bluuebunny/crossref_metadata_2025_split huggingface dataset:
Central Nervous System Complications in Miliary Pulmonary Tuberculosis: A Systematic Review Of Published Case Reports And Case Series
Authors: Garg Ravindra Kumar , Paliwal Vimal Kumar , Srivastava Anand , Garg Rajiv , Bhattacharya Sandeep , Jain Amita , Rizvi Imran 
Published: July 2024

AbstractBackgroundThis systematic review aims to evaluate central nervous system involvement in context of miliary pulmonary tuberculosis.MethodsWe included studies on central nervous system infections associated with miliary pulmonary tuberculosis involving human subjects in any language. Patients with disseminated tuberculosis involving two non-contiguous organs were excluded. Databases searched included PubMed, Scopus, Embase, and Google Scholar. Case reports, case series, and observational studies with confirmed diagnoses were included. The review follows PRISMA guidelines and is registered with PROSPERO (CRD42024542130).ResultsThe review included 158 records describing 161 patients. The mean age was 32.7 years, with 53.4% females. Key comorbid conditions included human immunodeficiency virus positivity (6.8%), immunosuppressive therapy (9.9%), and chronic kidney disease (2.5%). Common clinical features were fever (58.4%), headache or vomiting (41.6%), and altered sensorium (26.7%). Frequent neuroimaging abnormalities were miliary or multiple brain tuberculomas (66.5%), basal exudates (7.5%), vertebral tuberculosis (7.5%), cerebral infarcts (6.8%), and spinal cord tuberculoma or abscess (6.2%). Paradoxical manifestations occurred in one-third of cases, including new or enlarged brain lesions (22.4%) and paradoxical cerebral infarcts (2.5%). Cerebrospinal fluid findings were normal or unavailable in 45.3% of cases. Positive diagnostic tests included smear, culture, polymerase chain reaction, or GeneXpert in 25% of cases, with 5% showing drug resistance. Improvement was seen in 80.8% of patients, while 9.9% either died or did not improve.ConclusionThis review highlights diverse central nervous system involvement in miliary pulmonary tuberculosis, including tuberculous meningitis and spinal cord lesions, with common paradoxical manifestations and significant patient improvement with following treatment.
Autoencoder to Identify Sex-Specific Sub-phenotypes in Alzheimer’s Disease Progression Using Longitudinal Electronic Health Records
Authors: Meng Weimin , Xu Jie , Huang Yu , Wang Cankun , Song Qianqian , Ma Anjun , Song Lixin , Bian Jiang , Ma Qin , Yin Rui 
Published: July 2024

AbstractAlzheimer’s Disease (AD) is a complex neurodegenerative disorder significantly influenced by sex differences, with approximately two-thirds of AD patients being women. Characterizing the sex-specific AD progression and identifying its progression trajectory is a crucial step to developing effective risk stratification and prevention strategies. In this study, we developed an autoencoder to uncover sex-specific sub-phenotypes in AD progression leveraging longitudinal electronic health record (EHR) data from OneFlorida+ Clinical Research Consortium. Specifically, we first constructed temporal patient representation using longitudinal EHRs from a sex-stratified AD cohort. We used a long short-term memory (LSTM)-based autoencoder to extract and generate latent representation embeddings from sequential clinical records of patients. We then applied hierarchical agglomerative clustering to the learned representations, grouping patients based on their progression sub-phenotypes. The experimental results show we successfully identified five primary sex-based AD sub-phenotypes with corresponding progression pathways with high confidence. These sex-specific sub-phenotypes not only illustrated distinct AD progression patterns but also revealed differences in clinical characteristics and comorbidities between females and males in AD development. These findings could provide valuable insights for advancing personalized AD intervention and treatment strategies.
Library size can undermine accurate molecular and phenotypic subtyping in spatial transcriptomics data
Authors: Fisher Natalie C , Malla Sudhir B , Jamieson Nigel B , Dunne Philip D 
Published: July 2024

