bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic evolution analysis of hemagglutinin and neuraminidase genes of H9N2 avian influenza virus in external environment of some areas of Yunnan Province, China from 2020 to 2023
Authors: Liu Zhaosheng , Fu Xiaoqing , Chen Yaoyao , Sun Yanhong , Zhang Meiling , Han Xiaoyu , Zhao Xiaonan , Zhou Jienan 
Published: February 2024

ObjectiveTo understand the molecular characteristics and genetic variation of hemagglutinin (HA) and neuraminidase (NA) genes of H9N2 subtype avian influenza virus (AIV) in the external environment of Yunnan Province, and to provide evidence for the prevention and control of H9N2 subtype AIV in this area.ResultsThe HA and NA genes of 20 isolates belonged to Y280-like sub-branch. The nucleotide and amino acid homology of HA gene were 88.46%-99.81% and 89.08% -99.61%, respectively. The nucleotide and amino acid homology of NA gene were 88.85%-100% and 90.09%-100%, respectively. The HA protein cleavage site of 20 isolates was PSRSSRGLF, which was consistent with the molecular characteristics of low pathogenic avian influenza virus. The 226 th and 228 th positions of the receptor binding site are all L and G, which have the ability to bind to the mammalian sialic acid α-2,6 sialic acid receptor; HA protein had 7-8 glycosylation sites, and the main variation was the deletion of one site at 218 and the addition of one glycosylation site at 313 and 491. The main antigenic sites were G90E, S/T145D, D/N153G, A/S/F168N/E, T200R, N/D201G/T mutations. The NA protein neck of 20 isolates lacked 3 amino acids (TEI), which had the molecular characteristics of highly pathogenic avian influenza. NA protein had 6-8 glycosylation sites. The main variation was that two isolates increased a new glycosylation site NPTQ at the 2nd position, and one isolate increased a new glycosylation site NTTI at the 67th position. All isolates lost one site at the 402nd position, and some isolates lost at the 83rd and 365th positions. The amino acids at the active site and key site of NA protease were not mutated, and the isolates did not produce resistance to neuraminidase inhibitors.ConclusionThe HA and NA genes of H9N2 subtype avian influenza virus in Yunnan Province have evolved continuously, but they still belong to the Y280 branch of the Eurasian lineage. Mutations in key sites may cause increased infectivity and transmission. The monitoring of H9N2 subtype avian influenza virus should be strengthened to prevent it from breaking the interspecies barrier and spreading to humans and lower mammals, so as to prevent the outbreak of H9N2 subtype avian influenza.
Mesencephalic projections to the nucleus accumbens shell modulate value updating during probabilistic reversal learning
Authors: Zühlsdorff Katharina , Piller Sammy , Sala-Bayo Júlia , Zhukovsky Peter , Lamla Thorsten , Nissen Wiebke , von Heimendahl Moritz , Deiana Serena , Nicholson Janet R. , Robbins Trevor W. , Alsiö Johan , Dalley Jeffrey W. 
Published: February 2024

AbstractCognitive flexibility, the capacity to adapt behaviour to changes in the environment, is impaired in a range of brain disorders, including substance use disorder and Parkinson’s disease. Putative neural substrates of cognitive flexibility include mesencephalic pathways to the ventral striatum (VS) and dorsomedial striatum (DMS), hypothesised to encode learning signals needed to maximize rewarded outcomes during decision-making. However, it is unclear whether mesencephalic projections to the ventral and dorsal striatum are distinct in their contribution to flexible reward-related learning. Here, rats acquired a two-choice spatial probabilistic reversal learning (PRL) task, reinforced on an 80%:20% basis, that assessed the flexibility of behaviour to repeated reversals of response-outcome contingencies. We report that optogenetic stimulation of projections from the ventral tegmental area (VTA) to the nucleus accumbens shell (NAcbS) in the VS significantly impaired reversal learning when optical stimulation was temporally aligned with negative feedback (i.e., reward omission). Moreover, the exploitation-exploration parameter,β, was increased (indicating greater exploitation of information) when this pathway was optogenetically stimulated after a spurious loss (i.e. an incorrect (20%) response at the 80% reinforrced location) compared to after a spurious win (i.e. a correct (20%) response at the 20% reinforced location). VTA → NAcbS stimulation during other phases of the behavioural task was without effect. Optogenetic stimulation of projection neurons from the substantia nigra (SN) to the DMS, aligned either with reward receipt or omission or prior to making a choice, had no effect on reversal learning. These findings are consistent with the notion that enhanced activity in VTA → NAcbS projections leads to maladaptive perseveration as a consequence of an inappropriate bias to exploitationviapositive reinforcement.
Efficient 3ʹ-end tailing of RNA with modified adenosine for nanopore direct total RNA sequencing
Authors: Yuan Yinan , Arneson Reed , Burke Emma , Apostle Alexander 
Published: February 2024

