bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effect of Pulsed Power During Electrochemical Surface Modification on the Wettability of Aluminum and Titanium Alloy
Authors: Petrenko Anton , B. Kamaraj Abishek 
Published: February 2024

Abstract
Aluminum and especially titanium alloy are increasingly being used to replace traditional metals in many new applications due to their high strength-to-weight ratio and biocompatibility. Surgical implants need to have a hydrophilic nature when tissue growth is desired, while they need to be hydrophobic if tissue/microbial growth is not expected. Thus, there is a need to control the wettability of these metals. This study used a sodium chlorate electrolyte to control the wettability of 1-inch by 3-inch aluminum and titanium alloy samples using an electrochemical surface modification (ECSM) process. Duty cycle, frequency, and ECSM duration were modified while voltage was held constant at 10 V. Duty cycles of 25%, 50%, 75%, and 100% (or direct current) and frequencies of 1 kHz and 100 kHz were used. The time of processing was changed to allow the samples to have an equal active time with 2000, 1000, 667, and 500 seconds for 25%, 50%, 75%, and 100% duty cycles, respectively. A first principles-based theoretical model was developed in this study to predict the pulse power setting needed to achieve the desired wettability in the samples by measuring the sample mass before and after ECSM. The model was validated with experimental results. The surface’s wettability switched from superhydrophilic to hydrophilic after the sample was heated in a furnace. Both the metals showed a change in contact angle behavior after evaporation of the residual water. This study allows for the use of ECSM as a technique to modify the surface of implants with controlled wettability for improved osseointegration.
CFD-Based Optimization of the Kinematic Cycle of an Oscillating Foil Energy Harvesting Device
Authors: Rovito Nick , Walters D. Keith 
Published: February 2024

Abstract
This paper investigates the effects of kinematic operational parameters on oscillating foil energy harvester (OFEH) performance and presents a method for determining operating points corresponding to optimum performance. The optimization is carried out for an initial proof-of-concept OFEH design, and two different operating conditions are investigated with three and five degrees of freedom (DOF), respectively, represented by non-dimensional kinematic operating parameters. To determine OFEH efficiency at each operating condition, computational fluid dynamics (CFD) simulations were conducted using Ansys Fluent v. 22.1. Resulting optimum performance operating points and efficiencies are compared to numerical and experimental investigations previously documented in the open literature. Results from both the 3- and 5-DOF cases demonstrate that the optimization method is able to determine efficiency maxima iteratively with limited data. The efficiency optima and operating points obtained agree with the ranges reported in the open literature. Overall, the results suggest that implementation of an iterative optimization search using least-squares based localized response surface modeling may reduce computational resource and time requirements when using computational fluid dynamics in engineering design.
Foil Gas Bearing Damping Measurements and Analysis With Varied Configurations
Authors: Knechel Jared , Agrawal Giri , Sahay Chittaranjan , Ghosh Suhash 
Published: February 2024

Abstract
Predictions of bearing damping in turbomachinery are essential to developing reliable, efficient, and safe products. Analytic solutions are practically non-existent. Numerical solutions and simulations are very limited and experimental data is usually specific to a particular configuration. The present work intends to serve the turbomachinery designer in their selection and configuration of Foil Gas Bearings (FGBs), as it makes a connection between some common bearing configuration parameters, the applied load level and frequency, and the level of bearing damping they can expect.
To obtain the data required to build a model that captures these relationships, several configurations of foil gas journal bearings are subjected to oscillating loads through the use of an electro-mechanical shaker. The bearing displacement and load signals are recorded and analyzed to obtain a coefficient of equivalent viscous damping at frequencies between 20 and 400 Hz and at loads between 2 and 11 lbf. The bearing configuration variations include bump foil thickness, pitch, and height. The data is analyzed and a model developed using a non-linear regression method. The model captures the relationship between an equivalent viscous damping coefficient and a forcing frequency, load, and a non-dimensional geometry configuration parameter G. The findings may serve as a practical tool for designers of turbomachinery supported by FGBs.
Degradation of
Listeria monocytogenes
biofilm by phages belonging to the genus
Pecentumvirus
Authors: Cucić Stevan , Ells Tim , Guri Anilda , Kropinski Andrew M. , Khursigara Cezar M. , Anany Hany 
Published: February 2024

