bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring methanogenic archaea and their thermal responses in the glacier-fed stream sediments of Rongbuk River Basin, Mt. Everest
Authors: Ma Wei , Lin Miao , Shen Peihua , Chi Hongfei , Zhang Weizhen , Zhu Jingyi , Tian Shaoyi , Liu Pengfei 
Published: November 2024

AbstractGlacier-fed streams (GFS) are emergent sources of greenhouse gas methane, and methanogenic archaea in sediments contribute largely to stream methane emissions. However, little is known about the methanogenic communities in GFS sediments and their key environmental driving factors. This study analyzed stream sediments from the Rongbuk River basin on Mount Everest for methanogenic communities and their temperature responses through anaerobic microcosm incubations at 5°C and 15°C. Diverse methanogens were identified, including acetoclastic, hydrogenotrophic, and methylotrophic types. Substantial methane and CO2production were detected across altitudes and increased significantly at 15°C, with both methane and CO2production rate negatively correlated with altitude. While temperature sensitivity of CO2production but not CH4showed a negative altitude correlation. Methanogens increased substantially over long-term incubation, dominating the archaeal community. At 15°C, the relative abundance of several methanogenic groups was strongly correlated with altitude, with positive correlations observed forMethanomassiliicoccaceaeandMethanoregulaceae, and negative correlations forMethanocellaceaeandMethanotrichaceae, respectively. Besides altitude, factors like phosphorus, C-to-N ratio, and pH also affected methanogenic structure, methane and CO2production, and temperature sensitivities. This study offers new insights into methanogens and methane production in GFS sediments, improving our understanding of GFS carbon cycling and its potential responses to climate change.
A hierarchical multiscale model of forward and backward alpha-band traveling waves in the visual system
Authors: Schwenk Jakob C. B. , Alamia Andrea 
Published: November 2024

AbstractRecent studies have shown that low-frequency oscillations in the cortex are often organized as traveling waves. The dynamical properties of these waves, that span different scales, have been linked to both sensory processing and cognitive functions. In EEG recordings, alpha-band (∼10Hz) traveling waves propagate predominantly in both directions of the occipital-frontal axis, with forward waves being most prominent during visual processing, while backward waves dominate at rest and during sensory suppression. While a previous study has proposed a functional model to explain their generation and propagation, a multi-scale, biologically plausible implementation is still lacking. Here, we present a multi-scale network model with mean-field dynamics that, building on known interlaminar and cortico-cortical projections, reproduces the dynamics of alpha-band traveling waves observed in EEG recordings. We show that scalp-level forward and backward waves can arise from two distinct sub-networks that are connected in infragranular layers at each area. At rest, the network generates spontaneous backward waves and switches to a forward state upon bottom-up sensory stimulation, reproducing the dynamics we observed in EEG recordings in healthy participants.. We then expand our model to a cortico-thalamic network with a parallel feedforward pathway through the pulvinar. Our results show that this pathway biases the cortical dynamics to the forward state and that high pulvinar engagement leads to spontaneous forward waves without external input. This result is in line with previous studies suggesting a key role for the pulvinar in directing information flow in the cortex, and provide a computational basis to investigate the role of the pulvinar in cortical dynamics. In summary, our model provides a biologically plausible architecture for modeling the dynamics of macroscale traveling waves. Importantly, our study bridges the gap between distinct scales by connecting laminar mean-field activity to spatial patterns at the scalp level, providing a biologically grounded and comprehensive view of the generation and propagation of alpha-band traveling waves.
Alternative cGAS signaling promotes herpes simplex encephalitis
Authors: Shmuel-Galia Liraz , Jiang Zhaozhao , Stine Laurel , Cahill Sara , Ng Sze-Ling , Wilson Ruth , Kandasamy Richard Kumaran , Kurt-Jones Evelyn A. , Ramanjulu Joshi M. , Bertin John , Kasparcova Viera , Pesiridis G. Scott , Fitzgerald Katherine A. , Humphries Fiachra 
Published: November 2024

