bluuebunny/crossref_metadata_2025_split huggingface dataset:
Natural language processing tool for extracting information about opioid overdoses in the USA from case narratives in the violent death reporting system
Authors: Omaki Elise , Restrepo Felipe , Shields Wendy C. , Abrahams Alan 
Published: January 2025

BackgroundImproving the infrastructure for drug overdose surveillance is critical for identifying new threats and responding to emerging trends. We aimed to develop a prototype tool using the principles of natural language processing that can extract information from the death records of drug overdose victims.MethodsData were obtained from the Violent Death Reporting System on drug overdose deaths. Narratives were manually labelled for 12 attributes of interest, totalling 82 labels about the circumstances of the overdose. Narratives were passed through the ‘Excel Extractor’ to identify and extract a target phrase and subsequently map the extracted phrase to predetermined code values. The output from the Excel Extractor was compared with manually labelled data to determine accuracy. Performance was compared against multiple machine learning models.ResultsThe Excel Extractor performed well across the attributes of interest, achieving an F1 Score over 0.8 on nine of the 12 attributes. The Excel Extractor was the highest performing model on seven of the 12 attributes. The Excel Extractor achieved an F1 Score of 0.8 or higher on 46 of 82 (56%) of the labels, and a score of 0.9 or higher on nearly one-third (25 out of 82) of the labels.ConclusionThis work demonstrates it is feasible to develop a spreadsheet-formula-based natural language processing tool to accurately extract information about drug overdose deaths from narratives; for most attributes, a rule-based search performs well or better than deep learning. The Excel Extractor has the potential to streamline data abstraction for epidemiologists gathering data about drug overdose deaths.
Past, present and future of injury prevalence in high-income countries: insights and projections up to 2030 from the Global Burden of Disease Study
Authors: Saleib Suriel-Kyrillos M. , Charalampous Periklis , Van Vledder Mark G. , Halm Jens A. , Verhofstad Michael M.A. , Van Waes Oscar J.F. , Haagsma Juanita A. 
Published: January 2025

BackgroundInjury prevalence is a metric which can be used to understand healthcare utilisation and prioritise injuries based on the magnitude of the injury rate. Given the ageing population in high-income countries and subsequently ageing of the injured population, the probability of long-term or permanent consequences of injuries is also likely to increase. By understanding past trends and exploiting patterns of prevalence injury rates (PIRs), future PIRs can be predicted.DesignData on PIRs from the Global Burden of Disease Study 2019 (GBD2019) were collected. To understand past trends of GBD2019, joinpoint regression analysis was used to find trends expressed as annual per cent changes (APCs), averaged APCs and to compare trends across injuries. To project future PIRs up to 2030, autoregressive integrated moving average time series analysis was used on the GBD2019 data.ResultsAll injuries showed negative averaged APCs during 1990–2019, However, an increased PIR is found for the last APC period of the same time interval, the greatest being in amputations with 2.3 (2.1–2.4). All PIR trends were statistically neither parallel nor identical across the injuries. Forecasts showed an absolute and relative increase in PIR projection.ConclusionThe PIRs positively declined in the past. However, the latest past trends up to 2019 increased, as well as the forecasts to 2030. Reflection and advocating for strategies to mitigate the possible outcome of increased PIRs are given. This proactive approach will form the foundation for future resource allocation and planning. Additionally, there may be a need to adjust current treatment strategies and standards to address the expected increase in demand.
Differential impact of cervical cancer in immigrant women: a decade-long epidemiological study in the Marche Region, Italy
Authors: Di Biagio Katiuscia , Bracci Raffaella , Peconi Chiara , Gasperini Beatrice , Manasse Sonia , Pompili Marco , Sarti Donatella , Lanari Alice , Prospero Emilia 
Published: January 2025

