bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finite Element Model Validation of Cryogenic DOT-113 Tank Car Side Impact Tests
Authors: Eshraghi Shaun , Carolan Michael , Perlman Benjamin , González III Francisco 
Published: June 2024

Abstract
The U.S. Department of Transportation’s (USDOT’s) Federal Railroad Administration (FRA) has sponsored a series of four full-scale side impact tests on specification DOT-113 railroad tank cars. A DOT-113 is a specially designed tank car intended to transport cryogenic liquid commodities. For each side impact test, researchers at the USDOT’s Volpe National Transportation Systems Center (Volpe Center) created a pre-test finite element (FE) model to estimate the overall force-time response of the impactor, puncture/non-puncture outcomes of the impacted tank car, global motions of the tank car, internal pressures within the tank car, and the energy absorbed by the tank car during the impact. While researchers have previously compared FE model results to test measurements for tank car side impact tests, there are currently no formal guidelines on what measurable level of agreement is an acceptable demonstration of FE model validation. This paper presents FE model validation of DOT-113 and DOT-113 surrogate side impact tests using a publicly available software named Correlation and Analysis Plus (CORA) [1] which was originally developed for automotive crashworthiness using models of anthropomorphic test devices, i.e., crash test dummies.
The authors have previously presented FE model validation frameworks for impact simulations [2] and demonstrated FE model validation for non-cryogenic tank car side impacts [3] using CORA and another software called Roadside Verification and Validation Program (RSVVP) [4]. The authors have decided to use CORA in this paper because its validation metrics and rating procedures are included in an ISO technical specification for road vehicles (ISO/TS 18571:2014) [5]. Conversely, RSVVP is not incorporated in a US or international specification.
The results indicate that CORA can be directly applied to tank car side impact model results using the procedures in ISO/TS 18571:2014 when the model does not self-terminate due to puncture. The FE models achieved excellent and good CORA scores for cases without puncture of the tank car. However, early termination of the FE model due to puncture disrupted the automated post-processing of the model results for the two tests that produced a puncture outcome. Further consideration is necessary to develop guidelines that can produce useful validation scores for FE models that include a puncture outcome.
Modeling and Assessment for the Estimation of Heat Transfer Coefficients on Curved Downwards-Facing Heated Walls in Application to ERVC
Authors: Osman Sameer , Afgan Imran , Addad Yacine 
Published: June 2024

Abstract
External Reactor Vessel Cooling (ERVC) is a proposed technique for severe accident mitigation in nuclear power plants. ERVC is aimed at containing the molten corium inside the Reactor Pressure Vessel (RPV) by transporting heat through the coolant (water) which occupies the intentionally flooded reactor cavity and is in direct contact with the outer surface of the lower head. An experimental study along with a computational fluid dynamics (CFD) model are used in the present study to investigate the local convection heat transfer coefficient on curved heated upper walls during the early stages of this type of severe accidents. The CFD study is realized using the open-source code OpenFOAM, in which proper formulation of the physics in terms of mass, momentum, and energy conservation is implemented. Results from the CFD model are compared to the experimental data obtained from a flow-boiling test facility, commissioned, and operated at Khalifa University, in the single-phase regime. The experimental findings highlight that the flat plate correlations are inaccurate for the estimation of the heat transfer coefficient on RPV lower head, especially at high Reynolds number values. Furthermore, the fully resolved turbulence model k-omega SST is the most accurate in predicting the actual thermal boundary layer and turbulent mixing. Quantification of the uncertainty in the experimental measurements as well as the discretization error in the numerical results is provided. In addition, a sensitivity analysis is provided for the inlet turbulence conditions to highlight their importance for accurate solutions. This study provides a framework for the assessment and validation of CFD codes dealing with heat transfer in scenarios where the flow is affected by curved geometries and fluid properties’ variations. In addition, it paves the way for more accurate heat transfer correlations suitable for heat flux partitioning models that can accurately capture the boiling curve in ERVC systems.
Solution Verification Study for Finite Element Analysis of PLLA Stent Implantation
Authors: Osloub Ehsan , Teller Sean S. 
Published: June 2024

