bluuebunny/crossref_metadata_2025_split huggingface dataset:
m5c-iEnsem: 5-methylcytosine sites identification through ensemble models
Authors: Bilal Anas , Alarfaj Fawaz Khaled , Khan Rafaqat Alam , Suleman Muhammad Taseer , Long Haixia 
Published: December 2024

Abstract

Motivation
5-Methylcytosine (m5c), a modified cytosine base, arises from adding a methyl group at the 5th carbon position. This modification is a prevalent form of post-transcriptional modification (PTM) found in various types of RNA. Traditional laboratory techniques often fail to provide rapid and accurate identification of m5c sites. However, with the growing accessibility of sequence data, expanding computational models offers a more efficient and reliable approach to m5c site detection. This research focused on creating advanced in-silico methods using ensemble learning techniques. The encoded data was processed through ensemble models, including bagging and boosting techniques. These models were then rigorously evaluated through independent testing and 10-fold cross-validation.

Results
Among the models tested, the Bagging ensemble-based predictor, m5C-iEnsem, demonstrated superior performance to existing m5c prediction tools.

Availability and implementation
To further support the research community, m5c-iEnsem has been made available via a user-friendly web server at https://m5c-iensem.streamlit.app/.
Identification and annotation of centromeric hypomethylated regions with CDR-Finder
Authors: Mastrorosa Francesco Kumara , Oshima Keisuke K , Rozanski Allison N , Harvey William T , Eichler Evan E , Logsdon Glennis A 
Published: December 2024

Abstract

Motivation
Centromeres are chromosomal regions historically understudied with sequencing technologies due to their repetitive nature and short-read mapping limitations. However, recent improvements in long-read sequencing allow for the investigation of complex regions of the genome at the sequence and epigenetic levels.

Results
Here, we present Centromere Dip Region (CDR)-Finder: a tool to identify regions of hypomethylation within the centromeres of high-quality, contiguous genome assemblies. These regions are typically associated with a unique type of chromatin containing the histone H3 variant CENP-A, which marks the location of the kinetochore. CDR-Finder identifies the CDRs in large and short centromeres and generates a BED file indicating the location of the CDRs within the centromere. It also outputs a plot for visualization, validation, and downstream analysis.

Availability and implementation
CDR-Finder is available at https://github.com/EichlerLab/CDR-Finder.
SCARAP: scalable cross-species comparative genomics of prokaryotes
Authors: Wittouck Stijn , Eilers Tom , van Noort Vera , Lebeer Sarah 
Published: December 2024

Abstract

Motivation
Much of prokaryotic comparative genomics currently relies on two critical computational tasks: pangenome inference and core genome inference. Pangenome inference involves clustering genes from a set of genomes into gene families, enabling genome-wide association studies and evolutionary history analysis. The core genome represents gene families present in nearly all genomes and is required to infer a high-quality phylogeny. For species-level datasets, fast pangenome inference tools have been developed. However, tools applicable to more diverse datasets are currently slow and scale poorly.

Results
Here, we introduce SCARAP, a program containing three modules for comparative genomics analyses: a fast and scalable pangenome inference module, a direct core genome inference module, and a module for subsampling representative genomes. When benchmarked against existing tools, the SCARAP pan module proved up to an order of magnitude faster with comparable accuracy. The core module was validated by comparing its result against a core genome extracted from a full pangenome. The sample module demonstrated the rapid sampling of genomes with decreasing novelty. Applied to a dataset of over 31 000 Lactobacillales genomes, SCARAP showcased its ability to derive a representative pangenome. Finally, we applied the novel concept of gene fixation frequency to this pangenome, showing that Lactobacillales genes that are prevalent but rarely fixate in species often encode bacteriophage functions.

