bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiresolution dynamic mode decomposition approach for wind pressure analysis and reconstruction around buildings
Authors: Snaiki Reda , Mirfakhar Seyedeh Fatemeh 
Published: July 2024

AbstractAccurate wind pressure analysis on high‐rise buildings is critical for wind load prediction. However, traditional methods struggle with the inherent complexity and multiscale nature of these data. Furthermore, the high cost and practical limitations of deploying extensive sensor networks restrict the data collection capabilities. This study addresses these limitations by introducing a novel framework for optimal sensor placement on high‐rise buildings. The framework leverages the strengths of multiresolution dynamic mode decomposition (mrDMD) for feature extraction and incorporates a novel regularization term within an existing sensor placement algorithm under constraints. This innovative term enables the algorithm to consider real‐world system constraints during sensor selection, leading to a more practical and efficient solution for wind pressure analysis. mrDMD effectively analyzes the multiscale features of wind pressure data. The extracted mrDMD modes, combined with the enhanced constrained QR decomposition technique, guide the selection of informative sensor locations. This approach minimizes the required number of sensors while ensuring accurate pressure field reconstruction and adhering to real‐world placement constraints. The effectiveness of this method is validated using data from a scaled building model tested in a wind tunnel. This approach has the potential to revolutionize wind pressure analysis for high‐rise buildings, paving the way for advancements in digital twins, real‐time monitoring, and risk assessment of wind loads.
Clinical and microbiological characteristics of a hospital outbreak of Candida auris in a referral hospital in Lima, Peru
Authors: Pérez‐Lazo Giancarlo , Sandoval‐Ahumada Roxana , Soto‐Febres Fernando , Ballena‐López José , Morales‐Castillo Liliana , Trujillo‐Gregorio Lucy , Garay‐Quintana Rocio , Arenas‐Ramírez Berenice 
Published: July 2024

AbstractBackgroundCandida auris, a multidrug‐resistant fungal pathogen, has received considerable attention owing to its recent surge, especially in South America, which coincides with the ongoing global COVID‐19 pandemic. Understanding the clinical and microbiological characteristics of outbreaks is crucial for their effective management and control.ObjectiveThis retrospective observational study aimed to characterize a C. auris outbreak at a Peruvian referral hospital between January 2021 and July 2023.MethodsData were collected from hospitalized patients with positive C. auris culture results. Microbiological data and antifungal susceptibility test results were analysed. Additionally, infection prevention and control measures have been described. Statistical analysis was used to compare the characteristics between the infected and colonized patients.ResultsThirty‐three patients were identified, mostly male (66.7%), with a median age of 53 years. Among them, 18 (54.5%) were colonized, and 15 (45.5%) were infected. Fungemia was the predominant presentation (80%), with notable cases of fungemia in tuberculosis patients with long‐stay devices for parenteral anti‐tuberculosis therapy. Seventy‐five percent of the isolates exhibited fluconazole resistance. Echinocandins were the primary treatment, preventing fungemia recurrence within 30 days. Infected patients had significantly longer hospital stays than colonized patients (100 vs. 45 days; p = .023). Hospital mortality rates were 46.7% and 25% in the infected and fungemia patients, respectively. Simultaneous outbreaks of multidrug‐resistant bacteria were documented.ConclusionsThis study underscores the severity of a C. auris outbreak at a referral hospital in Peru, highlighting its significant impact on patient outcomes and healthcare resources. The high prevalence of fluconazole‐resistant isolates, leading to prolonged hospital stay and high mortality rates, particularly in cases of fungemia, underscores the critical need for effective infection prevention and control strategies.
Hijacking of the methylglyoxal detoxification pathway: a new tactic of Xoo pathogenesis in rice
Authors: Kumar Parvesh , Kumari Poonam , Mehra Rakesh , Singh Bahaderjeet , Kumar Rakesh 
Published: July 2024

AbstractXanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial blight (BB), has developed a unique strategy to infect rice by hijacking the host's methylglyoxal (MG) detoxification pathway. This results in an over‐accumulation of MG, which facilitates tissue colonization and evasion of host's immune responses. While MG role in abiotic stresses is well‐documented, its involvement in biotic stresses has not been extensively explored. Recently, Fu et al. (2024) provided the first evidence of MG role in promoting Xoo pathogenesis in rice. This new virulence strategy contributes to the pathogen's remarkable adaptability and survival. In this mechanism of hijacking of MG detoxification pathway, Xoo induces OsWRKY62.1 to inhibit OsGLY II expression, leading to MG overaccumulation in infected rice cells. This excess MG hinders plant cell organelle function, creating a favorable environment for Xoo by compromising the rice defense system. In this article, we have presented our perspectives on how the BB pathogen adapts its virulence mechanisms to infect and cause disease in rice.
Thoughts on the structure of the history of Africana philosophy
Authors: Jeffers Chike 
Published: July 2024

