bluuebunny/crossref_metadata_2025 huggingface dataset:
Microstructure and surface properties of Co-based brazed alloys coatings
Authors: Anghel (Petculescu) Iasmina-Mădălina , Uțu Ion-Dragos , Uțu Diana , Titus Constantin Albert
Published: November 2024

The paper investigates the characteristics of two different manufactured high temperature brazed coatings using a cobalt based powder applied onto the surface of a stainless-steel substrate (AISI 904L). The coatings are intended to shield components exposed to high temperatures in an atmosphere where wear is expected. Energy dispersive analysis (EDX) together with scanning electron microscopy (SEM) was used to characterise the coating microstructure and morphology, and X-ray diffraction was used to identify the phase composition. Properties evaluations were carried out on the coatings’ surface characteristics, including hardness, erosion behaviour and hot corrosion resistance. The hot corrosion test was conducted at 650°C in a salt mixture that contained 75 wt. % sodium sulphate (Na2SO4) and 25 wt.% sodium chloride (NaCl). Alumina particles were used in the erosion tests, which hit the samples surface with an impact angle of 90°.The degree of corrosion attack, erosion behavior and hardness depended on the microstructure of the manufactured vacuum brazed coatings.
Investigation of an Automotive Part Obtained by the WIG Process
Authors: Chepetean Florin , Ioana Feier Anamaria , Felicia Veronica Banciu
Published: November 2024

The paper presents a case study from the automotive industry, namely a part made of Inconel 713C and 18/8 L stainless steel and further focuses on the study and analysis the applicability of the WIG process in the automotive industry. The WIG process chosen for the joining of the two components and all the steps from pre-assembly to the examination part will be presented. In a context where quality and performance requirements are critical, WIG welding is a key element in manufacturing processes.
Effect of different parameters on mode I fracture toughness of resin samples manufactured by DLP
Authors: Vasile Baban Marian , Viorel Coşa Alexandru , Linul Emanoil
Published: November 2024

Additive manufacturing is spreading rapidly in almost all industries, from household to advanced engineering. Components produced by Digital Light Processing (DLP) are not comprehensively characterized, but exceed the capabilities of many AM processes. Its advantages include the ability to produce highly complex designs, superior precision, fast printing and lower operating costs. The present paper investigates the mode I fracture toughness (KIC) of UV-sensitive resin specimens obtained through DLP process. Single edge notch bending (SENB) specimen were 3D printed and tested according to the ASTM D5045 standard. The influence of printing orientation-PO (0°, 45° and 90°), resin color-RC (white, black and transparent) and corrosive environment-CE (air, water and saline solution) was studied. It was observed that all the studied parameters have some effect on the fracture properties. The highest KIC values were obtained for 45°-PO, white-RC (1.88 MPa•m0.5) and saline solution-CE (2.24 MPa•m0.5). However, the greatest influence is highlighted by RC (∼92%), while CE (∼32%) shows a minimal effect. The fracture surface of the investigated samples is influenced by the printing parameters.
Obtaining antimicrobial polymer composites based on copper oxide nanoparticles for sports medical devices.
Authors: Dzitac V , Rusu G I , Gherman V , Valean E , Vodă M , Șerban V-A
Published: November 2024

The beneficial effects of using antimicrobial materials in eliminating or inhibiting microbial proliferation on surfaces are well known, thus contributing to reducing the risk of diseases resulting from accidents involving pathogenic microorganisms. The addition of certain metal particles in various proportions, (for example, silver, copper, or their oxides), in polymer matrices represents an effective method for producing new high-quality antimicrobial materials. In this study, the aim was to obtain a polymer/copper oxide composite with superior biocidal behaviour by using proportions ranging from 3-10% of copper oxides and polymers with different characteristics. The composites were prepared by melt mixing at various temperatures, durations, and homogenization speeds. Subsequently, the necessary samples for investigations were obtained through thermoforming. To evaluate the composite, tests were performed to determine mechanical characteristics, to verify the uniformity of particles in the composite material, and to test antimicrobial efficacy. The results demonstrated that the PP/CuO composite exhibited improved properties compared to pure polymers. These obtained characteristics recommend its potential use in medical devices for prevention or protection (examples include finger, ankle, or tendon prostheses), which can be produced through additive manufacturing or thermoforming.
Statistical method of extracting assembly stresses in over-constrained solder-less press-fit pin technology for vibration reliability analysis
Authors: Drienovsky Mihai , Marius Pop Daniel , Sorin Nes Cristian , Davidescu Arjana
Published: November 2024

Solderless press-fit technology is increasingly favored over lead-free solder mountings due to cost-effective design benefits amid lead-free regulations. However, its over-constrained nature causes assembly issues and preload stress in pins, leading to fatigue failure under vibration. This paper extends previous research by presenting a method to evaluate the robustness of these assemblies under vibration-induced fatigue, considering assembly-induced stresses as static preload stress. The proposed statistical method uses Monte Carlo simulations to compute the distribution of pin failures due to fatigue, providing a comprehensive analysis that traditional worst-case FEA simulations cannot. This approach aids in identifying worst-case scenarios, predicting failure percentages, ranking designs, and improving design robustness through iterative feedback during the design phase.
Tensile properties of Romanian “Țurcana” sheep wool farm-waste fibers
Authors: Sosdean Corina , Galatanu Sergiu-Valentin
Published: November 2024

