bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconstruction Algorithm for Complex Dexel Models Based on Composite Block Partition
Authors: Yu Haiwen , Wu Dianliang , Xu Hanzhong 
Published: November 2023

Abstract
In machining simulations, dexel models are often used to represent objects to achieve high accuracy and real-time performance. However, this approach leads to the loss of original surface information and topological relationships, thereby affecting the visualization effect of simulations. Furthermore, existing reconstruction methods have the drawbacks of generalization or redundancy. To reconstruct the surface of dexel models efficiently and accurately, this paper proposes an algorithm based on “composite block” partition, which converts the dexel model into a polyhedral model. The algorithm begins by partitioning the entire dexel model within the grids into several composite blocks based on the “Connectivity Principle” and generating their end faces. Subsequently, the transitional zone’s surface is reconstructed based on the connectivity relationships of the boundaries of composite blocks. Finally, an optimization process refines the boundaries to generate smoother side faces at a low computational cost. The paper first validates the algorithm’s reconstruction capability and the effectiveness of edge refinement through the reconstruction of various dexel models with different precision levels. It is observed that edge refinement does not introduce excessive additional computation, doubling the overall efficiency compared to existing algorithms. Furthermore, by changing model volumes and performing separate reconstructions, it’s noted that as the volume increases, the incremental growth in conversion time gradually decreases. This makes the algorithm particularly suitable for reconstructing large-scale complex dexel models. Finally, the application of this algorithm in virtual-real simulation systems and industrial digital twin systems is briefly introduced.
Design Space Exploration and Evaluation Using Margin-Based Trade-Offs
Authors: Al Handawi Khalil , Brahma Arindam , Wynn David C. , Kokkolaras Michael , Isaksson Ola 
Published: November 2023

Abstract
Design space exploration and margin analysis can inform critical decisions early in engineering design, helping to handle the uncertainties of early design while ensuring design performance. In practice, the complexity of many products makes such decision-making challenging. This paper addresses the challenge with a new design framework that relies on the margin value method to evaluate sets of concepts that are combinatorially generated from an enhanced function-means tree. The basis for concept comparison is the margin value in each design alternative. The margin value method is expanded to address a broad class of design problems by using surrogate models and novel metrics for evaluating different conceptual alternatives. Visualization tools are introduced to support the evaluations. The efficacy of the framework is demonstrated using the design of a structural aero-engine component involving simulation models and uncertain load specifications. Overall, this paper shows how design concepts can be compared objectively and distilled to a set of alternatives that would retain their values throughout product development.
Structural Designs of Novel Deployable Polyhedral Grippers for Noncontact Capturing Missions
Authors: Tang Ruijie , Meng Qizhi , Xie Fugui , Liu Xin-Jun , Wang Jinsong 
Published: November 2023

Abstract
Deployable polyhedral grippers have attracted increasing attention for their priority in noncontact capturing missions. Enrichment of these grippers may benefit the conduction of various capturing tasks. In this paper, novel deployable polyhedral grippers are presented. A design flow is proposed for the structural designs of diverse grippers. The core problem during the construction is reducible to the structural designs and combination of multiple synchronously deployable modules. Each module, containing three faces connected by two revolute joints, can realize one-degree-of-freedom deployment. Type synthesis of synchronously deployable modules adopting different layouts of revolute joints is conducted. The mobility and kinematics of these modules are analyzed to verify the achieved motion. As examples, four deployable polyhedral grippers based on different polyhedrons and deployment diagrams are presented. The deployment performance of the prototype proves the validity of the proposed design method and exhibits the potential of these deployable polyhedral grippers for diverse capturing missions.
Involvement of endoplasmic reticulum and histone proteins in immunomodulation by TLR4-interacting SPA4 peptide against
Escherichia coli
Authors: Awasthi Shanjana , Singh Bhupinder , Ramani Vijay , Godbole Nachiket M. , King Catherine 
Published: November 2023