AbstractThis article seeks to comment insightfully on the way things hang together as we try to chart the history of Africana philosophy. It does so through reflections on the History of Africana Philosophy podcast, part of Peter Adamson's larger series, the History of Philosophy Without Any Gaps. The article is divided into three sections, corresponding to the three parts of the podcast. Important to the first section is a reply to recent criticism by Olúfẹ́mi Táíwò of use of the term “precolonial” in discussions of Africa's history. The second section includes extended reflection on the special roles of Ethiopia, Haiti, and Liberia in the history of Africana philosophy. The final section explores the significance of writing, in an attempt to explain why the third part of the podcast, which covers the twentieth century, was lengthier than the other two parts of the series combined.
LncRNA NEAT1 targets miR‐125/ADAM9 mediated NF‐κB pathway in inflammatory response of rosacea
Authors: Xu Sijia , Dong Wenxin 
Published: July 2024

AbstractObjectiveTo investigate the role of NEAT1 targeted regulation of miR‐125/ADAM9 mediated NF‐κB pathway in inflammatory response in rosacea.MethodHaCaT cell rosacea phenotype was induced by LL37. The connection targeted by NEAT1 and miR‐125a‐5p was confirmed by Double‐Luciferase report analysis. qPCR was employed to assess the levels of expression for NEAT1, miR‐125a‐5p, and ADAM9 genes. The levels of expression for ADAM9/TLR2/NF‐κB P65 pathway proteins in each batch of cells were determined by Western blotting. The levels of expression for inflammatory factors, including TNF‐α, IL‐1β, IL‐6, and IL‐18, were measured through ELISA experimentation.ResultsLL37 could successfully induce HaCaT cells to exhibit rosacea phenotype. The luciferase report experiment confirmed that NEAT1 could target and bind miR‐125a‐5p and inhibit its expression. ADAM9 exhibited increased expression in LL37‐induced HaCaT cells, showing a positive association with NEAT1 expression and inverse relationship with miR‐125a‐5p activation. LL37 treatment promoted the expression of ADAM9/TLR2/NF‐κB P65 pathway proteins. Silencing ADAM9 can inhibit the inflammatory signaling pathway and reduce the level of TNF‐α, IL‐1β, IL‐6, and IL‐18 in HaCaT cells.ConclusionNEAT1 can suppress the production of miR‐125a‐5p and activate the TLR2/NF‐κB inflammatory pathway mediated by ADAM9, thereby promoting the inflammatory response in rosacea.
A global polycenter identification method with single‐source data: The integration of local multisource data recognition
Authors: Ruan Yichen , Zhang Xiaoyi , Chen Qiuxiao , Zhang Mingyu 
Published: July 2024

AbstractWith the widespread application of multisource data, the identification of urban polycenters faces the challenge of increasing data costs. This study developed a cost‐effective model for identifying urban polycenters by employing a combination of the Random Forest algorithm and Local Moran's I index. Using point‐of‐interest data from Amap, our model was benchmarked against a multisource data model to verify its effectiveness and accuracy. The results indicate that the single‐source model possesses an accuracy comparable to that of the multisource model in determining the centrality and spatial distribution of urban centers, thus offering a substantial capability to reduce reliance on multisource data. The random forest method exhibits a significant accuracy advantage over traditional ordinary least squares regression methods. However, it also exhibited susceptibility to overfitting and variations in data sampling. This suggests that while the model is highly effective for large‐scale urban studies, it requires careful handling of data inputs. This model can be applied to actual urban planning and research, providing a useful instrument for investigating urban polycentric structures at different spatial scales. This will increase the usefulness of the model in real‐world scenarios and lower the expenses related to analyzing urban data.
Enhancing kernel oil and tailoring fatty acid composition by genomics‐assisted selection for dgat1‐2 and fatb genes in multi‐nutrient‐rich maize: new avenue for food, feed and bioenergy
Authors: Katral Ashvinkumar , Hossain Firoz , Zunjare Rajkumar U. , Mishra Subhra J. , Ragi Shridhar , Kasana Ravindra K. , Chhabra Rashmi , Thimmegowda Vinutha , Vasudev Sujata , Kumar Santosh , Bhat Jayant S. , Neeraja Chirravuri Naga , Yadava Devendra K. , Muthusamy Vignesh 
Published: July 2024

