bluuebunny/crossref_metadata_2025_split huggingface dataset:
Organ xenotransplantation acceptance in veterinary students: A multicentric opinion study in Spain
Authors: Martínez‐Alarcón Laura , Flores‐Medina Juan , Ramis Guillermo , Gómez‐Laguna Jaime , Moll Xavier , Falceto Victoria , San Román‐Ascaso Fidel , San Román‐Llorens Fidel , Quereda Juan José , Herrero Juan Manuel , Mendonça Livia , Martin‐Barrasa José Luis , Fernández Olga María , Muñoz Antonio , Ramírez Pablo , Gutiérrez Pedro , López‐Chicheri Isabel , López‐Navas Ana , Ríos Antonio 
Published: September 2023

AbstractBackgroundThe shortage of available transplant organs has made it necessary to search for alternatives, one of which is xenotransplantation. However, the use of animal organs could face rejection from society and the personnel involved in its implementation. Objectives: (a) to analyze the attitudes of Veterinary Degree students in six Spanish Universities towards xenotransplantation; and (b) to determine the factors that affect its acceptance.MethodsOf the 2815 students surveyed in the degree program, 2683 valid surveys were obtained. Attitudes towards organ xenotransplantation were evaluated using a validated questionnaire of organ donation.ResultsIf xenotransplantation was confirmed as a clinical reality, 93% (n = 2493) of those surveyed would accept a xenotransplanted organ, whilst 7% would not. If the results of xenotransplantation were worse than those obtained with human donors and it entailed more risk, 12% (n = 318) would be in favor. 56% (n = 1497) of the students would accept a xenotransplantation provisionally pending the arrival of a human organ. Attitudes towards xenotransplantation were affected by the academic year in which a student was studying, with more favorable attitudes among students in the last year (88% in first year vs. 95% in fifth year;p < .001). More favorable attitudes are also observed depending on the attitude they have towards organ transplantation, with those students being more in favor of donating their organs when they die (94% vs. 88%;p < .001).ConclusionVeterinary students would have a very favorable attitude toward xenotransplantation if these animal organs functioned as well as human organs. Therefore, these students could play an important role in the future promotion of this technique.
High-Dimensional Uncertainty Quantification of High-Pressure Turbine Vane Based on Multifidelity Deep Neural Networks
Authors: Li Zhihui , Montomoli Francesco , Casari Nicola , Pinelli Michele 
Published: September 2023

Abstract
In this work, a new multifidelity (MF) uncertainty quantification (UQ) framework is presented and applied to the LS89 nozzle modified by fouling. Geometrical uncertainties significantly influence the aerodynamic performance of gas turbines. One representative example is given by the airfoil shape modified by fouling deposition, as in turbine nozzle vanes, which generates high-dimensional input uncertainties. However, the traditional UQ approaches suffer from the curse of dimensionality phenomenon in predicting the influence of high-dimensional uncertainties. Thus, a new approach based on multifidelity deep neural networks (MF-DNN) was proposed in this paper to solve the high-dimensional UQ problem. The basic idea of MF-DNN is to ensure the approximation capability of neural networks based on abundant low-fidelity (LF) data and few high-fidelity (HF) data. The prediction accuracy of MF-DNN was first evaluated using a 15-dimensional benchmark function. An affordable turbomachinery UQ platform was then built based on key components including the MF-DNN model, the sampling module, the parameterization module and the statistical processing module. The impact of fouling deposition on LS89 nozzle vane flow was investigated using the proposed UQ framework. In detail, the MF-DNN was fine-tuned based on bi-level numerical simulation results: the 2D Euler flow field as low-fidelity data and the 3D Reynolds-averaged Navier–Stokes (RANS) flow field as high-fidelity data. The UQ results show that the total pressure loss of LS89 vane is increased by at most 17.1% or reduced by at most 4.3%, while the mean value of the loss is increased by 3.4% compared to the baseline. The main reason for relative changes in turbine nozzle performance is that the geometric uncertainties induced by fouling deposition significantly alter the intensity of shock waves near the throat area and trailing edge. The developed UQ platform could provide a useful tool in the design and optimization of advanced turbomachinery considering high-dimensional input uncertainties.
Oral administration of a 2-aminopyrimidine robenidine analogue (NCL195) significantly reduces
Staphylococcus aureus
infection and reduces
Escherichia coli
infection in combination with sub-inhibitory colistin concentrations in a bioluminescent mouse model
Authors: Nguyen Hang Thi , Venter Henrietta , Woolford Lucy , Young Kelly A. , McCluskey Adam , Garg Sanjay , Sapula Sylvia S. , Page Stephen W. , Ogunniyi Abiodun David , Trott Darren J. 
Published: September 2023

