bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic analysis of meiotic genes during the mitosis-to-meiosis transition inDrosophilafemales
Authors: Vallés Ana Maria , Rubin Thomas , Macaisne Nicolas , Toe Laurine Dal , Molla-Herman Anahi , Antoniewski Christophe , Huynh Jean-René 
Published: July 2024

AbstractGermline cells produce gametes, which are specialized cells essential for sexual reproduction. Germline cells first amplify through several rounds of mitosis before switching to the meiotic program, which requires specific sets of proteins for DNA recombination, chromosome pairing and segregation. Surprisingly, we previously found that some proteins of the synaptonemal complex, a prophase I meiotic structure, are already expressed and required in the mitotic region ofDrosophilafemales. Here, to assess if additional meiotic genes were expressed earlier than expected, we isolated mitotic and meiotic cell populations to compare their RNA content. Our transcriptomic analysis reveals that all known meiosis I genes are already expressed in the mitotic region, however, only some of them are translated. As a case study, we focused onmei-W68, theDrosophilahomologue ofSpo11, to assess its expression at both the mRNA and protein levels, and used different mutant alleles to assay for a pre-meiotic function. We could not detect any functional role for Mei-W68 during homologous chromosome pairing in dividing germ cells. Our study paves the way for further functional analysis of meiotic genes expressed in the mitotic region.Article SummaryGermline cells, crucial for sexual reproduction, were thought to switch to meiosis only after several rounds of mitosis. Surprisingly, a few meiotic proteins were found active in the mitotic phase of female flies. Here, we discovered that all known meiosis genes were expressed during mitosis, but only some produced proteins. This study suggests that genes related to reproduction are active earlier than expected, prompting further exploration into their functions during early cell division.
Simplest Model of Nervous System. IV. General Solution
Authors: Sinitskiy Anton V. 
Published: July 2024

AbstractIn this paper, we extend our previous work on a simplified model of the nervous system by solving the general optimization problem for the evolutionary cost of the nervous system. This optimization takes into account constraints on the scales of membrane potential kinetics and sensory response function to ensure finite, biologically plausible solutions. Our analysis reduces the variational problem to a system of two integro-differential equations, which we solve asymptotically using series expansions. This study confirms the emergence of sharp finite neuronal spikes and robust sensory and motor response functions as evolutionarily optimal solutions. We note that, in principle, alternative evolutionary solutions with different biophysical interpretations might exist for this optimization problem. This work provides a rigorous mathematical framework bridging evolutionary optimization with the fundamental properties of nervous systems.
A rapid method to determine the genetic lineage ofEscherichia coliusing open reading frame composition in the shallow sequencing
Authors: Yagi Nobuyoshi , Uechi Ayumi , Hirai Itaru 
Published: July 2024

AbstractDetermining the genetic background of bacterial isolates and evaluating the genetic relatedness among these isolates in a short time period are important to identify the spreading route(s) in cases of healthcare-associated infections and outbreaks caused by antimicrobial-resistant bacteria. Previously, we proposed a shallow sequencing (Shall-seq) procedure to determine the genetic backgrounds of clinical isolates using the minimum amount of sequence data. However, it took a longer time, such as longer than 10 h, to determine the genetic background of one clinical isolate. In this study, we developed a search procedure using open reading frame (ORF) composition to select the reference genome sequence with the highest matching ratio (>90%), the indicator genome sequence (IGS), for the examined bacterial isolate. Consequently, IGSs were selected for 28 (96.6%) of the examined 29 isolates and selection was performed within 30 min for each bacterial isolate. More importantly, the comparison of IGSs indicated that the IGSs, determined by ORF composition, of the examined bacterial isolates were closely related to the genome sequences determined using the Shall-seq procedure. Taken together, these results suggest that our newly developed search procedure can quickly determine the genetic background of bacterial isolates.
Proxiaml Temporary Occlusion using Balloon Guide Catheter for Mechanical Thrombectomy (PROTECT-MT): Study protocol for a multicenter randomized trial
Authors: Zhou Yu , Zhang Lei , Zhang Yongwei , Li Zifu , Xing Pengfei , Shen Hongjian , Zhu Xuan , Goyal Mayank , Liu Jianmin , Yang Pengfei ,   PROTECT-MT investigators
Published: July 2024