SUMMARYEnhancing maize kernel oil is vital for improving the bioavailability of fat‐soluble vitamins. Here, we combined favourable alleles of dgat1‐2 and fatb into parental lines of four multi‐nutrient‐rich maize hybrids (APTQH1, APTQH4, APTQH5 and APTQH7) using marker‐assisted selection (MAS). Parental lines possessed favourable alleles of crtRB1, lcyE, vte4 and opaque2 genes. Gene‐specific markers enabled successful foreground selection in BC1F1, BC2F1 and BC2F2, while background selection using genome‐wide microsatellite markers (127–132) achieved 93% recurrent parent genome recovery. Resulting inbreds exhibited significantly higher oil (6.93%) and oleic acid (OA, 40.49%) and lower palmitic acid (PA, 14.23%) compared to original inbreds with elevated provitamin A (11.77 ppm), vitamin E (16.01 ppm), lysine (0.331%) and tryptophan (0.085%). Oil content significantly increased from 4.80% in original hybrids to 6.73% in reconstituted hybrids, making them high‐oil maize hybrids. These hybrids displayed 35.70% increment in oil content and 51.56% increase in OA with 36.32% reduction in PA compared to original hybrids, while maintaining higher provitamin A (two‐fold), vitamin E (nine‐fold), lysine (two‐fold) and tryptophan (two‐fold) compared to normal hybrids. Lipid health indices showed improved atherogenicity, thrombogenicity, cholesterolaemic, oxidability, peroxidizability and nutritive values in MAS‐derived genotypes over original versions. Besides, the MAS‐derived inbreds and hybrids exhibited comparable grain yield and phenotypic characteristics to the original versions. The maize hybrids developed in the study possessed high‐yielding ability with high kernel oil and OA, low PA, better fatty acid health and nutritional properties, higher multi‐vitamins and balanced amino acids, which hold immense significance to address malnutrition and rising demand for oil sustainably in a fast‐track manner.
Design and Optimization of a Cable-Driven Parallel Polishing Robot With Kinematic Error Modeling
Authors: Zhou Bin , Wu Shuainan , Zi Bin , Zhu Weidong 
Published: July 2024

Abstract
This article presents the design and optimization of a cable-driven parallel polishing robot (CDPPR) with kinematic error modeling and introduces an improved nondominated sorting genetic algorithm II (NSGA-II) for multiobjective optimization. First, the mechanical design and kinematic and static modeling of the CDPPR are conducted. Subsequently, a kinematic error transfer model is established based on the evidence theory by considering the change of exit points of cables, and an error index is derived to measure the accuracy of the robot. Besides, another two performance indices including the workspace and static stiffness are proposed. Thus, a multiobjective optimization model is established to optimize the workspace, static stiffness, and error index, and an improved NSGA-II is developed. Finally, an experimental scaled prototype of the CDPPR is constructed, and numerical examples and experimental results demonstrate the effectiveness of the improved NSGA-II and the stability of the optimal configuration.
Crystal structure of the class A extended-spectrum β-lactamase CTX-M-96 in complex with relebactam at 1.03 Angstrom resolution
Authors: Ghiglione Barbara , Rodríguez María Margarita , Penzotti Pedro , Bethel Christopher R. , Gutkind Gabriel , Bonomo Robert A. , Klinke Sebastián , Power Pablo 
Published: July 2024