ABSTRACT

We have previously reported promising
in vivo
activity of the first-generation 2-aminopyramidine robenidine analogue NCL195 against Gram-positive bacteria (GPB) when administered via the systemic route. In this study, we examined the efficacy of oral treatment with NCL195 (± low-dose colistin) in comparison to oral moxifloxacin in bioluminescent
Staphylococcus aureus
and
Escherichia coli
peritonitis-sepsis models. Four oral doses of 50 mg/kg NCL195, commencing immediately post-infection, were administered at 4 h intervals in the
S. aureus
peritonitis-sepsis model. We used a combination of four oral doses of 50 mg/kg NCL195 and four intraperitoneal doses of colistin at 0.125 mg/kg, 0.25 mg/kg, or 0.5 mg/kg in the
E. coli
peritonitis-sepsis model. Subsequently, the dose rates of four intraperitoneal doses of colistin were increased to 0.5 mg/kg, 1 mg/kg, or 2 mg/kg at 4 h intervals to treat a colistin-resistant
E. coli
infection. In the
S. aureus
infection model, oral treatment of mice with NCL195 resulted in significantly reduced
S. aureus
infection loads (
P
< 0.01) and longer survival times (
P
< 0.001) than vehicle-only treated mice. In the
E. coli
infection model, co-administration of NCL195 and graded doses of colistin resulted in a dose-dependent significant reduction in colistin-susceptible (
P
< 0.01) or colistin-resistant (
P
< 0.05)
E. coli
loads compared to treatment with colistin alone at similar concentrations. Our results confirm that NCL195 is a potential candidate for further preclinical development as a specific treatment for multidrug-resistant infections, either as a stand-alone antibiotic for GPB or in combination with sub-inhibitory concentrations of colistin for Gram-negative bacteria.
Expression of V-nitrogenase and Fe-nitrogenase in
Methanosarcina acetivorans
is controlled by molybdenum, fixed nitrogen, and the expression of Mo-nitrogenase
Authors: Chanderban Melissa , Hill Christopher A. , Dhamad Ahmed E. , Lessner Daniel J. 
Published: September 2023

ABSTRACT

All nitrogen-fixing bacteria and archaea (diazotrophs) use molybdenum (Mo) nitrogenase to reduce dinitrogen (N
2
) to ammonia, with some also containing vanadium (V) and iron-only (Fe) nitrogenases that lack Mo. Among diazotrophs, the regulation and usage of the alternative V-nitrogenase and Fe-nitrogenase in methanogens are largely unknown.
Methanosarcina acetivorans
contains
nif
,
vnf
, and
anf
gene clusters encoding putative Mo-nitrogenase, V-nitrogenase, and Fe-nitrogenase, respectively. This study investigated nitrogenase expression and growth by
M. acetivorans
in response to fixed nitrogen, Mo/V availability, and CRISPRi repression of the
nif
,
vnf
, and/or
anf
gene clusters. The availability of Mo and V significantly affected growth of
M. acetivorans
with N
2
but not with NH
4
Cl.
M. acetivorans
exhibited the fastest growth rate and highest cell yield during growth with N
2
in medium containing Mo, and the slowest growth in medium lacking Mo and V. qPCR analysis revealed the transcription of the
nif
operon is only moderately affected by depletion of fixed nitrogen and Mo, whereas
vnf
and
anf
transcription increased significantly when fixed nitrogen and Mo were depleted, with removal of Mo being key. Immunoblot analysis revealed Mo-nitrogenase is detected when fixed nitrogen is depleted regardless of Mo availability, while V-nitrogenase and Fe-nitrogenase are detected only in the absence of fixed nitrogen and Mo. CRISPRi repression studies revealed that V-nitrogenase and/or Fe-nitrogenase are required for Mo-independent diazotrophy, and unexpectedly that the expression of Mo-nitrogenase is also required. These results reveal that alternative nitrogenase production in
M. acetivorans
is tightly controlled and dependent on Mo-nitrogenase expression.