AbstractBackground and RationaleUncertainty exists over balloon guide catheter(BGC) usage for Mechanical Thrombectomy(MT) in patients with acute ischemic stroke acute ischemic stroke due to anterior circulation large vessel occlusion.ObjectiveTo determine the effectiveness of balloon guide catheter(BGC) as compared to conventional guide catheter on functional outcome in patients with acute ischemic stroke and treated with MT.DesignProximal TEmporary oCclusion using balloon guide caTheter for Mechanical Thrombectomy (PROTECT-MT) is an investigator-initiated, multicenter, prospective, open label trial with blinded outcome assessment (PROBE design) assessing the effectiveness and safety of BGC in acute ischemic stroke. An estimated 1074 patients meet the inclusion criteria would be randomized (1:1) to receive either MT with BGC(intervention) or MT with conventional guide catheter(control). The primary outcome is an ordinal shift analysis of scores on the modified Rankin scale (mRS) at 90 days.ProgressRecruitment started on February 7, 2023. At a meeting of the independent Data and Safety Monitoring Board in November 2023 to review primary outcome data available for 169 patients, they recommended suspension of recruitment due to safety concerns, which was implemented by the Trial Steering Committee (TSC) with 329 randomized patients. The TSC stopped recruitment due to the safety concerns persisted on further review of the data on April 18, 2024.DiscussionPROTECT-MT is the largest RCT assessing the effectiveness of BGC versus conventional guide catheter on functional outcome in large vessel occlusion patients treated with MT, it will provide further randomized evidence on the role of BGC in AIS patients treated with MT.
Post-proline cleaving enzymes also show specificity to reduced cysteine
Authors: Kalaninová Zuzana , Portašiková Jasmína Mária , Jirečková Barbora , Polák Marek , Nováková Jana , Kavan Daniel , Novák Petr , Man Petr 
Published: July 2024

AbstractIn proteomics, post-proline cleaving enzymes (PPCEs) likeAspergillus nigerprolyl endopeptidase and neprosin complement proteolytic tools because proline is a stop site for many proteases. However, our systematic analysis of cleavage preferences showed that both PPCEs also display specificity to reduced cysteine. Post-cysteine cleavage was blocked by Cys alkylation, explaining why this activity has remained undetected. Our findings redefine their applicability and how we study and interpret their cleavage mechanism.
Stabilization Mechanism of Initiator Transfer RNA in the Small Ribosomal Subunit from Coarse-Grained Molecular Simulations
Authors: Mori Yoshiharu , Tanaka Shigenori 
Published: July 2024

AbstractProteins play a variety of roles in biological phenomena in cells. Proteins are synthesized by a ribosome, which is a large molecular complex composed of proteins and nucleic acids. Among many molecules involved in the process of protein synthesis, transfer RNA (tRNA) is one of the essential molecules. In this study, coarse-grained molecular dynamics simulations were performed to understand how the tRNA molecule is stabilized in the ribosome, and the free energy along the dissociation path of the tRNA was calculated. We found that some ribosomal proteins, which are components of the ribosome, are involved in the stabilization of the tRNA. The positively charged amino acid residues in the C-terminal region of the ribosomal proteins are particularly important for the stabilization. These findings contribute to our understanding of the molecular evolution of protein synthesis in terms of the ribosome, which is a universal component of life.TOC Graphic
Global Phylogeography and Microdiversity of the Marine Diazotrophic CyanobacteriaTrichodesmiumand UCYN-A
Authors: Nguyen Angie , Ustick Lucas J. , Larkin Alyse A. , Martiny Adam C. 
Published: July 2024

