bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel adaptive immune systems in pristine Antarctic soils
Authors: Van Goethem Marc W. , Bezuidt Oliver K. I. , Pierneef Rian , Vikram Surendra , Hopkins David W. , Aspray Thomas , Hall Grant , Woodborne Stephan , Hogg Ian D. , Northen Trent R. , Kong Weidong , Daffonchio Daniele , Cowan Don A. , Van de Peer Yves , Delgado-Baquerizo Manuel , Makhalanyane Thulani P. 
Published: January 2025

Abstract
Antarctic environments are dominated by microorganisms, which are vulnerable to viral infection. Although several studies have investigated the phylogenetic repertoire of bacteria and viruses in these poly-extreme environments with freezing temperatures, high ultra violet irradiation levels, low moisture availability and hyper-oligotrophy, the evolutionary mechanisms governing microbial immunity remain poorly understood. Using genome-resolved metagenomics, we test the hypothesis that Antarctic poly-extreme high-latitude microbiomes harbour diverse adaptive immune systems. Our analysis reveals the prevalence of prophages in bacterial genomes (Bacteroidota and Verrucomicrobiota), suggesting the significance of lysogenic infection strategies in Antarctic soils. Furthermore, we demonstrate the presence of diverse CRISPR-Cas arrays, including Class 1 arrays (Types I-B, I-C, and I-E), alongside systems exhibiting novel gene architecture among their effector cas genes. Notably, a Class 2 system featuring type V variants lacks CRISPR arrays, encodes Cas1 and Cas2 adaptation module genes. Phylogenetic analysis of Cas12 effector proteins hints at divergent evolutionary histories compared to classified type V effectors and indicates that TnpB is likely the ancestor of Cas12 nucleases. Our findings suggest substantial novelty in Antarctic cas sequences, likely driven by strong selective pressures. These results underscore the role of viral infection as a key evolutionary driver shaping polar microbiomes.
Association between herpes simplex virus infection and Alzheimer’s disease biomarkers: analysis within the MAPT trial
Authors: Linard Morgane , Garrigue Isabelle , Vellas Bruno , Coley Nicola , Zetterberg Henrik , Blennow Kaj , Ashton Nicholas James , Payoux Pierre , Salabert Anne-Sophie , Dartigues Jean-François , Mazere Joachim , Andrieu Sandrine , Helmer Catherine 
Published: January 2025

Abstract
In vitro and animal studies have suggested that inoculation with herpes simplex virus 1 (HSV-1) can lead to amyloid deposits, hyperphosphorylation of tau, and/or neuronal loss. Here, we studied the association between HSV-1 and Alzheimer’s disease biomarkers in humans. Our sample included 182 participants at risk of cognitive decline from the Multidomain Alzheimer Preventive Trial who had HSV-1 plasma serology and an amyloid PET scan. Plasma Aβ42/40 ratio, neurofilament light chain and p-tau181 were also available for a sub-sample of participants. Multivariate linear regressions were performed and stratified by APOE4 genotype. The median age was 74.0 years, 85.2% were infected with HSV-1. Infected participants tended to have a lower cortical amyloid load than uninfected participants (β = -0.08, p = 0.06), especially those suspected of reactivating HSV-1 most frequently (i.e. with a high anti-HSV-1 IgG level; n = 58, β = -0.09 p = 0.04). After stratification, the association was only significant in APOE4 carriers (n = 43, β = -0.21 p = 0.01). No association was found with the plasma biomarkers. The trend toward lower cortical amyloid load in HSV-1-infected participants was unexpected given the pre-existing literature and may be explained either by a modified immune response in HSV-1 infected subjects which could favour the clearance of amyloid deposits or by a selection bias.
Insights into the diverse roles of the terminal oxidases in Burkholderia cenocepacia H111
Authors: Paszti Sarah , Biner Olivier , Liu Yilei , Bolli Kim , Jeggli Sarah Dorothy , Pessi Gabriella , Eberl Leo 
Published: January 2025