Abstract
Numerical simulation models are extensively used in the medical device industry to support device design and reduce costs associated with prototype testing. Regulatory agencies such as the US Food and Drug Administration (FDA) require device manufacturers to follow rigorous simulation verification procedures to assess credibility of numerical simulations used to support submissions. Verification techniques are categorized into code and solution verification, the latter employed to ensure that the numerical solution has converged to the exact solution to the mathematical model. These verification techniques are used even though the exact solution cannot be derived. In other words, solution verification is a method to quantify and minimize discretization error, one of the main sources of numerical error.
In this work, we simulate the crimping of a Poly L-lactic Acid (PLLA) stent in the implantation process using an advanced viscoplastic constitutive model to model the PLLA in a quasi-static implicit scheme with Dassault Systèmes Abaqus 2023 using a reference stent geometry from the literature. We monitor and extract the crimping force and peak maximum principal stress in the stent as the quantities of interest for solution verification. We use Richardson extrapolation to estimate the discretization error between the numerical model and the exact solution. Discretization errors for three systematically refined mesh configurations are quantified and we demonstrate that the solution is in the asymptotic range.
Credibility Assessment of Machine Learning-Based Surrogate Model Predictions on NACA 0012 Airfoil Flow
Authors: Kirsch Jared , Rider William , Fathi Nima 
Published: June 2024

Abstract
The use of surrogate models in computational mechanics is an area of high interest due to the potential for significant savings in computational cost. However, assessment and presentation of evidence for surrogate model credibility has yet to reach a standard form. The present study utilizes a deep neural network as a surrogate for a computational fluid dynamics simulation in order to predict the coefficients of lift and drag on a NACA 0012 airfoil for various Reynolds numbers and angles of attack. Using best practices, the credibility of the underlying simulation predictions and of the surrogate model predictions are analyzed. Conclusions are drawn which should better inform future uses of surrogate models in the context of their credibility.
Complete coding sequence of an Aedes flavivirus strain isolated from
Aedes albopictus
collected in Northern Italy
Authors: Korhonen Essi M. , Truong Nguyen Phuoc T. , Faolotto Giulia , Suvanto Maija T. , Nicosia Anna Maria , Crobu Maria Grazia , Grasso Ivan , Vapalahti Olli , Smura Teemu , Ravanini Paolo , Huhtamo Eili 
Published: June 2024

ABSTRACT

Complete genome data for the globally distributed Aedes flavivirus (AEFV) is scarce. We analyzed a new Italian AEFV strain isolated from
Aedes albopictus
. The results demonstrated genetic diversity among Italian AEFVs. The high similarity between AEFV genomes across geographically distant regions suggests long distance spreading via invasive host mosquito species.
A panel of genotypically and phenotypically diverse clinical
Acinetobacter baumannii
strains for novel antibiotic development
Authors: Sun Chunli , Zhou Danyan , He Jintao , Liu Haiyang , Fu Ying , Zhou Zhihui , Leptihn Sebastian , Yu Yunsong , Hua Xiaoting , Xu Qingye 
Published: June 2024

ABSTRACT

Acinetobacter baumannii
is one of the most important pathogens worldwide. The intrinsic and acquired resistance of
A. baumannii
, coupled with the slow pace of novel antimicrobial drug development, poses an unprecedented and enormous challenge to clinical anti-infective therapy of
A. baumannii
. Recent studies in the field of pathogenicity, antibiotic resistance, and biofilms of
A. baumannii
have focused on the model strains, including ATCC 17978, ATCC 19606, and AB5075. However, these model strains represent only a limited portion of the heterogeneity in
A. baumannii
. Furthermore, variants of these model strains have emerged that show significant diversity not only at the genotypic level but also reflected in differences at the phenotypic levels of capsule, virulence, pathogenicity, and antibiotic resistance. Research on
A. baumannii
, a key pathogen, would benefit from a standardized approach, which characterizes heterogeneous strains in order to facilitate rapid diagnosis, discovery of new therapeutic targets, and efficacy assessment. Our study provides and describes a standardized, genomically and phenotypically heterogeneous panel of 45 different
A. baumannii
strains for the research community. In addition, we performed comparative analyses of several phenotypes of this panel. We found that the sequence type 2 (ST2) group showed significantly higher rates of resistance, lower fitness cost for adaptation, and yet less biofilm formation. The Macrocolony type E (MTE, flat center and wavy edge phenotype reported in the literature) group showed a less clear correlation of resistance rates and growth rate, but was observed to produce more biofilms. Our study sheds light on the complex interplay of resistance fitness and biofilm formation within distinct strains, offering insights crucial for combating
A. baumannii
infection.