AbstractCyanobacterial diazotrophs, specifically the generaTrichodesmiumand UCYN-A, play a pivotal role in marine nitrogen cycling through their capacity for nitrogen fixation. Despite their global distribution, the microdiversity and environmental drivers of these diazotrophs remain underexplored. This study provides a comprehensive analysis of the global diversity and distribution ofTrichodesmiumand UCYN-A using the nitrogenase gene (nifH) as a genetic marker. We sequenced 954 samples from the Pacific, Atlantic, and Indian Oceans as part of the Bio-GO-SHIP project. Our results reveal significant phylogenetic and biogeographic differences between and within the two genera.Trichodesmiumexhibited greater microdiversity compared to UCYN-A, with clades showing region-specific distribution.Trichodesmiumclades were primarily influenced by temperature and nutrient availability, and particularly frequent in regions of phosphorus stress. In contrast UCYN-A was found in regions of iron stress. UCYN-A clades demonstrated a more homogeneous distributions, with a single sequencing variant within the UCYN-A1 clade dominating across varied environments. The biogeographic patterns and environmental correlations ofTrichodesmiumand UCYN-A highlight the role of microdiversity in their ecological adaptation and reflect their different ecological strategies. This study underscores the importance of characterizing the global patterns of fine-scale genetic diversity to better understand the functional roles and distribution of marine nitrogen-fixing cyanobacteria.
Oxford Nanopore’s 2024 sequencing technology forListeria monocytogenesoutbreak detection and source attribution: progress and clone-specific challenges
Authors: Biggel Michael , Cernela Nicole , Horlbog Jule Anna , Stephan Roger 
Published: July 2024

AbstractWhole genome sequencing is an essential cornerstone of pathogen surveillance and outbreak detection. Established sequencing technologies are currently challenged by Oxford Nanopore Technologies (ONT), which offers an accessible and cost-effective alternative enabling gap-free assemblies of chromosomes and plasmids. Limited accuracy has hindered its use for investigating pathogen transmission, but recent technology updates have brought significant improvements. To evaluate its readiness for outbreak detection, we selected 78Listeria monocytogenesisolates from diverse lineages or known epidemiological clusters for sequencing with ONT’s V14 Rapid Barcoding Kit and R10.4.1 flow cells. The most accurate of several tested workflows generated assemblies with a median of one error (SNP or indel) per assembly. For 66 isolates, cgMLST profiles from ONT-only assemblies were identical to those generated from Illumina data. Eight assemblies were of lower quality with more than 20 erroneous sites each, primarily caused by methylations at the GAAGAC motif (5′-GAAG6mAC-3 / 3′-GT4mCTTC-5′). This led to inaccurate clustering, failing to group isolates from a persistence-associated clone that carried the responsible restriction-modification system. Out of 50 methylation motifs detected among the 78 isolates, only the GAAGAC motif was linked to substantially increased error rates. Our study shows that mostL. monocytogenesgenomes assembled from ONT-only data are suitable for high-resolution genotyping, but further improvements of chemistries or basecallers are required for reliable routine use in outbreak and food safety investigations.
Nitration of a ribosomal pentapeptide generates a noncanonical precursor for nonribosomal peptide synthesis
Authors: Padva Leo , Zimmer Lukas , Gullick Jemma , Zhao Yongwei , Sasi Vishnu Mini , Schittenhelm Ralf B. , Jackson Colin J. , Cryle Max , Crüsemann Max 
Published: July 2024