Abstract

Burkholderia cenocepacia H111 is an obligate aerobic bacterium which has been isolated from a cystic fibrosis (CF) patient. In CF lungs the environment is considered micro-oxic or even oxygen-depleted due to bacterial activities and limited oxygen diffusion in the mucus layer. To adapt to low oxygen concentrations, bacteria possess multiple terminal oxidases. In this study, we identified six terminal oxidases of B. cenocepacia H111 and constructed reporter strains to monitor their expression in different environments. While the heme-copper oxidase aa

3
(cta) was constitutively expressed, the bd-1 oxidase (cyd) was induced under oxygen-limited growth conditions. The cyanide-insensitive bd-type terminal oxidase (cio-1) was mainly expressed in cells grown on the surface of solid medium or in liquid cultures in presence of cyanide, which is known to be produced in the CF lung by the often co-residing CF pathogen Pseudomonas aeruginosa. Indeed, a cio-1 insertional mutant was not able to grow in the presence of cyanide confirming the important role of Cio-1 in cyanide resistance. The caa

3
oxidase (caa), was only expressed under nutrient limitation when cells were grown on the surface of solid medium. We also investigated the involvement of two regulatory systems, Anr and RoxS/RoxR, in the expression of cio-1 and cyd. Our data suggest, that, given that Cio-1 is only present in prokaryotes and plays an important role in the defense against cyanide-producing P. aeruginosa, it may be a valuable drug target for treatment of polymicrobial infections in CF patients.
Machine learning approach for predicting tramp elements in the basic oxygen furnace based on the compiled steel scrap mix
Authors: Schäfer Michael , Faltings Ulrike , Glaser Björn 
Published: January 2025

Abstract
In the blast furnace and basic oxygen furnace route, pig iron and steel scrap are used as resources for steel production. The scrap content can consist of many different types of scrap varying in origin and composition. This makes it difficult to compile the scrap mix and predict the future chemical analysis in the converter. When compiling the scrap mix, steel manufacturers often rely on experience and trials. In this paper, we present a machine learning approach based on XGBoost to predict the chemical element content in the converter. Data from around 115000 heats were analyzed and a model was developed to better predict the content of the tramp elements copper, chromium, molybdenum, phosphorus, nickel, tin and sulphur at the end of the basic oxygen furnace process. The study shows that it is possible to predict the chemical element content for tramp elements in the converter based solely on data available in advance and routinely collected without the necessity of additional sensors or analysis of input material. Given the nature of scrap classifications for (external) scrap types, this is non-trivial. Furthermore, an online model was implemented, accessible via a defined synchronous interface, which allows to optimize the use of different scrap types by predicting the chemical content at the end of the basic oxygen furnace process and simulating with new combinations of input material. Not all types of steel scrap are always available. With the model developed, new scrap input constellations can now be created to ensure that the quality of the melt is maintained. However, for very accurate predictions, the data from the upstream processes must be of high quality and quantity. Efficient scrap management, monitoring of the scrap input and confusion checks.
A pathway from fragmentation to interoperability through standards-based enterprise architecture to enhance patient safety
Authors: Wong Zoie Shui-Yee , Gong Yang , Ushiro Shin 
Published: January 2025

Abstract
Creating an ontology is the essential step in natural language processing (NLP). To improve patient safety in this era of generative AI, it is crucial to develop a standards-driven, ontology-based architecture for patient safety that can seamlessly integrate with health systems, thereby facilitating effective detection and monitoring potentially preventable harms in healthcare. This visionary, whole-system approach to patient safety addresses a significant gap in establishing resilient safety systems within the healthcare sector.
Strong-weak dual interface engineered electrocatalyst for large current density hydrogen evolution reaction
Authors: Ke Shaorou , Mi Ruiyu , Min Xin , Zhu Xinyu , Wu Congyi , Li Xin , Yang Bozhi , Wu Xiaowen , Liu Yangai , Huang Zhaohui , Fang Minghao 
Published: January 2025