With a long tradition in sheep farming, Romania is still one of the major sheep breeding countries in Easter Europe with the “T urcana” sheep breed playing a central role. In recent decades, wool has been increasingly considered waste from the shearing process, yet its potential as a natural, renewable, biodegradable fiber offers opportunities for its use as raw construction material due to its beneficial characteristics and eco-friendly nature. With a focus on reducing environmental impact and optimizing its functionality, this study conducts tensile testing on “T urcana” wool to evaluate its strength and explores the potential of utilizing wool fibres as reinforcement in newly developed composites.
A deep learning-based intelligent method for mining sentiment words in english translation texts
Authors: Li Xiaoli
Published: November 2024

The current conventional sentiment lexicon mining methods mainly achieve lexical extraction by mining the sentiment features of words, which leads to poor mining effect due to the lack of sentiment lexicon construction. In this regard, the intelligent mining method of sentiment lexicon of English translation text based on deep learning is proposed. The intelligent mining algorithm is optimized by extracting lexical templates with generality, constructing sentiment lexicon, and building convolutional network to extract lexical features. The experimental results showed that this mining method had an accuracy of over 85% in mining emotional vocabulary in translated texts, which was higher than other algorithms. Meanwhile, the mining time required for this algorithm was not yet 4.5 min. The above results indicated that the proposed method had higher accuracy and faster speed in mining emotional vocabulary in English translation texts.
Diverse Explanations From Data-Driven and Domain-Driven Perspectives in the Physical Sciences
Authors: Li Sichao , Wang Xin , Barnard Amanda S
Published: November 2024

Machine learning methods have been remarkably successful in material science, providing novel scientific insights, guiding future laboratory experiments, and accelerating materials discovery. Despite the promising performance of these models, understanding the decisions they make is also essential to ensure the scientific value of their outcomes. However, there is a recent and ongoing debate about the diversity of explanations, which potentially leads to scientific inconsistency. This Perspective explores the sources and implications of these diverse explanations in ML applications for physical sciences. Through three case studies in materials science and molecular property prediction, we examine how different models, explanation methods, levels of feature attribution, and stakeholder needs can result in varying interpretations of ML outputs. Our analysis underscores the importance of considering multiple perspectives when interpreting ML models in scientific contexts and highlights the critical need for scientists to maintain control over the interpretation process, balancing data-driven insights with domain expertise to meet specific scientific needs. By fostering a comprehensive understanding of these inconsistencies, we aim to contribute to the responsible integration of eXplainable Artificial Intelligence (XAI) into physical sciences and improve the trustworthiness of ML applications in scientific discovery.
Manipulation and Sexual Consent
Authors: Boonin David
Published: November 2024

This chapter discusses two kinds of case where consent to sex can seem problematic even if no coercion, deception, or incompetence is involved. The first section addresses cases involving positional inequality, like that between a therapist and their patient or between a professor and their student. It provides an explanation of, and a critical response to, David Archard’s argument for the claim that sexual consent is invalid in such cases because it involves a kind of exploitation. This section concludes that sex in such cases may well be wrong for other reasons but rejects the claim that it involves sex without valid consent if no coercion, deception, or incompetence is involved. The second section considers whether offering someone a large amount of money in exchange for sex invalidates the consent that the offer elicits. This section is divided into two parts. The first part explains and argues against the claim that such offers invalidate consent because they are, in effect, so good that they can’t be refused and thus coerce people into accepting them. The second part explains and argues against the claim that such offers invalidate consent because they impair the judgment of the people who receive them and thus leave them unable to competently consent to them. This section concludes that such offers do not invalidate the consent to sex that they elicit.
CP’s Account of Action Understanding and the Deflationary Challenge
Authors: Borg Emma
Published: November 2024

According to common-sense psychology (CP), to understand the actions of others we typically assign them appropriate reasons and reasoning (your jar-reaching behaviour makes sense because I think you want a cookie and believe there is one in the jar). Recently, however, this account has come under significant pressure and many theorists now hold that CP underpins (at best) only a tiny fragment of our understanding of the actions of others. This chapter sets out this challenge, first by clarifying what is involved in CP’s account of action understanding and then by introducing the idea of ‘deflationary’ accounts of action understanding. The chapter then looks at the arguments commonly adduced for the view that mental state attribution, particularly when it involves states like beliefs and desires, must be a highly complex and demanding skill (a skill which is too complex to explain action understanding in animals, infants, or adults under pressure).
Mild behavioural impairment in Parkinson’s disease: a systematic review
Authors: Yu Ruan-Ching , Chan Lung , Chou Szu-Yi , Lin Li-Fong , Hu Chaur-Jong , Hong Chien-Tai
Published: November 2024

Behavioural symptoms are common manifestations of Parkinson’s disease (PD). Early behavioural symptoms characterise mild behavioural impairment (MBI). The prevalence and intensity of MBI in people with PD (PwP) have been studied across various cohorts. However, methodological differences have obscured our understanding of MBI in these individuals. This systematic review examines and synthesises findings from relevant studies, enhancing understanding of the symptoms and implications of MBI in PD. Nine studies from five separate research institutions were identified. The conceptualisation of MBI varied considerably, affecting the reported prevalence rates of MBI in individuals with early-stage PD. Among PwP, MBI was associated higher education and impaired cognition. Affective dysregulation and impulse control disorders were primary contributors to MBI; abnormal perception was least contributor. This systematic review underscores the specific characteristics and incidence of MBI in early-stage PD. Mood and impulse control disorders are primary concerns associated with MBI. Future longitudinal studies are required to clarify the progression of these symptoms and evaluate MBI’s potential as an indicator for PD-related dementia or increased dependency.
“Bridging cultures with love”: Spirituality in fostering intercultural effectiveness. The effects of language
Authors: Wilczewski Michał , Gorbaniuk Oleg , Gut Arkadiusz , Wołońciej Mariusz
Published: November 2024