ABSTRACT

The use of β-lactam/β-lactamase inhibitors constitutes an important strategy to counteract β-lactamases in multidrug-resistant (MDR) Gram-negative bacteria. Recent reports have described ceftazidime-/avibactam-resistant isolates producing CTX-M variants with different amino acid substitutions (e.g., P167S, L169Q, and S130G). Relebactam (REL) combined with imipenem has proved very effective against Enterobacterales producing ESBLs, serine-carbapenemases, and AmpCs. Herein, we evaluated the inhibitory efficacy of REL against CTX-M-96, a CTX-M-15-type variant. The CTX-M-96 structure was obtained in complex with REL at 1.03 Å resolution (PDB 8EHH). REL was covalently bound to the S70-Oγ atom upon cleavage of the C7-N6 bond. Compared with apo CTX-M-96, binding of REL forces a slight displacement of the deacylating water inwards the active site (0.81 Å), making the E166 and N170 side chains shift to create a proper hydrogen bonding network. Binding of REL also disturbs the hydrophobic patch formed by Y105, P107, and Y129, likely due to the piperidine ring of REL that creates clashes with these residues. Also, a remarkable change in the positioning of the N104 sidechain is also affected by the piperidine ring. Therefore, differences in the kinetic behavior of REL against class A β-lactamases seem to rely, at least in part, on differences in the residues being involved in the association and stabilization of the inhibitor before hydrolysis. Our data provide the biochemical and structural basis for REL effectiveness against CTX-M-producing Gram-negative pathogens and essential details for further DBO design. Imipenem/REL remains an important choice for dealing with isolates co-producing CTX-M with other β-lactamases.
Complete genome sequencing of three methicillin-resistant
Staphylococcus aureus
isolated from the blood of patients with persistent bacteremia
Authors: Lee Soo In , Bae Seongman , Kim Yang Soo , Lee Sungkyoung 
Published: July 2024

ABSTRACT

We report the complete genome sequences of three molecular types of methicillin-resistant
Staphylococcus aureus
(MRSA) clinical strains isolated from the blood of three patients diagnosed with persistent MRSA bacteremia: KNIH_5618 (ST5-t5076-SCC
mec
II), KNIH_5844 (ST72-t664-SCC
mec
IV), and KNIH_6268 (ST89-t375-SCC
mec
II). These genome sequences contribute to an enhanced understanding of the underlying causes of persistent MRSA infection.
Characterization of
Ligilactobacillus salivarius
CRISPR-Cas systems
Authors: Roberts Avery , Spang Daniel , Sanozky-Dawes Rosemary , Nethery Matthew A. , Barrangou Rodolphe 
Published: July 2024

ABSTRACT

Ligilactobacillus
is a diverse genus among lactobacilli with phenotypes that reflect adaptation to various hosts. CRISPR-Cas systems are highly prevalent within lactobacilli, and
Ligilactobacillus salivarius
, the most abundant species of
Ligilactobacillus
, possesses both DNA- and RNA-targeting CRISPR-Cas systems. In this study, we explore the presence and functional properties of I-B, I-C, I-E, II-A, and III-A CRISPR-Cas systems in over 500
Ligilactobacillus
genomes, emphasizing systems found in
L. salivarius
. We examined the I-E, II-A, and III-A CRISPR-Cas systems of two
L. salivarius
strains and observed occurrences of split
cas
genes and differences in CRISPR RNA maturation in native hosts. This prompted testing of the single Cas9 and multiprotein Cascade and Csm CRISPR-Cas effector complexes in a cell-free context to demonstrate the functionality of these systems. We also predicted self-targeting spacers within
L. salivarius
CRISPR-Cas systems and found that nearly a third of
L. salivarius
genomes possess unique self-targeting spacers that generally target elements other than prophages. With these two
L. salivarius
strains, we performed prophage induction coupled with RNA sequencing and discovered that the prophages residing within these strains are inducible and likely active elements, despite targeting by CRISPR-Cas systems. These findings deepen our comprehension of CRISPR-Cas systems in
L. salivarius
, further elucidating their relationship with associated prophages and providing a functional basis for the repurposing of these Cas effectors for bacterial manipulation.

IMPORTANCE

Ligilactobacillus salivarius
is a diverse bacterial species widely used in the food and dietary supplement industries. In this study, we investigate the occurrence and diversity of their adaptive immune systems, CRISPR-Cas, in over 500 genomes. We establish their function and provide insights into their role in the interplay between the bacterial host and the predatory phages that infect them. Such findings expand our knowledge about these important CRISPR-Cas immune systems widespread across the bacterial tree of life and also provide a technical basis for the repurposing of these molecular machines for the development of molecular biology tools and the manipulation and engineering of bacteria and other life forms.
Diagnostic accuracy of Savanna RVP4 (QuidelOrtho) for the detection of Influenza A virus, RSV, and SARS-CoV-2
Authors: Köse Büsra , Schaumburg Frieder 
Published: July 2024