AbstractIn an era where transcriptomics-based subtyping, phenotyping and mechanistic understanding is increasingly being driven by state-of-the-art spatially resolved transcriptomic (ST) technologies, it is imperative that researchers, journals, and funders do all they can to ensure that as a community we are interpreting these exciting data as accurately as possible with awareness of their limitations. In this short report, we highlight one potential bias in ST data that could undermine accurateinterpretationof transcriptional signatures, providing the field with an opportunity to identify and avoid this issue prior to release of new mechanistic findings. This issue is particularly relevant for platforms that produce some of the most granular and high-resolution spatial information at single cell (and sub-cellular) resolution, with the compromise of a reduced transcriptome panel of genes (Figure 1A).
Discovery and mechanism of K63-linkage-directed deubiquitinase activity in USP53
Authors: Wendrich Kim , Gallant Kai , Recknagel Sarah , Petroulia Stavroula , Führer Siska , Bezstarosti Karel , O’Dea Rachel , Demmers Jeroen , Gersch Malte 
Published: July 2024

AbstractUbiquitin-specific proteases (USPs) are the largest class of human deubiquitinases (DUBs) and comprise its phylogenetically most distant members USP53 and USP54, which are annotated as catalytically inactive pseudo-enzymes. Conspicuously, mutations in the USP domain ofUSP53cause familial intrahepatic cholestasis. Here we report the discovery that USP53 and USP54 are in fact active DUBs with high specificity for K63-linked polyubiquitin. We demonstrate how USP53 patient mutations abrogate catalytic activity, implicating loss of DUB activity inUSP53-mediated pathology. Depletion of USP53 increases K63-linked ubiquitination of tricellular junction components. Assays with substrate-bound polyubiquitin reveal that USP54 cleaves within K63-linked chains, whereas USP53 can deubiquitinate a substrate in a K63-linkage-dependent manner. Biochemical and structural analyses uncover underlying K63-specific S2-ubiquitin-binding sites within their catalytic domains. Collectively, our work revises the annotation of USP53 and USP54, provides chemical reagents and a mechanistic framework to broadly investigate K63-polyubiquitin chain length decoding, and establishes K63-linkage-directed deubiquitination as novel DUB activity.
RNA genome expansion up to 64 kb in nidoviruses is host constrained and associated with new modes of replicase expression
Authors: Neuman Benjamin W. , Smart Alexandria , Vaas Josef , Bartenschlager Ralf , Seitz Stefan , Gorbalenya Alexander E. , Caliskan Neva , Lauber Chris 
Published: July 2024

AbstractPositive-strand RNA viruses of the orderNidoviraleswith genomes larger than ∼20 kb, including the largest known 36.7 kb RNA genome in vertebrate viruses, encode a proofreading exoribonuclease (ExoN). Here, we assemble 76 genome sequences of invertebrate nidoviruses from >500.000 published transcriptome experiments and triple the number of known nidoviruses with >36 kb genomes, including the largest known 64 kb RNA genome. We classify multi-cistronic ExoN-encoding nidoviruses into five groups, according to canonical and non-canonical modes of viral polymerase expression by ribosomes and genome segmentation. The largest group employing the canonical mode comprises invertebrate and vertebrate nidoviruses, including coronaviruses, with genomes ranging from 20-to-36 kb. Four groups with non-canonical expression modes include giant invertebrate nidoviruses with 31-to-64 kb genomes, some of which utilize dual ribosomal frameshifting that we validate experimentally. Thus, expansion of giant RNA virus genomes, the vertebrate/invertebrate host division, and the control of viral replicase expression are interconnected.
Phase I study on the pharmacokinetics of intravaginal, self-administered artesunate vaginal pessaries among women in Kenya
Authors: Mungo Chemtai , Sorgi Katherine , Misiko Brenda , Cheserem Cynthia , Rahangdale Lisa , Githongo George , Ogollah Cirilus , Omoto Jackton , Plesa Mihaela , Zamboni William 
Published: July 2024

