bluuebunny/crossref_metadata_2025_split huggingface dataset:
How to infer ocean freezing rates on icy satellites from measurements of ice thickness
Authors: Shibley Nicole C , Lai Ching-Yao , Culberg Riley 
Published: October 2024

ABSTRACT
Liquid-water oceans likely underlie the ice shells of Europa and Enceladus, but ocean properties are challenging to measure due to the overlying ice. Here, we consider gravity-driven flow of the ice shells of icy satellites and relate this to ocean freeze and melt rates. We employ a first-principles approach applicable to conductive ice shells in a Cartesian geometry. We derive a scaling law under which ocean freeze/melt rates can be estimated from shell-thickness measurements. Under a steady-state assumption, ocean freeze/melt rates can be inferred from measurements of ice thickness, given a basal viscosity. Depending on a characteristic thickness scale and basal viscosity, characteristic freeze/melt rates range from around O(10$^{-1}$) to O(10$^{-5}$) mm/yr. Our scaling is validated with ice-penetrating radar measurements of ice thickness and modelled snow accumulation for Roosevelt Island, Antarctica. Our model, coupled with observations of shell thickness, could help estimate the magnitudes of ocean freeze/melt rates on icy satellites.
Revisiting the effect of lens mass models in cosmological applications of strong gravitational lensing
Authors: Harvey-Hawes Christopher , Wiltshire David L 
Published: October 2024

ABSTRACT
Strong gravitational lens system catalogues are typically used to constrain a combination of cosmological and empirical power-law lens mass model parameters, often introducing additional empirical parameters and constraints from high resolution imagery. We investigate these lens models using Bayesian methods through a novel alternative that treats spatial curvature via the non-FLRW timescape cosmology. We apply Markov Chain Monte Carlo methods using the catalogue of 161 lens systems of Chen et al., in order to constrain both lens and cosmological parameters for: (i) the standard $\Lambda$CDM model with zero spatial curvature; and (ii) the timescape model. We then generate large mock data sets to further investigate the choice of cosmology on fitting simple power-law lens models. In agreement with previous results, we find that in combination with single isothermal sphere parameters, models with zero FLRW spatial curvature fit better as the free parameter approaches an unphysical empty universe, $\Omega _{\mathrm{M}0}\rightarrow 0$. By contrast, the timescape cosmology is found to prefer parameter values in which its cosmological parameter, the present void fraction, is driven to $f_{\mathrm{v}0}\rightarrow 0.73$ and closely matches values that best fit independent cosmological data sets: supernovae Ia distances and the cosmic microwave background. This conclusion holds for a large range of seed values $f_{\mathrm{v}0}\in \lbrace 0.1,0.9\rbrace$, and for timescape fits to both timescape and FLRW mocks. Regardless of cosmology, unphysical estimates of the distance ratios given from power-law lens models result in poor goodness of fit. With larger data sets soon available, separation of cosmology and lens models must be addressed.
How do the successive buckling events affect a galaxy bar and stellar disc? Potential observable signatures for spotting the buckling action – I
Authors: Kataria Sandeep Kumar 
Published: October 2024

ABSTRACT
Until now, observations have caught up only a handful of galaxies in ongoing buckling action. Interestingly, N-body simulations over the past several decades show that almost every bar buckles or vertically thickens as soon as it reaches its peak strength during its evolution and leads to box/peanut/x (BPX) shapes. In order to understand the effect of multiple buckling events on the observable properties of galactic bar and disc, we perform an N-body simulation of a Milky Way-type disc. The axisymmetric galaxy disc forms a bar within a Gyr of its evolution and the bar undergoes two successive buckling events. We report that the time-spans of these two buckling events are 220 Myr and 1 Gyr, which have almost similar strengths of the bending modes. As a result of these two buckling events, the full lengths of BPX shapes are around 5.8 and 8.6 kpc, which are around two-thirds of the full bar length at the end of each buckling event. We find that the first buckling occurs at a smaller scale (radius $\lt $3 kpc) with a shorter time-span affecting the larger length-scales of the disc, which is quantified in terms of changes in $m=$2 and $m=$ 4 Fourier modes. While the second buckling occurs at larger scales (radius $\approx$6 kpc) affecting the inner disc the most. Finally, we provide observable kinematic signatures (i.e. quadrupolar patterns of the line-of-sight velocities), which can potentially differentiate the successive buckling events.
Taurine hypomodification underlies mitochondrial tRNATrp-related genetic diseases
Authors: Lu Jia-Li , Dai Yichen , Ji Kunqian , Peng Gui-Xin , Li Hong , Yan Chuanzhu , Shen Bin , Zhou Xiao-Long 
Published: October 2024

