampered by the fragmented, erroneous, and incomplete B. dendrobatidis JEL423 genome assembly, which includes long stretches of ambiguous positions and poorly resolved telomeric regions. Here, we present and describe a substantially improved, near telomere-to-telomere genome assembly and gene annotation for B. dendrobatidis JEL423. Our new assembly is 24.5 Mb in length, ∼800 kb longer than the previously published assembly for this organism, comprising 18 nuclear scaffolds and 2 mitochondrial scaffolds and including an extra 839 kb of repetitive sequence. We discovered that the patterns of aneuploidy in B. dendrobatidis JEL423 have remained stable over approximately 5 years. We found that our updated assembly encodes fewer than half the number of M36 metalloprotease genes predicted in the previous assembly. In contrast, members of the crinkling and necrosis gene family were found in similar numbers to the previous assembly. We also identified a more extensive carbohydrate binding module 18 gene family than previously observed. We anticipate our findings, and the updated genome assembly will be a useful tool for further investigation of the genome evolution of the pathogenic chytrids.
A modular system to label endogenous presynaptic proteins using split fluorophores in Caenorhabditis elegans
Authors: Kurashina Mizuki , Snow Andrew W , Mizumoto Kota 
Published: December 2024

Abstract
Visualizing the subcellular localization of presynaptic proteins with fluorescent proteins is a powerful tool to dissect the genetic and molecular mechanisms underlying synapse formation and patterning in live animals. Here, we utilize split green and red fluorescent proteins to visualize the localization of endogenously expressed presynaptic proteins at a single-neuron resolution in Caenorhabditis elegans. By using CRISPR/Cas9 genome editing, we generated a collection of C. elegans strains in which endogenously expressed presynaptic proteins (RAB-3/Rab3, SNG-1/Synaptogyrin, CLA-1/Piccolo, SYD-2/Liprin-α, UNC-10/RIM, RIMB-1/RIM-BP, and ELKS-1/ELKS) are tagged with tandem repeats of GFP11 and/or wrmScarlet11. We show that the expression of GFP1-10 and wrmScarlet1-10 under neuron-specific promoters can robustly label presynaptic proteins in different neuron types. We believe that the combination of our knock-in strains and GFP1-10 and wrmScarlet1-10 plasmids is a versatile modular system useful for neuroscientists to examine the localization of endogenous presynaptic proteins in any neuron type in C. elegans.
‘Too Long a Sacrifice?’: Post-Transitional Justice and the Afterlives of Authoritarianism
Authors: Collins Cath , Durdiyeva Selbi 
Published: December 2024

ABSTRACT
In a field that of late appears beset by crises of confidence, this essay reviews three books that send transitional justice scholarship back to basics. The focus in the books on post-authoritarian settings sheds light on the effects of time on transitional justice expectations, actions and futures. The books also offer rear-view mirror vantage points on the assumptions, teleological and otherwise, that informed early praxis in the field. The common object of interest addressed by these volumes – authoritarian regimes and transitional responses to them, over time – is significant in itself. It also reminds us, firstly, that transitional justice dynamics are not reducible to immediate policy menus, and, secondly, that they do not disappear when intellectual fashions change.
Clinical impact of a subtype of urothelial carcinoma in nonmuscle-invasive bladder cancer
Authors: Minato Akinori , Yoshii Moena , Watanabe Shuki , Moriya Ryosuke , Kashiwagi Eiji , Fujimoto Naohiro 
Published: December 2024

Abstract

Objective
This study aimed to assess the oncological outcomes of the subtype of urothelial carcinoma (SUC), including divergent differentiation and histologic subtype, in comparison with those of pure urothelial carcinoma (PUC) in nonmuscle-invasive bladder cancer.

Methods
We retrospectively evaluated patients who were initially treated with transurethral resection of the bladder tumor (TURBT) between March 2005 and August 2020 at a single institution. Patients with PUC and SUC were compared in terms of recurrence-free survival (RFS), progression-free survival (PFS), and overall survival (OS).

Results
Out of 853 enrolled patients, 783 (91.8%) and 70 (8.2%) had PUC and SUC, respectively. SUC presence was significantly associated with old age, tumor size (≥3 cm), higher pT1 rate, high grade, concomitant carcinoma in situ, and lymphovascular invasion. RFS rates after TURBT did not significantly differ between the PUC and SUC groups. With a median follow-up period of 66 months (interquartile range, 38–103 months), the rates and median time of progression to muscle invasion were 6.9% and 22.5 months in the PUC group, and 22.9% and 10.0 months in the SUC group. Moreover, the incidence of progression to metastasis was 4.6% and 15.7% in the PUC and SUC groups, respectively. The 5-year PFS rates (64.5% and 81.9%, P &lt; .001) and 5-year OS rates (71.7% and 86.2%, P = .009) were lower in the SUC group than in the PUC group. On multivariate analysis, SUC presence independently predicted progression to muscle invasion and metastasis.