AbstractPeptide natural products possess a fascinating array of complex structures and diverse functions. Central to this is a repertoire of modified amino acid building blocks, which stem from fundamentally different biosynthesis pathways for peptides of nonribosomal and ribosomal origins. Given these origins, integration of nonribosomal and ribosomal pathways have previously been thought unlikely. Now, we demonstrate that ribosomal biosynthesis generates a key noncanonical 3-nitrotyrosine building block for the nonribosomal synthesis of rufomycin. In this pathway, a biarylitide-type ribosomal peptide is nitrated by a modified cytochrome P450 crosslinking enzyme, with the nitrated residue liberated by the actions of a dedicated protease found within the rufomycin gene cluster before being incorporated into rufomycin by the rufomycin nonribosomal peptide synthetase. This resolves the enigmatic origins of 3-nitrotyrosine within rufomycin biosynthesis and demonstrates unexpected integration of ribosomal peptide synthesis as a mechanism for the generation of noncanonical building blocks within nonribosomal synthesis pathways.
Psychological capital: a literature review and research trends
Authors: Nguyen Thanh D. , Cao Thi H. , Nguyen Tuan M. , Nguyen Tuan T. 
Published: July 2024

PurposeThis literature review aims to explore the various aspects of psychological capital (PsyCap), including its theoretical foundations, measurement methods, and the factors directly associated with PsyCap.Design/methodology/approachThe approach employed in this study is scientific document synthesis, with a specific emphasis on scholarly articles published between 2001 and 2023. The selection of articles is limited to those published in internationally renowned journals that are indexed by reputable databases, including ISI (WoS) and SJR (Scopus).FindingsPsychological capital is closely linked to other concepts at different levels. Scholars are investigating various factors associated with PsyCap, including health, project success, service marketing, banking services. It is important to note that different research areas have varying conceptualizations and scales when it comes to PsyCap.Originality/valueThis literature review of related studies reveals a growing global interest among researchers in the concept of positive psychological capital. The research results have shown significant interest in the items related to PsyCap, and and the factors directly associated with it, including antecedents, mediators, moderators, and outcomes.
Psychological need profiles during online shopping: exploring associations with word-of-mouth and loyalty
Authors: Ling Tianye , Zhao Rui , Jang Hyungshim 
Published: July 2024

PurposeDrawing on self-determination theory, a person-centered approach was used to investigate how the satisfaction and frustration of the basic psychological needs of autonomy and competence produce adaptive vs maladaptive consumer behavior during the online shopping experience.Design/methodology/approachWe collected questionnaire data from 1,399 respondents engaged in online shopping, including 65% females with an average age of 29.9. Latent profile analysis tested the hypotheses, using Mplus 8.3.FindingsThe online shopping experience sometimes satisfies and sometimes frustrates consumers’ basic psychological needs for autonomy and competence. This research used latent profile analysis to identify two profiles of the online shopping experience: “satisfied-dominant” and “moderately satisfied/frustrated.” Online shoppers who experienced only need satisfaction showed adaptive consumer behavior in terms of positive word-of-mouth and high loyalty, while online shoppers who experienced both moderate need satisfaction and frustration showed maladaptive consumer behavior.Originality/valueAn online shopping experience of need satisfaction vs frustration explains consumers’ adaptive vs maladaptive behavior. Specifically, when online shoppers experience only autonomy and competence need satisfaction, they engage in positive word-of-mouth and show high loyalty.
Support for housing recovery of home-based survivors: disaster case management after the 2011 Great East Japan Earthquake and tsunami
Authors: Uto Akihiro , Maly Elizabeth 
Published: July 2024