Research yields contradictory results on the relationship between an individual’s spirituality, that is, the relationship with God/the Transcendent, and their cultural development. To address this gap, we conceptualize a model that investigates the effects of two spirituality dimensions, namely felt love for God and love for others, on the behavioral aspect of intercultural competence, that is, intercultural effectiveness (IE), through ethnocentrism. This model undergoes testing using a sample of 144 international students who self-identify as Christians, Muslims, belonging to other religions, and non-religious. The results confirm the positive impact of spirituality on IE by reducing ethnocentrism. We establish suppressing effects of both love for God and love for others, suggesting intricate dynamics of these two spirituality dimensions within the intercultural communication model. Furthermore, we identify the direct effects of host language and English as a lingua franca proficiency on IE. We also define the mitigating effect of host language proficiency on the adverse impact of ethnocentrism on IE. This study underscores the importance of higher education institutions to nurture students’ relational spirituality and support them in overcoming ethnocentric perspectives.
Institutional escapes, breaks, and continuities: Reframing running away from residential child care institutions
Authors: Bartoszko Aleksandra , Herland Mari D
Published: November 2024

This article offers a novel approach to understand the phenomenon of running away from residential care institutions, challenging prevailing views that pathologize these incidents as individual deviance. Drawing on insights from the sociology of escape and Deleuze and Guattari’s concepts of rhizome and lines of escape, we examine spatial, temporal, and relational dimensions of institutions, revealing the porous nature of institutional boundaries and non-linear characteristics of runaways. By reframing runaways as integral to institutional life rather than isolated events, we argue against reducing them to individual traits. Running away serves as pivotal moments that disrupt and shape institutional norms, highlighting inherent limitations in care. Conceptualizing running away as running-around within the institutional assemblage, we challenge binary inside/outside distinctions and argue that they oversimplify institutional complexity. Our analysis underscores how institutions exert totalizing control through surveillance, while being transformed through acts of running away. Examining the employees’ experiences though five focus group interviews, we critique the conventional perception of institutions as places of care, emphasizing their unbounded and multifaceted social configurations. We discuss how institutional powers shape semiotic systems that govern young people’s behaviour, advocating for a nuanced understanding of residential institutions as rhizomatic formations, where individual actions continually reshape institutional practices and perceptions.
Bivalent RSVpreF Vaccine in Adults 18 to <60 Years Old With High-Risk Conditions
Authors: Davis Matthew , Towner William , DeHaan Elliot , Jiang Qin , Li Wen , Rahman Farah , Patton Michael , Wyper Hayley , Lino Maria Maddalena , Sarwar Uzma N , Majid-Mahomed Zaynah , Mehta Saumil , Howitt William , Cannon Kevin , Kalinina Elena , Cooper David , Swanson Kena A , Anderson Annaliesa S , Gurtman Alejandra , Munjal Iona ,   MONeT Study Team, Almeida Natalia Castillo , Cannon Kevin , Towner William , Davis Joseph , Malkin Elissa , Diemert David , Clark James , Boghara Haresh , Cohen Jonathan , Bailey Mary , Doust Matthew , Carter Michael , Smith William , Onoya Maria , Mehta Saumil , DeAtkine David , Stacey Helen , Howland William , Suplicy Felipe , Dever Michael , Davis Matthew , Mishkin David , Neutel Joel , Hulinsky Ilja , Chaudhry Abid , Juarez Erick , Mauri Monica , Rosen Jeffrey , Howitt William , Klein Terry , Taylor David , Denham Douglas
Published: November 2024

Background

Older individuals and adults with certain chronic or immunocompromising health conditions are at increased risk of severe respiratory syncytial virus (RSV) disease.

Methods

In this phase 3 randomized trial of RSVpreF safety and immunogenicity in 18–59-year-olds at high risk of severe RSV disease, participants were randomized 2:1 to 1 RSVpreF (120 µg) or placebo dose. Primary safety endpoints included reactogenicity events and adverse events (AEs) through 7 days and 1 month after vaccination, respectively, and serious AEs (SAEs) and newly diagnosed chronic medical conditions (NDCMCs) throughout the study. In primary analyses, immunogenicity elicited 1 month after RSVpreF was bridged to a randomly selected subset of ≥60-year-olds receiving RSVpreF from the immunogenicity subset in the pivotal phase 3 RENOIR trial, which demonstrated RSVpreF efficacy. Noninferiority was declared if 95% confidence interval (CI) lower bounds were >.667 (neutralizing titer adjusted geometric mean ratios) and >−10% (seroresponse rate differences) for RSV-A and RSV-B.

Results

Overall, 678 participants received RSVpreF (n = 453) or placebo (n = 225). Most reactogenicity events were mild/moderate; severe events occurred in ≤2.0% of participants overall. AE frequencies were similar in RSVpreF (7.1%) and placebo recipients (7.6%). No vaccine-related SAEs or NDCMCs were reported. One month after RSVpreF administration, noninferiority criteria were met in 18–59-year-olds versus ≥60-year-olds for RSV-A and RSV-B neutralizing titers and seroresponse rates.

