bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diurnal Regulation of SOS Pathway and Sodium Excretion Underlying Salinity Tolerance ofVigna marina
Authors: Noda Yusaku , Wang Fanmiao , Chankaew Sompong , Ariga Hirotaka , Muto Chiaki , Iki Yurie , Ohashi Haruko , Takahashi Yu , Sakai Hiroaki , Iseki Kohtaro , Ogiso-Tanaka Eri , Suzui Nobuo , Yin Yong-Gen , Miyoshi Yuta , Enomoto Kazuyuki , Kawachi Naoki , Somta Prakit , Furukawa Jun , Tomooka Norihiko , Naito Ken 
Published: March 2024

AbstractVigna marina(Barm.) Merr. is adapted to tropical marine beaches and has an outstanding tolerance to salt stress. Given there are growing demands for cultivating crops in saline soil or with saline water, it is important to understand how halophytic species are adapted to the saline environments. Here we revealed by positron emitting tracer imaging system (PETIS) thatV. marinaactively excretes sodium from the root during the light period but not in the dark period. The following whole genome sequencing accompanied with forward genetic study identified a QTL region harboringSOS1, encoding plasma membrane Na+/H+antiporter, which was associated with not only salt tolerance but also ability of sodium excretion. We also found the QTL region contained a large structural rearrangement that suppressed recombination across ∼20 Mbp, fixing multiple gene loci potentially involved in salt tolerance. RNA-seq and promoter analyses revealedSOS1inV. marinawas highly expressed even without salt stress and its promoter shared commoncis-regulatory motifs with those exhibiting similar expression profile. Interestingly, thecis-regulatory motifs seemed installed by a transposable element (TE) insertion. Though not identified by genetic analysis, the transcriptome data also revealedSOS2transcription was under diurnal regulation, explaining the pattern of sodium excretion together with up-regulated expression ofSOS1. Furthermore, we demonstrated that, under a condition of mild salt stress, the plants with the diurnally regulated SOS pathway outperformed those with the constitutively activated one.
Bacterial profiles of the oral, vaginal, and rectal mucosa and colostrum of periparturient sows
Authors: Piirainen Virpi , König Emilia , Husso Aleksi , Heinonen Mari , Iivanainen Antti , Pessa-Morikawa Tiina , Niku Mikael 
Published: March 2024

AbstractThe commensal microbiota influences the health, feeding efficiency, and reproductive performance of sows. The microbiota composition in the alimentary and genitourinary tracts and in colostrum/milk during pregnancy and lactation also impacts the developing microbiota and immune system of the piglets and subsequently their growth and health. Knowledge of the microbial compositions is important for evaluation of these effects and for discovering ways to improve the health and productivity of the sows.Oral, vaginal, and rectal mucosa were sampled from 32 sows of variable parity in late pregnancy on four commercial piglet-producing farms in Finland. Colostrum samples were taken within 6 hours of delivery of the first piglet. Microbial compositions were analyzed by 16S rRNA gene amplicon sequencing. Moderate differences in diversity and composition were observed between farms. The most abundant genera of the oral microbiota wereRothia,Moraxella, andStreptococcus.The rectal microbiota was dominated byClostridium sensu stricto 1. Streptococcuswas the most abundant genus in the vagina and colostrum. Differences in relative abundances of genera were detected between primiparous and multiparous sows. Some of these differences were detected across all the farms; in the multiparous sows, the relative abundances ofFusobacteriumandNeisseriawere lower in oral samples.Clostridium sensu stricto 1,Romboutsia, andLachnospiraceae_UCG_007were higher andPrevotellalower in rectal samples, andStreptococcushigher in colostrum samples. In vaginal samples, approximately half of the multiparous sows had significantly higher relative abundances of the generaFusobacteriumandStreptococcusthan the primiparous sows. Among the differentially abundant taxa,F. necrophorumandF. nucleatumwere identified in oral samples,Fusobacterium gastrosuisandFusobacterium necrophorumin vaginal samples, andStreptococcus dysgalactiaein colostrum samples. Most of the differences were due to unidentified species within the respective genus.This study provides a comprehensive overview of the mucosal and colostrum microbiota of periparturient sows during normal production conditions on Finnish commercial farms, including potentially interesting differences in the relative abundances of several genera at different mucosal sites between sows of low and high parity.
(p)ppGpp buffers cell division when membrane fluidity decreases inEscherichia coli
Authors: Singh Vani , Harinarayanan Rajendran 
Published: March 2024