Conclusion
At initial TURBT diagnosis, we must pay more attention to higher progression risk of SUC than that of PUC in nonmuscle-invasive bladder cancer.
Fungal hepatic abscess formation postlaparoscopic cholecystectomy
Authors: AlNuaimi Dana , Saeed Ghufran , Abdulghaffar Shareefa , AlKetbi Reem , Aleassa Essa M , Balci Numan Cem 
Published: December 2024

Abstract
Laparoscopic cholecystectomy is the preferred method for treating acute cholecystitis. Although the incidence of postoperative infections in laparoscopic cholecystectomy is low, serious postoperative surgical site infections are still reported. Hepatic abscesses, particularly fungal, can occur post-cholecystectomy leading to significant mortality and morbidity. We report a case of a 58-year-old female who underwent laparoscopic cholecystectomy and subsequently developed fever, jaundice, and right upper quadrant pain. Laboratory results showed deranged liver function tests with raised inflammatory markers. Radiographic investigations, including CT and MRI, revealed an irregular hilar lesion with periportal changes suggestive of an abscess with portal vein thrombosis. Histopathological examination of the biopsy obtained from the hilar lesion showed a fungal hepatic infection, and particularly conidiobolomycosis. To our best knowledge, this is the first case that reports this fungal infection as a complication of laparoscopic cholecystectomy. The patient was managed with a combination of intravenous antibiotics and antifungals, which yielded mild improvement. Unfortunately, the patient decided to leave the hospital against medical advice, limiting the information on the disease course.
VACStent closure of oesophageal defects by covered stent and endoscopic vacuum therapy: initial use and clinical outcomes
Authors: Ylli Kristali , AlQahtani Jowhara , Hraishawi Ihab , Murphy Thomas 
Published: December 2024

Abstract
Endoscopic management of transmural oesophageal defects following esophagectomy or spontaneous perforations, such as Boerhaave’s syndrome, is often complicated by stent migration and luminal occlusion [1]. The Vacuum-Assisted Closure (VAC) stent, which integrates a covered stent with endoscopic vacuum therapy, aims to address these issues by providing functional drainage and promoting wound healing [2]. This case series presents our initial experience with VACStent therapy in four patients treated between February 2023 and April 2024. Two patients had staple line defects post-esophagectomy, and two had Boerhaave’s syndrome. Treatment involved stent placement under general anaesthesia, followed by evaluations and scheduled stent exchanges every 6 days. All patients achieved successful defect closure, with no procedural complications noted. Three patients required one stent application, while one needed two applications. VACStent therapy appears to be a safe and effective treatment for transmural oesophageal defects, potentially establishing a new standard of care.
A Scoping Review of Methodologies Exploring Diet and Health Outcomes in Lactating Women: What Has Been Done and Where to Next?
Authors: Rahmannia Sofa , Arena Gina , Murray Kevin , Sakinah Ana D , Thariqi Yughni A , Diana Aly , Hickling Siobhan 
Published: December 2024

Abstract
Developing dietary guidelines for lactating women presents significant challenges, due to limited evidence being available on their specific nutrient needs and the biological impacts of various dietary dimensions. Current dietary recommendations often rely on data from nonlactating women, leading to potential inaccuracies. The relationship between diet and health outcomes in lactating women remains underexplored, particularly across different dietary dimensions, such as nutrients, food groups, dietary patterns, and other specific dietary variables. The aims of this scoping review were to map the diverse methodologies employed in research into maternal diet during lactation, to identify the current gaps, and to suggest areas for future investigation. The review focused on the dietary variables studied in relation to breastfeeding outcomes, and offers insights into the current state of lactation nutrition research. A comprehensive search was conducted in the CINAHL, MEDLINE, and Embase databases up to December 13, 2022. The included studies encompassed original quantitative research on dietary intake among lactating women and any associated outcomes. Data extracted included study characteristics, dietary variables, and outcome measures, and they were analyzed using descriptive statistics and pivot tables. Of the 1666 relevant studies identified, 231 met the inclusion criteria. Most research was conducted in high-income and upper-middle-income countries. Studies mainly focused on relatively short lactation durations, nutrient-based dietary dimensions, and maternal outcomes, particularly breast milk composition. Maternal metabolic status and child outcomes, such as infant micronutrient status and longitudinal growth, were underexplored. Specific dietary variables included meal frequency and nutrient intake from various food sources. Commonly adjusted covariates were maternal age and socio-economic status, while contraceptive use and sanitation were often overlooked. Many areas of research concerning the diet–health relationship in lactating women remain unexplored. Filling these gaps will gather evidence to inform the development of dietary guidelines for this population.