Conclusions

RSVpreF was well tolerated with no safety concerns and demonstrated immunobridging to efficacy in 18–59-year-olds at high risk of severe RSV disease versus ≥60-year-olds in whom efficacy was previously demonstrated, supporting use of RSVpreF to prevent RSV-associated disease in this population. NCT05842967.
Use of artificial intelligence to predict outcomes in mild aortic valve stenosis
Authors: Julakanti Raghav R , Padang Ratnasari , Scott Christopher G , Dahl Jordi , Al-Shakarchi Nader J , Metzger Coby , Lanyado Alon , Jackson John I , Nkomo Vuyisile T , Pellikka Patricia A
Published: November 2024

Aims

Aortic stenosis (AS) is a common and progressive disease, which, if left untreated, results in increased morbidity and mortality. Monitoring and follow-up care can be challenging due to significant variability in disease progression. This study aimed to develop machine learning models to predict the risks of disease progression and mortality in patients with mild AS.

Methods and results

A comprehensive database including 9611 patients with serial transthoracic echocardiograms was collected from a single institution across three clinical sites. The data set included parameters from echocardiograms, electrocardiograms, laboratory values, and diagnosis codes. Data from a single clinical site were preserved as an independent test group. Machine learning models were trained to identify progression to severe stenosis and all-cause mortality and tested in their performance for endpoints at 2 and 5 years. In the independent test group, the AS progression model differentiated those with progression to severe AS within 2 and 5 years with an area under the curve (AUC) of 0.86 for both. The feature of greatest importance was aortic valve mean gradient, followed by other valve haemodynamic measurements including valve area and dimensionless index. The mortality model identified those with mortality within 2 and 5 years with an AUC of 0.84 and 0.87, respectively. Smaller reduced-input validation models had similarly robust findings.

Conclusion

Machine learning models can be used in patients with mild AS to identify those at high risk of disease progression and mortality. Implementation of such models may facilitate real-time, patient-specific follow-up recommendations.
Impact of family mutual aid system for personal medical insurance accounts on paediatric patients’ outpatient utilization patterns and costs: a difference-in-differences analysis
Authors: Liu Xinyi , Gao Chunhui , Wei Mingyue , Li Guohong , Fan Xianqun
Published: November 2024

This study explores the effect of the transformation of paediatric healthcare through the implementation of the Family Mutual Aid System (FMAS) for personal medical insurance accounts among paediatric patients at a children’s hospital (Hospital A in Shanghai, China). We conducted a cohort study in the endocrinology department of Hospital A from August 2021 to July 2023 to assess the impact of FMAS enrolment on patients’ annual outpatient visits, annual outpatient expenditures, and the allocation of these costs among the basic medical insurance pooling fund and patients’ out-of-pocket expenses, with a further subdivision into online and offline consultations. Analysis employed a weighted difference-in-differences approach within a fixed-effects model following propensity score matching. The study encompassed 10 975 paediatric patients, divided into those enrolled in FMAS (observation group) and those not (control group). Enrolment in FMAS was associated with a statistically significant increase in annual outpatient visits by an average of 1.107, predominantly attributed to an uptick in offline consultations. Additionally, there was a substantial 38.9% rise in annual outpatient costs. Detailed analysis revealed a 52.5% increase in costs covered by the medical insurance pooling fund, while patients’ out-of-pocket expenses decreased by an average of 69.2%. These findings highlight the beneficial effects of FMAS enrolment on healthcare service utilization and the risk-sharing mechanisms of medical insurance.
One Health bottom-up analysis of the dissemination pathways concerning critical priority carbapenemase- and ESBL-producing Enterobacterales from storks and beyond
Authors: Martínez-Álvarez Sandra , Höfle Ursula , Châtre Pierre , Alonso Carla Andrea , Asencio-Egea María Ángeles , François Pauline , Cardona-Cabrera Teresa , Zarazaga Myriam , Madec Jean-Yves , Haenni Marisa , Torres Carmen
Published: November 2024

Background

‘One Health’ initiatives to tackle the rising risk of antimicrobial resistance (AMR) have flourished due to increasing detection of Enterobacterales producing extended-spectrum beta-lactamases (ESBLs) and carbapenemases (CPs).

Objectives

This study aimed to conduct an in-depth holistic analysis of Escherichia coli (Ec) and Klebsiella pneumoniae (Kp) isolates recovered from landfill-foraging white stork faecal samples and clinical isolates from a nearby hospital.

Methods

Faecal samples (n = 211) were collected from storks foraging at two landfills in Spain. Ec/Kp stork isolates were recovered on selective media and whole-genome sequencing (WGS), together with isolates obtained from the nearby hospital. These genomic data were compared with public genomes from different contexts (clinical, environmental, or animal hubs) to understand global transmission dynamics.

Results

A wide range of blaESBL/blapAmpC (blaCTX-M/blaSHV-12/blaDHA) were detected in 71 stork samples (33.6%), while blaCP (blaKPC/blaNDM/blaOXA-48/blaVIM) were identified in 28 (13.3%) samples. Clonal and plasmid transmissions were evidenced inside and between both landfills. Mapping against 10 624 public Ec/Kp genomes and from those of nearby hospital revealed that identical strains (<10 allelic differences with Ec-ST38/ST131 and Kp-ST512 lineages) and epidemic plasmids (full identity/coverage with IncN/blaKPC-2, IncF/blaKPC-3, IncX3/blaNDM-7, IncL/blaOXA-48) were found from clinical isolates in countries located along the storks’ migration routes.

