bluuebunny/crossref_metadata_2025_split huggingface dataset:
HoloST: holistic spatiotemporal learning-integrating long-short temporal dynamics and global-local spatial features for chemical process fault diagnosis
Authors: Chen Xiao , ren jia , Shi Qi , Wang Junjia 
Published: February 2025

Abstract
Owing to the inherent strong dynamics, nonlinearity, and spatiotemporal correlation of chemical process data, extracting effective features and achieving high-precision fault identification pose significant challenges. To tackle this problem, this paper presents a novel and effective spatiotemporal feature fusion model, HoloST. Specifically, the time series module integrates LSTM (Long Short-Term Memory), SEnet (Squeeze-and-Excitation Networks), and 1D CNN (One-Dimensional Convolutional Neural Network) to extract both long- and short-term temporal dependency information from the data. Meanwhile, the spatial module employs GS-CNN (Global Scale Convolutional Neural Network) and DSC (Depthwise Separable Convolution) to capture global and local spatial correlations. By integrating the temporal and spatial feature modules, the model can comprehensively extract long- and short-term temporal information as well as global and local spatial details, thereby significantly enhancing the effectiveness of feature extraction. Experiments conducted using the benchmark Tennessee Eastman process dataset and a three-phase flow dataset demonstrate the superiority of the proposed HoloST model over five other mainstream data-driven fault detection and diagnosis (FDD) approaches. Furthermore, k-fold cross-validation experiments and experiments with limited sample sizes verify the robustness and generalization capability of the model.
Trafficking of K63-polyubiquitin modified membrane proteins in a macroautophagy-independent pathway is linked to ATG9A
Authors: Scavone Francesco , Lian Sharon , Eskelinen Eeva-Liisa , Cohen Robert E. , Yao Tingting 
Published: February 2025

Cytoplasmic K63-linked polyubiquitin signals have well-established roles in endocytosis and selective autophagy. However, how these signals help to direct different cargos to different intracellular trafficking routes is unclear. Here we report that, when the K63-polyubiquitin signal is blocked by intracellular expression of a high-affinity sensor (named Vx3), many proteins originating from the plasma membrane are found trapped in clusters of small vesicles that co-localize with ATG9A, a transmembrane protein that plays an essential role in autophagy. Importantly, whereas ATG9A is required for cluster formation, other core autophagy machinery as well as selective autophagy cargo receptors are not required. Although the cargos are sequestered in the vesicular clusters in an ATG9-dependent manner, additional signals are needed to induce LC3 conjugation. Upon removal of the Vx3 block, K63-polyubiquitylated cargos are rapidly delivered to lysosomes. These observations suggest that ATG9A plays an unexpected role in the trafficking of K63-polyubiquitin modified membrane proteins. [Media: see text] [Media: see text] [Media: see text]
Shlomo Dykman’s Aeneid
Authors: Kenaan Vered Lev 
Published: February 2025

Abstract
The chapter focuses on Shlomo Dykman (b. Warsaw 1917–d. Jerusalem 1965) an influential and prolific Hebrew translator of Greek and Latin poetry. The chapter presents Dykman’s formative education in Warsaw until 1939 at the Tarbut Hebrew Gymnasium, the Institute of Jewish Studies, and Warsaw University. It considers Dykman’s vocation as a multilingual translator from Yiddish to Hebrew, from Hebrew to Polish, and from Greek and Latin to Hebrew. Dykman’s Hebrew translation of Virgil’s Aeneid is inseparable from his experience as a Jewish refugee fleeing Nazi-occupied Poland to Russia, and as a prisoner of the Vorkuta Gulag labour camp. The chapter examines the unique characteristics of Dykman’s translation of the Aeneid together with other Hebrew translations preceding Dykman’s translation. In using Holocaust imagery, Dykman not only Judaized the Trojan survivors but also united Roman and Zionist ideologies.
Ay de mi Alhama
Authors: Armstrong Richard H 
Published: February 2025