BackgroundCervical cancer is primarily caused by persistent human papilloma virus (HPV) infections, with significant disparities observed in its burden, especially affecting immigrant populations from high HPV prevalence regions. This study evaluates the incidence and severity of cervical cancer in immigrant women in the Marche region, Italy, from 2010 to 2019.MethodsWe employed a detailed analysis of population-based data from the Marche Cancer Registry using the age-standardised incidence rates (IRs) and Poisson regression models for in situ cervical cancer (ISCC) and infiltrating cervical cancer (ICC).ResultsThe IRs for ICC and ISCC among immigrant women are alarmingly higher compared with their Italian counterparts; IR for ICC in immigrant women is 26.5 per 100 000 women-years, compared with 7.9 in Italian women. For ISCC, the IR is 55.1 for immigrants versus 29.2 for Italians.Immigrant women showed a median age at diagnosis for ICC of 49 years, almost a decade younger than Italian women, and they were more likely to have squamous cell histology, which is linked to high-risk HPV strains.ConclusionsThe study reveals a substantially higher incidence of both ISCC and ICC among immigrant women with ICC diagnosed 8 years previously. These findings underscore the pressing need for culturally and linguistically tailored public health interventions, including improved access to screening and vaccination for HPV, to address the elevated risk and earlier onset of cervical cancer in immigrant women in Italy. The study highlights the critical role of preventive measures in reducing health disparities and enhancing the efficacy of public health policies.
Spatial and single-cell transcriptomics reveal cellular heterogeneity and a novel cancer-promoting Treg cell subset in human clear-cell renal cell carcinoma
Authors: Song Xiyu , Zhu Yumeng , Geng Wenwen , Jiao Jianhua , Liu Hongjiao , Chen Ruo , He Qian , Wang Lijuan , Sun Xiuxuan , Qin Weijun , Geng Jiejie , Chen Zhinan 
Published: January 2025

BackgroundClear cell renal cell carcinoma (ccRCC) is the most common histologic type of RCC. However, the spatial and functional heterogeneity of immunosuppressive cells and the mechanisms by which their interactions promote immunosuppression in the ccRCC have not been thoroughly investigated.MethodsTo further investigate the cellular and regional heterogeneity of ccRCC, we analyzed single-cell and spatial transcriptome RNA sequencing data from four patients, which were obtained from samples from multiple regions, including the tumor core, tumor-normal interface, and distal normal tissue. On the basis, the findings were investigated in vitro using tissue and blood samples from 15 patients with ccRCC and validated in the broader samples on tissue microarrays.ResultsIn this study, we revealed previously unreported subsets of both stromal and immune cells, as well as mapped their spatial location at finer resolution. In addition, we validated the clusters of tumor cells after removing batch effects according to six characterized gene sets, including epithelial-mesenchymal transitionhighclusters, metastatic clusters and proximal tubulehighclusters. Importantly, we identified a special regulatory T (Treg) cell subpopulation that has the molecular characteristics of terminal effector Treg cells but expresses multiple cytokines, such as interleukin (IL)-1β and IL-18. This group of Treg cells has stronger immunosuppressive function and was associated with a worse prognosis in ccRCC cohorts. They were colocalized withMRC1+FOLR2+tumor-associated macrophages (TAMs) at the tumor-normal interface to form a positive feedback loop, maintaining a synergistic procarcinogenic effect. In addition, we traced the origin of IL-1β+Treg cells and revealed that IL-18 can induce the expression of IL-1β in Treg cells via the ERK/NF-κB pathway.ConclusionsWe demonstrated a novel cancer-promoting Treg cell subset and its interactions withMRC1+FOLR2+TAMs, which provides new insight into Treg cell heterogeneity and potential therapeutic targets for ccRCC.
Tract-specific white matter hyperintensities and neuropsychiatric syndromes: a multicentre memory clinic study
Authors: Kan Cheuk Ni , Coenen Mirthe , Xu Xin , Hilal Saima , Barkhof Frederik , Benke Thomas , Dal-Bianco Peter , DeCarli Charles , Duering Marco , Enzinger Christian , Exalto Lieza G , Fletcher Evan F , Hofer Edith , Koek Huiberdina L , Kuijf Hugo J , Maillard Pauline M , Moonen Justine E F , Papma Janne M , Pijnenburg Yolande A L , Schmidt Reinhold , Steketee Rebecca M E , van den Berg Esther , van der Flier Wiesje M , Venketasubramanian Narayanaswamy , Vernooij Meike W , Wolters Frank J , Biessels Geert Jan , Chen Christopher Li-Hsian , Biesbroek J Matthijs , Tan Chin Hong 
Published: January 2025