Availability and implementation
The SCARAP toolkit is publicly available at https://github.com/swittouck/scarap.
Urban–rural diversification in response to nighttime dim light stress in Drosophila suzukii
Authors: Sato Ayame , Takahashi Yuma 
Published: December 2024

Abstract
Human disturbance in cities leads to environmental changes, such as habitat fragmentation, raised ambient temperature, night lighting, and noise. Here, we examine the plastic response to artificial light at night (ALAN) of morphological and reproductive traits in isofemale strains derived from four rural and four urban populations of Drosophila suzukii. The individuals from urban and rural populations were reared under 12 h daylight, followed by either 12 h darkness (control) or dim light (treatment). Adult morphology changed with ALAN exposure regardless of fly origin, but the impact on morphological traits was more pronounced in rural populations. The level of male courtship activities was decreased by ALAN exposure, although the response varied between the rural and urban populations. Egg size and shape were slightly affected by ALAN for both rural and urban populations. The number of eggs laid increased more under ALAN stress in rural populations compared with urban populations. Our results suggest that exposure to ALAN induces a plastic response in these traits and that individuals in urban populations have evolved to mitigate the impacts of ALAN stress. These findings highlight the potential for urban populations to adapt to human-induced environmental stressors, with important implications for predicting species responses to urbanization.
Eyespot function in butterflyfishes (Chaetodontidae): comparing evidence for aposematism, automimicry, and predator mimicry
Authors: Karan Elizabeth A , Hodge Jennifer R , Alfaro Michael E 
Published: December 2024

Abstract
Many species of butterflyfish display false eyespots, but factors underlying eyespot diversity remain poorly understood. Eyespots are thought to function in predator avoidance, but there are multiple ways in which this might occur. An eyespot can function as deflection when distracting predators away from the true eye of the fish by mimicking it elsewhere on the body (automimicry). It can also function as intimidation, either by mimicking the appearance of predator eyes (predator mimicry) or by serving as a conspicuous warning to predators that the fish is spiny (warning coloration). Colour patterns that conceal the eye are common among butterflyfishes. Eye concealment is predicted under automimicry and can also occur in predator mimicry but is not predicted under warning coloration. Long median fin spines and deep bodies can make many species of butterflyfishes unpalatable, as predicted under intimidation. We adopt a comparative approach to examine relationships between eyespot presence, conspicuousness, and position on the body with eye coverage and physical defences, in order to evaluate evidence under the deflection vs. intimidation hypotheses within different trait complexes. Our results suggest that eyespots and eye coverage have evolved in conjunction with traits that facilitate predator evasion. We did not find evidence to support eyespots functioning as warning coloration for physical defences.
Green tea polyphenols alleviate di (2-ethylhexyl) phthalate-induced testicular injury in mice via lncRNA–miRNA–mRNA axis
Authors: Shi Heng , Zhao Xin-Hai , Peng Qin , Zhou Xian-Ling , Liu Si-Si , Sun Chuan-Chuan , Cao Qiu-Yu , Zhu Shi-Ping , Sun Sheng-Yun 
Published: December 2024

Abstract
Di(2-ethylhexyl) phthalate (DEHP) is a commonly used plasticizer known for its toxic effects on the male reproductive system. Green tea polyphenols (GTPs), recognized for their antioxidant and anti-inflammatory properties, have demonstrated protective effects on various organs, but the mechanisms by which GTPs mitigate DEHP-induced testicular damage remain unclear. Healthy male C57BL/6J mice were divided into five groups: control, DEHP, DEHP + GTP treatment, GTP, and oil groups. Testicular histopathological changes were assessed using hematoxylin–eosin (H&E), periodic acid-Schiff (PAS), and Masson staining. Ultrastructural alterations were examined through transmission electron microscopy. High-throughput sequencing was performed to analyze the expression of mRNA, miRNA, and lncRNA and construct an lncRNA–miRNA–mRNA regulatory network for identifying key regulatory axes. Mice in the DEHP group exhibited significant testicular damage, including reduced sperm count, mitochondrial deformation, and endoplasmic reticulum dilation. GTP treatment notably improved testicular structural integrity, restored sperm count, and alleviated mitochondrial and endoplasmic reticulum damage. Additionally, DEHP significantly increased activated CD8+ T cells, which were reduced with GTP treatment. High-throughput sequencing revealed that GTP treatment exerted protective effects through the regulation of six key lncRNA–miRNA–mRNA axes. GTPs significantly protect against DEHP-induced testicular damage, and the lncRNA–miRNA–mRNA regulatory axes play a potential role in this process.
First Impressions Last? Lay-Judges’ Assessments of Credible Victimhood
Authors: Heber Anita , Fredriksson Tea 
Published: December 2024

