bluuebunny/crossref_metadata_2025_split huggingface dataset:
Independence of Centromeric and Pericentromeric Chromatin Stability on CCAN Components
Authors: Biggs Ronald J. , Sundararajan Kousik , Sun Mingxuan , Hendrix Eline , Straight Aaron F. , Marko John F. 
Published: December 2024

AbstractThe chromatin of the centromere provides the assembly site for the mitotic kinetochore that couples microtubule attachment and force production to chromosome movement in mitosis. The chromatin of the centromere is specified by nucleosomes containing the histone H3 variant CENP-A. The constitutive centromeric-associated network (CCAN) and kinetochore are assembled on CENP-A chromatin to enable chromosome separation. CENP-A chromatin is surrounded by pericentromeric heterochromatin and bound by the sequence specific binding protein CENP-B. We performed mechanical experiments on mitotic chromosomes while tracking CENP-A and CENP-B to observe the centromere’s stiffness and the role of the CCAN. We degraded CENP-C and CENP-N using auxin-inducible degrons, which we verified compromises the CCAN via observation of CENP-T loss. Chromosome stretching revealed that the CENP-A domain does not visibly stretch, even in the absence of CENP-C and/or CENP-N. Pericentromeric chromatin deforms upon force application, stretching approximately 3-fold less than the entire chromosome. CENP-C and/or CENP-N loss has no impact on pericentromere stretching. Chromosome-disconnecting nuclease treatments showed no structural effects on CENP-A. Our experiments show that the core-centromeric chromatin is more resilient and likely mechanically disconnected from the underlying pericentromeric chromatin, while the pericentric chromatin is deformable yet stiffer than the chromosome arms.
Promoting helmet usage in undergraduates with electric and non-electric bicycles and scooters: a single-site survey and intervention
Authors: Dorsey Alanna , Li Gabrielle , Cha Spencer , Ritter Victor , Flao Enora Le , Camarillo David B. 
Published: December 2024

AbstractCollege students report alarmingly low helmet usage while riding bikes and other open-wheeled forms of transportation (OWTs), increasing risk of brain injury and skull fracture. Despite prior interventions, this problem persists, necessitating an updated examination of the current barriers to helmet usage, and how to effectively mitigate them. This study aimed to determine the effect of class year on helmet usage in American college students, and explore emerging trends with electric bikes, skateboards, and scooters. We created and distributed an online survey to undergraduate students at Stanford University in California (N = 400) who regularly used electric or non-electric bikes, skateboards, or scooters. This survey collected information on helmet usage, attitudes on bike safety, and demographics, and the findings were used to design a pilot intervention. Students who regularly wore helmets were recruited as peer agents (N=3) and were trained to ask friends and classmates to pledge to wear a helmet. We observed bike, scooter, and skateboard rides (N = 4885), and followed up with students who pledged to analyze their behavior change. We confirmed prior trends that most college students never or rarely wear a helmet, and the most common reasons for not wearing a helmet were “Helmets mess up my hair” (44%), “I don’t see others wearing helmets” (43%), and “It’s unlikely I will fall/crash” (34%). We also found that helmet usage was similarly low (48% of participants reported never wearing a helmet) across class years, but class years reported different reasons for not wearing a helmet. Lastly, there was no difference in helmet usage between electric and non-electric OWT users for any of the frequency categories (p=0.43 for daily, p=0.44 for a few times a week, p=0.77 for a few times a month, p=0.23 for rarely, p=0.15 for never), revealing that previous trends in helmet behavior also apply to American college students with electric OWTs. The pilot intervention resulted in a non-significant yet positive trend, and students who pledged demonstrated a behavior change (as measured by follow-up surveys about helmet usage) that persisted 3 weeks after the conclusion of the intervention. In addition to finding that past trends about helmet behavior in college students are still present, we discovered new trends on electric OWTs and class years in American college students. We also found that our peer agent program shows promise in modifying the behavior of college students.
Spatial Perturb-Seq: Single-Cell Functional Genomics within Intact Tissue Architecture
Authors: Shen Kimberle , Seow Wan Yi , Keng Choong Tat , Shern Daryl Lim , Guo Ke , Meliani Amine , Hajis Irfan Muhammad Bin , Chen Kok Hao , Chew Wei Leong 
Published: December 2024