BackgroundWhite matter hyperintensities (WMH) have been implicated in the pathogenesis of neuropsychiatric symptoms of dementia but the functional significance of WMH in specific white matter (WM) tracts is unclear. We investigate whether WMH burden within major WM fibre classes and individual WM tracts are differentially associated with different neuropsychiatric syndromes in a large multicentre study.MethodNeuroimaging and neuropsychiatric data of seven memory clinic cohorts through the Meta VCI Map consortium were harmonised. Class-based analyses of major WM fibres (association, commissural and projection) and region-of-interest-based analyses on 11 individual WM tracts were used to evaluate associations of WMH volume with severity of hyperactivity, psychosis, affective and apathy syndromes.ResultsAmong 2935 patients (50.4% women; mean age=72.2 years; 19.8% subjective cognitive impairment, 39.8% mild cognitive impairment, and 40.4% dementia), larger WMH volume within projection fibres (B=0.24, SE=0.10, p=0.013) was associated with greater apathy. Larger WMH volume within association (B=0.31, SE=0.12, p=0.009), commissural (B=0.47, SE=0.17, p=0.006) and projection (B=0.39, SE=0.16, p=0.016) fibres was associated with greater hyperactivity, driven by the inferior fronto-occipital fasciculus (B=0.50, SE=0.18, p=0.006), forceps major (B=0.48, SE=0.18, p=0.009) and anterior thalamic radiation (B=0.49, SE=0.19, p=0.011), respectively. Larger WMH volume in the uncinate fasciculus (B=1.82, SE=0.67, p=0.005) and forceps minor (B=0.61, SE=0.19, p=0.001) were additionally associated with greater apathy. No associations with affective and psychosis were observed.ConclusionsTract-syndrome specificity of WMH burden with apathy and hyperactivity suggests that disruption of strategic neuronal pathways may be a potential mechanism through which small vessel disease affects emotional and behavioural regulation in memory clinic patients.
An In-Depth Analysis of Password Managers and Two-Factor Authentication Tools
Authors: Jubur Mohammed , Shrestha Prakash , Saxena Nitesh 
Published: January 2025

Passwords remain the primary authentication method in online services, a domain increasingly crucial in our digital age. However, passwords suffer from several well-documented security and usability issues. Addressing these concerns, password managers and two-factor authentication (2FA) have emerged as key solutions. This article examines these methods with a focus on enhancing password security without compromising usability. We utilize an adapted Bonneau et al. (IEEE S&P 2012) framework tailored to the specific challenges of password managers and 2FA. This allows us to categorize and evaluate prominent solutions from both academic research and industry practice, with a focus on their security, privacy, and usability. A crucial aspect of our study involves evaluating the effectiveness of a combined PM+2FA system in balancing security and usability. This study not only examines current trends but also suggests potential areas for future research, offering valuable insights to both users and developers in the evolving landscape of digital security.
FTO Alleviates Hepatic Ischemia‐Reperfusion Injury by Regulating Apoptosis and Autophagy
Authors: Wang Pi-Xiao , Zhu Ling , Xiang Mei , Zhang Rixin , Zheng Xiaolin , Zheng Zhi , Li Kai 
Published: January 2025

Objective: Despite N6‐methyladenosine (m6A) being closely involved in various pathophysiological processes, its potential role in liver injury is largely unknown. We designed the current research to study the potential role of fat mass and obesity‐associated protein (FTO), an m6A demethylase, on hepatic ischemia‐reperfusion injury (IRI).Methods: Wild‐type mice injected with an adeno‐associated virus carrying fat mass and obesity‐associated protein (AAV‐FTO) or adeno‐associated virus carrying green fluorescent protein (GFP) (AAV‐GFP) were subjected to a hepatic IRI model in vivo. Hematoxylin–eosin staining was performed to observe IRI. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining was used to observe the cell apoptosis. Reverse transcription polymerase chain reaction (RT‐PCR) was used to observe the expression of FTO. The protein levels of FTO, apoptosis, or autophagy‐associated signaling proteins were detected by western blot. Reactive oxygen species (ROS) levels were determined by flow cytometry, and immunohistochemistry was used to detect the FTO and LC3‐II expression. For in vitro experiments, cultured hepatocytes were subjected to hypoxia/reoxygenation (H/R) stimulation. Monodansylcadaverine (MDC) staining was used to visualize autophagic vesicles.Results: In the present study, we showed that FTO was involved in hepatic IRI, apoptosis, and autophagy. Specifically, the expression level of FTO was significantly reduced in the hepatic IRI. Besides, increasing FTO expression (AAV‐FTO) ameliorated the hepatic IRI in animal models, accompanied by decreased apoptosis and autophagy. Furthermore, the FTO inhibitor (FB23‐2) aggravated autophagy in hepatocytes upon H/R‐induced damage.Conclusion: FTO could act as a protective effector during hepatic IRI, associated with decreased apoptosis and autophagy. FTO‐mediated m6A demethylation modification may be an important therapeutic target for hepatic IRI.
NI-3201 Is a Bispecific Antibody Mediating PD-L1–Dependent CD28 Co-stimulation on T Cells for Enhanced Tumor Control
Authors: Majocchi Sara , Lloveras Pauline , Nouveau Lise , Legrand Margaux , Viandier Alizee , Malinge Pauline , Charreton Maud , Raymond Cecile , Pace Emily A. , Millard Bjorn L. , Svensson L. Anders , Kelpšas Vinardas , Anceriz Nadia , Salgado-Pires Susana , Daubeuf Bruno , Magistrelli Giovanni , Gueneau Franck , Moine Valéry , Masternak Krzysztof , Shang Limin , Fischer Nicolas , Ferlin Walter G. 
Published: January 2025