Abstract
This article explores how Swedish lay-judges assess victims’ credibility in district court. Previous studies have explored how biases and emotional expressions impact credibility assessments. Adding to this, the present study analyses how lay-judges assess courtroom credibility from an intersectional perspective. Based on 24 in-depth interviews with lay-judges, the study explores three intertwined layers of credibility: appearances, narratives and emotions. The analysis concludes that these layers actualize balancing acts for both victims and the lay-judges assessing them. These layers of credibility can compound for victims, making them particularly credible in the eyes of the lay-judges, especially if and when they perform victimhood in line with expectations set by their intersectional characteristics.
Diagnostic performance of simultaneous multislice diffusion-weighted imaging in differentiating breast lesions: a systematic review and meta-analysis
Authors: Tan Yuqi , Ye Zheng , Lv Xinyang , Zhang Yiteng , Zhang Meng , Xia Chunchao , Li Zhenlin 
Published: December 2024

Abstract

Objectives
To investigate the diagnostic performance of simultaneous multislice diffusion-weighted imaging (SMS-DWI) in differentiating malignant and benign breast lesions, and compare it with conventional single shot and readout segmented echo planar imaging without the SMS technique.

Methods
The literature search was performed in PubMed, Embase, and Web of Science to identify comparative studies reporting the diagnostic performance of SMS-DWI and conventional DWI in patients with breast lesions. Histopathological analysis was used as a reference standard for malignant breast lesions. The methodological quality was evaluated using QUADAS-2 scale. The summary sensitivity, summary specificity, and area under the curve (AUC) of the summarized receiver operating characteristic curve were calculated and compared between SMS-DWI and conventional DWI using a bivariate random-effects model. Heterogeneity was explored with meta-regression and subgroup analyses.

Results
Six studies with 626 patients and 649 breast lesions (benign: 222, malignant: 427) were included. The summary sensitivity, summary specificity, and AUC for SMS-DWI were 0.89 (95% CI: 0.78-0.95), 0.94 (95% CI: 0.81-0.98), and 0.96 (95% CI: 0.94-0.98), respectively, and those for conventional DWI were 0.90 (0.95 CI: 0.84-0.94), 0.87 (95% CI: 0.80-0.92), and 0.94 (95% CI: 0.92-0.96), respectively. The diagnostic performance was not significantly different between SMS-DWI and conventional DWI (P = .337).

Conclusions
SMS-DWI has high diagnostic performance in differentiating breast lesions, which is not significantly different from the conventional DWI.

Advances in knowledge
There is no significant difference between SMS-DWI and conventional DWI in differentiating breast lesions, suggesting SMS-DWI may be a potential alternative to conventional DWI in breast imaging.
Measurement of Serum Free Vitamin D Concentrations: Importance, Challenges, and the Emerging Role of Mass Spectrometry
Authors: Alexandridou Anastasia , Stokes Caroline S , Volmer Dietrich A 
Published: December 2024

Abstract

Background
Serum total 25-hydroxyvitamin D [25(OH)D] concentration is the most widely used clinical biomarker for vitamin D status. Under certain physiological and pathological conditions, however, total 25(OH)D may not always be the best index for vitamin D status. Instead, the nonprotein-bound (free) fraction of total 25(OH)D has been suggested as a more appropriate marker in certain clinical situations.

Content
Free 25(OH)D levels can either be calculated or measured directly. Calculated free 25(OH)D depends on the concentrations of total serum 25(OH)D, vitamin D binding protein (VDBP), and albumin, as well as the affinity between analyte and binding proteins. Differences in VDBP concentrations are observed between populations as a result of health status, gene polymorphisms, and the assay used for determination. Direct measurement methods for free 25(OH)D are often complicated (dialysis, ultrafiltration) or susceptible to interferences, cross-reactivity, and type of antibody (immunoassays). Therefore, it is very important to develop tools that allow either accurate and precise measurement of VDBP or direct measurement of free 25(OH)D. For the latter, liquid chromatography combined with tandem mass spectrometry (LC–MS/MS) has recently shown promise for analysis of free vitamin D. In the current review, we present the importance and challenges regarding free 25(OH)D determination and the role of LC–MS-based methods in future studies.

