bluuebunny/crossref_metadata_2025_split huggingface dataset:
Premigratory experiences with Civil War violence and social trust
Authors: Okundaye Gabriela , Ishiyama John 
Published: February 2024

AbstractDo experiences with civil war violence affect an individual's level of social trust? The literature on this topic suggests that being a victim of violence or being involved in violence has a profound effect on an individual's political behavior in the new host country. However, what has not been explored is how experiences with civil war and violence impact levels of social trust among immigrants. Building on prior research on premigratory experience and literature on experience with violence, we intend to determine if the premigratory experiences with violence in an immigrant's country of origin affect whether social trust is increased or decreased in an immigrant's country of residence. We investigate this question using the National Latino and Asian American Study. We find that immigrants who had experienced civil war as unarmed civilians and were persecuted due to their political beliefs were less likely to acculturate to the host country. Participation in combat also tended to reduce acculturation but did not affect social trust.
Haemolytic transfusion reactions caused by non‐ABO red cell antibodies reported to the Norwegian Haemovigilance System 2004–2020
Authors: Espinosa Aurora , Steinsvåg Christine Torsvik , Flesland Øystein 
Published: February 2024

AbstractBackground and ObjectivesThe aim of this study was to analyse the reports received in the Norwegian Haemovigilance System from 2004 to 2020 on acute and delayed haemolytic transfusion reactions caused by non‐ABO red cell antibodies.Materials and MethodsAntibody specificity, clinical symptoms and outcomes were included when available.ResultsAfter transfusion of 3.7 million red cell concentrates, reports on 78 cases of haemolytic transfusion reactions caused by non‐ABO red cell antibodies were received, corresponding to an incidence of 1 in 47,000 transfused red cell concentrates. There were 30 acute and 48 delayed haemolytic transfusion reactions. A total of 113 red cell antibodies were found: 82 alloantibodies, 6 autoantibodies and 25 cases where the antibody specificity could not be determined. Two fatalities occurred: one caused by anti‐Wra and one caused by an unidentified red cell antibody. The most frequently reported antibody specificities were those in the Rh and Kidd blood group systems, representing 24% and 14%, respectively, of all the antibodies identified. In six cases, errors occurred, leading to the issuing of blood units without the required phenotype match.ConclusionsDespite the possible underreporting, the low number of serious haemolytic transfusion reactions reflects an adequate pre‐transfusion practice by the Norwegian blood banks.
Vagotomy blunts cardiorespiratory responses to vagal afferent stimulation via pre‐ and postsynaptic effects in the nucleus tractus solitarii
Authors: Hofmann Gabrielle C. , Gama de Barcellos Filho Procopio , Khodadadi Fateme , Ostrowski Daniela , Kline David D. , Hasser Eileen M. 
Published: February 2024

AbstractViscerosensory information travels to the brain via vagal afferents, where it is first integrated within the brainstem nucleus tractus solitarii (nTS), a critical contributor to cardiorespiratory function and site of neuroplasticity. We have shown that decreasing input to the nTS via unilateral vagus nerve transection (vagotomy) induces morphological changes in nTS glia and reduces sighs during hypoxia. The mechanisms behind post‐vagotomy changes are not well understood. We hypothesized that chronic vagotomy alters cardiorespiratory responses to vagal afferent stimulation via blunted nTS neuronal activity. Male Sprague–Dawley rats (6 weeks old) underwent right cervical vagotomy caudal to the nodose ganglion, or sham surgery. After 1 week, rats were anaesthetized, ventilated and instrumented to measure mean arterial pressure (MAP), heart rate (HR), and splanchnic sympathetic and phrenic nerve activity (SSNA and PhrNA, respectively). Vagal afferent stimulation (2–50 Hz) decreased cardiorespiratory parameters and increased neuronal Ca2+ measured by in vivo photometry and in vitro slice imaging of nTS GCaMP8m. Vagotomy attenuated both these reflex and neuronal Ca2+ responses compared to shams. Vagotomy also reduced presynaptic Ca2+ responses to stimulation (Cal‐520 imaging) in the nTS slice. The decrease in HR, SSNA and PhrNA due to nTS nanoinjection of exogenous glutamate also was tempered following vagotomy. This effect was not restored by blocking excitatory amino acid transporters. However, the blunted responses were mimicked by NMDA, not AMPA, nanoinjection and were associated with reduced NR1 subunits in the nTS. Altogether, these results demonstrate that vagotomy induces multiple changes within the nTS tripartite synapse that influence cardiorespiratory reflex responses to afferent stimulation.
imageKey points
Multiple mechanisms within the nucleus tractus solitarii (nTS) contribute to functional changes following vagal nerve transection.
Vagotomy results in reduced cardiorespiratory reflex responses to vagal afferent stimulation and nTS glutamate nanoinjection.
Blunted responses occur via reduced presynaptic Ca2+ activation and attenuated NMDA receptor expression and function, leading to a reduction in nTS neuronal activation.
These results provide insight into the control of autonomic and respiratory function, as well as the plasticity that can occur in response to nerve damage and cardiorespiratory disease.
Nonsmooth Reduced Interface Models and Their Use in Co-Simulation of Mechanical Systems
Authors: Raoofian Ali , Dai Xu , Kövecses József 
Published: February 2024