AbstractWe develop Spatial Perturb-Seq, anin vivoCRISPR technology that interrogates multiple genes within single cells of intact tissues. We apply Spatial Perturb-Seq to screen risk genes for neurodegenerative diseases in the mouse brain, uncovering cell autonomous and cell-cell microenvironmental effects within the spatially intact tissue. Spatial Perturb-Seq functionally screens multiple genesin situandin vivo, identifying candidate genes underlying dysregulated neuronal intercellular communication pathways in Lrp1 signalling and ephrin-Eph receptor interactions.
Accurate and fast segmentation of filaments and membranes in micrographs and tomograms with TARDIS
Authors: Kiewisz Robert , Fabig Gunar , Conway Will , Johnston Jake , Kostyuchenko Victor A. , Bařinka Cyril , Clarke Oliver , Magaj Magdalena , Yazdkhasti Hossein , Vallese Francesca , Lok Shee-Mei , Redemann Stefanie , Müller-Reichert Thomas , Bepler Tristan 
Published: December 2024

AbstractIt is now possible to generate large volumes of high-quality images of biomolecules at near-atomic resolution and in near-native states using cryogenic electron microscopy/electron tomography (Cryo-EM/ET). However, the precise annotation of structures like filaments and membranes remains a major barrier towards applying these methods in high-throughput. To address this, we present TARDIS (Transformer-basedRapidDimensionlessInstanceSegmentation), a machine-learning framework for fast and accurate annotation of micrographs and tomograms. TARDIS combines deep learning for semantic segmentation with a novel geometric model for precise instance segmentation of various macromolecules. We develop pre-trained models within TARDIS for segmenting microtubules and membranes, demonstrating high accuracy across multiple modalities and resolutions, enabling segmentation of over 13,000 tomograms from the CZI Cryo-Electron Tomography data portal. As a modular framework, TARDIS can be extended to new structures and imaging modalities with minimal modification. TARDIS is open-source and freely available athttps://github.com/SMLC-NYSBC/TARDIS, and accelerates analysis of high-resolution biomolecular structural imaging data.
Phosphatidylinositol-3,5-bisphosphate mediated vacuolar morphology modulation is integral to ethanol stress response
Authors: Mandal Pritha , Hazra Babai , Ghosh Trisha , Patra Nabanita , Sarkar Srimonti 
Published: December 2024

ABSTRACTVacuoles enlarge in response to ethanol. We used quantitative imaging to show that even brief exposure to ethanol causes a rapid transition from multilobed vacuoles to a single compartment. Vacuole unlobing is essential as mutants restricted for vacuole fusion exhibit greater ethanol sensitivity. This response involves the inhibition of vacuole fission via downregulation of the activity of Fab1, a lipid kinase generating the signaling lipid phosphatidylinositol-3,5-bisphosphate. Ethanol exposure results in the redistribution of a phosphatidylinositol-3,5-bisphosphate sensor from the perivauolar dots to the cytoplasm and the dissociation of the effector of this lipid, Atg18, from the vacuolar membrane to the cytoplasm. Impaired Atg18 membrane recruitment also entails a loss of interaction between a scaffold of the Fab1 complex, Vac14, and Atg18. A hyperactive Fab1 mutant, with elevated pools of phosphatidylinositol-3,5-bisphosphate, shows delayed vacuole enlargement; the partial relocation of the phosphatidylinositol-3,5-bisphosphate probe to the perivacuolar dots and of Atg18 to the vacuole membrane. Since Atg18 is responsible for vacuole fragmentation, our results show that, under ethanol stress, cells actively regulate vacuole morphology by modulating phosphatidylinositol-3,5-bisphosphate levels.
Neuronal activation in the axolotl brain promotes spinal cord regeneration
Authors: Walker SE , Yu K , Burgess S , Echeverri K 
Published: December 2024