Summary
More research is required to determine the role of free 25(OH)D in the assessment of vitamin D status in healthy subjects and in various clinical conditions. Recent advances in technology, including mass spectrometry, can provide the required assays for this purpose.
Can LLMs deeply detect complex malicious queries? A framework for jailbreaking via obfuscating intent
Authors: Shang Shang , Zhao Xinqiang , Yao Zhongjiang , Yao Yepeng , Su Liya , Fan Zijing , Zhang Xiaodan , Jiang Zhengwei 
Published: December 2024

Abstract
This paper delves into a possible security flaw in large language models (LLMs), particularly in their capacity to identify malicious intent within intricate or ambiguous inquiries. We have discovered that LLMs might overlook the malicious nature of highly veiled requests, even without alterations to the malevolent text in those queries, thus exposing a significant weakness in their content analysis systems. To be specific, we pinpoint and scrutinize two aspects of this vulnerability: (i) LLMs’ diminished capability to perceive maliciousness when parsing extremely obscured queries, and (ii) LLMs’ inability to discern malicious intent in queries that have been intentionally altered to increase their ambiguity by modifying the malevolent content itself. To illustrate and tackle this problem, we propose a theoretical framework and analytical strategy, and introduce a novel black-box jailbreak attack technique called IntentObfuscator. This technique exploits the identified vulnerability by concealing the genuine intentions behind user prompts, thereby compelling LLMs to inadvertently produce restricted content and circumvent their inherent content safety protocols. We elaborate on two specific applications within this framework: ”Obscure Intention” and ”Create Ambiguity,” which skillfully manipulate the complexity and ambiguity of queries to effectively dodge the detection of malicious intent. We empirically confirm the efficacy of the IntentObfuscator approach across various models, including ChatGPT-3.5, ChatGPT-4, Qwen, and Baichuan, achieving an average jailbreak success rate of 69.21%. Remarkably, our tests on ChatGPT-3.5, boasting 100 million weekly active users, yielded an impressive success rate of 83.65%. Additionally, we verify our approach across a range of sensitive content categories, including graphic violence, racism, sexism, political sensitivity, cybersecurity threats, and criminal techniques, further highlighting the considerable impact of our findings on refining ”Red Team” tactics against LLM content security frameworks.
CXCR4-targeted sensitive magnetic particle imaging for abdominal aortic aneurysm early detection and prognosis evaluation by recognizing total inflammatory cells
Authors: Cao Genmao , Zhang Ruijing , Jia Xiaohua , Jiang Bo , Li Yaling , Xuan Xuezhen , Tian Jie , Hui Hui , Xin Shijie , Dong Honglin 
Published: December 2024

Abstract

Aims
The maximum aortic diameter remains the diagnostic criteria and the indicator for prognosis prediction of abdominal aortic aneurysms (AAAs). An additional imaging modality is currently needed to help evaluate the prognosis of AAA as well as early detection of AAA formation. This study evaluated the most effective inflammatory markers for AAA using single-cell sequencing and, from these, developed probes to facilitate in vivo multimodal imaging of AAA inflammation.

Methods and results
Single-cell RNA sequencing (scRNAseq) of the human aortic aneurysms, GSE155468 and GSE166676 data sets, identified CXCR4 as the most representative marker. Anti-CXCR4-PE antibody was conjugated to superparamagnetic iron oxide nanoparticles to synthesize Fe3O4-anti-CXCR4-PE probes. The biocompatibility and specificity of the probes were validated in vivo and in vitro. Magnetic particle imaging (MPI) and fluorescence imaging (FLI) were performed to assess inflammation in early and advanced AAA mouse models. CXCR4-specific receptor inhibitor, AMD3100, was used for confirming CXCR4 as an excellent target for AAA imaging and therapy. scRNAseq indicated that chemokine-related pathways were upregulated in aortic aneurysms, and CXCR4 was the chemokine receptor that marks all AAA-related immune cells and inflammatory vascular cells. Fe3O4-anti-CXCR4-PE effectively recognized immune cells and inflammatory vascular cells, as strong MPI and FLI signals corresponded to increased CXCR4, CD45, and CD68 levels that represented AAA severity and rupture risk. Importantly, Fe3O4-anti-CXCR4-PE can help identify early AAA formation when ultrasound is undiagnosable. Finally, AMD3100 treatment in AAA mouse model inhibited AAA expansion and rupture and reduced aortic wall inflammation by inhibiting accumulation of immune cells and haematopoietic stem cells.