Abstract
In a co-simulation setup, the entire system is decomposed into a collection of individual subsystems that are interfaced together, with each subsystem being modeled and integrated separately according to its own requirements. To maintain the interconnectivity and consolidation of the primary system, these subsystems must communicate with each other through the interface and transfer certain information at the end points of a defined time interval termed macro time step. Inside the macro time step, the evolution of the interface variables has to be approximated as information about them will only be available again at the end of the step. In real-time simulations, the size of the macro time step and the accuracy of the approximated interface variables are critical factors; if the interface variables are approximated accurately, the size of the macro time step can be kept large enough to provide interactive rates without loss of accuracy and stability. This work focuses on systems where unilateral contact interactions are important and proposes reduced interface model concepts for such nonsmooth systems. The use of the proposed reduced interface model (RIM) is demonstrated in co-simulation to provide model-based approximation of the interface variables. The advantages of the proposed method are demonstrated through two representative case studies.
Analysis of Thermomechanical Stress of High-Temperature Ignition Surface Caused by Drop–Wall Interaction at Engine Conditions
Authors: Ahamed Sheikh , Kong Song-Charng 
Published: February 2024

Abstract
Drop–wall interaction is a complex phenomenon encountered in diverse industrial applications. An important example is fuel droplets impinging on a high-temperature ignition plug in a direct-injection compression-ignition engine. The ignition plug, comprised of heat-resistant materials, will experience thermal shock due to abrupt temperature changes. The ensuing temperature fluctuation in the solid wall induces thermal stress, and if this stress surpasses the material's strength in that mode, failure can occur. Therefore, it is imperative to analyze the temperature dynamics on the high-temperature surface to enhance material durability. This study focuses on drop–wall interactions in the engine environment. Utilizing the Smoothed Particle Hydrodynamics (SPH) method, this research simulates fuel droplet impingement on an ignition plug with various materials to characterize heat transfer, thermal penetration, and temperature distributions in the heated wall. The investigation also delves into the behavior of ceramic material, specifically silicon nitride, assessing its thermomechanical stress and durability based on the stress–number of cycles (S-N) curve. Thermal stress is computed by considering temperature gradients and material properties, while mechanical stress is evaluated based on the bending momentum and momentum flux induced by the spray. A parametric study explores diverse materials such as tungsten carbide, iron, stainless steel, carbon steel, and aluminum. Results indicate that thermal stress outweighs bending and spray-induced stress. Moreover, the analysis reveals that silicon nitride exhibits the lowest thermal stress distribution and superior durability, potentially capable of operating for infinite cycles under engine-relevant conditions.
Active microbial population dynamics and life strategies drive the enhanced carbon use efficiency in high-organic matter soils
Authors: Xu Qicheng , Li Ling , Guo Junjie , Guo Hanyue , Liu Manqiang , Guo Shiwei , Kuzyakov Yakov , Ling Ning , Shen Qirong 
Published: February 2024