AbstractMaintenance of fluidity an inherent property of biological membranes by homeoviscous adaptation is important for optimal functioning of membrane-associated processes. Homeoviscous adaptation inE. coliinvolves an increase in the concentration of unsaturated fatty acid, cis-vaccenic acid (18:1) with decrease in temperature andvice versa. Lowering unsaturated fatty acid synthesis by inactivation of FadR reduced the proportion of unsaturated fatty acids in the membrane. In this study we show that when the proportion of unsaturated fatty acids in the membrane was reduced, cell division was dependent on the guanine nucleotide analogous (p)ppGpp. Combined expression of cell division genesftsQ,ftsAandftsZfrom plasmid rescued the growth defect that was associated with cell filamentation followed by lysis. To our knowledge, this is the first report of (p)ppGpp mediated regulation needed for the adaptation to membrane fluidity loss in bacteria.
A panel of phenotypically and genotypically diverse bioluminescent:fluorescentTrypanosoma cruzistrains as a resource for Chagas disease research
Authors: Olmo Francisco , Jayawardhana Shiromani , Khan Archie A. , Langston Harry C. , Francisco Amanda Fortes , Atherton Richard L. , Ward Alex I. , Taylor Martin C. , Kelly John M. , Lewis Michael D. 
Published: March 2024

ABSTRACTChagas disease is caused byTrypanosoma cruzi, a protozoan parasite that displays considerable genetic diversity. Infections result in a range of pathological outcomes, and different strains can exhibit a wide spectrum of anti-parasitic drug tolerance. The genetic determinants of infectivity, virulence and therapeutic susceptibility remain largely unknown. As experimental tools to address these issues, we have generated a panel of bioluminescent:fluorescent parasite strains that cover the diversity of theT. cruzispecies. These reporters allow spatio-temporal infection dynamics in murine models to be monitored in a non-invasive manner byin vivoimaging, provide a capability to detect rare infection foci at single-cell resolution, and represent a valuable resource for investigating virulence and host:parasite interactions at a mechanistic level. Importantly, these parasite reporter strains can also contribute to the Chagas disease drug screening cascade by ensuring that candidate compounds have pan-speciesin vivoactivity prior to being advanced into clinical testing. The parasite strains described in this paper are available on request.AUTHOR SUMMARYChagas disease results from infection with the protozoan parasiteTrypanosoma cruziand is a major public health problem throughout Latin America.T. cruziis a genetically diverse species and infection can result in a wide range of pathological outcomes, mainly associated with the heart and/or digestive tract. Research on Chagas disease, ranging from fundamental biology to drug development, has been greatly aided by the availability of genetically modified parasite reporter strains that express bioluminescent:fluorescent fusion proteins. In combination with mouse models and imaging technology, these strains allow infections to be monitored in real-time, with high sensitivity, and infection foci to be visualised at single-cell resolution. Here, we describe an extensive panel of bioluminescent and fluorescent strains that cover the diversity of theT. cruzispecies. These reporter strains, that are available on request, should have wide utility in many areas of Chagas disease research. In particular, as part of the drug development screening programme, they can be used to ensure that candidate compounds havein vivoactivity across the species prior to being advanced into clinical testing.
Multi-omics analysis reveals regime shifts in the gastrointestinal ecosystem in chickens following anticoccidial vaccination andEimeria tenellachallenge
Authors: Liu Po-Yu , Liaw Janie , Soutter Francesca , Ortiz José Jaramillo , Tomley Fiona M. , Werling Dirk , Gundogdu Ozan , Blake Damer P. , Xia Dong 
Published: March 2024