IMPORTANCE

Acinetobacter baumannii
is globally notorious, and in an effort to combat the spread of such pathogens, several emerging candidate therapies have already surfaced. However, the strains used to test these therapies vary across studies (the sources and numbers of test strains are varied and often very large, with little heterogeneity). The variation complicates the studies. Furthermore, the limited standardized resources of
A. baumannii
strains have greatly restricted the research on the physiology, pathogenicity, and antibiotic resistance. Therefore, it is crucial for the research community to acquire a standardized and heterogeneous panel of
A. baumannii
. Our study meticulously selected 45 diverse
A. baumannii
strains from a total of 2,197 clinical isolates collected from 64 different hospitals across 27 provinces in China, providing a scientific reference for the research community. This assistance will significantly facilitate scientific exchange in academic research.
Biodegradation of phenol-contaminated soil and plant growth promotion by
Myroides xuanwuensis
H13
Authors: Wang Zhonghua , Zhang Huihong , Zhang Dengxiao , Wang Yi , Han Yanlai , Xue Xia , Jiang Ying 
Published: June 2024

ABSTRACT

Physicochemical methods for remediating phenol-contaminated soils are costly and inefficient, making biodegradation an environmentally friendly alternative approach. This study aims to screen for potential phenol-degrading bacteria and to verify the removal capacities of a selected strain in a bioaugmentation experiment at the greenhouse level using
Brassica chinensis
L. (Chinese cabbage) as the model plant and phenol-contaminated soil. In parallel, pot experiments were conducted using a collaborative approach based on this model system. We found that
Myroides xuanwuensis
strain H13 showed a high degradation capability, with a 97.67% efficiency in degrading 100 mg/L phenol. Under shaking flask conditions, H13 facilitated the solubilization of tricalcium phosphate and potassium feldspar powder. Pot experiments suggested a phenol removal percentage of 89.22% and enhanced availability of soil phosphorus and potassium for plants with H13 inoculation. In this case, the abundance of soil microbes and the activity of soil enzymes significantly increased as well. Furthermore, both photosynthesis and the antioxidant system in Chinese cabbage were enhanced following H13 inoculation, resulting in its increased yield and quality. Partial least squares path modeling revealed that H13 can primarily affect plant root growth, with a secondary impact on photosynthesis. These findings highlight the potential of biodegradation from phenol-degrading bacteria as a promising strategy for efficient phenol removal from soil while promoting plant growth and health.

IMPORTANCE

This study is significant for environmental remediation and agriculture by its exploration of a more environmentally friendly and cost-effective bio-strategy in treating phenol-contaminated soil. These findings have essential implications for environmental remediation efforts and sustainable agriculture. By utilizing the biodegradation capabilities of
Myroides xuanwuensis
strain H13, it is possible to remove phenol contaminants from the soil efficiently, reducing their negative effects. Furthermore, the enhanced growth and health of the Chinese cabbage plants indicate the potential of this approach to promote sustainable crop production.
Risk factors for vancomycin treatment failure in heterogeneous vancomycin-intermediate
Staphylococcus aureus
bacteremia
Authors: Yun Ji Hyun , Chang Euijin , Bae Seongman , Jung Jiwon , Kim Min Jae , Chong Yong Pil , Kim Sung-Han , Choi Sang-Ho , Lee Sang-Oh , Kim Yang Soo 
Published: June 2024