Abstract
Escherichia coli MnmE and MnmG form a complex (EcMnmEG), generating transfer RNA (tRNA) 5-carboxymethylaminomethyluridine (cmnm5U) modification. Both cmnm5U and equivalent 5-taurinomethyluridine (τm5U, catalyzed by homologous GTPBP3 and MTO1) are found at U34 in several human mitochondrial tRNAs (hmtRNAs). Certain mitochondrial DNA (mtDNA) mutations, including m.3243A &gt; G in tRNALeu(UUR) and m.8344A &gt; G in tRNALys, cause genetic diseases, partially due to τm5U hypomodification. However, whether other mtDNA variants in different tRNAs cause a defect in τm5U biogenesis remains unknown. Here, we purified naturally assembled EcMnmEG from E. coli. Notably, EcMnmEG was able to incorporate both cmnm5U and τm5U into hmtRNATrp (encoded by MT-TW), providing a valuable basis for directly monitoring the effects of mtDNA mutations on U34 modification. In vitro, several clinical hmtRNATrp pathogenic mutations caused U34 hypomodification. A patient harboring an m.5541C &gt; T mutation exhibited hmtRNATrp τm5U hypomodification. Moreover, using mtDNA base editing, we constructed two cell lines carrying m.5532G &gt; A or m.5545C &gt; T mutations, both of which exhibited hmtRNATrp τm5U hypomodification. Taurine supplementation improved mitochondrial translation in patient cells. Our findings describe the third hmtRNA species with mutation-related τm5U-hypomodification and provide new insights into the pathogenesis and intervention strategy for hmtRNATrp-related genetic diseases.
GWAShug: a comprehensive platform for decoding the shared genetic basis between complex traits based on summary statistics
Authors: Cao Chen , Tian Min , Li Zhenghui , Zhu Wenyan , Huang Peng , Yang Sheng 
Published: October 2024

Abstract
The shared genetic basis offers very valuable insights into the etiology, diagnosis and therapy of complex traits. However, a comprehensive resource providing shared genetic basis using the accessible summary statistics is currently lacking. It is challenging to analyze the shared genetic basis due to the difficulty in selecting parameters and the complexity of pipeline implementation. To address these issues, we introduce GWAShug, a platform featuring a standardized best-practice pipeline with four trait level methods and three molecular level methods. Based on stringent quality control, the GWAShug resource module includes 539 high-quality GWAS summary statistics for European and East Asian populations, covering 54 945 pairs between a measurement-based and a disease-based trait and 43 902 pairs between two disease-based traits. Users can easily search for shared genetic basis information by trait name, MeSH term and category, and access detailed gene information across different trait pairs. The platform facilitates interactive visualization and analysis of shared genetic basic results, allowing users to explore data dynamically. Results can be conveniently downloaded via FTP links. Additionally, we offer an online analysis module that allows users to analyze their own summary statistics, providing comprehensive tables, figures and interactive visualization and analysis. GWAShug is freely accessible at http://www.gwashug.com.
A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain
Authors: Esler Morgan A , Belica Christopher A , Rollie Joseph A , Brown William L , Moghadasi Seyed Arad , Shi Ke , Harki Daniel A , Harris Reuben S , Aihara Hideki 
Published: October 2024