ABSTRACTCoccidiosis, caused byEimeriaparasites, poses significant economic and welfare challenges in poultry farming. Beyond its direct impact on health,Eimeriainfection disrupts enteric microbial populations leading to dysbiosis and increases vulnerability to secondary diseases such as necrotic enteritis, caused byClostridium perfringens. The impact ofEimeriainfection or anticoccidial vaccination on host gastrointestinal phenotypes and enteric microbiota remains understudied. In this study, the metabolomic profiles and microbiota composition of chicken caecal tissue and contents were evaluated concurrently during a controlled experimental vaccination and challenge trial. Cobb500 broilers were vaccinated with aSaccharomyces cerevisiae-vectored anticoccidial vaccine and challenged with 15,000Eimeria tenellaoocysts. Assessment of caecal pathology and quantification of parasite load revealed correlations with alterations to caecal microbiota and host metabolome linked to infection and vaccination status. Infection heightened microbiota richness with increases in potentially pathogenic species, while vaccination elevated beneficialBifidobacterium. Using a multi-omics factor analysis (MOFA) machine learning model, data on caecal microbiota and host metabolome were integrated and distinct profiles for healthy, infected, and recovering chickens were identified. Healthy and recovering chickens exhibited higher vitamin B metabolism linked to short-chain fatty acid-producing bacteria, whereas essential amino acid and cell membrane lipid metabolisms were prominent in infected and vaccinated chickens. Notably, vaccinated chickens showed distinct metabolites related to the enrichment of sphingolipids, important components of nerve cells and cell membranes. Our integrated multi-omics model revealed latent biomarkers indicative of vaccination and infection status, offering potential tools for diagnosing infection, monitoring vaccination efficacy, and guiding the development of novel treatments or controls.
Coordinated regulation of osmotic imbalance by c-di-AMP shapes ß-lactam tolerance in Group BStreptococcus
Authors: Brissac Terry , Guyonnet Cécile , Sadouni Aymane , Hernandez Montoya Ariadna , Jacquemet Elise , Legendre Rachel , Sismeiro Odile , Trieu-Cuot Patrick , Lanotte Philippe , Tazi Asmaa , Firon Arnaud 
Published: March 2024

ABSTRACTStreptococcus agalactiaeis among the few pathogens that have not developed resistance to ß-lactam antibiotics despite decades of clinical use. The molecular basis of this long-lasting susceptibility has not been investigated, and it is not known whether specific mechanisms constrain the emergence of resistance. In this study, we report the conserved role of the signaling nucleotide cyclic-di-AMP in susceptibility to ß-lactams, demonstrating that inactivation of the phosphodiesterase GdpP inS. agalactiaeconfers ß-lactam tolerance. Characterization of the c-di-AMP signaling pathway reveals antagonistic regulation by the transcriptional factor BusR, which is activated by c-di-AMP and negatively regulates ß-lactam susceptibility through the BusAB transporter and AmaP/Asp23 cell envelope stress complex. Furthermore, we show that the simultaneous inhibition of osmolyte transporters activity and transcription by c-di-AMP has an additive effect, sustaining ß-lactam tolerance. Finally, we expanded the analysis of ß-lactam tolerance using random transposon mutagenesis, uncovering a convergent pattern of mutations involving the KhpAB small RNA chaperone and the S protein immunomodulator. Overall, our results demonstrate that c-di-AMP acts as a turgor pressure rheostat, coordinating an integrated response to cell wall weakening due to ß-lactam activity, and identify mechanisms that may foster antibiotic resistance inS. agalactiae.
Real-space blocking of qubit variables on parallel lattice gauge theory links for quantum simulation
Authors: Shir Judy , Zohar Erez 
Published: March 2024