Abstract
This chapter follows a recursive chronology that contrasts two very different twentieth-century Jewish trajectories: the assimilated, Ashkenazi experience of the Freud family, and the Sephardic experience of the Jews of Thessaloniki, particularly Moshe Ha-Elion (1925–2022), a contemporary of Freud’s grandchildren. At the heart of this chapter is Freud’s ‘A Disturbance of Memory on the Acropolis’ of 1936 where Freud quotes from ‘Ay de mi Alhama’, the lament for the fall of Alhama. The Sephardic connection to Spain through the Ladino language keeps such romances alive in Jewish tradition. The chapter presents Moshe Ha-Elion, a Holocaust survivor, who was born in Salonica and immigrated to Palestine in 1946. Ha-Elion wrote poetry in Ladino to commemorate the Shoah, and in his final years, translated the entire Iliad and Odyssey into Ladino. The chapter connects Alhama, Granada, ancient Troy, Jewish Salonica/Thessaloniki, and Freud’s Vienna, all great cities whose populations suffered genocidal terror at the hands of their conquerors.
Translation in Exile
Authors: Kenaan Vered Lev , Nubani Ahlam 
Published: February 2025

Abstract
This chapter deals with the significance of Virgil’s Aeneid for Palestinian historical memory. This Arabic prose translation of Virgil’s Aeneid, by the Palestinian Maḥmūd ʿAli al-Ghūl (1923–83), is extremely important for uncovering a relationship between Roman and Palestinian memorialization of their painful past and offers access to a yet untold history of the reception of classical studies in Palestine before 1948. The chapter discusses the importance of the Arab College in Jerusalem for the transmission of classical learning among Palestinians. Maḥmūd ʿAli al-Ghūl was born in Silwan village near Jerusalem and received a classical education both at the Arab College in Jerusalem and at King Fuad I University in Cairo, Egypt. He composed his translation of the Aeneid from 1942 to 1951, yet the work was published only posthumously in 2015. He worked on his Arabic translation while wandering as a refugee from one academic position to another.
A structural mean modelling Mendelian randomization approach to investigate the lifecourse effect of adiposity: applied and methodological considerations
Authors: Power Grace M , Palmer Tom , Warrington Nicole , Heron Jon , Richardson Tom G , Didelez Vanessa , Tilling Kate , Smith George Davey , Sanderson Eleanor 
Published: February 2025

Abstract
Mendelian randomization (MR) is a technique that uses genetic variation to address causal questions about how modifiable exposures influence health. For some time-varying phenotypes, genetic effects may have differential importance at different periods in the lifecourse. MR studies often employ conventional instrumental variable (IV) methods designed to estimate lifelong effects. Recently, several extensions of MR have been proposed to investigate time-varying effects, including structural mean models (SMMs). SMMs exploit IVs through g-estimation and circumvent some of the parametric assumptions of other MR methods.
We apply g-estimation of SMMs to MR to estimate the period effects of adiposity measured at two life stages, childhood and adulthood, on cardiovascular disease (CVD), type 2 diabetes (T2D) and breast cancer. We found persistent period effects of higher adulthood adiposity on increased risk of CVD and T2D. Higher childhood adiposity had a protective period effect on breast cancer. We compare this method to an inverse variance weighted multivariable MR approach, a technique also using multiple IVs to assess time-varying effects but relying on a different set of assumptions. We highlight the strengths and limitations of each approach and conclude by emphasising the importance of underlying methodological assumptions in the application of MR to lifecourse research.
Determining the threshold time in restricted mean survival time analysis for two group comparisons with applications in clinical and epidemiology studies
Authors: Han Gang , Schell Michael J , Smith Matthew Lee , Hopkins Laura , Liu Yushi , Carroll Raymond J , Ory Marcia G 
Published: February 2025

Abstract
The restricted mean survival time analysis has been used extensively in clinical research involving time-to-event endpoints. The threshold time up to which the restricted mean survival is calculated has a critical impact on the analysis results. However, identifying an optimal threshold time for treatment comparison, which corresponds to the greatest restricted mean lifetime difference between groups, remains unclear in practice and no analytical method has been developed on this topic. We present a novel method for determining the threshold time in the restricted mean survival time analysis to compare two groups. Simulation studies indicate that this method leads to high statistical power and controlled type I error rate compared with existing methods. The proposed method is illustrated in two applications: 1) a clinical oncology study for non-small-cell lung cancer treatments comparison given a programmed death-ligand 1 biomarker measurement, and 2) a gerontology study of instrumental activities for care recipients with dementia.
Political participation on social media: conceptual and empirical state of the art and research agenda
Authors: Waeterloos Cato 
Published: February 2025