AbstractThe axolotl retains a remarkable capacity for regenerative repair and is one of the few vertebrate species capable of regenerating its brain and spinal cord after injury. To date, studies investigating axolotl spinal cord regeneration have placed particular emphasis on understanding how cells immediately adjacent to the injury site respond to damage to promote regenerative repair. How neurons outside of this immediate injury site respond to an injury remains unknown. Here, we identify a population of dpErk+/etv1+glutamatergic neurons in the axolotl telencephalon that are activated in response to tail amputation. Importantly, the activation of these neurons facilitates successful tail regeneration by promoting axon extension into the newly regenerated tissue. We demonstrate that these dpErk+neurons extend axons into the hypothalamus, which has a well-established role in hormone production. Furthermore, these neurons upregulate the neuropeptide neurotensin in response to injury, which in turn stimulates the production of multiple hormones in the hypothalamus to promote regenerative repair. Together, these findings identify a unique population of neurons in the axolotl brain whose activation is necessary for successful spinal cord regeneration, and sheds light on how neurons outside of the immediate injury site respond to a spinal cord injury.
Pulmonary fibroblast activation duringAspergillus fumigatusinfection enhances lung defense via immunomodulation and tissue remodeling
Authors: Guirao-Abad José P. , Shearer Shannon M. , Bowden Jon , Kasprovic Daniel A. , Grisham Christina , Ozdemir Mustafa , Tranter Michael , Wang Yunguan , Askew David S. , Kanisicak Onur 
Published: December 2024

ABSTRACTAspergillus fumigatusis the etiologic agent of invasive aspergillosis, a life- threatening fungal pneumonia that is initiated by the inhalation of conidia (spores) into the lung. If the conidia are not cleared, they secrete large quantities of hydrolytic enzymes and toxins as they grow, resulting in extensive damage to pulmonary tissue. Stromal fibroblasts are central responders to tissue damage in many organs, but their functional response to pulmonary injury caused byA. fumigatushas not been explored. In this study, we employed cell lineage tracing, targeted cell ablation, and single-cell RNA sequencing to monitor the dynamics of fibroblast behavior upon exposure toA. fumigatusin both immunocompetent and immunosuppressed hosts. The results demonstrate that a subset of pulmonary fibroblasts becomes activated in an immunocompetent host in response to a challenge withA. fumigatusconidia, acquiring a gene expression program reflecting the acquisition of new immunomodulatory properties as well as enhanced extracellular matrix (ECM)-secreting ability. Remarkably, through targeted ablation of fibroblasts that express the profibrotic activation marker periostin, we demonstrate that the progression of an invasiveA. fumigatusinfection in an immunosuppressed host is accelerated by the absence of periostin lineage cells and is accompanied by severe alveolar hemorrhage and angioinvasion. These findings uncover a novel protective role for fibroblasts in limiting the severity ofA. fumigatus-induced pulmonary injury and emphasize the importance of the pulmonary stroma in host defense against this invasive fungal infection.
Supervised non-negative matrix factorization on cell-free DNA fragmentomic features enhances early cancer detection
Authors: Tran Trung Hieu , Pham Ngoc Tan , Nguyen Van Thien Chi , Vo Dac Ho , Nguyen Thi Hue Hanh , Tran Thi Trang , Tran Thanh Truong , Vo Truong Dang Huy , Dao Thi Huyen , Nguyen Huu Tam Phuc , Phan Thi Van , Ha Thi Minh Thi , Ngo Thi Dieu Huong , Tran Nhat Huy , Tran Nhat-Thang , Hoang Thanh Quang , Nguyen Viet Binh , Le Van Cuong , Nguyen Xuan Chung , Nguyen Thi Minh Phuong , Nguyen Van Hung , Tran Nu Thien Nhat , Dang Thi Ngoc Quynh , Tran Manh Hoang , Nguyen Phuc Nguyen , Pham Thi Anh Tuyet , Vo Duy Long , Doan Thuy Nguyen , Nguyen Viet Hai , Tran Quang Dat , Dang Quang Thong , Ho Le Minh Quoc , Nguyen Vu Tuan Anh , Nguyen Sao Trung , Nguyen Hoai-Nghia , Tran Le Son , Giang Hoa , Phan Minh-Duy , Nguyen Trong Hieu 
Published: December 2024