ABSTRACT

Microbial carbon use efficiency (CUE) is a critical parameter that controls carbon storage in soil, but many uncertainties remain concerning adaptations of microbial communities to long-term fertilization that impact CUE. Based on H
2
18
O quantitative stable isotope probing coupled with metagenomic sequencing, we disentangled the roles of active microbial population dynamics and life strategies for CUE in soils after a long-term (35 years) mineral or organic fertilization. We found that the soils rich in organic matter supported high microbial CUE, indicating a more efficient microbial biomass formation and a greater carbon sequestration potential. Organic fertilizers supported active microbial communities characterized by high diversity and a relative increase in net growth rate, as well as an anabolic-biased carbon cycling, which likely explains the observed enhanced CUE. Overall, these results highlight the role of population dynamics and life strategies in understanding and predicting microbial CUE and sequestration in soil.

IMPORTANCE
Microbial CUE is a major determinant of global soil organic carbon storage. Understanding the microbial processes underlying CUE can help to maintain soil sustainable productivity and mitigate climate change. Our findings indicated that active microbial communities, adapted to long-term organic fertilization, exhibited a relative increase in net growth rate and a preference for anabolic carbon cycling when compared to those subjected to chemical fertilization. These shifts in population dynamics and life strategies led the active microbes to allocate more carbon to biomass production rather than cellular respiration. Consequently, the more fertile soils may harbor a greater microbially mediated carbon sequestration potential. This finding is of great importance for manipulating microorganisms to increase soil C sequestration.
Coding complete genome of a strain of ovine herpesvirus-2 associated with a clinical case of malignant catarrhal fever in a domestic lamb
Authors: Herndon David R. , Herndon Maria K. , Cunha Cristina W. 
Published: February 2024

ABSTRACT

Ovine herpesvirus-2 causes sheep-associated malignant catarrhal fever, a fatal disease of ruminants and pigs. The virus is carried by sheep, and infection is typically subclinical. Here, we report the coding complete genome sequence of a strain of OvHV-2 obtained from a clinically affected domestic lamb.
Draft genomes of meropenem-resistant
Pseudomonads
from the cloacae of turtles in Lake Opinicon, Canada
Authors: Ibrahim Asalia , Bradford Lauren , Bulté Grégory , Wong Alex 
Published: February 2024

ABSTRACT

We report the draft genome sequences of seven meropenem-resistant bacterial isolates from the cloacae of painted and musk turtles at Lake Opinicon, Canada. This study improves our understanding of the spread of meropenem-resistant bacteria in the wild.
Metagenome-assembled genome sequences of two cyanobacterial cultures from Homa Bay County, Kenya
Authors: Brown Katelyn M. , Ward Christopher S. , Bullerjahn George S. 
Published: February 2024

ABSTRACT

Metagenome-assembled genomes were generated for two xenic cyanobacterial strains collected from aquatic sources in Kenya and sequenced by NovaSeq S4. Here, we report the classification and genome statistics of
Microcystis panniformis
WG22 and
Limnospira fusiformis
LS22.
De novo
genome assembly of a probiotic
Lacticaseibacillus rhamnosus
ISO20, isolated from raw milk in South Africa
Authors: Makete Goitsemang , Mamphogoro Tshifhiwa Paris 
Published: February 2024

ABSTRACT

Lactic acid bacteria are known to exhibit probiotic properties through various mechanisms including production of antimicrobial substances and bile salts tolerance. Here, we report a draft genome sequence of
Lacticaseibacillus rhamnosus
ISO20, a lactic acid bacterium isolated from raw goat’s milk to provide genomic insight into its strategies as probiotic strain.
The role of the
C. albicans
transcriptional repressor
NRG1
during filamentation and disseminated candidiasis is strain dependent
Authors: Wakade Rohan S. , Wellington Melanie , Krysan Damian J. 
Published: February 2024