One of the methods proposed in recent years for studying nonperturbative gauge theory physics is quantum simulation, where lattice gauge theories are mapped onto quantum devices which can be built in the laboratory, or quantum computers. While being very promising and already showing some experimental results, these methods still face several challenges related to the interface between the technological capabilities and the demands of the simulated models; in particular, one such challenge is the need to simulate infinitely dimensional local Hilbert spaces, describing the gauge fields on the links in the case of compact Lie gauge groups, requiring some truncations and approximations which are not completely understood or controllable in the general case. This work proposes a way to obtain arbitrarily large such local Hilbert spaces by using coarse graining of simple, low-dimensional qubit systems, made of components available on most quantum simulation platforms, and thus opening the way to new types of lattice gauge theory quantum simulations.

Published by the American Physical Society
2024
Dark dimension and decaying dark matter gravitons
Authors: Obied Georges , Dvorkin Cora , Gonzalo Eduardo , Vafa Cumrun 
Published: March 2024

We explore the cosmology of the dark-dimension scenario taking into account perturbations in the linear regime. In the context of the dark-dimension scenario, a natural candidate for dark matter in our Universe is the excitations of a tower of massive spin-2 Kaluza-Klein (KK) gravitons. These dark gravitons are produced in the early Universe and decay to lighter KK gravitons during the course of cosmological evolution. The decay causes the average dark matter mass to decrease as the Universe evolves. In addition, the kinetic energy liberated in each decay leads to a kick velocity for the dark matter particles, leading to a suppression of structure formation. Using current cosmic microwave background (), baryon acoustic oscillation, and cosmic shear (KiDS-1000) data, we put a bound on the dark matter kick velocity today vtoday≤2.2×10−4c at 95% CL. This leads to rather specific regions of parameter space for the dark-dimension scenario. The combination of the experimental bounds from cosmology, astrophysics, and table-top experiments leads to the range l5∼1–10  μm for the size of the dark dimension. The dark-dimension scenario is found to be remarkably consistent with current observations and provides signatures that are within reach of near-future experiments.

Published by the American Physical Society
2024
Three-Dimensional Topological Field Theories and Nonunitary Minimal Models
Authors: Gang Dongmin , Kim Heeyeon , Stubbs Spencer 
Published: March 2024

We find an intriguing relation between a class of three-dimensional nonunitary topological field theories (TFTs) and Virasoro minimal models M(2,2r+3) with r≥1. The TFTs are constructed by topologically twisting 3D N=4 superconformal field theories (SCFTs) of rank-0, i.e., having zero-dimensional Coulomb and Higgs branches. We present ultraviolet (UV) field theory descriptions of the SCFTs with manifest N=2 supersymmetry, which we argue is enhanced to N=4 in the infrared. From the UV description, we compute various partition functions of the TFTs and reproduce some basic properties of the minimal models, such as their characters and modular matrices. We expect more general correspondence between topologically twisted 3d N=4 rank-0 SCFTs and 2D nonunitary rational conformal field theories.

Published by the American Physical Society
2024
Operator guidance systems in road construction: a technological mediation perspective
Authors: Voordijk Hans , Miller Seirgei , Vahdatikhaki Faridaddin 
Published: March 2024

PurposeUsing real-time support systems may help operators in road construction to improve paving and compaction operations. Nowadays, these systems transform from descriptive to prescriptive systems. Prescriptive or operator guidance systems propose operators actionable compaction strategies and guidance, based on the data collected. It is investigated how these systems mediate the perceptions and actions of operators in road pavement practice.Design/methodology/approachA case study is conducted on the specific application of an operator guidance system in a road pavement project. In this case study, comprehensive information is presented regarding the process of converting input in the form of data from cameras and sensors into useful output. The ways in which the operator guidance systems translate data into actionable guidance for operators are analyzed from the technological mediation perspective.FindingsOperator guidance systems mediate actions of operators physically, cognitively and contextually. These different types of action mediation are related to preconditions for successful implementation and use of these systems. Coercive interventions only succeed if there is widespread agreement among the operators. Persuasive interventions are most effective when collective and individual interests align. Contextual influence relates to designs of the operator guidance systems that determine human-technology interactions when using them.Originality/valueThis is the first study that analyzes the functioning of an operator guidance system using the technological mediation approach. It adds a new perspective on the interaction between this system and its users in road pavement practice.
Examining the adverse impact of social media: development of a theoretical model using conspiracy theory from socio-legal perspective
Authors: Chatterjee Sheshadri , Vrontis Demetris , Hussain Zahid , Basile Gianpaolo , Bianco Rosario 
Published: March 2024