AbstractDirect sequencing of total cellular RNA enables a better understanding of a broad spectrum of RNA species controlling cellular processes and organismal function. Current nanopore direct RNA sequencing method, however, only captures polyadenylated RNA for sequencing. To address this issue, we developed a unique 3’-end RNA tailing method to capture total RNA for nanopore direct RNA sequencing. Due to the distinct electrical signature of the added tail on nanopore, this method allows simultaneous detection of both non-polyadenylated and polyadenylated RNAs. We demonstrated the effectiveness of this method in capturing the dynamics of transcription and polyadenylation of chloroplast RNAs in plant cell. With its high efficiency in retaining total RNA on nanopore, this method has the potential to be broadly applied to RNA metabolism and functional genomics studies.
Developmentally stable representations of naturalistic image structure in macaque visual cortex
Authors: Lee Gerick M. , Rodríguez-Deliz C. L. , Bushnell Brittany N. , Majaj Najib J. , Movshon J. Anthony , Kiorpes Lynne 
Published: February 2024

AbstractWe studied visual development in macaque monkeys using texture stimuli, matched in local spectral content but varying in “naturalistic” structure. In adult monkeys, naturalistic textures preferentially drive neurons in areas V2 and V4, but not V1. We paired behavioral measurements of naturalness sensitivity with separately-obtained neuronal population recordings from neurons in areas V1, V2, V4, and inferotemporal cortex (IT). We made behavioral measurements from 16 weeks of age and physiological measurements as early as 20 weeks, and continued through 56 weeks. Behavioral sensitivity reached half of maximum at roughly 25 weeks of age. Neural sensitivities remained stable from the earliest ages tested. As in adults, neural sensitivity to naturalistic structure increased from V1 to V2 to V4. While sensitivities in V2 and IT were similar, the dimensionality of the IT representation was more similar to V4’s than to V2’s.
Simultaneous circulation and coinfection of Dengue clades and serotypes in Southern Brazil
Authors: Bermann Thales , Baethgen Ludmila Fiorenzano , Gregianini Tatiana Schäffer , Godinho Fernanda , Barcellos Regina Bones , Ruivo Amanda Pellenz , Bauerman Milena , Selayaran Taina Machado , dos Santos Franciellen Machado , Schoerer Julio Augusto , Möllmann Érica Bortoli , Martiny Fernanda Letícia , Lagranha Valeska Lizzi , de Oliveira Luiz Felipe Valter , da Veiga Ana Gorini , Zolet Andreia Carina Turchetto , Wallau Gabriel Luz , Salvato Richard Steiner 
Published: February 2024

ABSTRACTDengue is an arthropod-borne virus with worldwide urban transmission mediated by anthropophilic vectors of the genusAedes. Currently, there is a substantial genotype diversity that belongs to at least four known serotypes. Tropical regions, where several serotypes cocirculate in the population, are hyperendemic, driving multiple outbreaks with variable disease manifestations. Notably, the Dengue virus burden is increasing in subtropical and temperate regions of the globe due to climatic changes associated with new outbreaks in naive and previously unaffected human populations. The introduction and endemic transmission of different clades and serotypes in these regions is highly concerning due to the known and still unknown consequences of Dengue infection on populations with diverse genetic backgrounds. Here, we characterized the coinfection of different Dengue clades and serotypes in Rio Grande do Sul, Brazil’s southernmost and subtropical state, by combining serotype-specific RT-PCR and deep sequencing. We found five coinfected patients in four municipalities where these clades and serotypes circulated simultaneously. Our data suggests that coinfection events account for a minority of total cases, but these findings may reflect the early transmission phases of some Dengue clades. Hence, close monitoring is warranted to evaluate coinfection rates and associated clinical consequences as clade prevalence changes.
A comprehensive analysis of non-pharmaceutical interventions and vaccination on Ebolavirus disease outbreak: Stochastic modeling approach
Authors: Ko Youngsuk , Lee Jacob , Seo Yubin , Jung Eunok 
Published: February 2024

