bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient Mapping Between Void Shapes and Stress Fields Using Deep Convolutional Neural Networks With Sparse Data
Authors: Bhaduri Anindya , Ramachandra Nesar , Krishnan Ravi Sandipp , Luan Lele , Pandita Piyush , Balaprakash Prasanna , Anitescu Mihai , Sun Changjie , Wang Liping 
Published: January 2024

Abstract
Establishing fast and accurate structure-to-property relationships is an important component in the design and discovery of advanced materials. Physics-based simulation models like the finite element method (FEM) are often used to predict deformation, stress, and strain fields as a function of material microstructure in material and structural systems. Such models may be computationally expensive and time intensive if the underlying physics of the system is complex. This limits their application to solve inverse design problems and identify structures that maximize performance. In such scenarios, surrogate models are employed to make the forward mapping computationally efficient to evaluate. However, the high dimensionality of the input microstructure and the output field of interest often renders such surrogate models inefficient, especially when dealing with sparse data. Deep convolutional neural network (CNN) based surrogate models have shown great promise in handling such high-dimensional problems. In this paper, a single ellipsoidal void structure under a uniaxial tensile load represented by a linear elastic, high-dimensional and expensive-to-query, FEM model. We consider two deep CNN architectures, a modified convolutional autoencoder framework with a fully connected bottleneck and a UNet CNN, and compare their accuracy in predicting the von Mises stress field for any given input void shape in the FEM model. Additionally, a sensitivity analysis study is performed using the two approaches, where the variation in the prediction accuracy on unseen test data is studied through numerical experiments by varying the number of training samples from 20 to 100.
The Handwriting Legibility Scale: A Language and Age Extension for Students With and Without Specific Learning Difficulties
Authors: Stuart Nichola , Zoia Stefania , Biancotto Marina , Barnett Anna L. 
Published: January 2024

Handwriting is a useful skill through education, yet handwriting difficulties are common in students with Specific Learning Difficulties (SpLD), including Developmental Coordination Disorder. There are few practical tools to assess legibility, among these the Handwriting Legibility Scale (HLS) shows good reliability and validity for 9- to 14-year-olds in the United Kingdom. The aims of the current study were to investigate applicability of the HLS in students with and without SpLD in (a) another language and (b) older age groups. First, the HLS was translated and applied to writing scripts of 193 9- to 14-year-olds in Italy. Findings support previous work on reliability and validity. A principal component analysis confirmed a single component for the HLS at this age and there was differentiation between scripts from students with and without SpLD. Second, the HLS was applied to writing scripts of 80 15- to 16-year-olds and 120 17- to 25-year-olds in the United Kingdom. Results showed good reliability and differentiation between scripts from students with and without SpLD. A principal component analysis revealed two components for the HLS in the older age groups. Language and age differences in the use of the HLS are discussed, alongside other considerations when applying the tool to help identify handwriting difficulties in students.
Type I BREX system defends against antibiotic-resistant plasmids in
Escherichia coli
Authors: Jiang Xiaoying , Li Dan , Sun Zhewei , Lu Yanyan , Li Pei , Li Wanzhen , Wang Dongliang , Wei Lianhua , Xu Xiaogang , Yuan Yuan , Wang Minggui 
Published: January 2024

ABSTRACT

The Bacteriophage Exclusion (BREX) system is a novel antiphage defense system identified in
Bacillus cereus
in 2015. The purpose of this study was to investigate the presence of the BREX system defenses against antibiotic-resistant plasmids such as
bla
KPC
and
bla
NDM
invasion in
Escherichia coli
. The BREX system was present in 5.4% (23/424) of
E. coli
clinical isolates and 6.5% (84/1283) of
E. coli
strains with completely sequenced genomes in the GenBank database. All 23 BREX-positive
E. coli
clinical isolates were susceptible to carbapenems, while all five isolates carrying
bla
KPC
and 11 carrying
bla
NDM
were BREX-negative. For
E. coli
strains in the GenBank database, 37 of 38 strains carrying
bla
KPC
and 109 of 111 strains carrying
bla
NDM
were BREX negative. The recognition site sequence of methyltransferase PglX in a clinical
E. coli
3756 was 5′-CANC
A
TC-3′ using PacBio single-molecular real-time sequencing. The transformation efficiency of plasmid psgRNA-ColAori-target with the PglX recognition site was reduced by 100% compared with the plasmid without the recognition site in
E. coli
DH5α-pHSG398-BREX. The BREX showed lower defense efficacy against plasmid psgRNA-15Aori-target which had the same plasmid backbone but different surrounding sequences of recognition sites with psgRNA-ColAori-target. The conjugation frequency of the KPC-2 plasmid and NDM-5 plasmid in
E. coli
3756-ΔBREX was higher than that in
E. coli
3756 clinical isolate (1.0 × 10
−6
vs 1.3 × 10
−7
and 5.5 × 10
−7
vs 1.7 × 10
−8
, respectively). This study demonstrated that the type I BREX system defends against antibiotic-resistant plasmids in
E. coli
.
Characterization of the resistome and predominant genetic lineages of Gram-positive bacteria causing keratitis
Authors: André Camille , Van Camp Andrew G. , Ung Lawson , Gilmore Michael S. , Bispo Paulo J. M. 
Published: January 2024