ABSTRACT

Listeria monocytogenes
is a pathogenic foodborne bacterium that is a significant cause of mortality associated with foodborne illness and causes many food recalls attributed to a bacteriological cause. Their ability to form biofilms contributes to the persistence of
Listeria
spp. in food processing environments. When growing as biofilms,
L. monocytogenes
are more resistant to sanitizers used in the food industry, such as benzalkonium chloride (BAC), as well as to physical stresses like desiccation and starvation. Lytic phages of
Listeria
are antagonistic to a broad range of
Listeria
spp. and may, therefore, have utility in reducing the occurrence of
Listeria
-associated food recalls by preventing food contamination. We screened nine closely related
Listeria
phages, including the commercially available Listex P100, for host range and ability to degrade microtiter plate biofilms of
L. monocytogenes
ATCC 19111 (serovar 1/2a). One phage, CKA15, was selected and shown to rapidly adsorb to its host under conditions relevant to applying the phage in dairy processing environments. Under simulated dairy processing conditions (SDPC), CKA15 caused a 2-log reduction in
Lm
19111 biofilm bacteria. This work supports the biosanitation potential of phage CKA15 and provides a basis for further investigation of phage-bacteria interactions in biofilms grown under SDPC.

IMPORTANCE

Listeria monocytogenes
is a pathogenic bacterium that is especially dangerous for children, the elderly, pregnant women, and immune-compromised people. Because of this, the food industry takes its presence in their plants seriously. Food recalls due to
L. monocytogenes
are common with a high associated economic cost. In food-processing plants,
Listeria
spp. typically reside in biofilms, which are structures produced by bacteria that shield them from environmental stressors and are often attached to surfaces. The significance of our work is that we show a bacteriophage—a virus-infecting bacteria—can reduce
Listeria
counts by two orders of magnitude when the bacterial biofilms were grown under simulated dairy processing conditions. This work provides insights into how phages may be tested and used to develop biosanitizers that are effective but are not harmful to the environment or human health.
Culture-independent identification of bloodstream infections from whole blood: prospective evaluation in specimens of known infection status
Authors: Iyer Vidya , Castro Daniel , Malla Bipin , Panda Britta , Rabson Arthur R. , Horowitz Gary , Heger Nicholas , Gupta Kamlesh , Singer Alon , Norwitz Errol R. 
Published: February 2024

ABSTRACT

Sepsis caused by bloodstream infection (BSI) is a major healthcare burden and a leading cause of morbidity and mortality worldwide. Timely diagnosis is critical to optimize clinical outcome, as mortality rates rise every hour treatment is delayed. Blood culture remains the “gold standard” for diagnosis but is limited by its long turnaround time (1–7 days depending on the organism) and its potential to provide false-negative results due to interference by antimicrobial therapy or the presence of mixed (i.e., polymicrobial) infections. In this paper, we evaluated the performance of resistance and pathogen ID/BSI, a direct-from-specimen molecular assay. To reduce the false-positivity rate common with molecular methods, this assay isolates and detects genomic material only from viable microorganisms in the blood by incorporating a novel precursor step to selectively lyse host and non-viable microbial cells and remove cell-free genomic material prior to lysis and analysis of microbial cells. Here, we demonstrate that the assay is free of interference from host immune cells and common antimicrobial agents at elevated concentrations. We also demonstrate the accuracy of this technology in a prospective cohort pilot study of individuals with known sepsis/BSI status, including samples from both positive and negative individuals.

IMPORTANCE
Blood culture remains the “gold standard” for the diagnosis of sepsis/bloodstream infection (BSI) but has many limitations which may lead to a delay in appropriate and accurate treatment in patients. Molecular diagnostic methods have the potential for markedly improving the management of such patients through faster turnaround times and increased accuracy. But molecular diagnostic methods have not been widely adopted for the identification of BSIs. By incorporating a precursor step of selective lysis of host and non-viable microorganisms, our resistance and pathogen ID (RaPID)/BSI molecular assay addresses many limitations of blood culture and other molecular assay. The RaPID/BSI assay has an approximate turnaround time of 4 hours, thereby significantly reducing the time to appropriate and accurate diagnosis of causative microorganisms in such patients. The short turnaround time also allows for close to real-time tracking of pathogenic clearance of microorganisms from the blood of these patients or if a change of antimicrobial regimen is required. Thus, the RaPID/BSI molecular assay helps with optimization of antimicrobial stewardship; prompt and accurate diagnosis of sepsis/BSI could help target timely treatment and reduce mortality and morbidity in such patients.
Draft genome sequence of
Limosilactobacillus fermentum
isolated from subgingival biofilm
Authors: Jang Eun-Young , Yang Seok Bin , Chun Jeewan , Kim Cheul , Moon Ji-Hoi , Lee Jae-Hyung 
Published: February 2024