AbstractBackgroundCell-free circulating DNA (cfDNA) fragments exhibit non-random patterns in their length (FLEN), end-motif (EM), and distance to nucleosome position (ND). While these cfDNA features have shown promise as inputs for machine learning and deep learning models in early cancer detection, most studies utilize them as raw inputs, overlooking the potential benefits of pre-processing to extract cancer-specific features. This study aims to enhance cancer detection accuracy by developing a novel approach to feature extraction from cfDNA fragmentomics.MethodsWe implemented a supervised non-negative matrix factorization (SNMF) algorithm to generate embedding vectors capturing cancer-specific signals within cfDNA fragmentomic features. These embeddings served as input for a machine learning model to classify cancer patients from healthy individuals.ResultsWe validated our framework using two datasets: an in-house cohort of 431 cancer patients and 442 healthy individuals (dataset 1), and a published cohort comprising 90 hepatocellular carcinoma (HCC) patients and 103 individuals with cirrhosis or hepatitis B (dataset 2). In dataset 1, we achieved an AUC of 94% in pan-cancer detection. In dataset 2, our framework achieved an AUC of 100% for HCC vs healthy classification, 99% for HCC vs non-HCC patients classification, and 96% for identifying HCC patients among a mixed group of non-HCC patients and healthy donors.ConclusionThis study demonstrates the efficiency of SNMF-transformed features in improving both pan-cancer detection and specific HCC detection. Our approach offers a significant advancement in leveraging cfDNA fragmentomics for early cancer detection, potentially enhancing diagnostic accuracy in clinical settings.
Candida albicans: a comprehensive view of the proteome
Authors: Gomez-Artiguez Leticia , de la Cámara-Fuentes Samuel , Sun Zhi , Hernáez María Luisa , Borrajo Ana , Pitarch Aída , Molero Gloria , Monteoliva Lucía , Moritz Robert L. , Deutsch Eric W. , Gil Concha 
Published: December 2024

ABSTRACTWe describe a new release of theCandida albicansPeptideAtlas proteomics spectral resource (build 2024-03), providing a sequence coverage of 79.5% at the canonical protein level, matched mass spectrometry spectra, and experimental evidence identifying 3382 and 536 phosphorylated serine and threonine sites with false localization rates of 1% and 5.3%, respectively. We provide a tutorial on how to use the PeptideAtlas and associated tools to access this information. TheC. albicansPeptideAtlas summary web page provides “Build overview”, “PTM coverage”, “Experiment contribution”, and “Dataset contribution” information. The protein and peptide information can also be accessed via theCandidaGenome Database via hyperlinks on each protein page. This allows users to peruse identified peptides, protein coverage, post-translational modifications (PTMs), and experiments identifying each protein. Given the value of understanding the PTM landscape in the sequence of each protein, a more detailed explanation of how to interpret and analyse PTM results is provided in the PeptideAtlas of this important pathogen.Candida albicansPeptideAtlas web page:https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=578
A fully contained sample holder capable of electron-yield detection at soft X-ray energies
Authors: Gunther S. Olivia , Smith Patrick W. , Branson Jacob A. , Ditter Alexander S. , Minasian Stefan G. , N'Diaye Alpha T. , Schacherl Bianca , Shuh David K. 
Published: December 2024

A holder has been developed that enables electron yield-detected soft X-ray spectroscopy of fully contained samples at low temperature. Crucially, this design uses elements of the sample containment to collect ejected electrons, removing the need to expose samples directly to the vacuum environment of the spectrometer. The design is modular and should be adaptable to a number of different endstation configurations, enabling spectroscopy of air-sensitive, radioactive and vacuum-sensitive (biological) samples.
Intention to engage in inter-contractor cooperation: a belief elicitation study in the construction industry
Authors: Moshood T.D. , Ling Yee Voon , Chai Changsaar , Lee Chia Kuang 
Published: December 2024