Abstract
SARS-CoV-2 nucleocapsid (N) protein is a structural component of the virus with essential roles in the replication and packaging of the viral RNA genome. The N protein is also an important target of COVID-19 antigen tests and a promising vaccine candidate along with the spike protein. Here, we report a compact stem-loop DNA aptamer that binds tightly to the N-terminal RNA-binding domain of SARS-CoV-2 N protein. Crystallographic analysis shows that a hexanucleotide DNA motif (5′-TCGGAT-3′) of the aptamer fits into a positively charged concave surface of N-NTD and engages essential RNA-binding residues including Tyr109, which mediates a sequence-specific interaction in a uracil-binding pocket. Avid binding of the DNA aptamer allows isolation and sensitive detection of full-length N protein from crude cell lysates, demonstrating its selectivity and utility in biochemical applications. We further designed a chemically modified DNA aptamer and used it as a probe to examine the interaction of N-NTD with various RNA motifs, which revealed a strong preference for uridine-rich sequences. Our studies provide a high-affinity chemical probe for the SARS-CoV-2 N protein RNA-binding domain, which may be useful for diagnostic applications and investigating novel antiviral agents.
MicroEpitope: an atlas of immune epitopes derived from cancer microbiomes
Authors: Li Donghao , Cai Yangyang , Liu Kefan , Lv Dezhong , Zeng Mengqian , Wen Luan , Lv Chongwen , Guo Jiyu , Xu Kang , Ding Na , Li Yongsheng , Xu Juan 
Published: October 2024

Abstract
The majority of human cancers harbor molecular evidence of intratumoral microbiota. Microbiota-derived epitopes as molecular mimics of tumor antigens can bind human leukocyte antigen (HLA), thereby modulating host immunity. However, many questions remain regarding the mechanisms underlying the interactions between microbiota and the host's immune system in cancer. Here, MicroEpitope (http://bio-bigdata.hrbmu.edu.cn/MicroEpitope) was developed to provide and analyze the atlas of microbiota-derived epitopes in cancer. We manually collected available mass spectrometry (MS)-based HLA immunopeptidomes of 1190 samples across 24 cancer types. Alignment was performed against an in-house constructed theoretical library of human and intratumor microbiome encoded proteins, including 1298 bacterial and 124 viral species. Currently, MicroEpitope contains 51 497 bacteria and 767 virus-derived epitopes, mainly originating from Bacillus subtilis, Buchnera aphidicola and human cytomegalovirus. The common immunogenic features of epitopes were calculated, as well as their biochemical properties and the clinical relevance of corresponding bacteria and viruses across cancers. MicroEpitope also provides five analytical tools, and multiple visualization methods to facilitate understanding of the roles of microbiota-derived epitopes in cancer immunity. In summary, MicroEpitope represents a vital resource for investigating HLA-presented immunopeptidomes derived from cancer microbiomes, and could further enable rich insight in tumor antigen prioritization strategies.
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication
Authors: Sanchez-Londono Mariana , Rust Selina , Hernández-Tamayo Rogelio , Gomes-Filho José Vicente , Thanbichler Martin , Randau Lennart 
Published: October 2024

Abstract
Type IV CRISPR–Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) effector complexes are often encoded on plasmids and are proposed to prevent the replication of competing plasmids. The Type IV-A1 CRISPR–Cas system of Pseudomonas oleovorans additionally harbors a CRISPR RNA (crRNA) that tightly regulates the transcript levels of a chromosomal target and represents a natural CRISPR interference (CRISPRi) tool. This study investigates CRISPRi effects of this system using synthetic crRNAs against genome and plasmid sequences. Targeting of reporter genes revealed extended interference in P. oleovorans and Escherichia coli cells producing recombinant CRISPR ribonucleoprotein (crRNP) complexes. RNA sequencing (RNA-seq) analyses of Type IV-A1 CRISPRi-induced transcriptome alterations demonstrated highly effective long-range downregulation of histidine operon expression, whereas CRISPRi effects of dCas9 remained limited to the vicinity of its binding site. Single-molecule microscopy uncovered the localization dynamics of crRNP complexes. The tracks of fluorescently labeled crRNPs co-localized with regions of increased plasmid replication, supporting efficient plasmid targeting. These results identify mechanistic principles that facilitate the application of Type IV-A1 CRISPRi for the regulation of gene expression and plasmid replication.
Effectiveness and Experience of Implementing Digital Interventions to Promote Smoking Cessation Among Adults With Severe Mental Illness: A Systematic Review and Meta-analysis
Authors: Huddlestone Lisa , Shoesmith Emily , Pervin Jodi , Stevens Rosie , Gilbody Simon , Ratschen Elena 
Published: October 2024

Abstract

Introduction
Digital technology is increasingly used to support interventions targeting smoking cessation in people with severe mental illness (SMI). However, little is known about their implementation and effectiveness in this population. We aimed to determine the effectiveness, stakeholder experiences, factors influencing implementation, and quality of reporting of digital interventions for smoking cessation in adults living with SMI.