Abstract
Over the past decades, political participation in an online context has gained substantive attention. However, it is only recently that conceptual advancements have been made concerning the specific expressive and mobilizing practices that occur on social media. This article argues on the importance and implications of recognizing political participation on social media as a conceptually distinct mode of political participation, shaped by unique affordances that highlight its networked and political character. Specifically, the article provides a conceptual and normative state of the art regarding online and social media political participation. By discussing the empirical implications of prominent theoretical assumptions in the field, three key research gaps are identified and I propose a research agenda for the field of political communication.
HTSinfer: Inferring metadata from bulk illumina RNA-Seq libraries
Authors: Balajti Máté , Kandari Rohan , Jurič Boris , Zavolan Mihaela , Kanitz Alexander 
Published: February 2025

Abstract

Summary
The Sequencing Read Archive is one of the largest and fastest-growing repositories of sequencing data, containing tens of petabytes of sequenced reads. Its data is used by a wide scientific community, often beyond the primary study that generated them. Such analyses rely on accurate metadata concerning the type of experiment and library, as well as the organism from which the sequenced reads were derived. These metadata are typically entered manually by contributors in an error-prone process, and are frequently incomplete. In addition, easy-to-use computational tools that verify the consistency and completeness of metadata describing the libraries to facilitate data reuse, are largely unavailable. Here we introduce HTSinfer, a Python-based tool to infer metadata directly and solely from bulk RNA-sequencing data generated on Illumina platforms. HTSinfer leverages genome sequence information and diagnostic genes to rapidly and accurately infer the library source and library type, as well as the relative read orientation, 3’ adapter sequence and read length statistics. HTSinfer is written in a modular manner, published under a permissible free and open-source license and encourages contributions by the community, enabling easy addition of new functionalities, for example for the inference of additional metrics, or the support of different experiment types or sequencing platforms.

Availability and implementation
HTSinfer is released under the Apache License 2.0. Latest code is available via GitHub at https://github.com/zavolanlab/htsinfer, while releases are published on Bioconda. A snapshot of the HTSinfer version described in this article was deposited at Zenodo at 10.5281/zenodo.13985958.
The small molecule inhibitor 3PO is a modulator of neutrophil metabolism, ROS production and NET release
Authors: Fresneda Alarcon Michele , Abdullah Genna Ali , Nolan Andy , Linford Christina , Meschis Maria Martina , Cross Andrew L , Sellin Andrew , Phelan Marie M , Wright Helen L 
Published: February 2025

Abstract
Neutrophils are key effector leukocytes of the innate immune system and play a pivotal role in defending the host against microbial infections. Recent studies have identified a crucial link between glycolysis and neutrophil cellular functions. Using human neutrophils, we have investigated the intricate relationship between glycolysis, extracellular glucose availability, and the enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3), in the regulation of reactive oxygen species (ROS) and neutrophil extracellular trap (NET) production. We have identified that PFKFB3 is elevated in rheumatoid arthritis (RA) neutrophils and that the small molecule PFKFB3 inhibitor 3PO is a key regulator of neutrophil ROS and NET production. 3PO blocked the production of ROS and NETs in a dose-dependent manner in both RA and healthy (HC) neutrophils (p&lt;0.01), and RA neutrophils were more sensitive to lower concentrations of 3PO. Bacterial killing was only partially inhibited by 3PO, and the proportion of live neutrophils after 24h incubation was unchanged. Using NMR metabolomics, we identified that 3PO increases the concentration of lactate, phenylalanine and L-glutamine in neutrophils, as well as significantly decreasing intracellular glutathione (adj. p-value&lt;0.05). We also demonstrated that RA neutrophils produce ROS and NETs in culture conditions which mimic the low glucose environments encountered in RA synovial joints. Our results also suggest 3PO may have molecular targets beyond PFKFB3. By dissecting the intricate interplay between metabolism and neutrophil effector functions, this study advances the understanding of the molecular mechanisms governing pro-inflammatory neutrophil responses and identifies 3PO as a potential therapeutic for conditions characterized by dysregulated neutrophil activation.
Difelikefalin for CKD-aP: real world evidence of efficacy and safety in Italian patients
Authors: Aucella Filippo , Zerbi Simona , Monaco Maria Pia , Bonomini Mario , Alberici Federico , Losappio Vincenzo , Tagliente Federica , Urciuolo Federica , Grandaliano Giuseppe , Aucella Francesco , Nardella Maria , Manenti Lucio 
Published: February 2025

Abstract

Introduction
Chronic Kidney Disease Associated Pruritus (CKD-aP), defined as moderate to severe itching directly related to kidney disease, affects about 1/3 of haemodialysis patients and has been associated with poor quality of life, poor sleep, depression and increased mortality. Difelikefalin (DFK) is the first-in-class therapy approved by FDA and EMA for this condition. The aim of the present study was to evaluate DFK efficacy and safety in a real-world setting in Italy.