Abstract
Supported nanocatalysts are crucial for hydrogen production, yet their activity and stability are challenging to manage due to complex metal-support interfaces. Herein, we design Pt@ anatase&rutile-TiO2 with a strong-weak dual interface by modifying TiO2 using high-energy ball milling and in-situ reduction to vary surface energies. Experiments and density functional theory calculations reveal that the strong Pt-anatase TiO2 interface enhances hydrogen adsorption. In contrast, the weak Pt-rutile TiO2 interface facilitates hydrogen desorption, simultaneously preventing Pt agglomeration and increasing reaction rate. As a result, the tailored catalyst has a 529.3 mV overpotential at 1000 mA cm−2 in 0.5 M H2SO4, 0.69 times less than commercial Pt/C. It also possesses 8.8 times the mass activity of commercial Pt/C and maintains a low overpotential after 2000 cyclic voltammetry cycles, suggesting high activity and stability. This strong-weak dual interface engineering strategy shows potential for overall water splitting and proton exchange membrane water electrolyzer, advancing the design of efficient supported nanocatalysts.
Working-class youth participation in climate action: networks, civic experience, and equity
Authors: Naseif Rasha , Haddad Isabelle , Almeida Paul 
Published: January 2025

Abstract
Research on individual participation in climate action largely focuses on middle class environmental activism around protest events. To better understand the expansion of civic engagement on climate issues, more work needs to be carried out on wider sectors of the population. This study examines the drivers associated with involvement in climate action at the individual level with a survey sample of working-class youth of color. The findings suggest that youth embedded in pro-climate social networks, a history of civic engagement, and an equity belief system increase willingness to participate in several forms of climate action, including climate meetings, demonstrations, and inviting others to participate. For larger climate action initiatives to overcome the barriers of participation, linking to specific pools of sympathy in civil society that value economic equality may provide a mass base of support for policies consistent with just transition perspectives.
Comparison of Different Methods on Post-Activation Performance
Enhancement: A Meta-Analysis
Authors: Zhao Chunyu , Li Congying , Su Ronghai , Chen Lin , Wei Wei , Meng Meng , Chen Chen 
Published: January 2025

AbstractThis meta-analysis was aimed to compare the effects of two methods on
post-activation performance enhancement (PAPE). We conducted a comprehensive
search of PubMed, Web of Science, Cochrane Library, and China National Knowledge
Infrastructure from inception to December 2023. Two authors independently
selected the included studies, extracted data, and assessed the risk of bias and
certainty evidence. The primary meta-analysis compared the effects of blood flow
restriction combined with resistance training (BFR-RT) and high-load resistance
training (HL-RT) on the indicator jump height (JH) and power output (PO) of
PAPE. The secondary meta-analyses compared within-group differences by gender
and between-group differences between the optimal combined protocol of arterial
occlusion pressure (AOP) combined with resistance load and the HL-RT protocol.
This meta-analysis shows that both BFR-RT and HL-RT significantly improved JH
(standardized mean difference (SMD)=0.39, 95% confidence interval (CI) [0.20,
0.59]) (SMD=0.34, 95% CI [0.19, 0.48]) and PO (SMD=0.42, 95% CI [0.21, 0.62])
(SMD=0.37, 95%CI [0.19, 0.54]), and there was no significant difference between
them. However, subgroup analysis revealed that in terms of gender, BFR-RT was
more beneficial for PAPE in females, and in terms of combined protocol, BFR-RT
with 50% AOP+30% 1 repetition maximum had the greatest effect compared to
HL-RT.BFR-RT can serve as an effective alternative to HL-RT for inducing
PAPE.
Composite microRNA-genetic risk score model links to migraine and implicates its pathogenesis
Authors: Chen Shih-Pin , Chang Ya-Hsuan , Wang Yen-Feng , Chen Hsuan-Yu , Wang Shuu-Jiun 
Published: January 2025