PurposePartnering has been introduced to the construction field to improve project delivery efficiency. However, little research outlines the factors influencing the intention to form partnerships. This paper aims to investigate the relationships between attitude, subjective norm perceived behavioural control (PBC) and intention to form partnering, as well as to elicit behavioural, normative and control beliefs regarding partnering formation. The study also examines the relationships between these beliefs and their respective constructs within the Theory of Planned Behavior (TPB) framework.Design/methodology/approachIn order to achieve these objectives, a two-stage approach was employed. First, a belief elicitation study (BES) involving 20 construction industry professionals was conducted to elicit salient beliefs. Subsequently, a TPB survey was administered to 99 contractors from grades G4 to G7. Partial Least Square analysis assessed the factors influencing the intention to form partnering.FindingsThe results supported six hypotheses, while six others were unsupported. Perceived usefulness significantly influenced attitude towards intention to form partnering, followed by attitude itself, which also significantly influenced intention. The project management team and sole proprietors had significant effects on the subjective norms, while facilitating conditions and consensus on appropriation significantly affected PBC.Practical implicationsThis research contributes to the existing literature by providing empirical evidence on the role of intention in partnering formation. Moreover, by applying the BES, this research extends the TPB model of intention to form partnering in construction projects, offering valuable insights for future research and practice.Originality/valueThis study investigates the relationships between attitude, subjective norm PBC and intention to form partnering, as well as to elicit behavioural, normative and control beliefs regarding partnering formation. The study also examines the relationships between these beliefs and their respective constructs within the TPB framework.
The impact of quality management systems on organizational resilience
Authors: Al Balushi Mohammed 
Published: December 2024

PurposeFor decades, quality management systems (QMS) have played an important role in the performance of organizations. Yet, with the unprecedented uncertainty surrounding the business environment, organizational resilience has become vital for business continuity. As organizations need to ensure both high performance and resilience, this paper aims at investigating how ISO 9001 implementation impacts organizational resilience.Design/methodology/approachThe research deploys a qualitative methodology, with an outsider–insider approach. 32 semi-structured interviews were conducted, plus one final reflective interview. Interview questions dealt with resilience constructs: problem identification and prioritization, resource mobilization, organizational learning, sensemaking, self-organization, creativity and innovation, entrepreneurial spirit, mindfulness and coupling. The questions also dealt with how ISO 9001 implementation impacted each construct of organizational resilience.FindingsThe results show that ISO 9001 implementation enhanced resilience, mainly by promoting process-orientation and ensuring consistent practice of risk management across the organization. The results also suggest that at a certain point, when units became very highly process-oriented, ISO impact faded or disappeared as units had already been beyond that level before ISO implementation. This indicates a significant role played by the organizational structure when it comes to both ISO 9001 implementation and organizational structure.Originality/valueThis study is unique as it is the first – within the reviewed literature – to examine how a QMS, in particular ISO 9001, impacts firm’s ability to overcome adverse conditions. It also highlights the fundamental role the organizational structure plays to both effectively implement ISO 9001 and enhance organizational resilience.
Understanding criminogenic features: case studies of cryptocurrencies-based financial crimes
Authors: Carletti Rossella , Luo Xiaojun , Adelopo Ismail 
Published: December 2024

Purpose
This paper aims to comprehensively examine the intricate relationship between cryptocurrency and criminal enterprises, shedding light on the methods, mechanisms and implications of cryptocurrency use in various financial crimes.

Design/methodology/approach
This paper conducts a thematic analysis of 51 cryptocurrency-related financial crime cases to identify criminogenic features of cryptocurrencies, key tools and features of cryptocurrency-related financial crimes. Based on the case study, policy-changing recommendations and big-data analytics tools are proposed for law enforcement agencies to combat cryptocurrency crimes.

Findings
This study found that decentralisation, pseudo-anonymity and borderless nature of cryptocurrencies enable cross-border financial flows and make transaction tracking a complex challenge. Popularity and market capitalisation used to play a dominant role in criminals’ choice of cryptocurrency as Bitcoin was associated with most cryptocurrency-related crimes before 2019. An increasing number of other cryptocurrencies, such as privacy coins and stablecoins, have been utilised for financial crimes recently. Cryptocurrency has also become an essential source of terrorist financing.

Research limitations/implications
Due to the open access to cryptocurrency transaction data, powerful big-data analytics tools should be developed to help law enforcement departments proactively detect cryptocurrency-related crimes.

Practical implications
It is important and urgent for cryptocurrency exchange companies, mixing services and wallet providers to implement strict anti-money laundering and know-your-customer measures to help combat cryptocurrency-related crimes and create a sustainable future for cryptocurrencies.

Originality/value
There is a lack of studies to reveal the current trend of cryptocurrency crimes; the relationship between criminogenic features of cryptocurrency and types of financial crimes; as well as the approaches used to facilitate different types of cryptocurrency-related financial crimes. These gaps will be addressed through thematic analysis on 51 crypto crime cases.