Methods
Five online bibliographic databases were searched for articles published between December 31, 2000 and January 31, 2023. Studies involving adults accessing treatment for alcohol and substance use disorders, neurocognitive disorders, and terminal illnesses were excluded. Risk of bias was assessed using the Mixed Methods Appraisal Tool. A Mantel–Haenszel random-effects meta-analysis of randomized controlled trials was conducted. Participant experience and intervention implementation were explored using a narrative synthesis. Quality of reporting of interventions was assessed using the Template for Intervention Description and Replication checklist.

Results
Thirty-one studies enrolling 3794 participants were included. Meta-analysis of biochemically verified abstinence at longest follow-up (month 1 to month 6) did not find an overall effect in favour of intervention (risk ratio = 0.66, 95% confidence interval = −0.005 to 1.37). Interventions tailored to people with SMI were perceived as acceptable. Implementation strategies concentrated on overcoming practical challenges at the participant/user level.

Conclusions
No evidence of the effectiveness of digital interventions to support smoking cessation in people with SMI was found. The importance of tailoring interventions to the needs of people with SMI is highlighted. Robust reporting of implementation is required to enhance future efforts to support smoking cessation in adults with SMI.

Implications
The findings of this review add to the emerging evidence on digital interventions to support smoking cessation among people with SMI. We highlight the importance of tailoring interventions to the population, particularly considering the role of mental illness and the side effects of psychotropic medication in the accessibility and usability of digital interventions.
Attenuated melanopsin-mediated post-illumination pupillary response is associated with reduced actigraphic amplitude and mesor in older adults
Authors: Chan Joey W Y , Li Chun-Tung , Chau Steven Wai Ho , Chan Ngan Yin , Li Tim Man-ho , Huang Bei , Tsoh Joshua , Li Shirley X , Chong Kelvin K L , Roecklein Kathryn A , Wing Yun Kwok 
Published: October 2024

Abstract

Study Objectives
This study aimed to explore the relationship between post-illumination pupillary response (PIPR) with sleep and circadian measures in a community sample of healthy older adults.

Methods
Eligible participants were invited to complete a 1 week sleep diary and actigraphy, and provide an overnight urine sample to measure urinary 6-sulfatoxymelatonin (aMT6s). PIPR was defined as the (1) pupil constriction at 6 second poststimulus (PIPR-6s) and (2) for -30s beginning 10 seconds after stimulus (PIPR-30s), normalized as a percentage to the baseline pupil diameter, after 1 second of blue and 1 second of red light stimulus, respectively. The Net-PIPRs were reported by subtracting the PIPR to red stimulus from the PIPR to blue stimulus. The relationship between PIPR metrics to aMT6s and actigraphic rest-activity rhythm parameters was examined by generalized linear models.

Results
A total of 48 participants were recruited (mean age: 62.6 ± 7.1 years, male: 44%). Both Net PIPR-6s and Net PIPR-30s were significantly associated with actigraphic rest-activity amplitude (B = 0.03, p = .001 and B = 0.03, p = .01, respectively) and actigraphic rest-activity mesor (B = 0.02, p = .001 and B = 0.03, p = .004, respectively). Additionally, the Net PIPR-30s were positively associated with overnight aMT6s level (B = 0.04, p = .03) and negatively associated with actigraphic rest-activity acrophase (B = −0.01, p = .004) in the fully adjusted models.

