bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of multi‐layer porcine small intestinal submucosa for the reconstruction of deep corneal defects in cats
Authors: Luo JingWen , Zhou ZhenLei 
Published: February 2024

AbstractObjectiveThis study documented the application of porcine small intestinal submucosa (SIS) as a stand‐alone scaffold for treating deep corneal defects in cats.MethodsMedical records of 20 cats with deep stromal ulcers, perforations, or corneal sequestra that underwent surgical treatment with SIS grafts between 2021 and 2022 were retrospectively reviewed. Data on re‐epithelialization time, corneal transparency score, and complications were collected to analyze the reconstruction of deep corneal defects after SIS biomaterial implantation.ResultsAll cats were unilaterally affected. The corneal defects varied in size, with a median diameter of 8.3 mm (range: 3–15 mm). Re‐epithelialization of the SIS graft was completed 16–32 days after surgery (median, 22.3 days). No, mild, or moderate corneal transparency was detected in 90% of the cases. Complications were observed in eight cases (40%), including aqueous leakage (10%), partial SIS malacia (25%), and persistent bullous keratopathy (5%). The follow‐up period ranged 90–725 days, with a median duration of 255 days. The SIS graft was successfully applied as a single scaffold in 17 of 20 cases (85%).ConclusionThe results of this study suggest that the application of commercial SIS is an effective surgical technique for managing deep corneal defects in cats.
The Interaction of Turbulent Spots With Low-Speed Streaks
Authors: Suryanarayanan Saikishan , Settlemier Anthony , Goldstein David B. 
Published: February 2024

Abstract
Turbulent spots are regions of turbulence surrounded by laminar flow that appear during the late stages of boundary layer transition. While turbulent spots are often studied in isolation, they usually occur near low-speed streaks and other disturbances during transition. This paper investigates the interaction between a turbulent spot and a subcritical low-speed streak using direct numerical simulations. The results, analyzed from streak instability and vorticity points of view, reveal mechanisms of the destabilization of the streak by the spot and provide insights into spot evolution in a realistic environment. Additional simulations involving intentional local control of portions of the streak provide further insight into the interaction mechanisms and potential transition mitigation strategies.
Enhancing Axial Flow Fan Performance in Air-Cooled Condensers: Tip Vortex Manipulators and Comparative Analysis of Numerical Simulation and Experimental Testing
Authors: Pretorius Johannes P. , van der Spuy Sybrand J. 
Published: February 2024

Abstract
Direct dry-cooled power plants typically operate numerous large-diameter axial flow fans in air-cooled condensers (ACCs) to facilitate the condensation of steam in the plant's thermodynamic cycle. Enhanced fan efficiency may, at scale, lead to significant parasitic power reductions and subsequent increases in plant power output. The performance of these fans may be increased by adding blade-tip modifications, which act to control blade-tip leakage flow. Previous studies have shown that manipulating the tip leakage vortex (TLV) increases the blade-to-air momentum transfer and stabilizes the air flow structures as it traverses the fan blade. This paper takes a step toward the development of improved tip vortex manipulators for an ACC fan. Three-dimensional computational fluid dynamics (CFD) simulations, and experimental testing of the modified and unmodified fan within an ISO test facility are performed. The results are then utilized to assess the accuracy of the simulation model, visualize the manipulated flow structures at the blade tip, and ultimately quantify the effect of the endplate designs on fan performance. Excellent correlation between numerical and test results for the unmodified fan is observed, and the benefit of blade-tip modification on fan performance is again confirmed experimentally. The simulation model, however, fails to predict improvements in fan performance under modification, and simulated tip leakage flows are investigated for clarification. It is hypothesized that deflection of tip endplates under operation account for differences between simulation and experiment, and that fluid–structure interaction analyses could potentially resolve discrepancies.
A multifunctional flavoprotein monooxygenase HspB for hydroxylation and C-C cleavage of 6-hydroxy-3-succinoyl-pyridine
Authors: Ouyang Xingyu , Liu Gongquan , Guo Lihua , Wu Geng , Xu Ping , Zhao Yi-Lei , Tang Hongzhi 
Published: February 2024