ABSTRACT

Limosilactobacillus fermentum
is generally considered beneficial for vaginal and digestive health. However, strains isolated from the oral cavity, especially from periodontitis lesions, have not been thoroughly studied. Here, we report the draft genome sequence of strain KHUD_007 isolated from the subgingival biofilm of a Korean patient with periodontitis.
Draft genome sequence of the yeast
Schwanniomyces capriottii
strain UCD805, isolated from soil in Ireland
Authors: Heneghan Padraic G. , Ryan Adam P. , Ó Cinnéide Eoin , Davies Jordan , Bracken Cathal , Ogundipe Victoria , Doheny Maria , Lenihan Liam , Passalaris Anastasia , Walker Rosalind , Wolfe Kenneth H. , Butler Geraldine , Byrne Kevin P. 
Published: February 2024

ABSTRACT

Schwanniomyces capriottii
is a member of the Debaryomycetaceae family in the order Saccharomycetales. Here, we present the genome sequence of
S. capriottii
UCD805, which was isolated from soil in Dublin, Ireland. This genome is 12.2 Mb and was assembled into 14 scaffolds plus a mitochondrial genome scaffold.
Hepatitis B virus-targeting sodium taurocholate cotransporting polypeptide mediates HBV infection and damage in human renal podocytes
Authors: Wang Lifen , Wang Cheng , Wang Xu , Cao Yantao , Guo Xiaohua , Ye Zhiming 
Published: February 2024

ABSTRACT

Hepatitis B virus (HBV) may directly infect human podocytes (HPCs). However, the mechanism of direct infection is unclear. We found that HPCs express sodium taurocholate cotransporting polypeptide (NTCP), a specific receptor for HBV entry into hepatocytes. Thus, we investigated whether NTCP mediates HBV infection and damage in HPCs and further clarified the specific mechanism. We constructed shRNA-NTCP1,2, shRNA-NC, WT-NTCP, and MUT-NTCP and transfected them into HPCs. HPCs were infected with HBV, and HBV infection markers were detected by enzyme-linked immunosorbent assay (ELISA) and real-time quantitative PCR (RT-qPCR). The functional changes in HPCs were detected by Transwell migration and scratch assays, apoptosis was evaluated by flow cytometry (FCM), and podocytoskeletal proteins (nephrin, CD2AP, and synaptopodin) were determined by western blotting (WB). Compared with the control HPCs, HPCs infected with HBV showed increased levels of HBV infection markers and apoptosis along with decreased podocytoskeletal protein expressions, cell vitality, proliferation, and migration. Compared with the HPCs infected with HBV, the HPCs transfected with HBV + shRNA-NTCP, and HBV + MUT-NTCP showed decreased levels of HBV infection markers and apoptosis along with increased podocytoskeletal protein expressions, cell vitality, proliferation, and migration; the opposite effects were observed in the HPCs transfected with HBV + WT-NTCP. Overall, the changes to NTCP affected the susceptibility of HPCs to HBV and modulated HPC damage and repair. NTCP can mediate direct HBV infection and damage human podocytes, and the NTCP 157–165 locus is the main site of HBV entry. The findings provide a new target and theoretical basis for HBV-associated glomerulonephritis.