IMPORTANCE
Methanogens and closely related methanotrophs are the only archaea known or predicted to possess nitrogenase. Methanogens play critical roles in both the global biological nitrogen and carbon cycles. Moreover, methanogens are an ancient microbial lineage and nitrogenase likely originated in methanogens. An understanding of the usage and properties of nitrogenases in methanogens can provide new insight into the evolution of nitrogen fixation and aid in the development nitrogenase-based biotechnology. This study provides the first evidence that a methanogen can produce all three forms of nitrogenases, including simultaneously. The results reveal components of Mo-nitrogenase regulate or are needed to produce V-nitrogenase and Fe-nitrogenase in methanogens, a result not seen in bacteria. Overall, this study provides a foundation to understand the assembly, regulation, and activity of the alternative nitrogenases in methanogens.
Alterations in gp120 glycans or the gp41 fusion peptide-proximal region modulate the stability of the human immunodeficiency virus (HIV-1) envelope glycoprotein pretriggered conformation
Authors: Zhang Zhiqing , Wang Qian , Nguyen Hanh T. , Chen Hung-Ching , Chiu Ta-Jung , Smith III Amos B. , Sodroski Joseph G. 
Published: September 2023

ABSTRACT
The human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer mediates entry into host cells by binding receptors, CD4 and CCR5/CXCR4, and fusing the viral and cell membranes. In infected cells, cleavage of the gp160 Env precursor yields the mature Env trimer, with gp120 exterior and gp41 transmembrane Env subunits. Env cleavage stabilizes the State-1 conformation, which is the major target for broadly neutralizing antibodies, and decreases the spontaneous sampling of more open Env conformations that expose epitopes for poorly neutralizing antibodies. During HIV-1 entry into cells, CD4 binding drives the metastable Env from a pretriggered (State-1) conformation into more “open,” lower-energy states. Here, we report that changes in two dissimilar elements of the HIV-1 Env trimer, namely particular gp120 glycans and the gp41 fusion peptide-proximal region (FPPR), can independently modulate the stability of State 1. Individual deletion of several gp120 glycans destabilized State 1, whereas removal of a V1 glycan resulted in phenotypes indicative of a more stable pretriggered Env conformation. Likewise, some alterations of the gp41 FPPR decreased the level of spontaneous shedding of gp120 from the Env trimer and stabilized the pretriggered State-1 Env conformation. State-1-stabilizing changes were additive and could suppress the phenotypes associated with State-1-destabilizing alterations in Env. Our results support a model in which multiple protein and carbohydrate elements of the HIV-1 Env trimer additively contribute to the stability of the pretriggered (State-1) conformation. The Env modifications identified in this study will assist efforts to characterize the structure and immunogenicity of the metastable State-1 conformation.

IMPORTANCE
The elicitation of antibodies that neutralize multiple strains of HIV-1 is an elusive goal that has frustrated the development of an effective vaccine. The pretriggered shape of the HIV-1 envelope glycoprotein (Env) spike on the virus surface is the major target for such broadly neutralizing antibodies. The “closed” pretriggered Env shape resists the binding of most antibodies but is unstable and often assumes “open” shapes that elicit ineffective antibodies. We identified particular changes in both the protein and the sugar components of the Env trimer that stabilize the pretriggered shape. Combinations of these changes were even more effective at stabilizing the pretriggered Env than the individual changes. Stabilizing changes in Env could counteract the effect of Env changes that destabilize the pretriggered shape. Locking Env in its pretriggered shape will assist efforts to understand the Env spike on the virus and to incorporate this shape into vaccines.
Limiting viral replication in hepatocytes alters Rift Valley fever virus disease manifestations
Authors: Xu Lingqing , Paine Alden C. , Barbeau Dominique J. , Alencastro Frances , Duncan Andrew W. , McElroy Anita K. 
Published: September 2023