Methods
We retrospectively collected data of 20 patients treated with DFK in a compassionate manner, before the drug was commercialized, after obtaining approval by the relevant Ethics Committee for each individual case. Mean age and dialysis vintage were 72±11 years and 54±44 months, respectively, basal WI-NRS score being 8.2 and 5D-ITCH 18.6. Scratching lesions were detected in 15/20 patients. DFK was administered IV with weight-based dosing at the end of each dialysis session.

Results
18/20 patients were treated for 12 weeks, 2 patients stopped treatment for dizziness (n.1) and discomfort (n.1). WI-NRS score improved &gt;3 in 11/18 (61%) at week 4 and in 16/18 (88%) at week 12. 5D-ITCH decreased from basal 18,6 to 10,5 at week 12, while sleep quality at the same time points changed from 2,6 to 5,8; scratching lesions disappeared in 12/15 (80%). Except for the two early therapy breaks, no other side effects were reported.

Conclusions
In haemodialysis patients affected by CKD-aP, DFK is an effective and safe treatment that might clearly improve this distressing and overlooked condition.
Validating a variable-instar, climate-based phenology model for the Asian longhorned beetle (Coleoptera: Cerambycidae) using field data from South Carolina
Authors: Schmitt Lena R , Trotter R Talbot , Coyle David R 
Published: February 2025

Abstract
The Asian longhorned beetle, Anoplophora glabripennis (ALB, Coleoptera: Cerambycidae), is a federally regulated invasive species capable of infesting several different genera of hardwood trees. Accurate knowledge of ALB’s phenology is critical for the effective implementation of management and eradication plans. We updated the ALBLT prediction model and used empirical data collected in South Carolina, USA to validate ALBLT v. 2.0. The new model largely agreed with ALB life stages found in field collections, except for late instars and pupae. We also ran the model at 8 other potentially high-risk cities in the contiguous United States with latitudes ranging from 28°N (Tampa, FL) to 41°N (Chicago, IL) to predict how long a single ALB generation might take to develop in these environments. Model predictions ranged from a 2–3-yr lifecycle in Chicago to a potential life cycle of &lt; 1 yr in Tampa. These predictions can help inform managers and invasive species specialists should ALB be found in new environments, and these data can aid in developing an adequate management and eradication plan.
Aortic valve reconstruction with Cardiocel: midterm results
Authors: Irimie Vadim P , Nasra Wasim , Atieh Alaa , Ahmidou Akram , Lehmkuhl³ Lukas , Urbanski Paul P 
Published: February 2025

Abstract

OBJECTIVES
The aim of the study was to evaluate the outcomes of aortic valve repair techniques using cusp patch-plasty with CardioCel.

METHODS
Between September 2014 and June 2021, a total of 167 patients underwent aortic valve reconstruction using cusp repair. In all patients CardioCel patch was used exclusively. An isolated cusp repair was performed in 117 patients (70%), while 50 patients with concomitant aortopathy needed a combined valve and root repair. Seventy-two patients (43%) presented with tricuspid valve. The mean age of the entire cohort was 54.3 ± 12.3 years , 143 patients being males.

RESULTS
Early (30-day/in-hospital) mortality was 0.6%. The survival at 2, 4, and 6 years was 98.8%, 96.8%, and 95.7%, respectively. During the mean follow-up of 4.2 ± 1.7 years (resulting in 697 patient-years), a relevant aortic insufficiency occurred in 10 patients (8 of them presenting with bicuspid valve). All the patients underwent a valve replacement, resulting in a 7.8 ± 2.5% cumulative risk of aortic valve reoperation and/or insufficiency ≥3+ at 6 years. The causes of reoperation were cusp tear at the suture line, progressive valve pathology, endocarditis, and unknown in 4, 4, 1, and 1, respectively. Degeneration and/or calcification of the CardioCel has not been observed.