ABSTRACTDuring infection, foreign DNA is sensed by cyclic GMP-AMP synthase (cGAS) leading to the production of cGAMP, STING-dependent type I interferon and proinflammatory cytokine expression, and autophagy. To prevent a response to self-DNA, cGAS activity is tightly regulated. Dysregulation of cGAS underpins interferonopathies, such as Aicardi-Goutières syndrome, as well as Lupus and neurodegenerative diseases like Parkinson’s disease. Thus, cGAS and its product cGAMP are therapeutic targets. However, if cGAS functions independently of cGAMP signaling is undefined. Here, we identified an alternative signaling pathway that cGAS engages independent of cGAMP synthesis. We demonstrate that alternative cGAS signaling promotes hyperexpression of CXCL1 and enhanced neutrophil recruitment that facilitates viral dissemination during herpes simplex encephalitis. Our study is the first report of an alternative cGAS response independent of cGAMP highlighting a previously uncharacterized scaffold function for cGAS.
A novel class of allosteric glucosylceramidase beta 1 correctors that reduce cellular stress and enhance lysosomal function
Authors: Fregno Ilaria , Pérez-Carmona Natalia , Rudinskiy Mikhail , Soldà Tatiana , Bergmann Timothy J. , Ruano Ana , Delgado Aida , Cubero Elena , Bellotto Manolo , García-Collazo Ana María , Molinari Maurizio 
Published: November 2024

AbstractMutations in glucosylceramidase beta 1 (GCase) disrupt the protein’s conformational maturation in the endoplasmic reticulum (ER) and hinder its transport to the lysosome. The intralysosomal accumulation of glucocerebrosides, which are substrates of the GCase enzyme, impairs lysosomal function and is linked to Gaucher disease (GD). GCase mutations also increase the risk of Parkinson’s disease (PD) and Dementia with Lewy Bodies. We used Site-directed Enzyme Enhancement Therapy (SEE-Tx®) technology to design two structurally targeted allosteric regulators (STARs) of GCase. Administration of GT-02287 and GT-02329 to cultured GD patient-derived primary human fibroblasts enhances folding and protects the two most common disease-causing GCase variants, GCaseAsn370Serand GCaseLeu444Pro, from proteasomal degradation. Mechanistically, these treatments facilitate the lysosomal delivery of enzymatically active forms of mutant GCase, leading to improved lysosomal function and reduced cellular stress in GD patient-derived fibroblasts. The findings suggest that the allosteric pharmacologic regulators GT-02287 and GT-02329 hold promise for further development as potential therapeutic agents for GCase-related disorders, including GD, PD and Dementia with Lewy Bodies.
Identification of Novel Modulators of the ALT Pathway Through a Native FISH-Based Optical Screen
Authors: Azeroglu Benura , Khurana Simran , Wang Shih-Chun , Tricola Gianna M. , Sharma Shalu , Jubelin Camille , Cortolezzis Ylenia , Pegoraro Gianluca , Miller Kyle M. , Stracker Travis H. , Lazzerini Denchi Eros 
Published: November 2024

SummaryA significant portion of human cancers utilize a recombination-based pathway, Alternative Lengthening of Telomeres (ALT), to extend telomeres. To gain further insights into this pathway, we developed a high-throughput imaging-based screen named TAILS (Telomeric ALTIn situLocalization Screen), to identify genes that either promote or inhibit ALT activity. Screening over 1000 genes implicated in DNA transactions, TAILS revealed both well-established and novel ALT modulators. We have identified new factors that promote ALT, such as the nucleosome-remodeling factor CHD4 and the chromatin reader SGF29, as well as factors that suppress ALT, including the RNA helicases DDX39A/B, the replication factor TIMELESS, and components of the chromatin assembly factor CAF1. Our data indicate that defects in histone deposition significantly contribute to ALT-associated phenotypes. Based on these findings, we demonstrate that pharmacological treatments can be employed to either exacerbate or suppress ALT-associated phenotypes.
STABIX: Summary statistic-based GWAS indexing and compression
Authors: Schneider Kristen , Walker Simon , Gignoux Chris , Layer Ryan 
Published: November 2024