ABSTRACT

Flavoprotein monooxygenases catalyze reactions, including hydroxylation and epoxidation, involved in the catabolism, detoxification, and biosynthesis of natural substrates and industrial contaminants. Among them, the 6-hydroxy-3-succinoyl-pyridine (HSP) monooxygenase (HspB) from
Pseudomonas putida
S16 facilitates the hydroxylation and C-C bond cleavage of the pyridine ring in nicotine. However, the mechanism for biodegradation remains elusive. Here, we refined the crystal structure of HspB and elucidated the detailed mechanism behind the oxidative hydroxylation and C-C cleavage processes. Leveraging structural information about domains for binding the cofactor flavin adenine dinucleotide (FAD) and HSP substrate, we used molecular dynamics simulations and quantum/molecular mechanics calculations to demonstrate that the transfer of an oxygen atom from the reactive FAD peroxide species (C4a-hydroperoxyflavin) to the C3 atom in the HSP substrate constitutes a rate-limiting step, with a calculated reaction barrier of about 20 kcal/mol. Subsequently, the hydrogen atom was rebounded to the FAD cofactor, forming C4a-hydroxyflavin. The residue Cys218 then catalyzed the subsequent hydrolytic process of C-C cleavage. Our findings contribute to a deeper understanding of the versatile functions of flavoproteins in the natural transformation of pyridine and HspB in nicotine degradation.

IMPORTANCE

Pseudomonas putida
S16 plays a pivotal role in degrading nicotine, a toxic pyridine derivative that poses significant environmental challenges. This study highlights a key enzyme, HspB (6-hydroxy-3-succinoyl-pyridine monooxygenase), in breaking down nicotine through the pyrrolidine pathway. Utilizing dioxygen and a flavin adenine dinucleotide cofactor, HspB hydroxylates and cleaves the substrate’s side chain. Structural analysis of the refined HspB crystal structure, combined with state-of-the-art computations, reveals its distinctive mechanism. The crucial function of Cys218 was never discovered in its homologous enzymes. Our findings not only deepen our understanding of bacterial nicotine degradation but also open avenues for applications in both environmental cleanup and pharmaceutical development.
Utilizing cost-effective portable equipment to enhance COVID-19 variant tracking both on-site and at a large scale
Authors: Park Sung Yong , Faraci Gina , Ward Pamela , Lee Ha Youn 
Published: February 2024

ABSTRACT

Despite optimistic predictions on the eventual end of COVID-19 (Coronavirus Disease 2019), caution is necessary regarding the emergence of new variants to sustain a positive outlook and effectively address any potential future outbreaks. However, ongoing efforts to track COVID-19 variants are concentrated in developed countries and unique social practices and remote habitats of indigenous peoples present additional challenges. By combining small-sized equipment that is easily accessible and inexpensive, we performed SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) whole genome sequencing and measured the sample-to-answer time and accuracy of this portable variant tracking tool. Our portable design determined the variant of SARS-CoV-2 in an infected individual within 9 hours and 15 minutes without external power or internet connection, surpassing the speed of previous portable tools. It took only 16 minutes to complete sequencing run, whole genome assembly, and lineage determination using a single standalone laptop. We then demonstrated the capability to produce 289 SARS-CoV-2 whole genome sequences in a single portable sequencing run, representing a significant improvement over an existing throughput of 96 sequences per run. We verified the accuracy of portable sequencing by comparison with two other independent sequencing methods. We showed that our high-throughput data consistently represented the circulating variants in Los Angeles, United States, when compared with publicly available sequences. Our scheme is designed to be flexible, rapid, and accurate, making it a valuable tool for large-scale surveillance operations in low- and middle-income countries as well as targeted surveys for vulnerable populations in remote locations.

IMPORTANCE
There have been significant efforts to track COVID-19 (Coronavirus Disease 2019) variants, accumulating over 15 million SARS-CoV-2 sequences as of 2023. However, the distribution of global survey data is highly skewed, with nearly half of all countries having inadequate or low levels of genomic surveillance. In addition, indigenous peoples face more severe threats from COVID-19, due to their generally remote residence and unique social practices. Cost-effective portable sequencing tools have been used to investigate Ebola and Zika outbreaks. However, these tools have a sample-to-answer time of around 24 hours and require an internet connection for data transfer to an off-site cloud server. In our study, we rapidly determined COVID-19 variants using only small and inexpensive equipment, with a completion time of 9 hours and 15 minutes. Furthermore, we produced 289 near-full-length SARS-CoV-2 genome sequences from a single portable Nanopore sequencing run, representing a threefold increase in throughput compared with existing Nanopore sequencing methods.
The H9N2 avian influenza virus increases APEC adhesion to oviduct epithelia by viral NS1 protein-mediated activation of the TGF-β pathway
Authors: Han Jinjie , Chang Wenchi , Fang Junyang , Hou Xiaolan , Li Zhijun , Wang Jingyu , Deng Wen 
Published: February 2024