IMPORTANCE
This study identified for the first time that sodium taurocholate cotransporting polypeptide (NTCP) can mediate HBV direct infection and damage to human podocytes, and the NTCP157–165 locus is the main HBV entry site. The findings provide theoretical support for the pathogenesis of direct infection of HBV with kidney tissue. The findings provide a new target and theoretical basis for the treatment of HBV-related glomerulonephritis (HBV-GN). Blocking NTCP is a new target for the treatment of HBV-GN. We found that tacrolimus, a calcineurin inhibitor that blocks NTCP, can effectively treat HBV-GN. This study also provides a theoretical basis for the effective and safe treatment of immunosuppressant tacrolimus for HBV-GN.
Hydroxyhexylitaconic acids as potent IMP-type metallo-β-lactamase inhibitors for controlling carbapenem resistance in
Enterobacterales
Authors: Wachino Jun-ichi , Jin Wanchun , Norizuki Chihiro , Kimura Kouji , Tsuji Motonori , Kurosaki Hiromasa , Arakawa Yoshichika 
Published: February 2024

ABSTRACT

Metallo-β-lactamases (MBLs) represent one of the main causes of carbapenem resistance in the order
Enterobacterales
. To combat MBL-producing carbapenem-resistant
Enterobacterales
, the development of MBL inhibitors can restore carbapenem efficacy for such resistant bacteria. Microbial natural products are a promising source of attractive seed compounds for the development of antimicrobial agents. Here, we report that hydroxyhexylitaconic acids (HHIAs) produced by a member of the genus
Aspergillus
can suppress carbapenem resistance conferred by MBLs, particularly IMP (imipenemase)-type MBLs. HHIAs were found to be competitive inhibitors with micromolar orders of magnitude against IMP-1 and showed weak inhibitory activity toward VIM-2, while no inhibitory activity against NDM-1 was observed despite the high dosage. The elongated methylene chains of HHIAs seem to play a crucial role in exerting inhibitory activity because itaconic acid, a structural analog without long methylene chains, did not show inhibitory activity against IMP-1. The addition of HHIAs restored meropenem and imipenem efficacy to satisfactory clinical levels against IMP-type MBL-producing
Escherichia coli
and
Klebsiella pneumoniae
clinical isolates. Unlike EDTA and Aspergillomarasmine A, HHIAs did not cause the loss of zinc ions from the active site, resulting in the structural instability of MBLs. X-ray crystallography and
in silico
docking simulation analyses revealed that two neighboring carboxylates of HHIAs coordinated with two zinc ions in the active sites of VIM-2 and IMP-1, which formed a key interaction observed in MBL inhibitors. Our results indicated that HHIAs are promising for initiating the design of potent inhibitors of IMP-type MBLs.

IMPORTANCE

The number and type of metallo-β-lactamase (MΒL) are increasing over time. Carbapenem resistance conferred by MΒL is a significant threat to our antibiotic regimen, and the development of MΒL inhibitors is urgently required to restore carbapenem efficacy. Microbial natural products have served as important sources for developing antimicrobial agents targeting pathogenic bacteria since the discovery of antibiotics in the mid-20th century. MΒL inhibitors derived from microbial natural products are still rare compared to those derived from chemical compound libraries. Hydroxyhexylitaconic acids (HHIAs) produced by members of the genus
Aspergillus
have potent inhibitory activity against clinically relevant IMP-type MBL. HHIAs may be good lead compounds for the development of MBL inhibitors applicable for controlling carbapenem resistance in IMP-type MBL-producing
Enterobacterales
.
Detecting horizontal gene transfer with metagenomics co-barcoding sequencing
Authors: Han Kai , Li Jiarui , Yang Duo , Zhuang Qinghui , Zeng Hui , Rong Chengbo , Yue Jinglin , Li Na , Gu Chaoyang , Chen Liang , Chen Chen 
Published: February 2024

ABSTRACT

Horizontal gene transfer (HGT) is the process through which genetic information is transferred between different genomes and that played a crucial role in bacterial evolution. HGT can enable bacteria to rapidly acquire antibiotic resistance and bacteria that have acquired resistance is spreading within the microbiome. Conventional methods of characterizing HGT patterns include short-read metagenomic sequencing (short-reads mNGS), long-read sequencing, and single-cell sequencing. These approaches present several limitations, such as short-read fragments, high amounts of input DNA, and sequencing costs, respectively. Here, we attempt to circumvent present limitations to detect HGT by developing a metagenomics co-barcode sequencing workflow (MECOS) and applying it to the human and mouse gut microbiomes. In addition to that, we have over 10-fold increased contig length compared to short-reads mNGS; we also obtained exceeding 30 million paired reads with co-barcode information. Applying the novel bioinformatic pipeline, we integrated this co-barcoding information and the context information from long reads, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Specifically, we detected approximately 3,000 HGT blocks in individual samples, encompassing ~6,000 genes and ~100 taxonomic groups, including loci conferring tetracycline resistance through ribosomal protection. MECOS provides a valuable tool for investigating HGT and advance our understanding on the evolution of natural microbial communities within hosts.

