bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust Contact Computation in Non-Rigid Variation Simulation
Authors: Tabar Roham Sadeghi , Lorin Samuel , Lindkvist Lars , Wärmefjord Kristina , Söderberg Rikard 
Published: May 2024

Abstract
In non-rigid variation simulation, contact modeling is used to avoid the virtual penetration of the components in the adjacent areas. Numerical errors and convergence issues due to the deformation behavior of the interacting surfaces are limiting the computational efficiency of solving the contact problem. In this paper, a quadratic programming approach has been introduced based on the Lagrangian multiplier method for robust contact modeling in non-rigid variation simulation, and the performance of the proposed approach has been compared to the previously applied iterative and barrier function methods. The methods have been compared on three industrial reference cases, and the convergence and time-efficiency of each method are compared. The results show that robust optimization of the quadratic program associated with the contact model is highly dependent on the reduced stiffness matrix condition. Furthermore, it has been shown that robust and efficient contact computation in non-rigid variation simulation is achievable through the proposed augmented Lagrangian method.
Federated Learning on Distributed and Encrypted Data for Smart Manufacturing
Authors: Kuo Timothy , Yang Hui 
Published: May 2024

Abstract
Industry 4.0 drives exponential growth in the amount of operational data collected in factories. These data are commonly distributed and stored in different business units or cooperative companies. Such data-rich environments increase the likelihood of cyber attacks, privacy breaches, and security violations. Also, this poses significant challenges on analytical computing on sensitive data that are distributed among different business units. To fill this gap, this article presents a novel privacy-preserving framework to enable federated learning on siloed and encrypted data for smart manufacturing. Specifically, we leverage fully homomorphic encryption (FHE) to allow for computation on ciphertexts and generate encrypted results that, when decrypted, match the results of mathematical operations performed on the plaintexts. Multilayer encryption and privacy protection reduce the likelihood of data breaches while maintaining the prediction performance of analytical models. Experimental results in real-world case studies show that the proposed framework yields superior performance to reduce the risk of cyber attacks and harness siloed data for smart manufacturing.
The Study of Thermal–Structural Coupling Deformation Analysis for Flexible Space Manipulator in Orbit
Authors: Zhang Fuli , Zhang Fuzhi , Liang Na 
Published: May 2024

Abstract
The space manipulator can assist astronauts to accomplish space activities, including docking, fixing, and grasping. It is subjected to thermal radiation and produces thermal deformation during orbit operation, which makes the operation of the space manipulator deviate from the predetermined trajectory and further affects its positioning accuracy. Therefore, to solve the problem of bidirectional coupling thermal–structural deformation analysis and positioning accuracy for space manipulator, based on the thermal–structural bidirectional coupling deformation analysis, a method of its thermal deformation on the output positioning accuracy of space flexible manipulator is proposed. It analyzes the bidirectional coupling relationship between the temperature and thermal deformation of the manipulators. Then, the influence of thermal deformation on the output joint error and end positioning accuracy of the space manipulator is analyzed. Finally, the validity of this method is verified by numerical analysis. Compared with the unidirectional coupling model, the bidirectional coupling model comprehensively considers the structure, deformation, and temperature of manipulators. It is closer to the real system. Thermal deformation will reduce the reliable runtime of the space manipulator in orbit. The study provides a theoretical basis for its thermal design and control.
Evaluation of treatment of methicillin-resistant
Staphylococcus aureus
biofilms with intermittent electrochemically generated H
2
O
2
or HOCl
Authors: Anoy Md Monzurul Islam , Kim Won-Jun , Gelston Suzanne , Fleming Derek , Patel Robin , Beyenal Haluk 
Published: May 2024