AbstractCervical cancer remains a significant global health issue, especially in low- and middle-income countries (LMICs), where access to prevention and treatment is limited and women are at a higher risk of cervical cancer. Artesunate, a widely available drug used to treat malaria, has shown promise in treating human papillomavirus (HPV)-associated anogenital lesions including high-grade cervical precancer, in a recent Phase I studies in the United States. Data on the pharmacokinetics of artesunate following intravaginal use, and its implications on malaria resistance, are lacking.ObjectivesThe primary objective of this study is to investigate the pharmacokinetics of Artesunate (AS) and its active metabolite, dihydroartemisinin (DHA) following intravaginal use at the dosing and frequency intended for cervical precancer treatment. A secondary objective is to assess safety among study participants.MethodsWe are conducting a single-arm, phase I trial with a sample size of 12 female volunteers. Participants will self-administer artesunate vaginal pessaries in the study clinic daily for 5 consecutive days. Participants will have their blood drawn prior to receiving the first dose of artesunate on day one of the study and then will receive 8 blood draws on study day five, prior to artesunate administration and at 15 minutes, 30 minutes, 1 hour, 2 hours, 4 hours, 6 hours, and 8 hours after pessary administration. Pharmacokinetic parameters of artesunate and DHA will be calculated by way of quantitative analysis of with determination of maximum concentration (Cmax), time to Cmax (Tmax), area under the serum concentration versus time curve (AUC), apparent clearance, and elimination half-life (t1/2).
Structural basis for Vipp1 membrane binding: From loose coats and carpets to ring and rod assemblies
Authors: Junglas Benedikt , Kartte David , Kutzner Mirka , Hellmann Nadja , Ritter Ilona , Schneider Dirk , Sachse Carsten 
Published: July 2024

AbstractVipp1 (also known as IM30) is essential in most oxygenic photoautotrophic organisms. It is involved in membrane remodeling and fusion and is critical for thylakoid membrane biogenesis and maintenance. Vipp1 has recently been identified as a member of the ESCRT-III superfamily of membrane remodeling proteins, albeit it still is elusive how Vipp1 interacts with and finally remodels membranes. Here we present a series of cryo-EM structures of cyanobacterial Vipp1 interacting with bacterial membranes: first, we solved seven structures between 5 and 7 Å resolution of three unique helical and four types of stacked-ring assemblies engulfing membranes, and, second, using sub-tomogram averaging, we determined three ∼20 Å resolution structures compatible with previously observed carpet structures at three different membrane curvatures. By analyzing ten additional unique structures of N-terminally truncated Vipp1, we could show that helix α0 is essential for membrane tubulation and forms the membrane anchoring domain of Vipp1. Using a conformation-restrained Vipp1 mutant, we were able to reduce the structural plasticity of Vipp1 assemblies in the presence of lipids and determined two structures of Vipp1 at 3.0 Å resolution, resolving the molecular details of membrane anchoring and intersubunit contacts of helix α0. Our data reveal the molecular details of how Vipp1 interacts with membranes, showing membrane curvature-dependent structural transitions from carpets to rings and rods, some of which are capable of inducing and/or stabilizing high local membrane curvature triggering membrane fusion.SummaryBacterial ESCRT-III family member Vipp1 forms membrane-bound coats, carpets, ring complexes, stacked-ring assemblies and helical tubes capable of internalizing lipids and inducing high membrane curvature.
Structural plasticity of bacterial ESCRT-III protein PspA in higher-order assemblies
Authors: Junglas Benedikt , Hudina Esther , Schönnenbeck Philipp , Ritter Ilona , Heddier Anja , Santiago-Schübel Beatrix , Huesgen Pitter F. , Schneider Dirk , Sachse Carsten 
Published: July 2024