ABSTRACT

Candida albicans
is one of the most common causes of superficial and invasive fungal diseases in humans. Its ability to cause disease is closely linked to its ability to undergo a morphological transition from budding yeast to filamentous forms (hyphae and pseudohyphae). The extent to which
C. albicans
strains isolated from patients undergo filamentation varies significantly. In addition, the filamentation phenotypes of mutants involving transcription factors that positively regulate hyphal morphogenesis can also vary from strain to strain. Here, we characterized the virulence,
in vitro
and
in vivo
filamentation, and
in vitro
and
in vivo
hypha-associated gene expression profiles for four poorly filamenting
C. albicans
isolates and their corresponding deletion mutants of the repressor of filamentation
NRG1
. The two most virulent strains, 57055 and 78048, show robust
in vivo
filamentation but are predominately yeast phase under
in vitro
hypha induction; the two low-virulence strains (94015 and 78042) do not undergo filamentation well under either condition.
In vitro
, deletion of
NRG1
increases hyphae formation in the SC5314 derivative SN250, but only pseudohyphae are formed in the clinical isolates. Deletion of
NRG1
modestly increased the virulence of 78042, which was accompanied by increased expression of hypha-associated genes without an increase in filamentation. Strikingly, deletion of
NRG1
in 78048 reduced filamentation
in vivo
, expression of candidalysin (
ECE1
), and virulence without dramatically altering establishment of infection. Thus, the function of the conserved repressor
NRG1
in
C. albicans
shows strain-based heterogeneity during infection.

IMPORTANCE

Clinical isolates of the human fungal pathogen
Candida albicans
show significant variation in their ability to undergo
in vitro
filamentation and in the function of well-characterized transcriptional regulators of filamentation. Here, we show that Nrg1, a key repressor of filamentation and filament specific gene expression in standard reference strains, has strain-dependent functions, particularly during infection. Most strikingly, loss of
NRG1
function can reduce filamentation, hypha-specific gene expression such as the toxin candidalysin, and virulence in some strains. Our data emphasize that the functions of seemingly fundamental and well-conserved transcriptional regulators such as Nrg1 are contextual with respect to both environment and genetic backgrounds.
A CRISPR interference system for engineering biological nitrogen fixation
Authors: Russell Steven J. , Garcia Amanda K. , Kaçar Betül 
Published: February 2024

ABSTRACT

A grand challenge for the next century is in facing a changing climate through bioengineering solutions. Biological nitrogen fixation, the globally consequential, nitrogenase-catalyzed reduction of atmospheric nitrogen to bioavailable ammonia, is a vital area of focus. Nitrogen fixation engineering relies upon extensive understanding of underlying genetics in microbial models, including the broadly utilized gammaproteobacterium,
Azotobacter vinelandii
(
A. vinelandii
). Here, we report the first CRISPR interference (CRISPRi) system for targeted gene silencing in
A. vinelandii
that integrates genomically via site-specific transposon insertion. We demonstrate that CRISPRi can repress transcription of an essential nitrogen fixation gene by ~60%. Further, we show that nitrogenase genes are suitably expressed from the transposon insertion site, indicating that CRISPRi and engineered nitrogen fixation genes can be co-integrated for combinatorial studies of gene expression and engineering. Our established CRISPRi system fills an important gap for engineering microbial nitrogen fixation for desired purposes.

IMPORTANCE

All life on Earth requires nitrogen to survive. About 78% of the atmosphere alone is nitrogen, yet humans cannot use it directly. Instead, we obtain the nitrogen we need for our survival through the food we eat. For more than 100 years, a substantial portion of agricultural productivity has relied on industrial methods for nitrogen fertilizer synthesis, which consumes significant amounts of nonrenewable energy resources and exacerbates environmental degradation and human-induced climate change. Promising alternatives to these industrial methods rely on engineering the only biological pathway for generating bioaccessible nitrogen: microbial nitrogen fixation. Bioengineering strategies require an extensive understanding of underlying genetics in nitrogen-fixing microbes, but genetic tools for this critical goal remain lacking. The CRISPRi gene silencing system that we report, developed in the broadly utilized nitrogen-fixing bacterial model,
Azotobacter vinelandii
, is an important step toward elucidating the complexity of nitrogen fixation genetics and enabling their manipulation.
Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia
Authors: Schaan Ana Paula , Vidal Amanda , Zhang An-Ni , Poyet Mathilde , Alm Eric J. , Groussin Mathieu , Ribeiro-dos-Santos Ândrea 
Published: February 2024