AbstractEbolavirus disease (EVD) outbreaks have intermittently occurred since the first documented case in the 1970s. Due to its transmission characteristics, large outbreaks have not been observed outside Africa. However, within the continent, significant outbreaks have been attributed to factors such as endemic diseases with similar symptoms and inadequate medical infrastructure, which complicate timely diagnosis. In this study, we employed a stochastic modeling approach to analyze the spread of EVD during the early stages of an outbreak, with an emphasis on inherent risks. We developed a model that considers medical staff and unreported cases, and assessed the effect of non-pharmaceutical interventions (NPIs) using actual data. Our results indicate that the implementation of NPIs led to a decrease in the transmission rate and infectious period by 30% and 40% respectively, following the declaration of the outbreak. We also investigated the risks associated with delayed outbreak recognition. Our simulations suggest that, when accounting for NPIs and recognition delays, prompt detection could have resulted in a similar outbreak scale, with approximately 50% of the baseline NPIs effect. Finally, we discussed the potential effects of a vaccination strategy as a follow-up measure after the outbreak declaration. Our findings suggest that a vaccination strategy can reduce both the burden of NPIs and the scale of the outbreak.Author summaryOur research employs a stochastic model to analyze the early-stage spread of Ebolavirus Disease. We incorporated factors such as medical staffs and unreported cases, and utilized real data to evaluate the impact of non-pharmaceutical interventions on disease transmission. Our findings indicate that rapid outbreak recognition could effectively control disease spread with reduced efforts. Furthermore, we explored the potential implementation of a vaccination strategy following an outbreak declaration. Our results suggest that such a strategy could mitigate both the scale of the outbreak and the necessity for additional interventions.
Diverse Relationships Between Antibiotic Resistance and Host Age: A Meta-Analysis Across Antibiotic Classes and Bacterial Genera
Authors: Binsted Lucy E. , McNally Luke 
Published: February 2024

AbstractAntimicrobial resistance (AMR) poses an urgent public health challenge. To improve patient outcomes and design interventions we must identify patient characteristics which predict the presence of AMR pathogens. One potential and commonly collected patient characteristic is host age, consensus remains elusive regarding its impact on the probability of infecting pathogens being resistant to antimicrobials. Here, we employ a meta-analysis to consolidate and compare these previous studies and examine the relationship between antibiotic resistance and host age across bacteria and antibiotics. We show that although the probability that infecting bacteria are antimicrobial resistant increases with host age on average, diverse patterns exist across antibiotic classes and bacterial genera, including negative, humped, and U-shaped relationships. We further illustrate, using a compartmental epidemiological model, that this variation is likely driven by differences in antibiotic consumption or incidence of bacterial infection/carriage between age groups, combined with age assortative transmission. These findings imply that empirical antibiotic therapy could be improved by considering age-specific local resistance levels (compared with overall local resistance levels), resulting in improved treatment success and reduced spread of antibiotic resistance. They additionally display consequences of assuming population homogeneity in epidemiological models. Finally, they indicate that the landscape of the already severe resistance crisis is likely to change as the age distribution of the human population shifts.
Attentional inhibition by alpha power is modulated by faster theta rhythm and audio-visual congruency during natural speech perception
Authors: Byczynski Gabriel , Park Hyojin 
Published: February 2024

AbstractAudio-visual processing is an essential aspect of human communication, however the mechanisms that underlie attention and processing in the auditory and visual domains are still limited. In order to understand how the brain attends to and processes information while ignoring irrelevant information, we employed a complex audio-visual paradigm to understand how the brain monitors and integrates audio-visual information in congruent and incongruent conditions. In three conditions, participants watched a Ted Talk presentation while listening to 1) congruent audio in both ears, 2) congruent audio in one ear and incongruent in the other (attending to congruent) or 3) congruent audio in one ear and incongruent audio in the other (attending to the incongruent). In order to investigate correlates of attention and audio-visual processing, we developed a novel method of detecting audio-visual congruency in the fluctuation rhythms of alpha power during each condition. Employing this method, we found that higher frequency alpha power fluctuation, falling in the delta-theta range, corresponded regionally to the side of attention, suggesting a novel mechanism of processing in that alpha-band activity may act as a temporal filter or attentional mechanism during audio-visual attention.
Sand flies and Toscana virus: intra-vector infection dynamics and impact onPhlebotomus perniciosuslife-history traits
Authors: Laroche Lison , Bañuls Anne-Laure , Charrel Rémi , Fontaine Albin , Ayhan Nazli , Prudhomme Jorian 
Published: February 2024