AbstractEukaryotic members of theendosome sorting complex required for transportIII (ESCRT-III) family have been shown to form diverse oligomeric assemblies. The bacterialphage shock protein A(PspA) has recently been identified as a bacterial member of the ESCRT-III superfamily, and monomeric PspA homo-oligomerizes to form large rod-shaped assemblies. As observed for eukaryotic ESCRT-III, PspA forms different tubular assemblies with varying diameters. Using electron cryo-microscopy (cryo-EM), we determined a total of 61 PspA structures and observed in molecular detail how structural plasticity of PspA rods is mediated by conformational changes at three hinge regions in the monomer and by the fixed as well as changing molecular contacts between protomers. Moreover, we reduced and increased the structural plasticity of PspA rods by removing the loop connecting helices α3/α4 and the addition of nucleotides, respectively. Based on our analysis of PspA-mediated membrane remodeling, we suggest that the observed mode of structural plasticity is a prerequisite for the biological function of ESCRT-III superfamily members.SummaryA series of cryo-EM structures of PspA rods with induced diameter modulations reveals the molecular basis of structural plasticity.
Axion dark matter and additional BSM aspects in an extended 2HDM setup
Authors: Arcadi Giorgio , Khan Sarif 
Published: July 2024

We illustrate and discuss the phenomenology of a model featuring a two-Higgs doublet sector augmented by two SU(2) singlet scalars. The gauge symmetry group is extended as well with a U(1)Lμ−Lτ component whose spontaneous breaking leads to the gauge boson which has an important effect in the muon (g−2). A global PQ symmetry is introduced upon its breaking; we have the axion particle which is also dark matter (DM) in our work. In particular, we have focused on type-X and type-II 2HDM models and found out that (g−2) cannot be explained only by the scalar sector for type-II 2HDM mainly due to stringent constraint from b→sγ resulted in MH±>800  GeV. For type-II 2HDM, we can have axion coupling with the gluons which generates the axion potential and possible explanation for the strong CP problem. The proposed model accommodates neutrino masses via the type-I seesaw mechanism with an upper bound on the right-handed neutrino mass 1 GeV (1 TeV) for type-II (type-X) 2HDM due to the presence of Planck scale suppressed operators. Moreover, we also have additional scalars which affect the oblique parameters and hence the W-boson mass which leads us to explain the W-boson mass observed at the CDF-II detector. The most stringent constraints on the masses and quartic couplings come from the perturbativity and potential bound from the below conditions which leads to fine-tuning among the parameters in part of the parameter space. Finally, we discuss the possible detection prospects of the axion DM and the additional gauge boson.

Published by the American Physical Society
2024
Constraining neutrino-DM interactions with Milky Way dwarf spheroidals and supernova neutrinos
Authors: Heston Sean , Horiuchi Shunsaku , Shirai Satoshi 
Published: July 2024

We constrain the neutrino-dark matter cross section using properties of the dark matter density profiles of Milky Way dwarf spheroidal galaxies. The constraint arises from core-collapse supernova neutrinos scattering on dark matter as a form of energy injection, allowing the transformation of the dark matter density profile from a cusped profile to a flatter profile. We assume a standard cosmology of dark energy and cold, collisionless, and non-self-interacting dark matter. By requiring that the dark matter cores do not lose too much mass or overshoot constraints from stellar kinematics, we place an upper limit on the cross section of σν−DM(Eν=15  MeV,mχ≲130  GeV)≈3.4×10−23  cm2 and σν−DM(Eν=15  MeV,mχ≳130  GeV)≈3.2×10−27(mχ1  GeV)2  cm2, which is stronger than previous bounds for these energies. Consideration of baryonic feedback or host galaxy effects on the dark matter profile can strengthen this constraint.