Purpose
The purpose of this study is to develop a model for investigating the sharing of harmful messages by employees using social media using the conspiracy theory from a socio-legal perspective. This study also examines the moderating role of different demographic parameters such as age, gender and education toward sharing harmful messages using social media.

Design/methodology/approach
Using the conspiracy theory and social impact theory as the foundation of this study, the authors developed theoretical model and validated it using the structural equation modeling technique with 342 participants from various organizations across Europe and Asia. The study also used different statistical measures to understand the demographic impacts toward sharing harmful messages.

Findings
It was found that epistemic, existential and social motives significantly and positively influence employees’ inappropriate message-sharing and seeking behavior, which in turn influences them to share harmful messages on social media. The study also indicates that there are some moderating impacts of employee demography toward sharing harmful messages using social media platforms.

Research limitations/implications
This study investigates the antecedents of sharing harmful messages using social media by employees. The present study could be useful for the organizations leaders as well as policymakers and legal fraternity. The study uses a limited number of feedback to validate the model. Also, this is a cross-sectional study which is another limitation of this study.

Originality/value
This study has proposed and validated a theoretical model by using the conspiracy theory as well as the social impact theory which is unique. Moreover, this study adds value to the existing literature on the harmful impacts of social media and its societal impacts. Besides, the validated model of this study has a high explanatory power which is another uniqueness of this study.
Development of in-country logistics performance index for emerging economies: a case of Indian states
Authors: Nayak Nikesh , Pant Pushpesh , Sarmah Sarada Prasad , Tulshan Raj 
Published: March 2024

PurposeLogistics sector is recognized as one of the core enablers of the economic development of a nation. However, inefficiency in logistics operations impedes the achievement of intended targets by increasing the cost of doing business. Also, it is difficult to improve the efficiency of a country’s logistics operations without a metric for evaluating and understanding logistics capabilities and efficiency. Therefore, the present study has developed In-country Logistics Performance Index (ILP Index) to propose a benchmarking tool to measure the in-country logistics competitiveness, particularly in the setting of emerging economies, i.e. India.Design/methodology/approachThis study has developed a unified index using principal component analysis and quintile approach. In addition, the proposed index relies on several dimensions that are developed and illustrated using quantitative secondary panel data.FindingsThe findings of this study reveal that the quality of infrastructure, economy, and telecommunications are the three most important dimensions that may significantly support the growth of the transportation and logistics sector. The results reveal that Gujarat, Tamil Nadu, and Maharashtra are the top performers whereas, Bihar, Jharkhand, and Jammu and Kashmir scores the least due to the insufficient logistics infrastructure as compared to other Indian states.Originality/valueGiven the extensive focus on international-level logistics index (like World Bank’s LPI) in the existing literature, this study intends to develop in-country logistics index to evaluate the logistics capabilities at the regional and state level. In addition, unlike prior studies, this study utilizes quantitative secondary data to eliminate cognitive and opinion bias. Moreover, this benchmarking tool would assist decision-makers in idealizing standard practices toward sustainable logistics operations. Additionally, the ILP index could serve the international investors in crucial decision-making, as it provides valuable insights into a country’s logistics readiness, influencing their investment choices and trade preferences. Finally, the proposed approach is adaptable to measuring the overall performance of any other industry/economy.