ABSTRACT

Chronic wound infections can be difficult to treat and may lead to impaired healing and worsened patient outcomes. Novel treatment strategies are needed. This study evaluated the effects of intermittently produced hydrogen peroxide (H
2
O
2
) and hypochlorous acid (HOCl), generated via an electrochemical bandage (e-bandage), against methicillin-resistant
Staphylococcus aureus
biofilms in an agar membrane biofilm model. By changing the working electrode potential, the e-bandage generated either HOCl (1.5 V
Ag/AgCl
) or H
2
O
2
(−0.6 V
Ag/AgCl
). The degree of biocidal activity of intermittent treatment with HOCl and H
2
O
2
correlated with HOCl treatment time; HOCl treatment durations of 0, 1.5, 3, 4.5, and 6 hours (with the rest of the 6-hour total treatment time devoted to H
2
O
2
generation) resulted in mean biofilm reductions of 1.36 ± 0.2, 2.22 ± 0.16, 3.46 ± 0.38, 4.63 ± 0.74, and 7.66 ± 0.5 log CFU/cm
2
, respectively, vs. non-polarized controls, respectively. However, application of H
2
O
2
immediately after HOCl treatment was detrimental to biofilm removal. For example, 3 hours HOCl treatment followed by 3 hours H
2
O
2
resulted in a 1.90 ± 0.84 log CFU/cm
2
lower mean biofilm reduction than 3 hours HOCl treatment followed by 3 hours non-polarization. HOCl generated over 3 hours exhibited biocidal activity for at least 7.5 hours after e-bandage operation ceased; 3 hours of HOCl generation followed by 7.5 hours of non-polarization resulted in a biofilm cell reduction of 7.92 ± 0.12 log CFU/cm
2
vs. non-polarized controls. Finally, intermittent treatment with HOCl (i.e., interspersed with periods of e-bandage non-polarization) for various intervals showed similar effects (approximately 6 log CFU/cm
2
reduction vs. non-polarized control) to continuous treatment with HOCl for 3 hours, followed by 3 hours of non-polarization. These findings suggest that timing and sequencing of HOCl and H
2
O
2
treatments are crucial for maximizing biofilm control when using an e-bandage strategy.
Microbial central carbon metabolism in a tidal freshwater marsh and an upland mixed conifer soil under oxic and anoxic conditions
Authors: Martinez Ayla , Dijkstra Paul , Megonigal Patrick , Hungate Bruce A. 
Published: May 2024

ABSTRACT

The central carbon (C) metabolic network is responsible for most of the production of energy and biosynthesis in microorganisms and is therefore key to a mechanistic understanding of microbial life in soil communities. Many upland soil communities have shown a relatively high C flux through the pentose phosphate (PP) or the Entner-Doudoroff (ED) pathway, thought to be related to oxidative damage control. We tested the hypothesis that the metabolic organization of the central C metabolic network differed between two ecosystems, an anoxic marsh soil and oxic upland soil, and would be affected by altering oxygen concentrations. We expected there to be high PP/ED pathway activity under high oxygen concentrations and in oxic soils and low PP/ED activity in reduced oxygen concentrations and in marsh soil. Although we found high PP/ED activity in the upland soil and low activity in the marsh soil, lowering the oxygen concentration for the upland soil did not reduce the relative PP/ED pathway activity as hypothesized, nor did increasing the oxygen concentration in the marsh soil increase the PP/ED pathway activity. We speculate that the high PP/ED activity in the upland soil, even when exposed to low oxygen concentrations, was related to a high demand for NADPH for biosynthesis, thus reflecting higher microbial growth rates in C-rich soils than in C-poor sediments. Further studies are needed to explain the observed metabolic diversity among soil ecosystems and determine whether it is related to microbial growth rates.

IMPORTANCE
We observed that the organization of the central carbon (C) metabolic processes differed between oxic and anoxic soil. However, we also found that the pentose phosphate pathway/Entner-Doudoroff (PP/ED) pathway activity remained high after reducing the oxygen concentration for the upland soil and did not increase in response to an increase in oxygen concentration in the marsh soil. These observations contradicted the hypothesis that oxidative stress is a main driver for high PP/ED activity in soil communities. We suggest that the high PP/ED activity and NADPH production reflect higher anabolic activities and growth rates in the upland soil compared to the anaerobic marsh soil. A greater understanding of the molecular and biochemical processes in soil communities is needed to develop a mechanistic perspective on microbial activities and their relationship to soil C and nutrient cycling. Such an increased mechanistic perspective is ecologically relevant, given that the central carbon metabolic network is intimately tied to the energy metabolism of microbes, the efficiency of new microbial biomass production, and soil organic matter formation.
Identifying components of the
Shewanella
phage LambdaSo lysis system
Authors: Thöneböhn Svenja , Fischer Dorian , Kreiling Vanessa , Kemmler Alina , Oberheim Isabella , Hager Fabian , Schmid Nicole E. , Thormann Kai M. 
Published: May 2024