ABSTRACTGenome-Wide Association Studies (GWAS) are widely used to investigate the role of genetics in disease traits, but the resulting file sizes from these studies are large, posing barriers to efficient storage, sharing, and querying. This issue is especially important for biobanks like the UK Biobank that publish GWAS for thousands of traits, increasing the volume of data that must be effectively managed. Current compression and query methods reduce file sizes and allow for quick genomic position-based queries but do not provide utility for quickly finding loci based on their summary statistics. For example, finding all SNVs in a particular p-value range would require decompressing and scanning the whole file. We propose a new tool, STABIX, which introduces summary-statistic-based queries and improves upon the standard bgzip compression and tabix query tool in both compression ratio and decompression speed. When applied to ten GWAS files from PanUKBB, STABIX created smaller compressed data and indices than tabix for all files, where bgzip and tbi files were an average of 1.2 times the size of STABIX compressed files and indexes. In the same ten files, STABIX per gene decompression was, on average 7x faster than tabix per gene decompression, and achieved faster per gene decompression times for over 99% of nearly 20,000 genes.
Membrane fusion reactions limited by defective SNARE zippering or stiff lipid fatty acyl composition have distinct requirements for Sec17, Sec18, and adenine nucleotide
Authors: Lopes Karina , Orr Amy , Wickner William 
Published: November 2024

AbstractIntracellular membrane fusion is catalyzed by SNAREs, Rab GTPases, SM proteins, tethers, Sec18/NSF and Sec17/SNAP. Membrane fusion has been reconstituted with purified vacuolar proteins and lipids to address 3 salient questions: whether ATP hydrolysis by Sec18 affects its promotion of fusion, whether fusion promotion by Sec17 and Sec18 is only seen with mutant SNAREs or can also be seen with wild-type SNAREs, and whether Sec17 and Sec18 only promote fusion when they work together or whether they can each work separately. Fusion is driven by two engines, completion of SNARE zippering (which does not need Sec17/Sec18) and Sec17/Sec18-mediated fusion (needing SNAREs but not the energy from their complete zippering). Sec17 is required to rescue fusion that is blocked by incomplete zippering, though optimal rescue also needs the ATPase Sec18. ATP is an essential Sec18 ligand, but at limiting Sec17 levels Sec18 ATP hydrolysis also drives release of Sec17 without concomitanttrans-SNARE complex disassembly. At higher (physiological) Sec17 levels, or without ATP hydrolysis, fusion prevails over Sec17 release. Stiff 16:0, 18:1 fatty acyl chain lipids provide an alternative route to suppressing fusion, with entirely wild-type SNAREs and without impediment to zippering. In this case, Sec17 and Sec18 restore comparable fusion with either ATP or a nonhydrolyzable analog. Fusion blocked by impaired zippering can be restored by concentrated Sec17 alone (but not by Sec18), while fusion inhibited by stiff fatty acyl chains is partially restored by Sec18 alone (but not by Sec17). With distinct fusion impediments, Sec18 and Sec17 have both shared roles and independent roles in promoting fusion.SignificanceSec17/SNAP and Sec18/NSF catalyzecis-SNARE complex disassembly through ATP hydrolysis, but also drive fusion itself without ATP hydrolysis. Fusion can be inhibited by either “stiff” fatty acyl chains while allowing full zippering of entirely wild-type SNAREs or by incomplete SNARE zippering. In either case, Sec17 and Sec18 restore full fusion, but with clear differences. With defective zippering, high levels of Sec17 can restore fusion without Sec18. With stiff fatty acyl chains, Sec18 alone can restore fusion but Sec17 alone will not. In both cases, Sec17 and Sec18 are more efficient together. SNARE-dependent membrane fusion thus relies on two energy sources, complete SNARE zippering and interactions with Sec17 and Sec18.
Redesigning quick commerce fresh and short food supply chains: circular economy strategies for sustainable last-mile operations
Authors: Chavhan Rahul , Dutta Pankaj 
Published: November 2024