ABSTRACT

Seasonal increase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza virus A/B (Flu A/B), and respiratory syncytial virus (RSV) require rapid diagnostic test methods for the management of respiratory tract infections. In this study, we compared the diagnostic accuracy of Savanna RVP4 (RVP4, QuidelOrtho) with Xpert Xpress Plus SARS-CoV-2/Flu/RSV (Xpert, Cepheid). Nasopharyngeal swabs from patients treated at a tertiary care hospital (Germany) were tested for SARS-CoV-2, Flu A/B, and RSV by RVP4 to assess diagnostic accuracy (reference standard: Xpert). The intra and inter assay precision of Ct-values was assessed by repeated test in triplicates (on day 1) and duplicates (days 2–3). All patients with a physician’s order for a multiplex test for SARS-CoV-2, Flu, and RSV test were included. Duplicate swabs from the same patient, samples with a total volume ≤1 mL, or inappropriate shipment/storage were excluded. In total, 229 swabs were included between September 2023 and February 2024. The concordance between both tests was 96.5% (SARS-CoV-2), 98.7% (Flu A), and 99.6% (RSV). Flu B was not detected by both tests. The RVP4 test had a sensitivity of 85%–95% and a specificity of 100% for the detection of SARS-CoV-2, Flu A, and RSV. The intra and inter assay precision of Ct-values from RVP4 was 3% and 2% (SARS-CoV-2), 5% and 4% (Flu A), and 0% and 3% (RSV), respectively. The Savanna RVP4 has a favorable diagnostic accuracy for the detection of SARS-CoV-2, Flu A, and RSV.

IMPORTANCE
We assessed the diagnostic accuracy of a new point-of-care test for the rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza virus A/B (Flu A/B), and respiratory syncytial virus (RSV). The new test has a concordance with the reference standard of 96.5% (SARS-CoV-2), 98.7% (Flu A), and 99.1% (RSV). The sensitivity of 85%–95% and specificity of 100% for the detection of SARS-CoV-2, Flu A, and RSV is comparable with similar nucleic acid amplification-based point of care tests but at lower costs.
Rescue of pyrimidine-defective
Pseudomonas aeruginosa
through metabolic complementation
Authors: Mahmud Hafij Al , Garcia Randy , Garcia Alexsis , Baishya Jiwasmika , Wakeman Catherine A. 
Published: July 2024

ABSTRACT

Chronic infections harbor multiple pathogens where dynamic interactions between members of the polymicrobial community play a major role in determining the infection outcome. For example, in a nutrient-rich polymicrobial infection, bacteria have the potential to undergo evolutionary changes that impair their ability to synthesize essential metabolites. This adaptation may facilitate metabolic interdependencies between neighboring pathogens and lead to difficult-to-treat chronic infections. Our research group previously demonstrated that
Pseudomonas aeruginosa
(PA) and
Staphylococcus aureus
(SA), typically considered classical competitors, can adopt a cooperative lifestyle through bi-directional purine exchange medicated by exogenous DNA (eDNA) release. To further validate our initial findings, in this study, we investigated the potential exchange of pyrimidine between PA and other pathogens, which is another constituent of DNA. In our findings, we observed that a pyrimidine-deficient transposon mutant strain of PA showed improved growth when co-cultured with wild-type PA, SA,
Acinetobacter baumannii
(AB), and
Enterococcus faecalis
(EF). Additionally, improved fitness of pyrimidine-deficient PA was further observed in chemical complementation with eDNA and uridine-5′-monophosphate. Interestingly, the rescue of PA growth through eDNA complementation is not as effective as in intact cells, such as SA, AB, EF, and wild-type PA, implying that eDNA is a lesser contributor to this metabolic complementation. Also, the exchange mechanism between pathogens involves more active mechanisms beyond simple eDNA or metabolite release. Our data further highlights the importance of cell-to-cell contact for effective and increased metabolic complementation.

IMPORTANCE

This research holds crucial implications for combating chronic infections, where multiple pathogens coexist and interact within the same environment. By uncovering the dynamic exchange of pyrimidines between
Pseudomonas aeruginosa
(PA) and
Staphylococcus aureus
(SA), our study reveals a previously unrecognized aspect of interspecies cooperation. The observed enhanced growth of a pyrimidine-deficient PA strain when co-cultured with SA suggests potential avenues for understanding and disrupting bacterial metabolic interdependencies in chronic infection settings. Furthermore, our findings highlight the mechanisms involved in metabolic exchange, emphasizing the importance of cell-to-cell contact. This research explored essential metabolic interactions to address the challenges posed by difficult-to-treat chronic infections.