ABSTRACT

Phage-induced lysis of Gram-negative bacterial hosts usually requires a set of phage lysis proteins, a holin, an endopeptidase, and a spanin system, to disrupt each of the three cell envelope layers. Genome annotations and previous studies identified a gene region in the
Shewanella oneidensis
prophage LambdaSo, which comprises potential holin- and endolysin-encoding genes but lacks an obvious spanin system. By a combination of candidate approaches, mutant screening, characterization, and microscopy, we found that LambdaSo uses a pinholin/signal-anchor-release (SAR) endolysin system to induce proton leakage and degradation of the cell wall. Between the corresponding genes, we found that two extensively nested open-reading frames encode a two-component spanin module Rz/Rz1. Unexpectedly, we identified another factor strictly required for LambdaSo-induced cell lysis, the phage protein Lcc6. Lcc6 is a transmembrane protein of 65 amino acid residues with hitherto unknown function, which acts at the level of holin in the cytoplasmic membrane to allow endolysin release. Thus, LambdaSo-mediated cell lysis requires at least four protein factors (pinholin, SAR endolysin, spanin, and Lcc6). The findings further extend the known repertoire of phage proteins involved in host lysis and phage egress.

IMPORTANCE
Lysis of bacteria can have multiple consequences, such as the release of host DNA to foster robust biofilm. Phage-induced lysis of Gram-negative cells requires the disruption of three layers, the outer and inner membranes and the cell wall. In most cases, the lysis systems of phages infecting Gram-negative cells comprise holins to disrupt or depolarize the membrane, thereby releasing or activating endolysins, which then degrade the cell wall. This, in turn, allows the spanins to become active and fuse outer and inner membranes, completing cell envelope disruption and allowing phage egress. Here, we show that the presence of these three components may not be sufficient to allow cell lysis, implicating that also in known phages, further factors may be required.
Group B
Streptococcus
transcriptome when interacting with brain endothelial cells
Authors: Vollmuth Nadine , Bridgers Bailey E. , Armstrong Madelyn L. , Wood Jacob F. , Gildea Abigail R. , Espinal Eric R. , Hooven Thomas A. , Barbieri Giulia , Westermann Alexander J. , Sauerwein Till , Foerstner Konrad U. , Schubert-Unkmeir Alexandra , Kim Brandon J. 
Published: May 2024

ABSTRACT

Bacterial meningitis is a life-threatening infection of the central nervous system (CNS) that occurs when bacteria are able to cross the blood–brain barrier (BBB) or the meningeal–cerebrospinal fluid barrier (mBCSFB). The BBB and mBCSFB comprise highly specialized brain endothelial cells (BECs) that typically restrict pathogen entry. Group B
Streptococcus
(GBS or
Streptococcus agalactiae
) is the leading cause of neonatal meningitis. Until recently, identification of GBS virulence factors has relied on genetic screening approaches. Instead, we here conducted RNA-seq analysis on GBS when interacting with induced pluripotent stem cell-derived BECs (iBECs) to pinpoint virulence-associated genes. Of the 2,068 annotated protein-coding genes of GBS, 430 transcripts displayed significant changes in expression after interacting with BECs. Notably, we found that the majority of differentially expressed GBS transcripts were downregulated (360 genes) during infection of iBECs. Interestingly,
codY
, encoding a pleiotropic transcriptional repressor in low-G + C Gram-positive bacteria, was identified as being highly downregulated. We conducted qPCR to confirm the
codY
downregulation observed via RNA-seq during the GBS–iBEC interaction and obtained
codY
mutants in three different GBS background parental strains. As anticipated from the RNA-seq results, the

∆

codY
strains were more adherent and invasive in two
in vitro
BEC models. Together, this demonstrates the utility of RNA-seq during the BEC interaction to identify GBS virulence modulators.