Abstract
Despite advances in cancer immunotherapy, such as targeting the PD-1/PD-L1 axis, a substantial number of patients harbor tumors that are resistant or relapse. Selective engagement of T-cell co-stimulatory molecules with bispecific antibodies may offer novel therapeutic options by enhancing signal 1–driven activation occurring via T-cell receptor engagement. In this study, we report the development and preclinical characterization of NI-3201, a PD-L1×CD28 bispecific antibody generated on the κλ-body platform that was designed to promote T-cell activity and antitumor function through a dual mechanism of action. We confirmed that NI-3201 blocks the PD-L1/PD-1 immune checkpoint pathway and conditionally provides T-cell co-stimulation via CD28 (signal 2) when engaging PD-L1+ tumors or immune cells. In systems with signal 1–primed T cells, NI-3201 enhanced potent effector functionality: in vitro through antigen-specific recall assays with cytomegalovirus-specific T cells and in vivo by inducing tumor regression and immunologic memory in tumor-associated antigen–expressing MC38 syngeneic mouse models. When T-cell engagers were used to provide synthetic signal 1, the combination with NI-3201 resulted in synergistic T cell–dependent cytotoxicity and potent antitumor activity in two humanized mouse tumor models. Nonhuman primate safety assessments showed favorable tolerability and pharmacokinetics at pharmacologically active doses. Quantitative systems pharmacology modeling predicted that NI-3201 exposure results in antitumor activity in patients, but this remains to be investigated. Overall, this study suggests that by combining PD-L1 blockade with safe and effective CD28 co-stimulation, NI-3201 has the potential to improve cancer immunotherapy outcomes, and the clinical development of NI-3201 for PD-L1+ solid tumors is planned.
AMETIS Preplanned Ancillary Study: Impact of Agitation During Mechanical Thrombectomy Under Sedation
Authors: Tabillon Caroline , Bernard Rémy , Jacquens Alice , Pommier Maxime , Begard Marc , Balança Baptiste , Rapido Francesca , Tavernier Benoit , Molliex Serge , Velly Lionel , Verdonk Franck , Lukaszewicz Anne-Claire , Perrigault Pierre-François , Albucher Jean-François , Cognard Christophe , Guyot Adrien , Fernandez Charlotte , Masgrau Aurélie , Moreno Ricardo , Ferrier Anna , Jaber Samir , Pereira Bruno , Futier Emmanuel , Chabanne Russel , Degos Vincent 
Published: January 2025

BACKGROUND:
Mechanical thrombectomy is the treatment of choice for ischemic strokes of the anterior circulation with proximal occlusion. Mechanical thrombectomy can be performed under sedation, which can lead to episodes of periprocedural agitation. The aim of this study is to describe the prevalence of agitation and determine the consequences during and after mechanical thrombectomy.

METHODS:
This is an ancillary study to the AMETIS study (Anesthesia Management in Endovascular Therapy for Ischemic Stroke). We evaluated the patients from the sedation group of this randomized trial; some patients presented at least 1 episode of agitation during the procedure (determined by a Richmond Agitation-Sedation Scale score >1) prospectively collected. We explored the association between agitation and a composite outcome (Thrombolysis in Cerebral Infarction score <2b and/or arterial perforation) through univariate and multivariate analyses, accounting for confounders (agitation, age, National Institutes of Health Stroke Scale score, local thrombus) identified a priori by the acyclic diagram method.