PurposeFresh and short food supply chains in grocery quick commerce (q-grocery FSFSCs), while valued for swift delivery, face challenges in sustainability, resource efficiency and scalability. This study aims to redesign the last mile of q-grocery FSFSCs by identifying and validating a framework of applicable circular economy (CE) practices. Furthermore, the study assesses the impact of these practices across various sustainability dimensions to understand their level of contribution to sustainable livelihoods and supply chain resilience.Design/methodology/approachThe study employs a multi-phase approach. First, an integrative literature review identifies CE practices and strategies. Second, a survey gathers data on the relationship between these practices and strategies and their impact on sustainability. Third, the framework is validated using the partial least squares structural equation modeling (PLS-SEM) method in WarpPLS 8.0. Finally, k-means cluster analysis in Tableau 2019.4 groups CE practices based on their impact across five sustainability dimensions: environmental, economic, social, resource efficiency and scalability.FindingsThe study validates a framework and identifies high-impact CE practices, such as waste reduction, sustainable packaging, sustainable sourcing, route optimization, sustainable processes and customer convenience. Medium-impact practices include energy efficiency, sustainable fleet, resale and redistribution and information flow. Low-impact practices cover composting, reverse logistics and appropriate storage.Research limitations/implicationsThe findings assist q-grocery companies to adopt CE practices and strategies that support sustainable livelihoods and strengthen supply chain resilience while offering policymakers guidance to promote circularity.Originality/valueThis study is unique in the exploration of the intersection of quick commerce, FSFSCs and CE principles, providing actionable insights for sustainability in the q-grocery industry.
Beyond blueprints: unveiling sustainable housing ambitions – a TAM and EMGB fusion among paraprofessionals in urban construction landscape
Authors: Sharmila Devi R. , Perumandla Swamy 
Published: November 2024

PurposeThis study explores the factors influencing the investment intentions of potential home buyers among paraprofessionals in sustainable housing within urban construction. By combining the technology acceptance model (TAM) and the extended model of goal-directed behavior (EMGB), the research seeks to understand how technological perceptions, personal motivations and behavioral intentions intersect to shape these investment decisions.Design/methodology/approachA quantitative, cross-sectional and descriptive research design was employed in this study. The study surveyed 641 paraprofessionals as potential home buyers in various Indian cities using a multi-stage stratified sampling technique. It incorporated variables from the TAM and EMGB, modifying some aspects to include financial self-efficacy, hedonic motivation and anticipated regret, alongside adding location as a new factor to examine its impact. For data analysis, partial least squares structural equation modeling was utilized. The analysis focused on hypothesis testing to examine the relationships between the constructs of interest. Bootstrap t-values and effect sizes were used to assess these relationships’ significance and magnitude.FindingsThe study found that perceived usefulness and ease of use significantly enhance attitudes toward sustainable homes, while subjective norms have a minimal effect on such investments in India, emphasizing personal rather than societal influences. Financial self-efficacy, anticipated regret and hedonic motivation are key drivers, indicating that economic capacity and the pursuit of a satisfying lifestyle are crucial for investment intentions. Additionally, the importance of location is highlighted, with infrastructural aspects notably affecting sustainable housing appeal. These insights reveal unique dynamics in India’s sustainable housing sector, diverging from trends in developed countries.Originality/valueThe study lies in its unique fusion of the TAM and EMGB specifically tailored to the Indian urban construction context. It introduces financial self-efficacy, hedonic motivation and anticipated regret as novel variables within these frameworks, alongside emphasizing the significant role of location in sustainable housing decisions. This approach offers new insights into the psychological and socioeconomic factors driving sustainable housing investments in developing countries.
Cybersecurity awareness and fear of cyberattacks among online banking users in Malaysia
Authors: Vafaei-Zadeh Ali , Nikbin Davoud , Teoh Kit Yik , Hanifah Haniruzila 
Published: November 2024