ABSTRACT

H9N2 avian influenza is a low-pathogenic avian influenza circulating in poultry and wild birds worldwide and frequently contributes to chicken salpingitis that is caused by avian pathogenic
Escherichia coli
(APEC), leading to huge economic losses and risks for food safety. Currently, how the H9N2 virus contributes to APEC infection and facilitates salpingitis remains elusive. In this study,
in vitro
chicken oviduct epithelial cell (COEC) model and
in vivo
studies were performed to investigate the role of H9N2 viruses on secondary APEC infection, and we identified that H9N2 virus enhances APEC infection both
in vitro
and
in vivo
. To understand the mechanisms behind this phenomenon, adhesive molecules on the cell surface facilitating APEC adhesion were checked, and we found that H9N2 virus could upregulate the expression of fibronectin, which promotes APEC adhesion onto COECs. We further investigated how fibronectin expression is regulated by H9N2 virus infection and revealed that transforming growth factor beta (TGF-β) signaling pathway is activated by the NS1 protein of the virus, thus regulating the expression of adhesive molecules. These new findings revealed the role of H9N2 virus in salpingitis co-infected with APEC and discovered the molecular mechanisms by which the H9N2 virus facilitates APEC infection, offering new insights to the etiology of salpingitis with viral-bacterial co-infections.

IMPORTANCE
H9N2 avian influenza virus (AIV) widely infects poultry and is sporadically reported in human infections. The infection in birds frequently causes secondary bacterial infections, resulting in severe symptoms like pneumonia and salpingitis. Currently, the mechanism that influenza A virus contributes to secondary bacterial infection remains elusive. Here we discovered that H9N2 virus infection promotes APEC infection and further explored the underlying molecular mechanisms. We found that fibronectin protein on the cell surface is vital for APEC adhesion and also showed that H9N2 viral protein NS1 increased the expression of fibronectin by activating the TGF-β signaling pathway. Our findings offer new information on how AIV infection promotes APEC secondary infection, providing potential targets for mitigating severe APEC infections induced by H9N2 avian influenza, and also give new insights on the mechanisms on how viruses promote secondary bacterial infections in animal and human diseases.
Ceramide-1-phosphate is a regulator of Golgi structure and is co-opted by the obligate intracellular bacterial pathogen
Anaplasma phagocytophilum
Authors: Read Curtis B. , Ali Anika N. , Stephenson Daniel J. , Macknight H. Patrick , Maus Kenneth D. , Cockburn Chelsea L. , Kim Minjung , Xie Xiujie , Carlyon Jason A. , Chalfant Charles E. 
Published: February 2024

ABSTRACT

Many intracellular pathogens structurally disrupt the Golgi apparatus as an evolutionarily conserved promicrobial strategy. Yet, the host factors and signaling processes involved are often poorly understood, particularly for
Anaplasma phagocytophilum
, the agent of human granulocytic anaplasmosis. We found that
A. phagocytophilum
elevated cellular levels of the bioactive sphingolipid, ceramide-1-phosphate (C1P), to promote Golgi fragmentation that enables bacterial proliferation, conversion from its non-infectious to infectious form, and productive infection.
A. phagocytophilum
poorly infected mice deficient in ceramide kinase, the Golgi-localized enzyme responsible for C1P biosynthesis. C1P regulated Golgi morphology via activation of a PKCα/Cdc42/JNK signaling axis that culminates in phosphorylation of Golgi structural proteins, GRASP55 and GRASP65. siRNA-mediated depletion of Cdc42 blocked
A. phagocytophilum
from altering Golgi morphology, which impaired anterograde trafficking of
trans
-Golgi vesicles into and maturation of the pathogen-occupied vacuole. Cells overexpressing phosphorylation-resistant versions of GRASP55 and GRASP65 presented with suppressed C1P- and
A. phagocytophilum
-induced Golgi fragmentation and poorly supported infection by the bacterium. By studying
A. phagocytophilum
, we identify C1P as a regulator of Golgi structure and a host factor that is relevant to disease progression associated with Golgi fragmentation.