ABSTRACT

Increasing levels of industrialization have been associated with changes in gut microbiome structure and loss of features thought to be crucial for maintaining gut ecological balance. The stability of gut microbial communities over time within individuals seems to be largely affected by these changes but has been overlooked among transitioning populations from low- to middle-income countries. Here, we used metagenomic sequencing to characterize the temporal dynamics in gut microbiomes of 24 individuals living an urban non-industrialized lifestyle in the Brazilian Amazon. We further contextualized our data with 165 matching longitudinal samples from an urban industrialized and a rural non-industrialized population. We show that gut microbiome composition and diversity have greater variability over time among non-industrialized individuals when compared to industrialized counterparts and that taxa may present diverse temporal dynamics across human populations. Enterotype classifications show that community types are generally stable over time despite shifts in microbiome structure. Furthermore, by tracking genomes over time, we show that levels of bacterial population replacements are more frequent among Amazonian individuals and that non-synonymous variants accumulate in genes associated with degradation of host dietary polysaccharides. Taken together, our results suggest that the stability of gut microbiomes is influenced by levels of industrialization and that tracking microbial population dynamics is important to understand how the microbiome will adapt to these transitions.

IMPORTANCE
The transition from a rural or non-industrialized lifestyle to urbanization and industrialization has been linked to changes in the structure and function of the human gut microbiome. Understanding how the gut microbiomes changes over time is crucial to define healthy states and to grasp how the gut microbiome interacts with the host environment. Here, we investigate the temporal dynamics of gut microbiomes from an urban and non-industrialized population in the Amazon, as well as metagenomic data sets from urban United States and rural Tanzania. We showed that healthy non-industrialized microbiomes experience greater compositional shifts over time compared to industrialized individuals. Furthermore, bacterial strain populations are more frequently replaced in non-industrialized microbiomes, and most non-synonymous mutations accumulate in genes associated with the degradation of host dietary components. This indicates that microbiome stability is affected by transitions to industrialization, and that strain tracking can elucidate the ecological dynamics behind such transitions.
Characterization, taxonomic classification, and genomic analysis of two newly isolated bacteriophages with potential to infect
Escherichia coli
Authors: Nazir Amina , Li Lulu , Li Fei , Tong Yigang , Liu Yuqing , Chen Yibao 
Published: February 2024

ABSTRACT

Escherichia coli
is a pathogenic bacterium that is widely distributed and can lead to serious illnesses in both humans and animals. As there is rising incidence of multidrug resistance among these bacteria, it has become imperative to discover alternative therapies beyond antibiotics to effectively treat such infections. Bacteriophage (phage) therapy has the potential to treat infections caused by
E. coli
, as phages contain enzymes that can cause lysis or destruction of bacterial cells. Simultaneously, the easy accessibility and cost-effectiveness of next-generation sequencing technologies have led to the accumulation of a vast amount of phage sequence data. Here, phages IME177 and IME267 were isolated from sewage water of a hospital in China. Modern phylogenetic approaches and key findings from the genomic analysis revealed that phages IME177 and IME267 are classified as members of the
Kayfunavirus
genus,
Autographiviridae
family, and a newly proposed
Suseptimavirus
genus under subfamily
Gordonclarkvirinae
, respectively. Further, the Kuravirus genus reshaped into three different genera:
Kuravirus
,
Nieuwekanaalvirus
, and
Suspeptimavirus
, which are classified together under a higher taxonomic rank (subfamily) named
Gordonclarkvirinae
. No genes related to virulence were detected in the genomes of the phages IME177 and IME267. Both phages exhibited a high degree of resilience to a wide range of conditions, including pH, temperature, exposure to chloroform, and UV radiation. Phages IME177 and IME267 are promising biological agents that can infect
E. coli
, making them suitable candidates for use in phage therapies.

IMPORTANCE

Biological and taxonomic characterization of phages is essential for facilitating the development of effective strategies for phage therapy and disease control.
Escherichia coli
phages are incredibly diverse, and their isolation and classification help us understand the scope and nature of this diversity. By identifying new phages and grouping them into families, we can better understand the genetic and structural variations between phages and how they affect their infectivity and interactions with bacteria. Overall, the isolation and classification of
E. coli
phages have broad implications for both basic and applied research, clinical practice, and public health.