Published by the American Physical Society
2024
When cobweb meets oligopoly
Authors: Zhang Qianqian , Lin Faqin , Wang Xiuqing , Xin Xian 
Published: July 2024

PurposeThe purpose of this paper is to present an oligopolistic version of the cobweb model that departs from the strict assumptions of perfect competition in the traditional cobweb model.Design/methodology/approachIntroducing a model where n identical producers engage in Cournot competition, with output decisions influencing market prices. The paper retains the original assumptions of naive expectations and a linear model where price expectations of Cournot competitors are made simultaneously with production decisions. The investigation focuses on the model's behavior as the number of producers decreases or industry concentration increases. The authors also show empirical evidence when drawing the data from the pig sector in China and the USA.FindingsThe findings indicate that the cobweb model undergoes a transition from divergent to continuous and even convergent as the number of producers decreases or industry concentration increases. The incorporation of costs related to entry and exit from the market contributes to achieving a more stable equilibrium state.Originality/valueThe cobweb model has been primarily studied in an idealized market structure of perfect competition, and the assumptions that they share are not obviously appropriate to many agriculture markets. This study presents an alternative version of the cobweb model in an oligopolistic market that relaxes the strict assumptions of perfect competition. The authors show the dynamics of reduced competitor numbers or increased industry concentration on the convergence of the cobweb model based on subtle variations in parameters.
Robot adoption of family firms: the role of family non-executive directors
Authors: Du Shanzhong , Cao June 
Published: July 2024

PurposeIndustrial robots are of great significance to the long-term development of family firms. Drawing on the lens of the principal–principal conflict, this paper aims to investigate the influence of family non-executive directors on robot adoption in Chinese family firms.Design/methodology/approachThis paper selects the family firms in China from 2011 to 2019 as the sample. Furthermore, the authors manually collected the family non-executive directors and constructed the robot adoption variable utilizing data sourced from the International Federation of Robotics. In brief, this paper constructs a comprehensive framework of the mechanisms and additional tests pertaining to the influence of family non-executive directors on robot adoption.FindingsThis paper finds that family non-executive directors can promote robot adoption in family firms. The underlying mechanism analysis shows that family non-executive directors promote robot adoption by exerting financial and human effects. This paper further finds that the characteristics of family non-executive directors, such as kinship, differential shareholding and excessive directors, affect the role of family non-executive directors. Finally, robot adoption can improve future performance, and the promotional effect is more evident when family members are non-executive directors.Originality/valueThis paper contributes to the related literature from the following two aspects. Firstly, this paper decomposes the types of family directors to understand the role of family non-executive directors, which challenges the assumption that family board members are homogeneous in family firms. Second, this paper expands the research on the factors that influence robot adoption in emerging economies from the micro-enterprise level. In addition, the findings in this paper have managerial implications for family firms to optimize their strategic decisions with the help of the mode of board right allocation.
Artificial intelligence literacy: a proposed faceted taxonomy
Authors: Shiri Ali 
Published: July 2024

Purpose
The purpose of this paper is to propose a taxonomy of artificial intelligence (AI) literacy to support AI literacy education and research.

Design/methodology/approach
This study makes use of the facet analysis technique and draws upon various sources of data and information to develop a taxonomy of AI literacy. The research consists of the following key steps: a comprehensive review of the literature published on AI literacy research, an examination of well-known AI classification schemes and taxonomies, a review of prior research on data/information/digital literacy research and a qualitative and quantitative analysis of 1,031 metadata records on AI literacy publications. The KH Coder 3 software application was used to analyse metadata records from the Scopus multidisciplinary database.

Findings
A new taxonomy of AI literacy is proposed with 13 high-level facets and a list of specific subjects for each facet.

Research limitations/implications
The proposed taxonomy may serve as a conceptual AI literacy framework to support the critical understanding, use, application and examination of AI-enhanced tools and technologies in various educational and organizational contexts.

Practical implications
The proposed taxonomy provides a knowledge organization and knowledge mapping structure to support curriculum development and the organization of digital information.

Social implications
The proposed taxonomy provides a cross-disciplinary perspective of AI literacy. It can be used, adapted, modified or enhanced to accommodate education and learning opportunities and curricula in different domains, disciplines and subject areas.

Originality/value
The proposed AI literacy taxonomy offers a new and original conceptual framework that builds on a variety of different sources of data and integrates literature from various disciplines, including computing, information science, education and literacy research.