PurposeDrawing on protection motivation theory (PMT), this study aims to explore the factors that enhance cybersecurity awareness among online banking users in Malaysia. More specifically, it investigates the influences of perceived vulnerability, perceived severity, technical knowledge, privacy intrusions and privacy awareness on perceived threats and then examines the effects of perceived threats, along with response efficacy and self-efficacy, on cybersecurity awareness, considering the moderating role of fear of cyberattacks.Design/methodology/approachA survey-based research approach was applied, and the hypotheses were tested using a sample of 324 respondents, employing partial least squares structural equation modeling (PLS-SEM).FindingsThe results show that perceived vulnerability, perceived severity, privacy intrusions and privacy awareness significantly influence perceived threats, while technical knowledge does not influence perceived threats. Furthermore, it was found that response efficacy and self-efficacy both enhance cybersecurity awareness, while perceived threats have no influence on it. Finally, our research confirmed the moderating role of fear of cyberattacks in the relationship between self-efficacy and cybersecurity awareness.Practical implicationsFor individuals, the study highlights the significance of fear, privacy awareness and response efficacy in shaping cybersecurity perceptions, paving the way for enhanced and tailored awareness programs. Moreover, the understanding of relationships between perceived threats, response efficacy and self-efficacy empowers individuals to craft personalized risk mitigation strategies, fostering confidence in navigating the digital landscape. Businesses can leverage the insights for informed design of employee training programs and data-driven decision-making in cybersecurity investments. Government entities, recognizing the nuanced relationship between perceived threats and cybersecurity awareness, are encouraged to formulate context-specific policies and foster cross-sector collaboration for comprehensive cybersecurity initiatives.Originality/valueThis research extends PMT by incorporating additional antecedent variables – namely, technical knowledge, privacy intrusions and privacy awareness within the online banking context that have been overlooked thus far. Furthermore, it delves into the unique role of fear of cyberattack as a moderating variable, thereby enhancing our understanding of PMT.
Improved 3D laser point cloud reconstruction for autonomous mobile robot applications by using SVM-R technique
Authors: Singh Mandeep , Nagla K.S. 
Published: November 2024

PurposeIn autonomous mobile robots, high-level accuracy and precision in 3D perception are required for object detection, shape estimation and obstacle distance measurement. However, the existing methods suffer from limitations like inaccurate point clouds, noise in sensor data and synchronization problems between 2D LiDAR and servomotor. These factors can lead to the wrong perception and also introduce noise during sensor registration. Thus, the purpose of this study is to address these limitations and enhance the perception in autonomous mobile robots.Design/methodology/approachA new sensor mounting structure is developed for 3D mapping by using a 2D LiDAR and servomotor. The proposed method uses a support vector machine regression (SVM-R) technique to optimize the waypoints of the servomotor for the point cloud reconstruction process and to obtain a highly accurate and detailed representation of the environment.FindingsThe study includes an analysis of the SVM-R model, including Linear, radial basis function (RBF) and Polynomial kernel. Results show that the Linear kernel performs better with the lowest 3.67 mean absolute error (MAE), 26.24 mean squared error (MSE) and 5.12 root mean squared error (RMSE) values than the RBF and Polynomial kernels. The 2D to 3D point cloud reconstruction shows that the proposed method with a new sensor mounting structure performs better in perception accuracy and achieves an error of 0.45% in measuring the height of the target objects whereas in previous techniques the error was very large.Originality/valueThe study shows the effectiveness of SVM-R in the 3D point cloud reconstruction process and exhibits remarkable performance for object height measurement. Further, the proposed technique is applicable for future advanced visual applications and has a superior performance over the other conventional methods.