Conclusions

Storks may be contaminated by bacterial isolates from a likely human origin and become non-human reservoirs of critical genes, which can be dispersed over long distances. Identifying strains/plasmids along the stork’s routes that are identical or closely related to those described here opens new perspectives for large-scale research to understand the AMR transmission dynamics.
In vitro monitoring of drug resistance emergence during stepwise induction of bedaquiline and clofazimine, alone and in combination: a phenotypic and genotypic analysis
Authors: Chen Suting , Shang Yuanyuan , Zheng Jifang , Huo Fengmin , Xue Yi , Zhao Liping , Jiang Guanglu , Chu Naihui , Huang Hairong
Published: November 2024

Objectives

The co-resistance between bedaquiline and clofazimine raises significant concerns, as they are commonly co-administered as core drugs in drug-resistant TB regimens. The present study aimed to monitor drug resistance-associated gene mutations and the phenotypic change in Mycobacterium tuberculosis (Mtb) under a stepwise drug resistance induction in vitro using bedaquiline, clofazimine or combined drugs.

Methods

Drug-resistant Mtb strains were gradually induced in vitro on a drug-containing solid medium with a 2-fold increasing concentration of bedaquiline, clofazimine and their combination. The MIC of the induced drug-resistant Mtb strains was determined. The drug resistance-associated genes, including Rv0678, Rv1979c, atpE and pepQ, were sequenced and analysed.

Results

Unlike exposure to bedaquiline alone or the combination of these two drugs, clofazimine alone resulted in drug resistance gene mutations occurring later, specifically in the fourth round of induction as opposed to the second round of induction. Besides, nucleotide deletion or insertion in Rv0678 was the main mutation type for induction under the two-drug combination, while single-nucleotide polymorphisms (SNPs) in Rv0678 were the major mutation types when induced by bedaquiline or clofazimine alone. Rv0678 mutation happened at a relatively lower bedaquiline concentration exposure alone, while atpE mutation occurred at a higher bedaquiline concentration. Regardless of the drug exposure manner, a strong correlation between bedaquiline MICs and clofazimine MICs was observed in all drug resistance strains.

Conclusions

Combined exposure to bedaquiline and clofazimine developed Rv0678 mutation as early as exposure to bedaquiline alone. However, rather than SNPs, deletion and insertion were the dominant mutation types in dual-drug exposure strain.
SV4GD: a comprehensive structural variation database specially for genetic diseases
Authors: Shi Lei , Zhang Sainan , Li Ying , Li Hailong , Wang Xin , Du Meiyu , Zhang Meiyi , Ke Liyan , Zhang Yueni , Xu Chao , Tan Senwei , Zhang Zitong , Zhang Duoyi , Wang Jiaping , Qi Changlu , Liu Xingwang , Wang Xin , Qian Kai , Cheng Liang , Zhang Xue
Published: November 2024

Structural variations (SVs) contribute to a large extent to genomic diversity and are highly relevant for various human genetic diseases. The sensitivity and specificity of SV identification have significantly improved with the development and widespread application of high-throughput sequencing, making clinical diagnosis and treatment more accurate. Therefore, the SV4GD (Structural Variation for Genetic Diseases, https://bio-computing.hrbmu.edu.cn/SV4GD/), a manually curated database, was constructed to provide a comprehensive, standardized and user-friendly data resource for selective batch browsing, searching, downloading and comparing those genetic disease-relevant SVs. This database compiles 10 305 records of germline structural variants from 58 human neoplastic diseases and 232 non-neoplastic genetic diseases, including 2695 disease-related SVs, and other 7610 pending research SVs detected from patients. SV4GD provides a browser and search engine to query for the detailed information of SVs, human genetic diseases and the clinical information of patients, providing an easy-to-use online tool for clinical and molecular genetics research.
Rfam 15: RNA families database in 2025
Authors: Ontiveros-Palacios Nancy , Cooke Emma , Nawrocki Eric P , Triebel Sandra , Marz Manja , Rivas Elena , Griffiths-Jones Sam , Petrov Anton I , Bateman Alex , Sweeney Blake
Published: November 2024

The Rfam database, a widely used repository of non-coding RNA families, has undergone significant updates in release 15.0. This paper introduces major improvements, including the expansion of Rfamseq to 26 106 genomes, a 76% increase, incorporating the latest UniProt reference proteomes and additional viral genomes. Sixty-five RNA families were enhanced using experimentally determined 3D structures, improving the accuracy of consensus secondary structures and annotations. R-scape covariation analysis was used to refine structural predictions in 26 families. Gene Ontology (GO) and Sequence Ontology annotations were comprehensively updated, increasing GO term coverage to 75% of families. The release adds 14 new Hepatitis C Virus RNA families and completes microRNA family synchronization with miRBase, resulting in 1603 microRNA families. New data types, including FULL alignments, have been implemented. Integration with APICURON for improved curator attribution and multiple website enhancements further improve user experience. These updates significantly expand Rfam’s coverage and improve annotation quality, reinforcing its critical role in RNA research, genome annotation and the development of machine learning models. Rfam is freely available at https://rfam.org.
CRISPRoffT: comprehensive database of CRISPR/Cas off-targets
Authors: Wang Grant , Liu Xiaona , Wang Aoqi , Wen Jianguo , Kim Pora , Song Qianqian , Liu Xiaona , Zhou Xiaobo
Published: November 2024

The CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated protein) programmable nuclease system continues to evolve, with in vivo therapeutic gene editing increasingly applied in clinical settings. However, off-target effects remain a significant challenge, hindering its broader clinical application. To enhance the development of gene-editing therapies and the accuracy of prediction algorithms, we developed CRISPRoffT (https://ccsm.uth.edu/CRISPRoffT/). Users can access a comprehensive repository of off-target regions predicted and validated by a diverse range of technologies across various cell lines, Cas enzyme variants, engineered sgRNAs (single guide RNAs) and CRISPR editing systems. CRISPRoffT integrates results of off-target analysis from 74 studies, encompassing 29 experimental prediction techniques, 368 guide sequences, 226 164 potential guide and off-target pairs and 8840 validated off-targets. CRISPRoffT features off-target data from different CRISPR approaches (knockout, base editing and prime editing) applied under diverse experimental conditions, including 85 different Cas/guide RNA (gRNA) combinations used across 34 different human and mouse cell lines. CRISPRoffT provides results of comparative analyses for individual guide sequences, genes, cell types, techniques and Cas/gRNA combinations under different conditions. CRISPRoffT is a unique resource providing valuable insights that facilitate the safety-driven design of CRISPR-based therapeutics, inform experimental design, advance the development of computational off-target prediction algorithms and guide RNA design algorithms.
iDog: a multi-omics resource for canids study
Authors: Liu Yanhu , Wang Yibo , Sun Jiani , Kong Demian , Zhou Bowen , Ding Mengting , Meng Yuyan , Duan Guangya , Cui Ying , Fan Zhuojing , Zhang Ya-Ping , Zhao Wenming , Tang Bixia
Published: November 2024

iDog (https://ngdc.cncb.ac.cn/idog/) is a comprehensive public resource for domestic dogs (Canis lupus familiaris) and wild canids, designed to integrate multi-omics data and provide data services for the worldwide canine research community. Notably, iDog 2.0 features a 15-fold increase in genomic samples, including 29.55 million single nucleotide polymorphisms (SNPs) and 16.54 million insertions/deletions (InDels) from 1929 modern samples and 29.09 million SNPs from 111 ancient Canis samples. Additionally, 43487 breed-specific SNPs and 530 disease/trait-associated variants have been identified and integrated. The platform also includes data from 141 BioProjects involving gene expression analyses and a single-cell transcriptome module containing data from 105 057 Beagle hippocampus cells. iDog 2.0 also includes an epignome module that evaluates DNA methylation patterns across 547 samples and chromatin accessibility across 87 samples for the analysis of gene expression regulation. Additionally, it provies phenotypic data for 897 dog diseases, 3207 genotype-to-phenotype (G2P) pairs, and 349 dog disease-associated genes, along with two newly constructed ontologies for breed and disease standardization. Finally, 13 new analytical tools have been added. Given these enhancements, the updated iDog 2.0 is an invaluable resource for the global cannie research community.
NCBI RefSeq: reference sequence standards through 25 years of curation and annotation
Authors: Goldfarb Tamara , Kodali Vamsi K , Pujar Shashikant , Brover Vyacheslav , Robbertse Barbara , Farrell Catherine M , Oh Dong-Ha , Astashyn Alexander , Ermolaeva Olga , Haddad Diana , Hlavina Wratko , Hoffman Jinna , Jackson John D , Joardar Vinita S , Kristensen David , Masterson Patrick , McGarvey Kelly M , McVeigh Richard , Mozes Eyal , Murphy Michael R , Schafer Susan S , Souvorov Alexander , Spurrier Brett , Strope Pooja K , Sun Hanzhen , Vatsan Anjana R , Wallin Craig , Webb David , Brister J Rodney , Hatcher Eneida , Kimchi Avi , Klimke William , Marchler-Bauer Aron , Pruitt Kim D , Thibaud-Nissen Françoise , Murphy Terence D
Published: November 2024

Reference sequences and annotations serve as the foundation for many lines of research today, from organism and sequence identification to providing a core description of the genes, transcripts and proteins found in an organism's genome. Interpretation of data including transcriptomics, proteomics, sequence variation and comparative analyses based on reference gene annotations informs our understanding of gene function and possible disease mechanisms, leading to new biomedical discoveries. The Reference Sequence (RefSeq) resource created at the National Center for Biotechnology Information (NCBI) leverages both automatic processes and expert curation to create a robust set of reference sequences of genomic, transcript and protein data spanning the tree of life. RefSeq continues to refine its annotation and quality control processes and utilize better quality genomes resulting from advances in sequencing technologies as well as RNA-Seq data to produce high-quality annotated genomes, ortholog predictions across more organisms and other products that are easily accessible through multiple NCBI resources. This report summarizes the current status of the eukaryotic, prokaryotic and viral RefSeq resources, with a focus on eukaryotic annotation, the increase in taxonomic representation and the effect it will have on comparative genomics. The RefSeq resource is publicly accessible at https://www.ncbi.nlm.nih.gov/refseq.
CAZac: an activity descriptor for carbohydrate-active enzymes
Authors: Lombard Vincent , Henrissat Bernard , Garron Marie-Line
Published: November 2024