AbstractToscana virus (TOSV) is a leading cause of summer viral meningitis in central Italy and south of France, and can cause severe neurological cases. Within the Mediterranean basin, it is transmitted by hematophagous sand flies belonging to thePhlebotomusgenus. Despite the identification of the primary TOSV vectors, the virus’s developmental cycle in vector species remains largely unknown. Limited research has been conducted on transmission dynamics and the vectorial competence and capacity of the principal TOSV vector,Phlebotomus perniciosus. In this context, we investigated the intra-vector TOSV infection dynamics inPh. perniciosus, as well as its impact on the vector’s life history traits. Female sand flies were experimentally infected with TOSV though an artificial blood meal. Systemic dissemination of the virus was observed approximately three days post-infection, potentially resulting in a shorter extrinsic incubation period. Moreover, the study revealed a longer hatching time for eggs laid by infected females. This research not only confirmed the vector competence ofPh. perniciosusbut also provided the first insight into TOSV’s developmental cycle and its impact on the vector. These findings prompt further exploration of TOSV transmission dynamics, raise new hypotheses on the virus transmission and highlight the importance of follow-up studies.Author summaryToscana virus (TOSV) is a reemerging sandfly-borne virus causing neuroinvasive infections in humans. This virus is endemic in the Mediterranean basin, with a potential risk of introduction in northern Europe and Asia. Despite decades of research, few studies have focused on the development cycle of TOSV in sand flies and the dynamics of transmission. Here, we provide a comprehensive study of the intra-vector dynamics of TOSV infection and its impact on both vector biology and transmission. Through experimental infections of the major vectorPhlebotomus perniciosus, we not only confirmed vector competence but also provided the first insight into the TOSV developmental cycle in the vector by estimating the extrinsic incubation period at six days. Our study reveals an impact of TOSV infection on vector hatching time leading to a delayed emergence of infected sand flies, with a potential impact on transmission. Our findings encourage further exploration of transmission dynamics, raise new hypotheses on alternative transmission pathways, and emphasize the importance of follow-up studies.
The energy metabolism ofCupriavidus necatorin different trophic conditions
Authors: Jahn Michael , Crang Nick , Gynnå Arvid H. , Kabova Deria , Frielingsdorf Stefan , Lenz Oliver , Charpentier Emmanuelle , Hudson Elton P. 
Published: February 2024

SummaryThe ‘knallgas’ bacteriumCupriavidus necatoris attracting interest for biotechnological applications due to its extremely versatile metabolism.C. necatorcan use hydrogen or formic acid as an energy source, fixes CO2viathe Calvin-Benson-Bassham (CBB) cycle, and also grows well on various other organic acids and sugars. Its tri-partite genome is notable for its size and manifold duplications of key genes (CBB cycle, hydrogenases, nitrate reductases). Comparatively little is known about which of these (iso-) enzymes and their cofactors are actually utilized for growth on different energy sources.Here, we investigated the energy metabolism ofC. necatorH16 by growing a barcoded transposon knockout library on various substrates including succinate, fructose, hydrogen (H2/CO2) and formic acid. The fitness contribution of each gene was determined from enrichment or depletion of the corresponding mutants. Fitness analysis revealed that 1) some, but not all, molybdenum cofactor biosynthesis genes were essential for growth on formate and nitrate respiration. 2) Soluble formate dehydrogenase (FDH) was the dominant enzyme for formate oxidation, not membrane-bound FDH. 3) For hydrogenases, both soluble and membrane-bound enzymes were beneficial for lithoautotrophic growth. 4) Of the six terminal respiratory complexes inC. necatorH16, only some are utilized and utilization depends on the energy source. 5) Deletion of hydrogenase-related genes boosted heterotrophic growth, and we show that the relief from associated protein cost is responsible for this phenomenon.This study evaluates the contribution of each ofC. necator’s genes to fitness in biotechnologically relevant growth regimes. Our results illustrate the genomic redundancy of this generalist bacterium, and may inspire future strategies for strain engineering.Graphical AbstractHighlightsa barcoded transposon library was used to assess gene fitness for hydrogenase, formate dehydrogenase and electron transport chain complexesthe utilization of terminal respiratory complexes is substrate specificsoluble formate dehydrogenase is more important than the membrane-bound enzymesoluble hydrogenase and membrane-bound hydrogenase are equally utilizedinactivation of hydrogenase and its accessory genes leads to faster heterotrophic growthwe demonstrate that faster growth is caused by the relief of protein synthesis burdenfitness data is available in an interactive app athttps://m-jahn.shinyapps.io/ShinyLib/
rf and thermal design studies of a 704.4 MHz,
β≈0.2
, continuous-wave rf quadrupole accelerator for frequency jump
Authors: Zhou Bowen , Zhang Chuan 
Published: February 2024