Abstract
The neurobiological mechanisms driving the ictal-interictal fluctuations and the chronification of migraine remain elusive. We aimed to construct a composite genetic-microRNA model that could reflect the dynamic perturbations of the disease course and inform the pathogenesis of migraine.
We prospectively recruited four groups of participants, including interictal episodic migraine (i.e., headache-free for &gt; 72 hrs apart from prior and subsequent attacks), ictal episodic migraine (i.e., during moderate to severe migraine attacks), chronic migraine, and controls in the discovery cohort. Next-generation sequencing (NGS) was used for microRNA profiling. The candidate microRNAs were validated with quantitative PCR (qPCR) in an independent validation cohort. Biological pathways associated with the microRNA regulome and interaction networks were explored. In addition, all participants received genotyping with the Axiom Genome-Wide Array TWB chip. A composite model was established, combining disease-associated microRNAs and genetic risk scores (GRS) indicative of genetic susceptibility, with the objective of differentiating migraine from controls using a binary outcome.
From a total of 120 participants in the discovery cohort and 197 participants in the validation cohort, we identified disease-state microRNA signatures (including miR-183, miR-25, and miR-320) that were ubiquitously higher or lower in patients with migraine compared to controls. We have also validated four disease-activity miRNA signatures (miR-1307-5p, miR-6810-5p, let-7e, and miR-140-3p) that were differentially expressed only during the ictal stage of episodic migraine. Functional analysis suggested that prolactin and estrogen signaling pathways might play important roles in the pathogenesis. Moreover, the composite microRNA-GRS model differentiated patients from controls, achieving a positive predictive value of over 90%.
To conclude, we developed a composite microRNA-genetic risk score model, which may serve as a predictive tool for identifying high-risk individuals. Our findings may help illuminate potential pathogenic mechanisms underlying the dysfunctional allostasis of migraine and pave the way for future precision medicine.
LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations
Authors: Nourani Esmaeil , Makri Evangelia-Mantelena , Mao Xiqing , Pyysalo Sampo , Brunak Søren , Nastou Katerina , Jensen Lars Juhl 
Published: January 2025

Abstract
Lifestyle factors (LSFs) are increasingly recognized as instrumental in both the development and control of diseases. Despite their importance, there is a lack of methods to extract relations between LSFs and diseases from the literature, a step necessary to consolidate the currently available knowledge into a structured form. As simple co-occurrence-based relation extraction (RE) approaches are unable to distinguish between the different types of LSF-disease relations, context-aware models such as transformers are required to extract and classify these relations into specific relation types. However, no comprehensive LSF–disease RE system existed, nor a corpus suitable for developing one. We present LSD600 (available at https://zenodo.org/records/13952449), the first corpus specifically designed for LSF–disease RE, comprising 600 abstracts with 1900 relations of eight distinct types between 5027 diseases and 6930 LSF entities. We evaluated LSD600’s quality by training a RoBERTa model on the corpus, achieving an F-score of 68.5% for the multilabel RE task on the held-out test set. We further validated LSD600 by using the trained model on the two Nutrition-Disease and FoodDisease datasets, where it achieved F-scores of 70.7% and 80.7%, respectively. Building on these performance results, LSD600 and the RE system trained on it can be valuable resources to fill the existing gap in this area and pave the way for downstream applications.
Database URL: https://zenodo.org/records/13952449
Assessment and reporting of extraintestinal manifestations and fatigue in phase 3 inflammatory bowel disease clinical trials
Authors: Chhibba Tarun , Sachdeva Karan , Ananthakrishnan Ashwin N 
Published: January 2025

Abstract

Background
Extraintestinal manifestations (EIMs) of inflammatory bowel disease (IBD) are frequently experienced by patients and may lead to severe symptoms and fatigue. However, the reporting patterns of these outcomes in IBD randomized controlled trials (RCTs) are not clear.

Methods
We searched placebo-controlled phase 3 RCTs of advanced therapies in IBD and assessed the frequency and means of reporting EIM and fatigue data in these studies.

Results
Thirty-three phase 3 RCTs for Crohn’s disease (CD) (n = 16) or ulcerative colitis (UC) (n = 16) were identified between 2002 and 2023. While all trials (16/16) in CD collected some EIM data, we could only ascertain 6/16 (38%) collected EIM data in UC trials. Fewer than one-third (9/32, 28%) reported EIM prevalence at baseline; fewer reported the improvement with active treatment (9%). Fatigue was measured in 20/32 trials (63%).