ABSTRACT

The incidence of heterogeneous vancomycin-intermediate
Staphylococcus aureus
(hVISA) infection is increasing and is associated with vancomycin treatment failures. However, studies investigating the risk factors for treatment failure in hVISA infection are limited. Patients with hVISA bacteremia treated with vancomycin over 7 days between August 2008 and June 2020 were enrolled in this study. Clinical and microbiological characteristics were compared between vancomycin treatment failure and success groups to identify the risk factors for vancomycin treatment failure. Among the 180 patients with hVISA bacteremia, 102 patients treated with vancomycin over 7 days were included. Vancomycin treatment failed in 80 (78%) patients. Patients in the vancomycin treatment failure group were older (
P
< 0.001) and more frequently had solid cancer (
P
= 0.04) than those in the vancomycin treatment success group. Solid organ transplantation (SOT) was more frequent (
P
< 0.001) in the vancomycin treatment success group. The Charlson comorbidity index (
P
= 0.01) and Acute Physiology and Chronic Health Evaluation II scores (
P
< 0.001) were higher in the vancomycin treatment failure group. In multivariate analysis, independent risk factors for vancomycin treatment failure were old age and severity of bacteremia. SOT and vancomycin minimal inhibitory concentration (MIC) ≤ 1.0 mg/L using the broth microdilution (BMD) method were associated with successful vancomycin treatment. Old age and infection severity were independent risk factors for vancomycin treatment failure. Vancomycin MIC using the BMD method is an important risk factor for vancomycin treatment failure, and its use should be considered in hVISA bacteremia.

IMPORTANCE

In this study, we assessed the clinical and microbiological characteristics of heterogeneous vancomycin-intermediated
Staphylococcus aureus
(hVISA) bacteremia and identified risk factors for vancomycin treatment failure. We found that advanced age and severity of infection were independent risk factors for vancomycin treatment failure. On the other hand, solid organ transplantation and a low vancomycin minimal inhibitory concentration were associated with successful vancomycin treatment. This study highlights the importance of vancomycin minimal inhibitory concentration in hVISA bacteremia.
Emergence of a novel GIII Getah virus variant in pigs in Guangdong, China, 2023
Authors: Chu Pin-Pin , Guo Hongyuan , Zhou Xia , Chen Sheng-Nan , Sun Xinran , Tian Sicheng , Zou Yu-Gen , Li Chun-Ling , Zhang Rong , Zhai Shao-Lun 
Published: June 2024

ABSTRACT

From May to July of 2023, one pig farm in Heyuan city, Guangdong Province of China, suffered severe piglet death and sow reproductive disorders. The common pig viruses and bacteria tested negative. To uncover the possible cause of the disease, a metagenomic analysis was performed in the pooled small intestine samples from three 8-day-old diseased piglets. The results showed that Getah virus (GETV), an RNA virus, might be the potential pathogen that affects pig health. Subsequently, GETV nucleotide was detected in all of the 15 samples collected from three diseased piglets using quantitative reverse transcription PCR, suggesting GETV as the main pathogen of the disease. A GETV strain, designated as GDHYLC23, was successfully isolated using the swine testicle cell line. Sequence analysis showed that the epidemic strain had a unique 32-nucleotide repeat insertion in the 3′ noncoding region. Phylogenetic analysis showed that GDHYLC23 belonged to the pandemic group III. The identification of GETV with new variations implies the continuous evolution of the virus, which poses potential threats to the swine industry.

IMPORTANCE
Pig farms are faced with emerging and re-emerging viruses that may cause substantial economic loss. The identification of potentially pathogenic viruses helps to prevent and control the spread of diseases. In this study, by using metagenomic analysis, we found that a neglected virus, GETV with a unique insertion in the genome, was the main pathogen in one pig farm that suffered severe piglet death and sow reproductive disorders. Although the potential impact of such an insertion on viral pathogenicity is unknown, the surveillance of the continuing evolution of GETV in pig farms cannot be ignored.
The
dmsEFABGH
operon encodes an essential and modular electron transfer pathway for extracellular iodate reduction by
Shewanella oneidensis
MR-1
Authors: Hou Lingyu , Zheng Beiling , Jiang Zhou , Hu Yidan , Shi Liang , Dong Yiran , Jiang Yongguang 
Published: June 2024