Conclusion
CXCR4 marks immune cells and inflammatory vascular cells in AAA and is associated with AAA prognosis in a mouse model of AAA. CXCR4-targeting multimodal MPI/FLI provides a novel approach for AAA prognosis prediction and early detection.
Tofacitinib versus Vedolizumab Among Bio-naïve Patients with Ulcerative Colitis: A Real-World Propensity-Weighted Comparison
Authors: Gros Beatriz , Constantine-Cooke Nathan , Kennedy Jake , Elford Alexander T , O’Hare Claire , Noble Colin , Jones Gareth-Rhys , Arnott Ian D , Lees Charlie W , Plevris Nikolas 
Published: December 2024

Abstract

BACKGROUND AND AIMS
Over the last decade, treatment options for moderate-to-severe ulcerative colitis (UC) have expanded. However, comparative studies between these agents are limited, especially among biologic-naïve patients. We aimed to compare the persistence, effectiveness and safety of tofacitinib and vedolizumab as the first advanced treatment for patients with UC.

METHODS
Patients who received either tofacitinib or vedolizumab as their first advanced therapy for UC in NHS Lothian were included. We used inverse probability of treatment weighting (IPTW). The probability of treatment assignment was calculated via logistic regression using age, sex, UC duration, Montreal extent, CRP, concomitant corticosteroids, and partial Mayo score at drug commencement.

RESULTS
We included n=158 patients, of whom n=81 (51.3%) received vedolizumab and n=77 (48.7%) tofacitinib. Median follow-up for vedolizumab patients was 3.1 years (IQR 1.6-4.8) and for tofacitinib patients 1.5 years (IQR 0.3-2.3). The cohort was 59.5% male with a median age of 41.1 years (IQR 31.5-51.8). At two years, vedolizumab persistence was superior to tofacitinib (p=0.005). At week 12 and week 52 clinical, biochemical and fecal biomarker steroid free remission were comparable between groups. Primary non-response and secondary loss of response were 9.9% and 17.3% for vedolizumab and 23.4% and 13% for tofacitinib respectively. Frequency of adverse events was comparable (11 [13.6%] vedolizumab vs 19 [24.7%] tofacitinib, p=0.629).

CONCLUSIONS
We found that the persistence and tolerability of vedolizumab was superior to tofacitinib in bio-naïve UC, although the rates of clinical and biomarker remission were comparable. These data may help inform positioning of advanced therapy.
The Partially-Matched-Sample Correction in Pseudo Panel Minimum Distance Estimation
Authors: Jia Fei 
Published: December 2024

Abstract
Certain repeated cross-sectional data sets, such as the Current Population Survey (CPS), use special sampling designs by which samples from different times periods are partially-matched. This paper proposes a correction to the optimal weighting matrix in minimum distance (MD) estimation of pseudo panel models to account for such partially-matched samples. This partially-matched-sample correction may be needed if the sample matching rate is nontrivial and, at the same time, there is a fixed effect, a serially correlated idiosyncratic error, or both in the underlying linear panel data model data generating process, all of which lead to a block diagonal structure of the optimal weighting matrix. Using the correction can result in considerable efficiency gains both in finite sample and asymptotically. Furthermore, it is shown that this correction is needed not only for the optimal MD estimator but for any MD estimator to make the inference right. As an illustration, the correction is applied to the classical question of estimating the monetary return to education using the yearly Merged Outgoing Rotation Group (MORG) files from CPS.