CONCLUSIONS
The intermediate results of aortic cusp repair using CardioCel are good. Anatomo-pathology of the aortic valve and quality of the cusps seem to be main reason of repair failure. Further investigations are needed to assess the long-term durability of CardioCel patch-plasty as an alternative to biological valve replacement in specific aortic valve pathologies.
Non-invasive vagus nerve stimulation and exercise capacity in healthy volunteers: a randomized trial
Authors: Ackland Gareth L , Patel Amour B U , Miller Stuart , Gutierrez del Arroyo Ana , Thirugnanasambanthar Jeeveththaa , Ravindran Jeuela I , Schroth Johannes , Boot James , Caton Laura , Mein Chas A , Abbott Tom E F , Gourine Alexander V 
Published: February 2025

Abstract

Background and Aims
Vagal parasympathetic dysfunction is strongly associated with impaired exercise tolerance, indicating that coordinated autonomic control is essential for optimizing exercise performance. This study tested the hypothesis that autonomic neuromodulation by non-invasive transcutaneous vagus nerve stimulation (tVNS) can improve exercise capacity in humans.

Methods
This single-centre, randomized, double-blind, sham-controlled, crossover trial in 28 healthy volunteers evaluated the effect of bilateral transcutaneous stimulation of vagal auricular innervation, applied for 30 min daily for 7 days, on measures of cardiorespiratory fitness (peak oxygen consumption (VO2peak)) during progressive exercise to exhaustion. Secondary endpoints included peak work rate, cardiorespiratory measures, and the whole blood inflammatory response to lipopolysaccharide ex vivo.

Results
tVNS applied for 30 min daily over 7 consecutive days increased VO2peak by 1.04 mL/kg/min (95% CI: .34–1.73; P = .005), compared with no change after sham stimulation (−0.54 mL/kg/min; 95% CI: −1.52 to .45). No carry-over effect was observed following the 2-week washout period. tVNS increased work rate (by 6 W; 95% CI: 2–10; P = .006), heart rate (by 4 bpm; 95% CI: 1–7; P = .011), and respiratory rate (by 4 breaths/min; 95% CI: 2–6; P &lt; .001) at peak exercise. Analysis of the whole blood transcriptomic response to lipopolysaccharide in serial samples obtained from five participants showed that tVNS reduced the inflammatory response.

Conclusions
Non-invasive vagal stimulation improves measures of cardiorespiratory fitness and attenuates inflammation, offering an inexpensive, safe, and scalable approach to improve exercise capacity.
Periodontitis-related myocardial fibrosis by expansion of collagen-producing SiglecF+ neutrophils
Authors: Wang Xuekui , Xu Yue , Yu Canqing , Deng Ruhua , Chen Yang , Jiang Kai , Liang Jiayi , Hu Congjiao , Yang Xingbo , Zhang Baowei , Yuan Xun , Pan Cancan , Wang Dandan , Sun Yao , Xiang Yaozu 
Published: February 2025

Abstract

Backgrounds and Aims
Patients with periodontitis (PD) are prone to developing myocardial infarction (MI), yet the prognosis and mechanisms remain unclear. Given the presumed close association of neutrophils with both conditions, this study aims to elucidate the roles of neutrophils in mediating the interaction between PD and MI.

Methods
Three prospective cohorts and PD + MI mouse model were investigated to assess the effects of PD on MI prognosis. Single-cell-RNA sequencing and genome-wide association study were employed to identify the neutrophil subtype involved. To characterize the function of SiglecF+ neutrophils, bone marrow transplantation, Edu-pulse chasing, lineage tracing, and collagen contraction assay were utilized. Adoptive neutrophil transfer, conditional Siglecf knockout and lipid nanoparticles facilitating local SiglecF+ neutrophils depletion was harnessed to explore the roles of SiglecF+ neutrophils in MI repair.

Results
Persisting but not short-term PD upset MI prognosis (cardiac fibrosis and function) in human and mice. Bone marrow neutrophils of PD were intrinsically skewed toward longer-lived SiglecF+ neutrophil differentiation, a subtype that was converted by GMCSF or TGFβ in PPARγ-dependent manner. SiglecF+ neutrophils were expanded in infarcted PD heart where they deposit collagen and activate fibroblasts to instigate excessive fibrosis. SiglecF+ neutrophil depletion was efficacious for mitigating fibrosis.

Conclusions
This study demonstrated that long-lasting PD-aggravated MI prognosis by expanding scar-associated SiglecF+ neutrophils into the heart and highlighted the clinical relevance of oral health examination for treating MI in a holistic fashion.