IMPORTANCE

Group B
Streptococcus
(GBS) meningitis remains the leading cause of neonatal meningitis. Research work has identified surface factors and two-component systems that contribute to GBS disruption of the blood–brain barrier (BBB). These discoveries often relied on genetic screening approaches. Here, we provide transcriptomic data describing how GBS changes its transcriptome when interacting with brain endothelial cells. Additionally, we have phenotypically validated these data by obtaining mutants of a select regulator that is highly down-regulated during infection and testing on our BBB model. This work provides the research field with a validated data set that can provide an insight into potential pathways that GBS requires to interact with the BBB and open the door to new discoveries.
Sequence polymorphisms in the reovirus σ1 attachment protein modulate encapsidation efficiency and replication in mice
Authors: Welsh Olivia L. , Roth Alexa N. , Sutherland Danica M. , Dermody Terence S. 
Published: May 2024

ABSTRACT

Many functions of viral attachment proteins are established, but less is known about the biological importance of viral attachment protein encapsidation efficiency. The mammalian orthoreovirus (reovirus) σ1 attachment protein forms filamentous trimers that incorporate into pentamers of the λ2 capsid protein. Reovirus strains vary in the efficiency of σ1 encapsidation onto progeny virions, which influences viral stability during entry into cells and the efficacy of tumor cell lysis. While the role of σ1 encapsidation has been evaluated in studies using cultured cells, the contribution of attachment protein encapsidation efficiency to viral infection in animals is less clear. Polymorphisms in reovirus σ1 at residues 22 and 249 have been implicated in viral dissemination in mice and susceptibility to proteolysis in the murine intestine, respectively. To determine whether these residues contribute to σ1 encapsidation efficiency, we engineered σ1 mutant viruses with single- and double-residue substitutions at sites 22 and 249. We found that substitutions at these sites alter the encapsidation of σ1 and that reoviruses encapsidating higher amounts of σ1 bind cells more avidly and have a modest replication advantage in a cell-type-specific manner relative to low σ1-encapsidating reoviruses. Furthermore, we found that a high σ1-encapsidating reovirus replicates and disseminates more efficiently in mice relative to a low σ1-encapsidating reovirus. These findings provide evidence of a relationship between viral attachment protein encapsidation efficiency and viral replication in cell culture and animal hosts.

IMPORTANCE
Viral attachment proteins can serve multiple functions during viral replication, including attachment to host cells, cell entry and disassembly, and modulation of host immune responses. The relationship between viral attachment protein encapsidation efficiency and viral replication in cells and animals is poorly understood. We engineered and characterized a panel of reoviruses that differ in the capacity to encapsidate the σ1 attachment protein. We found that strains encapsidating σ1 with higher efficiency bind cells more avidly and replicate and spread more efficiently in mice relative to those encapsidating σ1 with lower efficiency. These results highlight a function for σ1 attachment protein capsid abundance in viral replication in cells and animals, which may inform future use of reovirus as an oncolytic therapeutic.
Development of a mutant aerosolized ACE2 that neutralizes SARS-CoV-2
in vivo
Authors: Kober Daniel L. , Caballero Van Dyke Marley C. , Eitson Jennifer L. , Boys Ian N. , McDougal Matthew B. , Rosenbaum Daniel M. , Schoggins John W. 
Published: May 2024