ABSTRACT

Bacterial keratitis is a vision-threatening infection mainly caused by Gram-positive bacteria (GPB). Antimicrobial therapy is commonly empirical using broad-spectrum agents with efficacy increasingly compromised by the emergence of antimicrobial resistance. We used a combination of phenotypic tests and genome sequencing to identify the predominant lineages of GPB causing keratitis and to characterize their antimicrobial resistance patterns. A total of 161 isolates, including
Staphylococcus aureus
(
n
= 86), coagulase-negative staphylococci (CoNS;
n
= 34),
Streptococcus
spp. (
n
= 34), and
Enterococcus faecalis
(
n
= 7), were included. The population of
S. aureus
isolates consisted mainly of clonal complex 5 (CC5) (30.2%). Similarly, the population of
Staphylococcus epidermidis
was homogenous with most of them belonging to CC2 (78.3%). Conversely, the genetic population of
Streptococcus pneumoniae
was highly diverse. Resistance to first-line antibiotics was common among staphylococci, especially among CC5
S. aureus
. Methicillin-resistant
S. aureus
was commonly resistant to fluoroquinolones and azithromycin (78.6%) and tobramycin (57%). One-third of the CoNS were resistant to fluoroquinolones and 53% to azithromycin. Macrolide resistance was commonly caused by
erm
genes in
S. aureus
,
mphC
and
msrA
in CoNS, and
mefA and msr(D
) in streptococci. Aminoglycoside resistance in staphylococci was mainly associated with genes commonly found in mobile genetic elements and that encode for nucleotidyltransferases like
ant(4′)-Ib
and
ant(9)-Ia
. Fluroquinolone-resistant staphylococci carried from 1 to 4 quinolone resistance-determining region mutations, mainly in the
gyrA
and
parC
genes. We found that GPB causing keratitis are associated with strains commonly resistant to first-line topical therapies, especially staphylococcal isolates that are frequently multidrug-resistant and associated with major hospital-adapted epidemic lineages.
A single locus determines praziquantel response in
Schistosoma mansoni
Authors: Chevalier Frédéric D. , Le Clec’h Winka , Berriman Matthew , Anderson Timothy J.C. 
Published: January 2024

ABSTRACT

We previously performed a genome-wide association study (GWAS) to identify the genetic basis of praziquantel (PZQ) response in schistosomes, identifying two quantitative trait loci situated on chromosomes 2 and 3. We reanalyzed this GWAS using the latest (version 10) genome assembly showing that a single locus on chromosome 3, rather than two independent loci, determines drug response. These results reveal that PZQ response is monogenic and demonstrates the importance of high-quality genomic information.
Effect of glutathione-transport-related gene
gsiD
on desiccation tolerance of
Cronobacter sakazakii
and its related regulatory mechanism
Authors: Wang Xiao-yi , Li Ping , Du Xin-jun , Wang Shuo 
Published: January 2024

ABSTRACT

The outstanding desiccation tolerance of
Cronobacter sakazakii
(
C. sakazakii
) enables long-term persistence in food products with low-water activity to increase the infection risk, especially in low-birth-weight, immuno-compromised neonates, and infants less than 4 weeks of age. In our previous study, the disruption of glutathione transport-related gene
gsiD
by transposon was found to significantly increase its inactivation rate under drying stress challenges. However, the mechanism underlying the association between glutathione transport and desiccation tolerance of
C. sakazakii
remains to be clarified. In this study, the mechanism underlying their association was investigated in detail by constructing the
gsiD
gene deletion mutant.
gsiD
gene deletion was found to cause the dysfunction of the glutathione transport system GsiABCD and the limitation of glutathione import. The resulting decrease in intracellular glutathione caused the decreased potassium ions uptake and increased potassium ions efflux, inhibited the proline synthesis process, limited extracellular glutathione utilization, increased oxidant stress, reduced biofilm formation, and increased outer membrane permeability, which may be the main reasons for the significant reduction of the desiccation tolerance of
C. sakazakii
.