The Carbohydrate-Active enZYme database (CAZy; www.cazy.org) has been providing the reference classification of carbohydrate-active enzymes (CAZymes) for >30 years. Based on literature survey, the sequence-based families of CAZymes are enriched with functional data by using the International Union of Biochemistry and Molecular Biology Enzyme Commission (EC) number system. However, this system was not developed to search or compare functional information. To better harness functional information, we have developed CAZac (CAZyme activity descriptor), a multicriterion system that describes CAZymes’ mechanisms, glycosidic bond orientations, subsites and inter-residue connectivities. This new system, implemented for glycoside hydrolases, glycoside phosphorylases, transglycosidases, polysaccharide lyases and lytic polysaccharide monooxygenases allows complex searches in the CAZy database to uncover the evolution of substrate specificity and mechanisms of CAZymes across families.
EPCO-06. DIFFUSE MIDLINE GLIOMAS: FROM CELL CYCLE TO THERAPEUTIC OPPORTUNITIES
Authors: Hains Anastasia , Marques Joana , Chetal Kashish , Junior Carlos Biagi , Gonzalez-Sandoval Adriana , Pillai Renjitha , Gatto Alberto , Sadreyev Ruslan , Filbin Mariella , Van Rechem Capucine
Published: November 2024

The fatal Diffuse Midline Gliomas (DMG) are characterized by an undruggable H3K27M mutation in H3.1 or H3.3. K27M impairs normal development by stalling of differentiation. As replication timing influences gene expression, cell fate, and cellular response to therapeutics, we undertook a multi-omics approach (Repli-seq, cell cycle RNA-seq, single cell RNA-seq) in DMG cells (H3.1K27M and H3.3K27M subgroups) and tumors in comparison to normal brain to gain an appreciation for targetable pathways in DMG. DMG cells presented differential replication timing in each subgroup, which, in turn, correlated with significant differential gene expression including the cholesterol biosynthesis pathway. Consistent with these findings, DMG tumors presented high replication stress and cholesterol biosynthesis pathway signatures. Moreover, DMG cells were specifically vulnerable to an inhibitor of the cholesterol pathway and to a replication stress therapy, singly and in combination. In conclusion, this combinatorial genomics approach revealed insights into therapeutic opportunities for this incurable disease.
EPCO-11. BIASES IN HEALTHY BRAIN SINGLE-CELL DATASETS: FINDING THE BEST COMPARISON FOR GLIOBLASTOMA STUDIES
Authors: Carcanholo Felipe , Simões Renan , Santos Emerson , Malta Tathiane
Published: November 2024

Tumor cells undergo metabolic alterations that support their proliferation and simultaneously modify immune populations, resulting in an immunosuppressive tumor microenvironment. This study aims to compare the metabolic expression of immune cells within the tumor microenvironment to those in a healthy environment. However, there is a lack of single-cell transcriptomic data for normal brain cells, necessitating an analysis of different methods to compare immune cells in tumors with those in a healthy brain. To address this, we explored cell-to-cell metabolic variability using public single-cell RNA-seq (scRNA-seq) data of glioblastoma (n=338564), and from immune cells in the brains of post-mortem individuals (n=14177), fetuses (n=40000), and epilepsy patients (n=466), as well as from immune blood cells (n=329762). We employed ssGSEA to generate activity scores for 70 key metabolic pathways from KEGG for each individual cell. Known marker genes were utilized to identify normal cell populations (macrophages, T cells, oligodendrocytes) in datasets lacking cell type annotations. Our results revealed that blood cells exhibited high metabolic activity in macrophages but showed moderate activity in other cell types. Immune blood cells also demonstrated high oxidative phosphorylation (OXPHOS) but low fatty acid activity. Fetal brain cells displayed a lack of heterogeneity and showed high fatty acid activity with low OXPHOS activity. Brain cells from post-mortem individuals displayed heterogeneity but exhibited low metabolic activity across nearly all cells and pathways. Additionally, the hierarchy of pathway activity differed from the other datasets. Epilepsy data revealed a metabolic activity pattern similar to tumor-infiltrating immune cells, with comparable activity hierarchy and heterogeneity, although the sample size was limited for detailed comparison. Understanding the differences between types of datasets is important to choose the most appropriate comparison, allowing us to observe the metabolic alterations in immune cells caused by glioblastoma and to develop better immunotherapy strategies.
EPCO-20. MUTANT IDH INHIBITORS INDUCE LINEAGE DIFFERENTIATION IN IDH-MUTANT OLIGODENDROGLIOMA
Authors: Spitzer Avishay , Gritsch Simon , Nomura Masashi , Jucht Alexander , Fortin Jerome , Raviram Ramya , Weisman Hannah R , Castro L Nicolas Gonzalez , Druck Nicholas , Chanoch-Myers Rony , Lee John J Y , Mylvaganam Ravindra , Servis Rachel Lee , Fung Jeremy Man , Lee Christine K , Nagashima Hiroaki , Miller Julie J , Arrillaga-Romany Isabel , Louis David N , Wakimoto Hiroaki , Pisano Will , Wen Patrick Y , Mak Tak W , Sanson Marc , Touat Mehdi , Landau Dan A , Ligon Keith L , Cahill Daniel P , Suvà Mario L , Tirosh Itay
Published: November 2024