IMPORTANCE

Ceramide-1-phosphate (C1P), a bioactive sphingolipid that regulates diverse processes vital to mammalian physiology, is linked to disease states such as cancer, inflammation, and wound healing. By studying the obligate intracellular bacterium
Anaplasma phagocytophilum
, we discovered that C1P is a major regulator of Golgi morphology.
A. phagocytophilum
elevated C1P levels to induce signaling events that promote Golgi fragmentation and increase vesicular traffic into the pathogen-occupied vacuole that the bacterium parasitizes. As several intracellular microbial pathogens destabilize the Golgi to drive their infection cycles and changes in Golgi morphology is also linked to cancer and neurodegenerative disorder progression, this study identifies C1P as a potential broad-spectrum therapeutic target for infectious and non-infectious diseases.
Draft genome of three isolates of
Listeria monocytogenes
isolated from
Stenella coeruleoalba
in Italy
Authors: Scarpa Fabio , Grattarola Carla , Arillo Alessandra , Mattioda Virginia , Testori Camilla , Terracciano Giuliana , Senese Matteo , Giorda Federica , Zoppi Simona , Sanna Daria , Casu Marco , Peletto Simone 
Published: February 2024

ABSTRACT

Listeria monocytogenes
is the etiological agent of the listeriosis. Here, we described three draft genome sequences of
L. monocytogenes
isolated in Italy from stranded individuals of the striped dolphin
Stenella coeruleoalba
. All the genomes have been molecular typed through the multilocus sequence typing to identify the phylogenetic lineage, clonal complex, sublineage, and serogroup.
Interpreting and reporting fission-track chronological data
Authors: Kohn Barry P. , Ketcham Richard A. , Vermeesch Pieter , Boone Samuel C. , Hasebe Noriko , Chew David , Bernet Matthias , Chung Ling , Danišík Martin , Gleadow Andrew J.W. , Sobel Edward R. 
Published: February 2024

Abstract
Fission-track dating is based on the analysis of tracks—linear damage trails—produced by the spontaneous fission of 238U in a range of natural accessory minerals and glasses. The retention of tracks is sensitive to elevated temperatures, and the data serve principally as a tool for recording thermal histories of rocks, potentially over the range of ~20–350 °C, depending on the specific minerals studied. As such, in most cases, fission-track data generally bear little or no direct relationship to the original formation age of the material studied. The age range of fission-track dating is related to the product of age and uranium content, and ages from several tens of years to older than 1 Ga are reported. Fission-track analysis led to the development of powerful modeling techniques. When used with appropriate geological constraints, these modeling techniques allow important geological processes to be addressed in a broad range of upper crustal settings.
Since early attempts to standardize the treatment of fission-track data and system calibration over more than 30 years ago, major advancements were made in the methodology, necessitating the development of new, updated data reporting requirements. Inconsistencies in reporting impede public data transparency, accessibility and reuse, Big Data regional syntheses, and interlaboratory analytical comparisons.
This paper briefly reviews the fundamentals of fission-track dating and applications to provide context for recommended guidelines for reporting and supporting essential meta fission-track data for publication and methodological archiving in structured formats that conform with FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. Adopting such practices will ensure that data can be readily accessed, interrogated, and reused, allowing for further integration with other numerical geoscience techniques.
Subduction erosion revealed by exhumed lower arc crustal rocks in an accretionary complex, northeastern China
Authors: Xu Mengyu , Xiao Wenjiao , Liu Kai , Wan Bo , Mitchell Ross N. , Rosenbaum Gideon , Wang Hao 
Published: February 2024