ABSTRACT

Pulmonary host defense is critical for the control of lung infection and inflammation. An increased expression and activity of Toll-like receptor 4 (TLR4) induce phagocytic uptake/clearance and inflammation against Gram-negative bacteria. In this study, we addressed the mechanistic aspect of the immunomodulatory activity of the TLR4-interacting SPA4 peptide (amino acid sequence GDFRYSDGTPVNYTNWYRGE) against
Escherichia coli
. Binding of the SPA4 peptide to bacteria and direct anti-bacterial effects were investigated using flow cytometric, microscopic, and bacteriological methods. The bacterial uptake and inflammatory cytokine response were studied in dendritic cells expressing endogenous basal level of TLR4 or overexpressing TLR4. The subcellular distribution and co-localization of TLR4 and bacteria were investigated by immunocytochemistry. Furthermore, we studied the cellular expression and co-localization of endoplasmic reticulum (ER) molecules (calnexin and ER membrane protein complex subunit 1; EMC1) with lysosomal-associated membrane protein 1 (LAMP1) in cells infected with
E. coli
and treated with the SPA4 peptide. Simultaneously, the expression of histone H2A protein was quantitated by immunoblotting. Our results demonstrate no binding or direct killing of the bacteria by SPA4 peptide. Instead, it induces the uptake and localization of
E. coli
in the phagolysosomes for lysis and simultaneously suppresses the secreted levels of TNF-α. Overexpression of TLR4 further augments the pro-phagocytic and anti-inflammatory activity of SPA4 peptide. A time-dependent change in subcellular distribution of TLR4 and an increased co-localization of TLR4 with
E. coli
in SPA4 peptide-treated cells suggest an enhanced recognition and internalization of bacteria in conjugation with TLR4. Furthermore, an increased co-localization of calnexin and EMC1 with LAMP1 indicates the involvement of ER in pro-phagocytic activity of SPA4 peptide. Simultaneous reduction in secreted amounts of TNF-α coincides with suppressed histone H2A protein expression in the SPA4 peptide-treated cells. These results provide initial insights into the plausible role of ER and histones in the TLR4-immunomodulatory activity of SPA4 peptide against Gram-negative bacteria.
Pathogenesis of
Achromobacter xylosoxidans
respiratory infections: colonization, persistence, and transcriptome profiling in synthetic cystic fibrosis sputum medium
Authors: Billiot Caitlin E. , Novak Lea , McDaniel Melissa S. , Lindgren Natalie R. , Swords W. Edward 
Published: November 2023

ABSTRACT

Cystic fibrosis (CF) is a genetic disease affecting epithelial ion transport, resulting in thickened mucus and impaired mucociliary clearance. Persons with CF (pwCF) experience life-long infections of the respiratory mucosa caused by a diverse array of opportunists, which are leading causes of morbidity and mortality. In recent years, there has been increased appreciation for the range and diversity of microbes causing CF-related respiratory infections. The introduction of new therapeutics and improved detection methodology has revealed CF-related opportunists such as
Achromobacter xylosoxidans
(
Ax
).
Ax
is a Gram-negative bacterial species which is widely distributed in environmental sources and has been increasingly observed in sputa and other samples from pwCF, typically in patients in later stages of CF disease. In this study, we characterized CF clinical isolates of
Ax
and tested colonization and persistence of
Ax
in respiratory infection using immortalized human CF respiratory epithelial cells and BALB/c mice. Genomic analyses of clinical
Ax
isolates showed homologs for factors including flagellar synthesis, antibiotic resistance, and toxin secretion systems.
Ax
isolates adhered to polarized cultures of CFBE41o- human immortalized CF bronchial epithelial cells and caused significant cytotoxicity and depolarization of cell layers.
Ax
colonized and persisted in mouse lungs for up to 72 h post infection, with inflammatory consequences that include increased neutrophil influx in the lung, lung damage, cytokine production, and mortality. We also identified genes that are differentially expressed in synthetic CF sputum media. Based on these results, we conclude that
Ax
is an opportunistic pathogen of significance in CF.
miR-155 facilitates the synergistic replication between avian leukosis virus subgroup J and reticuloendotheliosis virus by targeting a dual pathway
Authors: Xue Jingwen , Zhou Defang , Zhou Jing , Du Xusheng , Zhang Xinyue , Liu Xiaoyang , Ding Longying , Cheng Ziqiang 
Published: November 2023