ABSTRACT

Rift Valley fever virus (RVFV) causes mild to severe disease in humans and livestock. Outbreaks of RVFV have been reported throughout Africa and have spread outside Africa since 2000, calling for urgent worldwide attention to this emerging virus. RVFV directly infects the liver, and elevated transaminases are a hallmark of severe RVFV infection. However, the specific contribution of viral replication in hepatocytes to pathogenesis of RVFV remains undefined. To address this, we generated a recombinant miRNA-targeted virus, RVFVmiR-122, to limit hepatocellular replication. MicroRNAs are evolutionarily conserved non-coding RNAs that regulate mRNA expression by targeting them for degradation. RVFVmiR-122 includes an insertion of four target sequences of the liver-specific miR-122. In contrast to control RVFVmiR-184, which contains four target sequences of mosquito-specific miR-184, RVFVmiR-122 has restricted replication
in vitro
in primary mouse hepatocytes. RVFVmiR-122-infected C57BL/6 mice survived acute hepatitis and instead developed late-onset encephalitis. This difference in clinical outcome was eliminated in
Mir-122 KO
mice, confirming the specificity of the finding. Interestingly, C57BL/6 mice infected with higher doses of RVFVmiR-122 had a higher survival rate which was correlated with faster clearance of virus from the liver, suggesting a role for activation of host immunity in the phenotype. Together, our data demonstrate that miR-122 can specifically restrict the replication of RVFVmiR-122 in liver tissue both
in vitro
and
in vivo
, and this restriction alters the clinical course of disease following RVFVmiR-122 infection.

IMPORTANCE
Rift Valley fever virus (RVFV) is a hemorrhagic fever virus that causes outbreaks in humans and livestock throughout Africa and has spread to continents outside Africa since 2000. However, no commercial vaccine or treatment is currently available for human use against RVFV. Although the liver has been demonstrated as a key target of RVFV, the contribution of viral replication in hepatocytes to overall RVFV pathogenesis is less well defined. In this study we addressed this question by using a recombinant miRNA-targeted virus with restricted replication in hepatocytes. We gained a better understanding of how this individual cell type contributes to the development of disease caused by RVFV. Techniques used in this study provide an innovative tool to the RVFV field that could be applied to study the consequences of limited RVFV replication in other target cells.
PARP12 is required to repress the replication of a Mac1 mutant coronavirus in a cell- and tissue-specific manner
Authors: Kerr Catherine M. , Parthasarathy Srivatsan , Schwarting Nancy , O'Connor Joseph J. , Pfannenstiel Jessica J. , Giri Emily , More Sunil , Orozco Robin C. , Fehr Anthony R. 
Published: September 2023

ABSTRACT

ADP-ribosyltransferases (ARTs) mediate the transfer of ADP-ribose from NAD
+
to protein or nucleic acid substrates. This modification can be removed by several different types of proteins, including macrodomains. Several ARTs, also known as PARPs, are stimulated by interferon indicating ADP-ribosylation is an important aspect of the innate immune response. All coronaviruses (CoVs) encode for a highly conserved macrodomain (Mac1) that is critical for CoVs to replicate and cause disease, indicating that ADP-ribosylation can effectively control coronavirus infection. Our siRNA screen indicated that PARP12 might inhibit the replication of a murine hepatitis virus (MHV) Mac1 mutant virus in bone-marrow-derived macrophages (BMDMs). To conclusively demonstrate that PARP12 is a key mediator of the antiviral response to CoVs both in cell culture and
in vivo
, we produced PARP12
−/−
mice and tested the ability of MHV A59 (hepatotropic/neurotropic) and JHM (neurotropic) Mac1 mutant viruses to replicate and cause disease in these mice. Notably, in the absence of PARP12, Mac1 mutant replication was increased in BMDMs and mice. In addition, liver pathology was also increased in A59-infected mice. However, the PARP12 knockout did not restore Mac1 mutant virus replication to WT virus levels in all cell or tissue types and did not significantly increase the lethality of Mac1 mutant viruses. These results demonstrate that while PARP12 inhibits MHV Mac1 mutant virus infection, additional PARPs or innate immune factors must contribute to the extreme attenuation of this virus in mice.

IMPORTANCE
Over the last decade, the importance of ADP-ribosyltransferases (ARTs), also known as PARPs, in the antiviral response has gained increased significance as several were shown to either restrict virus replication or impact innate immune responses. However, there are few studies showing ART-mediated inhibition of virus replication or pathogenesis in animal models. We found that the CoV macrodomain (Mac1) was required to prevent ART-mediated inhibition of virus replication in cell culture. Using knockout mice, we found that PARP12, an interferon-stimulated ART, was required to repress the replication of a Mac1 mutant CoV both in cell culture and in mice, demonstrating that PARP12 represses coronavirus replication. However, the deletion of PARP12 did not fully rescue Mac1 mutant virus replication or pathogenesis, indicating that multiple PARPs function to counter coronavirus infection.
The major role of
Listeria monocytogenes
folic acid metabolism during infection is the generation of N-formylmethionine
Authors: Feng Ying , Chang Shannon K. , Portnoy Daniel A. 
Published: September 2023