The radio-frequency quadrupole (RFQ) linac is often used as the first radio-frequency (rf) structure for both bunching and preaccelerating proton or heavy ion beams directly behind an ion source or a low-energy beam transport section. Typically, RFQ linacs operate at frequencies below 450 MHz and beam velocity ranges from β=0.01–0.08. Taking the MYRRHA project as an example, a 704.4 MHz continuous-wave (cw) RFQ linac has been recently proposed to realize an efficient fourfold frequency jump at β≈0.2. Due to its high frequency, small dimensions, and cw operation mode, careful design studies for the RFQ cavity structure including the water-cooling channels have been further performed, integrating the idea of using additive manufacturing technology for future construction. Systematic rf and thermal simulations and analysis demonstrated the reliability of the 704.4 MHz RFQ linac at cw operation and the frequency tuning ability via water-speed adjustments. This investigation shows that it could be a highly promising solution to perform an efficient frequency jump with a high-frequency RFQ accelerator at β≈0.2 for large-scale hadron linacs, which could potentially shorten the low- and medium-β parts of the whole facility.

Published by the American Physical Society
2024
Towards a high-intensity muon source
Authors: Cai Han-Jie , He Yuan , Liu Shuhui , Jia Huan , Qin Yuanshuai , Wang Zhijun , Wang Fengfeng , Zhao Lixia , Pu Neng , Niu Jianwei , Chen Liangwen , Sun Zhiyu , Zhao Hongwei , Zhan Wenlong 
Published: February 2024

A high-intensity muon source driven by a continuous-wave superconducting linac holds the potential to significantly advance the intensity frontier of muon sources. Alongside advancements in accelerator technologies, breakthroughs in muon production target and collection schemes are essential. After a brief introduction to the development of the accelerator-driven system superconducting linac, a novel muon production target is proposed, utilizing a free-surface liquid lithium jet capable of handling the heat power generated by a proton beam with an energy of 600 MeV and a current of 5 mA. It is predicted by our simulation studies that the lithium target is more efficient in surface muon production compared to the rotating graphite target. The parameter space of the front end consisting of a lithium target and a large-aperture capture solenoid is explored, from the perspective of production efficiency, capture efficiency, and characteristics of the surface muon beam.

Published by the American Physical Society
2024
Top Yukawa coupling determination at high energy muon collider
Authors: Liu Zhen , Lyu Kun-Feng , Mahbub Ishmam , Wang Lian-Tao 
Published: February 2024

The Top Yukawa coupling profoundly influences several core mysteries linked to the electroweak scale and the Higgs boson. We study the feasibility of measuring the Top Yukawa coupling at high energy muon colliders by examining the high energy dynamics of the weak boson fusion to top quark pair processes. A deviation of the Top Yukawa coupling from the Standard Model would lead to a modified VV→tt¯ process, violating unitarity at high energy. Our analysis reveals that utilizing a muon collider with a center-of-mass energy of 10 TeV and an integrated luminosity of 10  ab−1 allows us to investigate the Top Yukawa coupling with a precision surpassing 1.5%, more than one order of magnitude better than the precision from tt¯h channel at muon colliders. This precision represents a notable enhancement compared to the anticipated sensitivities of the High-Luminosity LHC (3.4%) and those at muon colliders derived from the tt¯H process.

Published by the American Physical Society
2024