ABSTRACT
Co-infection of avian leukosis virus subgroup J (ALV-J) and reticuloendotheliosis virus (REV) in poultry flocks induces synergistic replication, which worsens immunosuppression, growth inhibition, and increased mortality. However, the synergistic replication mechanism between ALV-J and REV is still not fully understood. We showed that microRNA-155 (miR-155) targets a dual pathway, PRKCI-MAPK8 and TIMP3-MMP2, which interacts with the U3 region of ALV-J and REV to promote synergistic replication between ALV-J and REV. Initially, we found that the RNA levels of ALV-J and REV increased significantly in ALV-J and REV co-infected cells and tissues compared with mono-infected cells and tissues. Next, miRNAomics showed that ALV-J and REV synergistically increased miR-155 levels. In co-infected cells, miR-155 promoted synergistic replication of ALV-J and REV. All structural proteins of the two viruses activated the expression of miR-155, especially gag proteins, rather than insertional activation. Proteomic study of cells co-infected with ALV-J and REV and transfected with miR-155 indicated that miR-155 directly suppressed PRKCI and TIMP3 and that PRKCI directly prevented MAPK8 expression, while TIMP3 directly interfered MMP2 expression. We also found that MAPK8 and MMP2 co-interacted with ALV-J and REV’s U3 to enhance synergistic replication. In conclusion, ALV-J and REV synergistically activate miR-155, facilitating the synergistic replication of ALV-J and REV by PRKCI-MAPK8 and TIMP3-MMP2 dual-pathway interaction with the U3 region of ALV-J and REV. This discovery will assist in explaining how two retroviruses replicate synergistically.

IMPORTANCE
The synergy of two oncogenic retroviruses is an essential phenomenon in nature. The synergistic replication of ALV-J and REV in poultry flocks increases immunosuppression and pathogenicity, extends the tumor spectrum, and accelerates viral evolution, causing substantial economic losses to the poultry industry. However, the mechanism of synergistic replication between ALV-J and REV is still incompletely elusive. We observed that microRNA-155 targets a dual pathway, PRKCI-MAPK8 and TIMP3-MMP2, interacting with the U3 region of ALV-J and REV, enabling synergistic replication. This work gives us new targets to modulate ALV-J and REV’s synergistic replication, guiding future research on the mechanism.
Hypoxia and HIF-1α promote lytic
de novo
KSHV infection
Authors: Lee See-Chi , Naik Nenavath Gopal , Tombácz Dóra , Gulyás Gábor , Kakuk Balázs , Boldogkői Zsolt , Hall Kevin , Papp Bernadett , Boulant Steeve , Toth Zsolt 
Published: November 2023

ABSTRACT

The impact of different stress conditions on the oncogenic Kaposi’s sarcoma-associated herpesvirus (KSHV) primary infection that can occur
in vivo
remains largely unknown. We hypothesized that KSHV can establish a latency or lytic cycle following
de novo
infection, depending on the conditions of the cellular environment. Previous studies showed that hypoxia is a natural stress condition that promotes lytic reactivation and contributes to KSHV pathogenesis, but its effect on
de novo
KSHV infection is unknown. To test the effect of hypoxia on KSHV infection, we infected cells under normoxia and hypoxia, performed a comparative analysis of viral gene expression and viral replication, and tested chromatinization of the KSHV genome during infection. We found that hypoxia induces viral lytic gene expression and viral replication following
de novo
infection in several biologically relevant cell types, in which the virus normally establishes latency under normoxia. We also found that hypoxia reduces the level of repressive heterochromatin and promotes the formation of a transcriptionally permissive chromatin on the incoming viral DNA during infection. We demonstrate that silencing hypoxia-inducible factor-1α (HIF-1α) during hypoxia abrogates lytic KSHV infection, while the overexpression of HIF-1α under normoxia is sufficient to drive lytic KSHV infection. Also, we determined that the DNA-binding domain and the N-terminal but not the C-terminal transactivation domain of HIF-1α are required for HIF-1α-induced lytic gene expression. Altogether, our data indicate that HIF-1α accumulation, which can be induced by hypoxia, prevents the establishment of latency and promotes lytic KSHV infection following primary infection.