Conclusions
EIM and fatigue data are inconsistently collected in RCTs of IBD. Standardizing collection methods across RCTs would provide greater insight on these agents and their efficacy in treating these manifestations of disease.
Preliminary results of a novel sphincter-sparing technique—fistula occlusion with the internal sphincter flap (FOISF)—for high complex anal fistulas
Authors: Huang Dandan , Wang Ning , Li Yiping , Ren Donglin , Yang Yong , Wei Kaikai , Li Yanzhu , Liu Zhimin 
Published: January 2025

Abstract

Background and aim
High complex anal fistula is a clinical challenge for proctologists and a nightmare for patients. Although the sphincter-sparing approach seems an ideal surgical intervention, there remains room for improvement in treatment efficacy. Herein, we introduce an enhanced sphincter-sparing approach, namely the fistula occlusion with the internal sphincter flap (FOISF), for treating high complex anal fistulas.

Methods
This study evaluated 15 patients with high complex anal fistulas who underwent FOISF between October 2021 and December 2022 in the Sixth Affiliated Hospital, Sun Yat-sen University (Guangzhou, P. R. China). Data on success rates, anal function, and various surgical characteristics were subjected to rigorous analysis.

Results
All patients underwent the FOISF procedure, with a median operation time of 53 min. Fourteen patients achieved primary intention healing, while one patient healed by second intention. No recurrence was observed over a follow-up period of 14–30 months. All patients exhibited satisfactory anal continence, with no statistically significant difference observed between preoperative and postoperative Wexner scores (P = 0.331). A significant improvement in the quality of life was observed when compared with the preoperative assessment (P &lt; 0.001).

Conclusion
The preliminary results of the FOISF procedure present an effective approach to treat high complex anal fistula.
Non-canonical imprinting, manifesting as post-fertilization placenta-specific parent-of-origin dependent methylation, is not conserved in humans
Authors: Daskeviciute Dagne , Chappell-Maor Louise , Sainty Becky , Arnaud Philippe , Iglesias-Platas Isabel , Simon Carlos , Okae Hiroaki , Arima Takahiro , Vassena Rita , Lartey Jon , Monk David 
Published: January 2025

Abstract
Genomic imprinting is the parent-of-origin dependent monoallelic expression of genes often associated with regions of germline-derived DNA methylation that are maintained as differentially methylated regions (gDMRs) in somatic tissues. This form of epigenetic regulation is highly conserved in mammals and is thought to have co-evolved with placentation. Tissue-specific gDMRs have been identified in human placenta, suggesting that species-specific imprinting dependent on unorthodox epigenetic establishment or maintenance may be more widespread than previously anticipated. Non-canonical imprinting, reliant on differential allelic H3K27me3 enrichment, has been reported in mouse and rat pre-implantation embryos, often overlapping long terminal repeat (LTR)-derived promoters. These non-canonical imprints lose parental allele-specific H3K27me3 specificity, subsequently gaining DNA methylation on the same allele in extra-embryonic tissues resulting in placenta-specific, somatically acquired maternal DMRs. To determine if similar non-canonical imprinting is present in the human placenta, we interrogated allelic DNA methylation for a selected number of loci, including (i) the human orthologues of non-canonical imprinted regions in mouse and rat, (ii) promoters of human LTR-derived transcripts, and (iii) CpG islands with intermediate placenta-specific methylation that are unmethylated in gametes and pre-implantation embryos. We failed to identify any non-canonical imprints in the human placenta whole villi samples. Furthermore, the assayed genes were shown to be biallelically expressed in human pre-implantation embryos, indicating they are not imprinted at earlier time points. Together, our work reiterates the continued evolution of placenta-specific imprinting in mammals, which we suggest is linked to epigenetic differences during the maternal-to-embryo transition and species-specific integration of retrotransposable elements.
On Interrelations Between Graph Complexes
Authors: Merkulov Sergei A 
Published: January 2025

Abstract
We study Maxim Kontsevich’s graph complex $\textsf{GC}_{d}$ for any integer $d$ as well as its oriented and targeted versions, and show new short proofs of the theorems due to Thomas Willwacher and Marko živković which establish isomorphisms of their cohomology groups. A new result relating the cohomology of the sourced-targeted graph complex in dimension $d+1$ with the direct sum of two copies of the cohomology group of Maxim Kontsevich’s graph complex $\textsf{GC}_{d}$ in dimension $d$ is obtained. We introduce a new graph complex spanned by purely trivalent graphs and show that its cohomology is isomorphic to $H^{\bullet }(\textsf{GC}_{d})$.