Conclusions
Attenuated PIPR is associated with a reduced actigraphic amplitude and mesor. The reduced retinal light responsivity may be a potential pathway contributing to impaired photic input to the circadian clock and resulted in age-related circadian changes in older adults.
3Digital Humanities
Authors: Roy Dibyadyuti , Deshbandhu Aditya 
Published: October 2024

Abstract
Current conversations around the manifestations of artificial intelligence have led to binary viewpoints that either predict apocalyptic visions of imminent human obsolescence or forthcoming machinic sentience and technological singularity. Amid these polarized perspectives, the materiality of massive digital infrastructures that regularly exploit vulnerable labour forces and the environmental costs driving such emerging forms of digitality are being systematically erased. As a field bridging humanistic enquiry and computational methods, digital humanities finds itself at the epicentre of such debates around the potentials and pitfalls of what artificial intelligence and its futures imply for scholarly and humanistic practices. Therefore, this chapter identifies and reviews interventions from 2023 and early 2024, across both discursive and physical locations, to show how current disciplinary conversations in digital humanities must emerge from both traditional and unconventional sites, which navigate the intersections between artificial and human domains, while emphasizing the provocations and issues that will shape the future of the field.
New theropod dinosaur remains from the Upper Cretaceous of the Kem Kem Group (Eastern Morocco) clarify spinosaurid morphology
Authors: Lacerda Mauro B S , Isasmendi Erik , Delcourt Rafael , Fernandes Marcelo A , Hutchinson John R 
Published: October 2024

AbstractThe Kem Kem Group is a lowermost lithostratigraphic unit from the Upper Cretaceous that extends along the border between Algeria and Morocco, in the northern region of Africa. This geological unit has yielded several tetrapod fossils, including a well-represented assemblage of theropod dinosaurs, after more than eight decades of research. Here, we report new occurrences of spinosaurid theropods from the spinosaurine clade in the Kem Kem Group by providing anatomical descriptions and taxonomic identifications of 11 new specimens derived from the Tafilalt region of Morocco. Among the findings, we describe a cervical vertebra of Sigilmassasaurus, in addition to several cranial, axial, and appendicular elements that can safely be attributed to Spinosaurinae. Moreover, based on a unique combination of characteristics, we also describe an isolated and partial ischium belonging to an indeterminate carcharodontosaurid. We also deliver a detailed redescription of one of the most complete snouts of a spinosaurine known to date. Therefore, the theropod dinosaurs of the Kem Kem Group show considerable diversity, but many questions, especially related to the diversity of spinosaurids and the general abundance of carnivorous dinosaurs in this region, remain unclear until new materials are discovered and complete descriptions are made.
Overexpression of CPT1A disrupts the maintenance and regenerative function of muscle stem cells
Authors: Qiu Jiamin , Yue Feng , Kim Kun Ho , Chen Xiyue , Khedr Mennatallah A. , Chen Jingjuan , Gu Lijie , Ren Junxiao , Ferreira Christina R. , Ellis Jessica , Kuang Shihuan 
Published: October 2024

AbstractThe skeletal muscle satellite cells (SCs) mediate regeneration of myofibers upon injury. As they switch from maintenance (quiescence) to regeneration, their relative reliance on glucose and fatty acid metabolism alters. To explore the contribution of mitochondrial fatty acid oxidation (FAO) pathway to SCs and myogenesis, we examined the role of carnitine palmitoyltransferase 1A (CPT1A), the rate‐limiting enzyme of FAO. CPT1A is highly expressed in quiescent SCs (QSCs) compared with activated and proliferating SCs, and its expression level decreases during myogenic differentiation. Myod1Cre‐driven overexpression (OE) of Cpt1a in embryonic myoblasts (Cpt1aMTG) reduces muscle weight, grip strength, and contractile force without affecting treadmill endurance of adult mice. Adult Cpt1aMTG mice have reduced number of SC, impairing muscle regeneration and promoting lipid infiltration. Similarly, Pax7CreER‐driven, tamoxifen‐inducible Cpt1a‐OE in QSCs of adult muscles (Cpt1aPTG) leads to depletion of SCs and compromises muscle regeneration. The reduced proliferation of Cpt1a‐OE SCs is associated with elevated level of acyl‐carnitine, and acyl‐carnitine treatment impedes proliferation of wildtype SCs. These findings indicate that aberrant level of CPT1A elevates acyl‐carnitine to impair the maintenance, proliferation and regenerative function of SCs.