IMPORTANCE

The current view is that the default pathway of Kaposi’s sarcoma-associated herpesvirus (KSHV) infection is the establishment of latency, which is a prerequisite for lifelong infection and viral oncogenesis. This view about KSHV infection is supported by the observations that KSHV latently infects most of the cell lines cultured
in vitro
in the absence of any environmental stresses that may occur
in vivo
. The goal of this study was to determine the effect of hypoxia, a natural stress stimulus, on primary KSHV infection. Our data indicate that hypoxia promotes euchromatin formation on the KSHV genome following infection and supports lytic
de novo
KSHV infection. We also discovered that hypoxia-inducible factor-1α is required and sufficient for allowing lytic KSHV infection. Based on our results, we propose that hypoxia promotes lytic
de novo
infection in cells that otherwise support latent infection under normoxia; that is, the environmental conditions can determine the outcome of KSHV primary infection.
Complete mitochondrial genome sequence of the Agaricomycetes brown rot fungus
Fomitopsis pinicola
isolate FBCC1181
Authors: Österman-Udd Janina , Lundell Taina Kristina 
Published: November 2023

ABSTRACT

The mitochondrial genome of the brown rot fungus
Fomitopsis pinicola
isolate FBCC 1181 is a 66.5 kbp circular chromosome. It contains 64 predicted genes, including a set typical for Basidiomycota Agaricomycetes mitogenomes. Introns of
cox
and
cob
genes contain several homing endonucleases of both LAGLIDADG and GIY-YIG types.
Draft genome sequence of multidrug-resistant
Citrobacter portucalensis
BAU_133-2 strain isolated from a domestic duck (
Anas platyrhynchos domesticus
) in Bangladesh
Authors: Ahmed Tarana , Islam Md. Saiful , Nuruzzaman Mohammad , Sadekuzzaman Mohammad , Kabir S. M. Lutful , Rahman Md. Tanvir , Khan Md. Shahidur Rahman 
Published: November 2023

ABSTRACT

We announce the genome sequence of the
Citrobacter portucalensis
BAU_133-2 strain isolated from a domestic duck. Our assembled genome contained a length of 4.8 Mb, 110.0× genome coverage, 51.91% of an average GC content, 1 plasmid, 1 CRISPR array, 8 prophages, 27 antibiotic resistance genes, and 75 virulence factor genes.
Engineered probiotic
Lactobacillus plantarum
WCSF I for monitoring and treatment of
Staphylococcus aureus
infection
Authors: Li Haoran , Jia Minjun , Qi Qingsheng , Wang Qian 
Published: November 2023

ABSTRACT

Lactobacillus plantarum
is one of the most thoroughly researched species of the genus
Lactobacillus
, which possesses the characteristics of easy genetic transformation, high-density growth, and high intestinal tract survival.
L. plantarum
has been proven to play a potential role as a probiotic delivery vector.
Staphylococcus aureus
is a common Gram-positive pathogenic bacterium. It uses an autoinducer peptide (AIP) produced by its Agr quorum-sensing (AgrQS) system to sense the population density. Using the quorum-sensing mechanism exclusive to
S. aureus
, we constructed an AgrQS system in
L. plantarum
WCSF induction and killing modules based on AIP sensing and regulation so that
L. plantarum
could effectively eliminate
S. aureus
when detecting exogenous AIP at nanomolar concentrations. By optimizing the expression strength of the two-component system AgrAC using different
L. plantarum
-derived promoters and replacing the core promoter of the AgrA-activating promoter, the activation strength of AgrQS increased from the initial 1.2-fold to 5.3-fold. By introducing the signal peptide N20-guided lysostaphin aureus protein, engineered
L. plantarum
was able to effectively control the release of lysostaphin aureus protein and inhibit the growth of
S. aureus
. For the first time, engineered
L. plantarum
can detect and treat
S. aureus
infection, laying the groundwork for the future development of engineered probiotics for the monitoring and therapy of intestinal pathogens.

IMPORTANCE

Bacterial infection and the emergence of drug-resistant strains are major problems in clinical treatment.
Staphylococcus aureus
, which typically infects the skin and blood of animals, is also a potential intestinal pathogen that needs to be addressed by the emergence of a new treatment approach. Probiotic therapy is the most likely alternative to antibiotic therapy to solve the problem of bacterial drug resistance in clinical practice. In this study, the engineered
Lactobacillus plantarum
can not only sense the signal AIP to detect
S. aureus
but also kill
S. aureus
by secreting the lysostaphin enzyme. Our strategy employed an Agr quorum-sensing genetic circuit to simultaneously detect and treat pathogenic bacteria, which provided a theoretical possibility for solving practical clinical bacterial infection cases in the future.
The fourth COVID-19 vaccine dose increased the neutralizing antibody response against the SARS-CoV-2 Omicron (B.1.1.529) variant in a diverse Brazilian population
Authors: Pires Farias Jéssica , Andreata-Santos Robert , Dalety da Silva Brito Ruth , Silva Souza Milena , Moreira Costa Fogaça Mayanna , Ramos Pinheiro Josilene , Ferreira da Cruz Edgar , Liang Willian , Simões Rafael da Conceição , Barros Luiz Wilson , Birbrair Alexander , Oliveira Vidal Paloma , Terzi Maricato Juliana , Torres Braconi Carla , Ferreira Luís Carlos de Souza , Ramos Janini Luiz Mário , Amorim Jaime Henrique 
Published: November 2023