IMPORTANCE

Contributing to its superior environmental adaptability,
Cronobacter sakazakii
can survive under many abiotic stress conditions. The outstanding desiccation tolerance makes this species persist in low-water activity foods, which increases harm to humans. For decades, many studies have focused on the desiccation tolerance of
C. sakazakii
, but the existing research is still insufficient. Our study found that
gsiD
gene deletion inhibited glutathione uptake and further decreased intracellular glutathione content, causing a decrease in desiccation tolerance and biofilm formation and an increase in outer membrane permeability. Moreover, the expression level of relative genes verified that
gsiD
gene deletion made the mutant not conducive to surviving in dry conditions due to restricting potassium ions uptake and efflux, inhibiting the conversion of glutamate to compatible solute proline, and increasing the oxidative stress of
C. sakazakii
. The above results enrich our knowledge of the desiccation tolerance mechanism of
C. sakazakii
.
HtrAs are essential for the survival of the haloarchaeon
Natrinema gari
J7-2 in response to heat, high salinity, and toxic substances
Authors: Luo Hongyi , Qu Xiaoyi , Deng Xi , He Liping , Wu Yi , Liu Yang , He Dan , Yin Jing , Wang Bingxue , Gan Fei , Tang Bing , Tang Xiao-Feng 
Published: January 2024

ABSTRACT

Bacterial and eukaryotic HtrAs can act as an extracytoplasmic protein quality control (PQC) system to help cells survive in stress conditions, but the functions of archaeal HtrAs remain unknown. Particularly, haloarchaea route most secretory proteins to the Tat pathway, enabling them to fold properly in well-controlled cytoplasm with cytosolic PQC systems before secretion. It is unclear whether HtrAs are required for haloarchaeal survival and stress response. The haloarchaeon
Natrinema gari
J7-2 encodes three Tat signal peptide-bearing HtrAs (NgHtrA, NgHtrB, and NgHtrC), and the signal peptides of NgHtrA and NgHtrC contain a lipobox. Here, the
in vitro
analysis reveals that the three HtrAs show different profiles of temperature-, salinity-, and metal ion-dependent proteolytic activities and could exhibit chaperone-like activities to prevent the aggregation of reduced lysozyme when their proteolytic activities are inhibited at low temperatures or the active site is disrupted. The gene deletion and complementation assays reveal that NgHtrA and NgHtrC are essential for the survival of strain J7-2 at elevated temperature and/or high salinity and contribute to the resistance of this haloarchaeon to zinc and inhibitory substances generated from tryptone. Mutational analysis shows that the lipobox mediates membrane anchoring of NgHtrA or NgHtrC, and both the membrane-anchored and free extracellular forms of the two enzymes are involved in the stress resistance of strain J7-2, depending on the stress conditions. Deletion of the gene encoding NgHtrB in strain J7-2 causes no obvious growth defect, but NgHtrB can functionally substitute for NgHtrA or NgHtrC under some conditions.

IMPORTANCE

HtrA-mediated protein quality control plays an important role in the removal of aberrant proteins in the extracytoplasmic space of living cells, and the action mechanisms of HtrAs have been extensively studied in bacteria and eukaryotes; however, information about the function of archaeal HtrAs is scarce. Our results demonstrate that three HtrAs of the haloarchaeon
Natrinema gari
J7-2 possess both proteolytic and chaperone-like activities, confirming that the bifunctional nature of HtrAs is conserved across all three domains of life. Moreover, we found that NgHtrA and NgHtrC are essential for the survival of strain J7-2 under stress conditions, while NgHtrB can serve as a substitute for the other two HtrAs under certain circumstances. This study provides the first biochemical and genetic evidence of the importance of HtrAs for the survival of haloarchaea in response to stresses.
Impaired neutrophil extracellular trap-forming capacity contributes to susceptibility to chronic vaginitis in a mouse model of vulvovaginal candidiasis
Authors: Yano Junko , Fidel Paul L. 
Published: January 2024