ABSTRACT

The rapid evolution of SARS-CoV-2 variants highlights the need for new therapies to prevent disease spread. SARS-CoV-2, like SARS-CoV-1, uses the human cell surface protein angiotensin-converting enzyme 2 (ACE2) as its native receptor. Here, we design and characterize a mutant ACE2 that enables rapid affinity purification of a dimeric protein by altering the active site to prevent autoproteolytic digestion of a C-terminal His
10
epitope tag. In cultured cells, mutant ACE2 competitively inhibits lentiviral vectors pseudotyped with spikes from multiple SARS-CoV-2 variants and infectious SARS-CoV-2. Moreover, the protein can be nebulized and retains virus-binding properties. We developed a system for the delivery of aerosolized ACE2 to K18-hACE2 mice and demonstrated protection by our modified ACE2 when delivered as a prophylactic agent. These results show proof-of-concept for an aerosolized delivery method to evaluate anti-SARS-CoV-2 agents
in vivo
and suggest a new tool in the ongoing fight against SARS-CoV-2 and other ACE2-dependent viruses.

IMPORTANCE

The rapid evolution of SARS-CoV-2 variants poses a challenge for immune recognition and antibody therapies. However, the virus is constrained by the requirement that it recognizes a human host receptor protein. A recombinant ACE2 could protect against SARS-CoV-2 infection by functioning as a soluble decoy receptor. We designed a mutant version of ACE2 with impaired catalytic activity to enable the purification of the protein using a single affinity purification step. This protein can be nebulized and retains the ability to bind the relevant domains from SARS-CoV-1 and SARS-CoV-2. Moreover, this protein inhibits viral infection against a panel of coronaviruses in cells. Finally, we developed an aerosolized delivery system for animal studies and show the modified ACE2 offers protection in an animal model of COVID-19. These results show proof-of-concept for an aerosolized delivery method to evaluate anti-SARS-CoV-2 agents
in vivo
and suggest a new tool in the ongoing fight against SARS-CoV-2.
Draft genome sequence of uropathogenic
Escherichia coli
U13824, a multidrug-resistant (MDR) and extended-spectrum-β-lactamase (ESBL)-producing UPEC strain isolated from an adult woman with urinary tract infection
Authors: Magaña-Lizárraga José Antonio , Gómez-Gil Bruno , Enciso-Ibarra Julisa , Sánchez-Lugo Yesenia , Parra-Unda Jesús Ricardo , Rodríguez-Atondo José Trinidad , Beltrán-Fernández Saúl , Báez-Flores María Elena 
Published: May 2024

ABSTRACT

Urinary tract infections (UTIs) caused by multidrug-resistant and extended-spectrum β-lactamase-producing uropathogenic
Escherichia coli
are a worldwide concern. We report the draft genome of
E. coli
U13824 isolated from a female outpatient with UTI. This genome’s availability strengthens the genomic surveillance of antimicrobial resistance and the spreading of these strains.
Genome sequences of the 15 bluetongue virus vaccine strains incorporated in the South African live-attenuated vaccine
Authors: Mlingo Tendai A. M. , Beeton-Kempen Natasha , Nthangeni M. Bethuel , Theron Jacques , Mokoena Nobalanda B. 
Published: May 2024

ABSTRACT

Bluetongue disease in endemic areas is predominantly controlled through vaccination with live-attenuated vaccines. Sequencing of the original master seed viruses used in the production of Onderstepoort Biological Products vaccine was conducted. Nucleotide identities of 82.97%–100% were obtained for all sequences when compared to South African reference strains.
Metatranscriptomes of California grassland soil microbial communities in response to rewetting
Authors: Chuckran Peter F. , Estera-Molina Katerina , Huntemann Marcel , Foster Brian , Roux Simon , Mukherjee Supratim , Hajek Patrick , Reddy T. B. K. , Daum Chris , Chen I-Min A. , Pennacchio Christa , Eloe-Fadrosh Emiley A. , Dijkstra Paul , Firestone Mary K. , Blazewicz Steven J. , Pett-Ridge Jennifer 
Published: May 2024

ABSTRACT

When very dry soil is rewet, rapid stimulation of microbial activity has important implications for ecosystem biogeochemistry, yet associated changes in microbial transcription are poorly known. Here, we present metatranscriptomes of California annual grassland soil microbial communities, collected over 1 week from soils rewet after a summer drought—providing a time series of short-term transcriptional response during rewetting.