ABSTRACT

Folic acid and its derivatives (folates) play central roles in one-carbon metabolism, necessary for the synthesis of purines, pyrimidines, and some amino acids. Antifolate drugs are widely used as broad-spectrum antibiotics for bacterial infections, including listeriosis, a disease caused by the facultative intracellular pathogen
Listeria monocytogenes
. However, folate-derived metabolites required during bacterial infection are poorly understood. Here, we report that
L. monocytogenes
encodes two enzymes, methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase (FolD) and formyltetrahydrofolate synthetase (Fhs), that catalyze the formation of N10-formyltetrahydrofolate, a critical intermediate in folate metabolism. N10-formyltetrahydrofolate is an essential carbon donor for biosynthesis of purines and N-formylmethionine, the amino acid used during initiation of bacteria translation. While
L. monocytogenes
mutants lacking Fhs had no observable defects and mutants lacking FolD had moderate virulence defects, mutants lacking both were highly attenuated in mice, especially in the liver. We compared the growth and virulence of mutants that were unable to synthesize folates with mutants unable to generate folate downstream products, including purines, thymidine, and N-formylmethionine. Mutants unable to synthesize N-formylmethionine behaved almost identically to FolD/Fhs double mutants during growth in broth or macrophages, but most importantly, were similarly attenuated to mutants unable to make folates, both of which had approximately 4-log
10
less colony-forming units in the livers compared with wild-type
L. monocytogenes
. The purine auxotrophic mutants were only 1.5-log
10
less virulent, and the thymidine mutants were fully virulent in the mouse infection model. These results strongly suggest that the main role of
L. monocytogenes
folates during infection is the generation of N-formylmethionine.

Importance

Folic acid is an essential vitamin for bacteria, plants, and animals. The lack of folic acid leads to various consequences such as a shortage of amino acids and nucleotides that are fundamental building blocks for life. Though antifolate drugs are widely used for antimicrobial treatments, the underlying mechanism of bacterial folate deficiency during infection is unclear. This study compares the requirements of different folic acid end-products during the infection of
Listeria monocytogenes
, a facultative intracellular pathogen of animals and humans. The results reveal the critical importance of N-formylmethionine, the amino acid used by bacteria to initiate protein synthesis. This work extends the current understanding of folic acid metabolism in pathogens and potentially provides new insights into antifolate drug development in the future.
Targeted curation of the gut microbial gene content modulating human cardiovascular disease
Authors: Borton Mikayla A. , Shaffer Michael , Hoyt David W. , Jiang Ruisheng , Ellenbogen Jared B. , Purvine Samuel , Nicora Carrie D. , Eder Elizabeth K. , Wong Allison R. , Smulian A. George , Lipton Mary S. , Krzycki Joseph A. , Wrighton Kelly C. 
Published: September 2023

ABSTRACT
Despite the promise of the gut microbiome to predict human health, few studies expose the molecular-scale processes underpinning such forecasts. We mined over 200,000 gut-derived genomes from cultivated and uncultivated microbial lineages to inventory the gut microorganisms and their gene content that control trimethylamine-induced cardiovascular disease. We assigned an atherosclerotic profile to the 6,341 microbial genomes that encoded metabolisms associated with heart disease, creating the Methylated Amine Gene Inventory of Catabolism database (MAGICdb). From microbiome gene expression data sets, we demonstrate that MAGICdb enhanced the recovery of disease-relevant genes and identified the most active microorganisms, unveiling future therapeutic targets. From the feces of healthy and diseased subjects, we show that MAGICdb predicted cardiovascular disease status as effectively as traditional lipid blood tests. This functional microbiome catalog is a public, exploitable resource, designed to enable a new era of microbiota-based therapeutics and diagnostics.

IMPORTANCE
One of the most-cited examples of the gut microbiome modulating human disease is the microbial metabolism of quaternary amines from protein-rich foods. By-products of this microbial processing promote atherosclerotic heart disease, a leading cause of human mortality globally. Our research addresses current knowledge gaps in our understanding of this microbial metabolism by holistically inventorying the microorganisms and expressed genes catalyzing critical atherosclerosis-promoting and -ameliorating reactions in the human gut. This led to the creation of an open-access resource, the Methylated Amine Gene Inventory of Catabolism database, the first systematic inventory of gut methylated amine metabolism. More importantly, using this resource we deliver here, we show for the first time that these gut microbial genes can predict human disease, paving the way for microbiota-inspired diagnostics and interventions.