IMPORTANCE
In this study, to better identify horizontal gene transfer (HGT) in individual samples, we introduce a new co-barcoding sequencing system called metagenomics co-barcoding sequencing (MECOS), which has three significant improvements: (i) long DNA fragment extraction, (ii) a special transposome insertion, (iii) hybridization of DNA to barcode beads, and (4) an integrated bioinformatic pipeline. Using our approach, we have over 10-fold increased contig length compared to short-reads mNGS, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Our results indicate the presence of approximately 3,000 HGT blocks, involving roughly 6,000 genes and 100 taxonomic groups in individual samples. Notably, these HGT events are predominantly enriched in genes that confer tetracycline resistance via ribosomal protection. MECOS is a useful tool for investigating HGT and the evolution of natural microbial communities within hosts, thereby advancing our understanding of microbial ecology and evolution.
Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023
Authors: Arantes Ighor , Gomes Marcelo , Ito Kimihito , Sarafim Sharbilla , Gräf Tiago , Miyajima Fabio , Khouri Ricardo , de Carvalho Felipe Cotrim , de Almeida Walquiria Aparecida Ferreira , Siqueira Marilda Mendonça , Resende Paola Cristina , Naveca Felipe Gomes , Bello Gonzalo ,   COVID-19 Fiocruz Genomic Surveillance Network
Published: February 2024

ABSTRACT

The SARS-CoV-2 XBB is a group of highly immune-evasive lineages of the Omicron variant of concern that emerged by recombining BA.2-descendent lineages and spread worldwide during 2023. In this study, we combine SARS-CoV-2 genomic data (
n =
11,065 sequences) with epidemiological data of severe acute respiratory infection (SARI) cases collected in Brazil between October 2022 and July 2023 to reconstruct the space-time dynamics and epidemiologic impact of XBB dissemination in the country. Our analyses revealed that the introduction and local emergence of lineages carrying convergent mutations within the Spike protein, especially F486P, F456L, and L455F, propelled the spread of XBB* lineages in Brazil. The average relative instantaneous reproduction numbers of XBB* + F486P, XBB* + F486P + F456L, and XBB* + F486P + F456L + L455F lineages in Brazil were estimated to be 1.24, 1.33, and 1.48 higher than that of other co-circulating lineages (mainly BQ.1*/BE*), respectively. Despite such a growth advantage, the dissemination of these XBB* lineages had a reduced impact on Brazil’s epidemiological scenario concerning previous Omicron subvariants. The peak number of SARI cases from SARS-CoV-2 during the XBB wave was approximately 90%, 80%, and 70% lower than that observed during the previous BA.1*, BA.5*, and BQ.1* waves, respectively. These findings revealed the emergence of multiple XBB lineages with progressively increasing growth advantage, yet with relatively limited epidemiological impact in Brazil throughout 2023. The XBB* + F486P + F456L + L455F lineages stand out for their heightened transmissibility, warranting close monitoring in the months ahead.

IMPORTANCE
Brazil was one the most affected countries by the SARS-CoV-2 pandemic, with more than 700,000 deaths by mid-2023. This study reconstructs the dissemination of the virus in the country in the first half of 2023, a period characterized by the dissemination of descendants of XBB.1, a recombinant of Omicron BA.2 lineages evolved in late 2022. The analysis supports that XBB dissemination was marked by the continuous emergence of indigenous lineages bearing similar mutations in key sites of their Spike protein, a process followed by continuous increments in transmissibility, and without repercussions in the incidence of severe cases. Thus, the results suggest that the epidemiological impact of the spread of a SARS-CoV-2 variant is influenced by an intricate interplay of factors that extend beyond the virus's transmissibility alone. The study also underlines the need for SARS-CoV-2 genomic surveillance that allows the monitoring of its ever-shifting composition.