ABSTRACT

Vulvovaginal candidiasis (VVC), caused by
Candida albicans,
is characterized by aberrant inflammation by polymorphonuclear neutrophils (PMNs) in the vaginal lumen. Data from the established murine model shows that despite potent antifungal properties, PMNs fail to clear
C. albicans
due to local heparan sulfate that inhibits the interaction between PMNs and
C. albicans
, resulting in chronic vaginal immunopathology. To understand the role of neutrophil extracellular traps (NETs) in defense against
C. albicans
at the vaginal mucosa, we investigated the NET-forming capacity of PMNs in chronic VVC-susceptible (CVVC-S/C3H) and -resistant (CVVC-R/CD-1) mouse strains. Immunofluorescence revealed the formation of NETs (release of DNA with PMN-derived antimicrobial proteins) in PMN
–C. albicans
cocultures using vaginal conditioned medium (VCM) generated from CVVC-R/CD-1 mice, similar to NET-inducing positive controls. Under these NETotic conditions, PMNs released high levels of double-stranded DNA bound with NET-associated proteins, concomitant with substantial
C. albicans
killing activity. In contrast, PMN
–C. albicans
cocultures in VCM from CVVC-S/C3H mice lacked NET formation together with reduced antifungal activity. Similar results were observed
in vivo
: active NET
–C. albicans
interaction followed by fungal clearance in inoculated CVVC-R/CD-1 mice, and sustained high vaginal fungal burden and no evidence of NETs in inoculated CVVC-S/C3H mice. Furthermore, the level of Ki67 expression, a putative NETotic PMN marker, was significantly reduced in vaginal lavage fluid from CVVC-S/C3H mice compared to CVVC-R/CD-1 mice. Finally, scanning electron microscopy revealed that PMNs in CVVC-R, but not CVVC-S, conditions exhibited NETs in direct contact with
C. albicans
hyphae
in vitro
and
in vivo
. These results suggest that VVC-associated immunopathology includes impaired NET-mediated antifungal activity.
Layering vaccination with antibiotic therapy results in protection and clearance of
Burkholderia pseudomallei
in Balb/c mice
Authors: Barnes Kay B. , Brett Paul , Burtnick Mary , Vente Andreas , Bentley Christine , Richards Mark I. , Flick-Smith Helen C. , Burgess Gary , Thwaite Joanne E. , Laws Thomas R. , Maishman Thomas C. , Nelson Michelle , Harding Sarah V. 
Published: January 2024

ABSTRACT

Melioidosis is a disease that is difficult to treat due to the causative organism,
Burkholderia pseudomallei
being inherently antibiotic resistant and it having the ability to invade, survive, and replicate in an intracellular environment. Combination therapy approaches are routinely being evaluated in animal models with the aim of improving the level of protection and clearance of colonizing bacteria detected. In this study, a subunit vaccine layered with the antibiotic finafloxacin was evaluated
in vivo
against an inhalational infection with
B. pseudomallei
in Balb/c mice. Groups of mice vaccinated, infected, and euthanized at antibiotic initiation had a reduced bacterial load compared to those that had not been immunized. In addition, the subunit vaccine provided a synergistic effect when it was delivered with a CpG ODN and finafloxacin was initiated at 48 h post-challenge. Vaccination was also shown to improve the outcome, in a composite measure of survival and clearance. In summary, layering a subunit vaccine with the antibiotic finafloxacin is a promising therapeutic alternative for use in the treatment of
B. pseudomallei
infections.
Enhanced antigen-specific CD8 T cells contribute to early protection against FMDV through swine DC vaccination
Authors: Mu Suyu , Chen Lingbo , Dong Hu , Li Shuai , Zhang Yun , Yin Shuanghui , Tian Yunfei , Ding Yaozhong , Sun Shiqi , Shang Shaobin , Guo Huichen 
Published: January 2024