IDH-mutant gliomas exhibit variable responses to mutant-IDH inhibitor (IDHi) therapy; yet, the molecular mechanisms underlying these responses remain poorly understood. Here, we investigate the cellular underpinnings of response by leveraging single cell/nuclei RNA-sequencing of on-treatment IDH-mutant oligodendroglioma tumor samples resected from three patients who benefited clinically from treatment. We integrate these findings with single cell and bulk RNA-seq data from independent cohorts and experimental models. We find that IDHi treatment promotes robust differentiation towards the astrocytic lineage, accompanied by stem-like cell depletion and reduced proliferation. Notably, NOTCH1 mutations are associated with impaired astrocytic differentiation, potentially negatively impacting response to IDHi. This study unveils the differentiating effects of IDHi on oligodendroglioma cellular hierarchies and identifies a potential genetic marker for optimizing patient selection. Paper was recently published in Cancer Cell (10.1016/j.ccell.2024.03.008).
EPCO-25. TRANSPOSABLE ELEMENTS INDUCE ONCO-EXAPTATION EVENTS IN MALIGNANT ATRX-DEFICIENT GLIOMAS
Authors: Malgulwar Prit Benny , Johnson William E , Dharmaiah Sharvari , Machado Annette A , Barathi Bhargavi Brahmendra , Lu Lina , Singh Anand , Saw Ajay , Danussi Carla , Irwin David , Rai Kunal , Gao Ruli , Huse Jason T
Published: November 2024

Deficiency of ATRX (Alpha Thalassemia/Mental Retardation Syndrome X-linked), a core member of SWI/SNF family chromatin regulator is altered in diffuse gliomas and coexist with IDH1/2 mutations in adults and histone G34R/V alterations in pediatric populations. Loss of ATRX has been associated with global alterations in chromatin accessibility and epigenomics landscape, however, the detail mechanism behind the oncogenic transformation remains elusive. Integrating transcriptomics and in-depth positional epigenome analysis over repetitive DNA sequences in progenitor and tumors models of murine and human gliomas, we describe ATRX-deficient gliomas is fundamentally a disease of altered Transposable Elements (TE’s) and regulates neuronal differentiation and cell motility in gliomas, as validated pharmacologically and genetically. Epigenome assessment reported de-repression of LINE-1 (Long interspersed nuclear elements-1), specifically at Lamina-Associated Domains (LADs) with gain of enhancer histone marks, with association in chromatin loops/topology in ATRX-deficient glioma cells. Moreover, our single cell-RNA seq analysis focusing on TE’s and molecular docking studies in human glioma stem cells demonstrated LINE-1 regulates oncogenic alternative splicing events and neuro-developmental signatures. Expanding the analysis, we identified a subset of evolutionary young regulatory TE’s to play critical role in ATRX-deficient gliomas involved in neuronal differentiation phenotype. To summarize, our cross-species analysis establishes tangible links between ATRX deficiency and multiscale dysregulated 3D-epigenomic architecture that hijack regulates onco-exaptation programs in gliomas. We further discover that enhancer-like TE’s fine-tune the transcriptional program with important clinical implications, that could help in developing treatment options in malignant gliomas.
EPCO-26. LONGITUDINAL SINGLE-CELL ANALYSES IDENTIFY DRIVERS OF GENETIC, EPIGENOMIC, AND CELLULAR EVOLUTION IN IDH-MUTANT GLIOMA
Authors: Johnson Kevin , Spitzer Avishay , Varn Frederick , Nomura Masashi , Garofano Luciano , Chowdhury Tamrin , Anderson Kevin , D’Angelo Fulvio , Bussema Lillian , Gritsch Simon , Oh Young Taek , Moon Hyo-Eun , Paek Sun Ha , Bielle Franck , Laurenge Alice , Stefano Anna-Luisa Di , Mathon Bertrand , Picca Alberto , Sanson Marc , Lipsa Anuja , Hertel Frank , Zhao Zheng , Wang Qianghu , Jiang Tao , Hermes Beth , Sanai Nader , Golebiewska Anna , Niclou Simone , Huse Jason , Yung W K Alfred , Lasorella Anna , Suvà Mario , Iavarone Antonio , Tirosh Itay , Verhaak Roel
Published: November 2024

Despite standard treatment, IDH-mutant gliomas inevitably recur. Previous studies suggest that therapeutic resistance may result from a combination of intratumoral cellular heterogeneity, epigenetic evolution, and acquired genetic alterations. However, how these multilayered molecular features interact to influence the evolutionary paths of IDH-mutant gliomas remains incompletely understood. To chart this evolution, 75 glioma samples were longitudinally collected from 35 patients (n = 13 oligodendroglioma, n = 22 astrocytoma) and profiled using single nucleus RNA sequencing, ATAC sequencing, and bulk DNA sequencing. Analysis of 331,016 nuclei (snRNA) revealed eight tumor microenvironment cell types and five pan-IDH-mutant malignant cellular states. The malignant states were distributed along a cellular hierarchy of stem-like populations (neural progenitor cell-like, oligodendrocyte progenitor cell-like, and undifferentiated) and more differentiated populations (mesenchymal-like and astrocyte-like) with cycling cells enriched in the stem-like populations. Joint open chromatin accessibility data (snATAC) was available for a subset of malignant cells (71,088 nuclei) and state-specific differentially accessible peaks supported that these states are epigenetically encoded. Across both subtypes, higher tumor grade was associated with reduced malignant cell differentiation and increased cycling populations. Between the two time points, we identified that there was a longitudinal increase in the cycling, undifferentiated, and mesenchymal-like populations with a corresponding decrease in the astrocyte-like population. Longitudinal genetic analysis revealed that 19 of 35 tumors acquired at least one of the following genetic alterations: treatment-associated hypermutation, cell cycle alteration, or large changes in copy number alterations. Importantly, tumors that acquired these key genetic alterations demonstrated significant shifts towards reduced differentiation and increased cycling populations while those tumors that did not had more stable malignant profiles. Collectively, our results suggest a common cellular hierarchy across IDH-mutant gliomas with a shift towards reduced differentiation, increased cycling populations during disease progression that is driven by acquired genetic alterations.