PurposeAfter the Great East Japan Earthquake (GEJE), the need for disaster case management (DCM) was highlighted through the efforts of the Sendai Bar Association, which investigated the situation of survivors. This paper provides an overview of DCM in Japan since the GEJE, including key findings from investigations and legal consultations conducted by the Sendai Bar Association and the first author, who took part in the surveys with survivors in Ishinomaki City, clarifying the large number of homebound survivors and their needs. Design/methodology/approachIn recent years there has been growing attention to the importance of DCM for supporting life and housing recovery of disaster survivors. Along with the expansion of DCM activities over several decades in Japan, the need for DCM was increasingly recognized after the 2011 GEJE and tsunami, especially for home-based survivors left out of government-provided disaster recovery support programs. As one-on-one advice to support individual recovery needs, the focus of DCM in Japan is legal advice to help survivors effectively navigate support policies.FindingsSince the GEJE, there has been growing support for DCM in Japan, including from practitioners, scholars, and regional and national governments. However, although DCM can be an effective way to support housing recovery, even 12 years after the GEJE, there are still survivors in need of additional support.Originality/valueDrawing on a detailed case study and action research of the first author, this paper contributes to the still limited international literature on DCM in Japan.
Neural networks for emergent behavior in biological microstructures
Authors: Kumar Manik , Sgarrella Joe , Peco Christian 
Published: July 2024

PurposeThis paper develops a neural network surrogate model based on a discrete lattice approach to investigate the influence of complex microstructures on the emergent behavior of biological networks.Design/methodology/approachThe adaptability of network-forming organisms, such as, slime molds, relies on fluid-to-solid state transitions and dynamic behaviors at the level of the discrete microstructure, which continuum modeling methods struggle to capture effectively. To address this challenge, we present an optimized approach that combines lattice spring modeling with machine learning to capture dynamic behavior and develop nonlinear constitutive relationships.FindingsThis integrated approach allows us to predict the dynamic response of biological materials with heterogeneous microstructures, overcoming the limitations of conventional trial-and-error lattice design. The study investigates the microstructural behavior of biological materials using a neural network-based surrogate model. The results indicate that our surrogate model is effective in capturing the behavior of discrete lattice microstructures in biological materials.Research limitations/implicationsThe combination of numerical simulations and machine learning endows simulations of the slime mold Physarum polycephalum with a more accurate description of its emergent behavior and offers a pathway for the development of more effective lattice structures across a wide range of applications.Originality/valueThe novelty of this research lies in integrating lattice spring modeling and machine learning to explore the dynamic behavior of biological materials. This combined approach surpasses conventional methods, providing a more holistic and accurate representation of emergent behaviors in organisms.
Impact of activation energy and cross-diffusion effects on 3D convective rotating nanoliquid flow in a non-Darcy porous medium
Authors: Sivanandam Sivasankaran , Alqurashi Turki J. , Alshehri Hashim M. 
Published: July 2024

Purpose
This study aims to investigate numerically the impact of the three-dimensional convective nanoliquid flow on a rotating frame embedded in the non-Darcy porous medium in the presence of activation energy. The cross-diffusion effects, i.e. Soret and Dufour effects, and heat generation are included in the study. The convective heating condition is applied on the bounding surface.

Design/methodology/approach
The control model consisted of a system of partial differential equations (PDE) with boundary constraints. Using suitable similarity transformation, the PDE transformed into an ordinary differential equation and solved numerically by the Runge–Kutta–Fehlberg method. The obtained results of velocity, temperature and solute concentration characteristics plotted to show the impact of the pertinent parameters. The heat and mass transfer rate and skin friction are also calculated.

Findings
It is found that both Biot numbers enhance the heat and mass distribution inside the boundary layer region. The temperature increases by increasing the Dufour number, while concentration decreases by increasing the Dufour number. The heat transfer is increased up to 8.1% in the presence of activation energy parameter (E). But, mass transfer rate declines up to 16.6% in the presence of E.

Practical implications
The applications of combined Dufour and Soret effects are in separation of isotopes in mixture of gases, oil reservoirs and binary alloys solidification. The nanofluid with porous medium can be used in chemical engineering, heat exchangers and nuclear reactor.

Social implications
This study is mainly useful for thermal sciences and chemical engineering.

Originality/value
The uniqueness in this research is the study of the impact of activation energy and cross-diffusion on rotating nanoliquid flow with heat generation and convective heating condition. The obtained results are unique and valuable, and it can be used in various fields of science and technology.