RESULTS:

Among the 138 participants (average age, 71±14 years; 72 [52%] male; average National Institutes of Health Stroke Scale score, 15±6), 53 (38%) experienced at least 1 agitation episode. Agitation was neither a risk factor of Thrombolysis in Cerebral Infarction score <2b and/or arterial perforation in univariate and multivariate analyses (adjusted odds ratio, 1.29 [0.57–2.92];
P
=0.5), nor a risk of unfavorable outcome (adjusted OR, 0.7 [0.18–2.56];
P
=0.56). Although, agitated patients had a higher incidence of conversion with intubation (21% versus 5%; OR, 5.3 [1.7–20];
P
<0.01) and significantly worse radiological image quality (62% versus 17%; OR, 8.37 [3.9–19.1];
P
<0.01).

CONCLUSIONS:
Our study found a high frequency of agitation during mechanical thrombectomy under sedation. Despite the absence of any significant link with prognosis, Thrombolysis in Cerebral Infarction score, and perforations, there is more conversion to general anesthesia with intubation and poorer quality images.
Novel Vascular Territory Mapping Algorithm as a Predictive Tool for Identification of Antegrade Flow in Middle Cerebral Artery Occlusion
Authors: Valente Michael , Bivard Andrew , Yan Bernard , Chen Chushuang , Visser Milanka , Ma Henry , Lin Longting , Parsons Mark 
Published: January 2025

BACKGROUND:
Vascular territory mapping (VTM) software estimates which intracerebral vessel provides predominant arterial flow to a brain voxel. The presence of antegrade flow in the setting of acute middle cerebral artery (MCA) occlusion is associated with improved outcomes. We identify whether VTM software is a determinant of antegrade flow in patients with proximal MCA occlusion.

METHODS:
Consecutive patients with the first branch of MCA (M1) occlusion were analyzed from the International Stroke Perfusion Imaging Registry with their computed tomography perfusion reprocessed through VTM software. Authors reviewed dynamic 4-dimensional computed tomography angiography for the presence of an acute M1 thrombus and also for the presence of residual antegrade flow. The VTM software assigned regions of the brain to an estimated feeding vessel (anterior cerebral artery, MCA, and posterior cerebral artery). A binomial logistic regression was performed to determine the effects of VTM, ischemic core (cerebral blood flow <30), and perfusion lesion (delay time >3) on the likelihood that patients had the presence of any antegrade flow in the MCA territory. A secondary analysis was performed to assess the relationship between imaging variables and 3-month modified Rankin Scale outcomes.

RESULTS:
The final data set included 130 patients with M1 occlusion. The median age of participants was 74 years (interquartile range, 62–81) with an onset-to-scan time of 2.1 hours (interquartile range, 1.4–3.8) and a National Institutes of Health Stroke Scale score of 15 (interquartile range, 12–20). Eighteen patients were identified with antegrade flow on 4-dimensional digital subtraction angiography. Patients with antegrade flow had significantly larger VTM volume normal side MCA, 101 (72–180) mL, compared with those with complete occlusion, 41 (21–71) mL. VTM volume normal side MCA volume significantly predicted antegrade flow and outcome, and 1 mL VTM volume normal side MCA volume increased odds of antegrade flow by 1.024 (95% CI, 1.013–1.036). Ischemic core and the perfusion lesion volumes did not predict antegrade flow.

CONCLUSIONS:
VTM software was more effective than traditional perfusion parameters in the detection of antegrade flow. The results demonstrate a potential clinical utility for VTM; however, larger cohorts will be required to detect whether VTM can predict clinical outcome after reperfusion treatment.
The residential patterns of Swiss urban elites. Continuity and change
across elite categories (1890-2000)
Authors: Benz Pierre , Di Capua Roberto , Mach André , Michael A. Strebel 
Published: January 2025

Abstract
Numerous studies have focused on wealth elites' housing, including their spatial and social exclusiveness. The insertion of the power elite in urban space has, however, largely been left unexplored. By combining positional and residential information on over 7,400 urban elites, we study how academic, economic, and political elites' residential patterns have evolved from 1890 to 2000 in the three largest Swiss cities (Basel, Geneva, Zurich). First, we uncover a long-term dynamic of suburbanization, which however does not result in even spatial dispersion: while gradually abandoning center cities, elites do not randomly disperse in the surrounding municipalities. Rather, they tend to settle in very specific areas. Second, we find that spatial differentiation of urban elites' residences varies across elite categories: economic elites tend to geographically segregate from both academic and political elites over the course of the twentieth century and settle in more privileged areas. At the same time, academic and left political elites, while historically living in distinct neighborhoods, tend to converge at the end of the century, echoing new similarities in their profile. This highlights the importance of studying the urban power elites' residential patterns in a long-term perspective.