ABSTRACT
Most of the original immunization regimens against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were composed of two doses, followed by a subsequent third booster dose to control the Omicron variant and hence coronavirus disease 2019 (COVID-19). However, most data generated regarding the fourth dose were not based on the general population. Therefore, this study aimed to verify the effect of the fourth COVID-19 vaccine dose in a diverse Brazilian population. This retrospective observational study was conducted between May and September 2022. We gathered data on the vaccine regimens and COVID-19 serologic status from 266 healthy volunteers who received three or four vaccine doses, as well as COVID-19 diagnosis and viral genome sequencing from 457 patients with flu-like symptoms. In addition, we conducted immunoinformatic analysis to assess the conserved epitopes in the locally circulating viruses. We showed that the fourth dose did not increase the serum levels of antiviral antibodies, as measured by enzyme-linked immunosorbent assay. However, it significantly increased neutralizing antibody (NAb) titers against the Omicron variant. All viral sequences generated in this study were Omicron subvariants, mainly B.A.5.1. Notably, most NAb epitopes present in the wild-type SARS-CoV-2 were not detected among the circulating Omicron subvariants. None of the volunteers who received the third or fourth doses presented COVID-19 for at least 1 year before the study period. Altogether, these results indicate that the fourth vaccine dose increases the serum levels of NAbs that recognize highly conserved epitopes in Omicron subvariants.

IMPORTANCE
Several additional COVID-19 vaccine doses were administered in the Brazilian population to prevent the disease caused by the B.1.1.529 (Omicron) variant. The efficacy of a third dose as a booster is already well described. However, it is important to clarify the humoral immune response gain induced by a fourth dose. In this study, we evaluate the effect of the fourth COVID-19 vaccine dose in a diverse Brazilian population, considering a real-life context. Our study reveals that the fourth dose of the COVID-19 vaccine increased the neutralizing antibody response against SARS-CoV-2 Omicron and significantly contributed in the reduction of the disease caused by this variant.
High-resolution chronostratigraphy of late Mesozoic sequences in northern North China: Implications for the linkages among intracontinental orogeny, volcanism, Jehol Biota, and Pacific plate subduction
Authors: Ma Qiang , Zhong Yuting , Yin Qingzhu , Huyskens Magdalena H. , Ma Liang , Xia Xiaoping , Meng Qing-Ren , Zhou Zhong-He , Xu Yi-Gang 
Published: November 2023

Abstract
Subduction of the paleo-Pacific plate during the late Mesozoic is thought to have been responsible for the destruction of the North China craton, manifested by intense volcanism, lithospheric deformation, and dramatic changes in surface morphology and terrestrial ecosystems. However, the timing and correlations of these consequential events remain obscure. This issue was addressed here by carrying out a high-resolution geochronologic study on the Upper Jurassic–Lower Cretaceous sequences of the Luanping basin, northern Hebei Province, China. Secondary ion mass spectrometry (SIMS) and chemical abrasion–isotope dilution–isotope ratio mass spectrometry (CA-ID-IRMS) zircon U-Pb ages from samples near the boundaries of the stratigraphic units help to redefine the chronostratigraphic framework of this basin and more importantly reveal that the second phase of the Yanshanian orogeny, representing a tectonic transition from flat to steep subduction of the paleo-Pacific plate, occurred within 0.87 ± 0.10 m.y. between 134.162 ± 0.091 Ma and 133.295 ± 0.043 Ma. Crustal extension then followed and resulted in development of rift basins and vigorous volcanism. The Jehol Biota came into being in Lower Cretaceous successions formed after ca. 130 Ma. The late Mesozoic Luanping basin therefore records how the subduction of the paleo-Pacific plate drove intracontinental orogeny, volcanism, basin development, and ecosystem evolution.