Abstract
Subduction erosion at convergent margins is a leading mechanism for the destruction (recycling and reworking) of continental crust. But because of the lack of direct evidence, it is not straightforward to identify erosive events and their intensities in fossil subduction zones. The Heilongjiang accretionary complex in northeastern China was formed during the early Mesozoic subduction of the Paleo-Pacific Ocean. We investigated amphibolites from this accretionary complex, whose protoliths (based on whole-rock trace elements and Sr-Nd-Hf isotopes) were mafic continental arc magmatic rocks (255–249 Ma; zircon core U-Pb ages) from the upper plate. Phase equilibria modeling constrained by mineral geochemistry indicates that the amphibolites and their wall rocks were first heated to low granulite facies (750–800 °C, ~7 kbar) at 251–244 Ma (zircon rim U-Pb ages) and then cooled to ~700 °C with increasing pressure (8–9 kbar) before 213–187 Ma (titanite and apatite U-Pb ages). To explain the occurrence of the lower arc crustal lithologies in the accretionary complex and their metamorphic history, we propose that the subducting plate strongly eroded the forearc crust, allowing the plate interface to advance landward and scrape the amphibolites and wall rocks formed under the old arc, which finally were exhumed along the subduction channel and became components of the complex. The case study exemplifies direct petrological evidence of strong subduction erosion occurring in an ancient orogen, thus implying that consumption of the entire forearc crust could occur within only ~50 m.y.
Factors that impact second attempt success for neonatal intubation following first attempt failure: a report from the National Emergency Airway Registry for Neonates
Authors: Johnson Mitchell David , Tingay David Gerald , Perkins Elizabeth J , Sett Arun , Devsam Bianca , Douglas Ellen , Charlton Julia K , Wildenhain Paul , Rumpel Jennifer , Wagner Michael , Nadkarni Vinay , Johnston Lindsay , Herrick Heidi M , Hartman Tyler , Glass Kristen , Jung Philipp , DeMeo Stephen D , Shay Rebecca , Kim Jae H , Unrau Jennifer , Moussa Ahmed , Nishisaki Akira , Foglia Elizabeth E 
Published: February 2024

ObjectiveTo determine the factors associated with second attempt success and the risk of adverse events following a failed first attempt at neonatal tracheal intubation.DesignRetrospective analysis of prospectively collected data on intubations performed in the neonatal intensive care unit (NICU) and delivery room from the National Emergency Airway Registry for Neonates (NEAR4NEOS).SettingEighteen academic NICUs in NEAR4NEOS.PatientsNeonates requiring two or more attempts at intubation between October 2014 and December 2021.Main outcome measuresThe primary outcome was successful intubation on the second attempt, with severe tracheal intubation-associated events (TIAEs) or severe desaturation (≥20% decline in oxygen saturation) being secondary outcomes. Multivariate regression examined the associations between these outcomes and patient characteristics and changes in intubation practice.Results5805 of 13 126 (44%) encounters required two or more intubation attempts, with 3156 (54%) successful on the second attempt. Second attempt success was more likely with changes in any of the following: intubator (OR 1.80, 95% CI 1.56 to 2.07), stylet use (OR 1.65, 95% CI 1.36 to 2.01) or endotracheal tube (ETT) size (OR 2.11, 95% CI 1.74 to 2.56). Changes in stylet use were associated with a reduced chance of severe desaturation (OR 0.74, 95% CI 0.61 to 0.90), but changes in intubator, laryngoscope type or ETT size were not; no changes in intubator or equipment were associated with severe TIAEs.ConclusionsSuccessful neonatal intubation on a second attempt was more likely with a change in intubator, stylet use or ETT size.
Association between age-related macular degeneration and risk of incident cancer
Authors: Park Junhee , Jung Wonyoung , Han Kyungdo , Kim Bongseong , Lee Seung-Yeon , Yoon Je Moon , Lim Dong Hui , Shin Dong Wook 
Published: February 2024

Background/aimsAge-related macular degeneration (AMD) and cancer may share similar risk factors, indicating possible common pathogenic pathways. We aimed to describe the site-specific cancer risk based on the relationship of AMD with visual disability (VD) status.MethodsThis was a population-based cohort study using data from the Korean National Health Insurance Service database (2009–2019) including patients who participated in a national health screening programme in 2009. The subjects were categorised based on the presence of AMD and VD. The occurrence of cancer was identified using principal diagnosis according to the International Classification of Disease, 10th revision codes in claims data. The Cox regression hazard model was used to compare HRs of site-specific cancer.ResultsAmong 4 088 814 participants, 51 596 had AMD of which 3683 subjects had VD. The mean follow-up period was 9.6 years. The overall cancer risk was generally null, but the risk of hypervascular cancer such as thyroid cancer (adjusted HR (aHR) 1.10, 95% CI 1.00 to 1.20) and renal cancer (aHR 1.16, 95% CI 1.00 to 1.33) was higher and the risk of stomach cancer (aHR 0.89, 95% CI 0.84 to 0.94) was lower in the AMD group than in the non-AMD group.ConclusionThis study demonstrated a possible association between AMD and several cancers. Increased renal and thyroid cancer risk among patients with AMD could indicate that AMD is associated with hypervascular cancer. Further studies in which additional databases are used and the underlying detailed mechanisms evaluated are needed to validate our results.