ABSTRACT

Extracellular iodate reduction by
Shewanella
spp. contributes to iodide generation in the biogeochemical cycling of iodine. However, there is a disagreement on whether
Shewanella
spp. use different extracellular electron transfer pathways with dependence on electron donors in iodate reduction. In this study, a series of gene deletion mutants of
Shewanella oneidensis
MR-1 were created to investigate the roles of
dmsEFABGH
,
mtrCAB,
and
so4357–so4362
operons in iodate reduction. The iodate-reducing activity of the mutants was tested with lactate, formate, and H
2
as the sole electron donors, respectively. In the absence of single-
dms
gene, iodate reduction efficiency of the mutants was only 12.9%–84.0% with lactate at 24 hours, 22.1%–85.9% with formate at 20 hours, and 19.6%–57.7% with H
2
at 42 hours in comparison to complete reduction by the wild type. Progressive inhibition of iodate reduction was observed when the
dms
homolog from the
so4357–so4362
operon was deleted in the single-
dms
gene mutants. This result revealed complementation of
dmsEFABGH
by
so4357–so4362
at the single-gene level, indicating modularity of the extracellular electron transfer pathway encoded by
dmsEFABGH
operon. Under the conditions of all electron donors, significant inhibition of iodate reduction and accumulation of H
2
O
2
were detected for Δ
mtrCAB
. Collectively, these results demonstrated that the
dmsEFABGH
operon encodes an essential and modular iodate-reducing pathway without electron donor dependence in
S. oneidensis
MR-1. The
mtrCAB
operon was involved in H
2
O
2
elimination with all electron donors. The findings in this study improved the understanding of molecular mechanisms underlying extracellular iodate reduction.

IMPORTANCE

Iodine is an essential trace element for human and animals. Recent studies revealed the contribution of microbial extracellular reduction of iodate in biogeochemical cycling of iodine. Multiple reduced substances can be utilized by microorganisms as energy source for iodate reduction. However, varied electron transfer pathways were proposed for iodate reduction with different electron donors in the model strain
Shewanella oneidensis
MR-1. Here, through a series of gene deletion and iodate reduction experiments, we discovered that the
dmsEFABGH
operon was essential for iodate reduction with at least three electron donors, including lactate, formate, and H
2
. The
so4357–so4362
operon was first demonstrated to be capable of complementing the function of
dmsEFABGH
at single-gene level.
Pangenome-wide association study reveals the selective absence of CRISPR genes (Rv2816c-19c) in drug-resistant
Mycobacterium tuberculosis
Authors: Bhalla Nikhil , Nanda Ranjan Kumar 
Published: June 2024

ABSTRACT

The presence of intermittently dispersed insertion sequences and transposases in the
Mycobacterium tuberculosis
(Mtb) genome makes intra-genome recombination events inevitable. Understanding their effect on the gene repertoires (GR), which may contribute to the development of drug-resistant Mtb, is critical. In this study, publicly available WGS data of clinical Mtb isolates (endemic region
n
= 2,601; non-endemic region
n
= 1,130) were
de novo
assembled, filtered, scaffolded into assemblies, and functionally annotated. Out of 2,601 Mtb WGS data sets from endemic regions, 2,184 (drug resistant/sensitive: 1,386/798) qualified as high quality. We identified 3,784 core genes, 123 softcore genes, 224 shell genes, and 762 cloud genes in the pangenome of Mtb clinical isolates from endemic regions. Sets of 33 and 39 genes showed positive and negative associations (
P
< 0.01) with drug resistance status, respectively. Gene ontology clustering showed compromised immunity to phages and impaired DNA repair in drug-resistant Mtb clinical isolates compared to the sensitive ones. Multidrug efflux pump repressor genes (Rv3830c and Rv3855c) and CRISPR genes (Rv2816c-19c) were absent in the drug-resistant Mtb. A separate WGS data analysis of drug-resistant Mtb clinical isolates from the Netherlands (
n
= 1130) also showed the absence of CRISPR genes (Rv2816c-17c). This study highlights the role of CRISPR genes in drug resistance development in Mtb clinical isolates and helps in understanding its evolutionary trajectory and as useful targets for diagnostics development.

IMPORTANCE
The results from the present Pan-GWAS study comparing gene sets in drug-resistant and drug-sensitive Mtb clinical isolates revealed intricate presence-absence patterns of genes encoding DNA-binding proteins having gene regulatory as well as DNA modification and DNA repair roles. Apart from the genes with known functions, some uncharacterized and hypothetical genes that seem to have a potential role in drug resistance development in Mtb were identified. We have been able to extrapolate many findings of the present study with the existing literature on the molecular aspects of drug-resistant Mtb, further strengthening the relevance of the results presented in this study.