ABSTRACT

Foot-and-mouth disease virus (FMDV) remains a challenge for cloven-hooved animals. The currently licensed FMDV vaccines induce neutralizing antibody (NAb)-mediated protection but show defects in the early protection. Dendritic cell (DC) vaccines have shown great potency in inducing rapid T-cell immunity in humans and mice. Whether DC vaccination could enhance early protection against FMDV has not been elaborately explored in domestic pigs. In this study, we employed DC vaccination as an experimental approach to study the roles of cellular immunity in the early protection against FMDV in pigs. Autologous DCs were differentiated from the periphery blood mononuclear cells of each pig, pulsed with inactivated FMDV (iFMDV-DC) and treated with LPS, and then injected into the original pigs. The cellular immune responses and protective efficacy elicited by the iFMDV-DC were examined by multicolor flow cytometry and tested by FMDV challenge. The results showed that autologous iFMDV-DC immunization induced predominantly FMDV-specific IFN-γ-producing CD4
+
T cells and cytotoxic CD8
+
T cells (CTLs), high NAb titers, compared to the inactivated FMDV vaccine, and accelerated the development of memory CD4 and CD8 T cells, which was concomitantly associated with early protection against FMDV virulent strain in pigs. Such early protection was associated with the rapid proliferation of secondary T-cell response after challenge and significantly contributed by secondary CD8 effector memory T cells. These results demonstrated that rapid induction of cellular immunity through DC immunization is important for improving early protection against FMDV. Enhancing cytotoxic CD8
+
T cells may facilitate the development of more effective FMDV vaccines.

IMPORTANCE

Although the currently licensed FMDV vaccines provide NAb-mediated protection, they have defects in early immune protection, especially in pigs. In this study, we demonstrated that autologous swine DC immunization augmented the cellular immune response and induced an early protective response against FMDV in pigs. This approach induced predominantly FMDV-specific IFN-γ-producing CD4
+
T cells and cytotoxic CD8
+
T cells, high NAb titers, and rapid development of memory CD4 and CD8 T cells. Importantly, the early protection conferred by this DC immunization is more associated with secondary CD8
+
T response rather than NAbs. Our findings highlighted the importance of enhancing cytotoxic CD8
+
T cells in early protection to FMDV in addition to Th1 response and identifying a strategy or adjuvant comparable to the DC vaccine might be a future direction for improving the current FMDV vaccines.
The small RNA PrrH aggravates
Pseudomonas aeruginosa
-induced acute lung injury by regulating the type III secretion system activator ExsA
Authors: Shi Qixuan , Zeng Shenghe , Yu Ruiqi , Li Mo , Shen Cong , Zhang Xuan , Zhao Chanjing , Zeng Jianming , Huang Bin , Pu Jieying , Chen Cha 
Published: January 2024

ABSTRACT

Pseudomonas aeruginosa
is an opportunistic pathogen that causes acute and chronic infections in immunocompromised individuals. Small regulatory RNAs (sRNAs) regulate multiple bacterial adaptations to environmental changes, especially virulence. Our previous study showed that sRNA PrrH negatively regulates the expression of a number of virulence factors, such as pyocyanin, rhamnolipid, biofilm, and elastase in the
P. aeruginosa
strain PAO1. However, previous studies have shown that the
prrH
-deficient mutant attenuates virulence in an acute murine lung infection model. All Δ
prrH
-infected mice survived the entire 28-day course of the experiment, whereas all mice inoculated with the wild-type or the complemented mutant succumbed to lung infection within 4 days of injection, but the specific mechanism is unclear. Herein, we explored how PrrH mediates severe lung injury by regulating the expression of virulence factors.
In vivo
mouse and
in vitro
cellular assays demonstrated that PrrH enhanced the pathogenicity of PAO1, causing severe lung injury. Mechanistically, PrrH binds to the coding sequence region of the mRNA of
exsA
, which encodes the type III secretion system master regulatory protein. We further demonstrated that PrrH mediates a severe inflammatory response and exacerbates the apoptosis of A549 cells. Overall, our results revealed that PrrH positively regulates ExsA, enhances the pathogenicity of
P. aeruginosa
, and causes severe lung injury.

IMPORTANCE

Pseudomonas aeruginosa
is a Gram-negative bacterium and the leading cause of nosocomial pneumonia. The pathogenicity of
P. aeruginosa
is due to the secretion of many virulence factors. Small regulatory RNAs (sRNAs) regulate various bacterial adaptations, especially virulence. Therefore, understanding the mechanism by which sRNAs regulate virulence is necessary for understanding the pathogenicity of
P. aeruginosa
and the treatment of the related disease. In this study, we demonstrated that PrrH enhances the pathogenicity of
P. aeruginosa
by binding to the coding sequence regions of the ExsA, the master regulatory protein of type III secretion system, causing severe lung injury and exacerbating the inflammatory response and apoptosis. These findings revealed that PrrH is a crucial molecule that positively regulates ExsA. Type III-positive strains are often associated with a high mortality rate in
P. aeruginosa
infections in clinical practice. Therefore, this discovery may provide a new target for treating
P. aeruginosa
infections, especially type III-positive strains.