bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk-Informing Nuclear Reactor Safety: The Prediction of the Probability of Core Damage Due to Loss of Power and Cooling
Authors: Duffey Romney B. , Zio Enrico 
Published: February 2024

Abstract
The modern idea of risk-informed decision-making (RIDM) is here critically examined for all existing, advanced and, generation-IV nuclear reactor systems. Motivated by the predictive difficulties of probabilistic risk assessment (PRA) in regard to occurred accidents, it is evident that the real (not hypothetical) consequences of nuclear core damage accidents that must be considered and quantified are the financial losses, infrastructure damages, societal disruptions, and adverse political policies, and not solely the traditional exceedance of regulated radiation release or public exposure limits. With this perspective, a new dynamic analysis is presented for estimating the probability of core damage due to extended loss of power and cooling in a modern nuclear reactor, giving results different from current standardized PRA/PSA analyses. Using existing data, we approach the multitude of different events in a new way: whatever the initial event in the finite event set {external flood, fire, hurricane, ice storm, typhoon, earthquake, cyber attack…}, the fundamental concerns are the consequent loss and nonrestoration of power, and the inadequate cooling of the core. The present proposed quantitative evaluation uses applicable and fully “exchangeable” severe event data for nuclear and nonnuclear systems, including active and passive emergency back-up systems for a wide range of power losses that lead to widespread damage and societal disruption. While not design-specific, this new independent “order-of-magnitude” estimate for the probability of core damage is some two to two hundred times larger than that shown or reported in recent modern and formal PSA/PRA for licensing submissions using generic failure rate data rather than actual severe event data. This new finding suggests greater uncertainties exist than presently assumed for risk-informed decision-making (RIDM), and points to the need for a major reconsideration and updating of risk assessment and regulatory risk-informed approaches for nuclear plant safety evaluation.
Simulation Test Research on Typical Simulator NS-2 in Urban Vehicle Ad Hoc Network Based on Big Data
Authors: Wang Xiaoting , Jin Junxia , Zhao Zhan 
Published: February 2024

Abstract
Vehicle ad hoc network (VANET) has gradually become a prominent research topic in the fields of wireless networks and intelligent vehicles. VANETs are unique mobile ad hoc networks with vehicles as their mobile nodes, presenting distinctive performance characteristics compared to traditional wireless self-organizing networks. In recent years, VANETs have gained significant attention in the wireless network and intelligent transportation domain. As an integral aspect of autonomous driving technology, vehicle-to-everything (V2X) communication spans multiple disciplines and is closely related to intelligent transportation, assisted driving, active safety, and smart vehicles. Evaluating VANET protocols and applications in real-world settings can be challenging. Therefore, utilizing simulation tools for VANET research is an effective approach. In this paper, we have designed and developed an optimized platform that uses IEEE 802.11a and IEEE 802.11p protocols for communication within a simulated urban traffic environment created with NS-2. The simulation results confirm the feasibility and rationale of applying the IEEE 802.11p protocol to wireless vehicular ad hoc networks. Within a distance of 300 m, at 0.0000 s, 14 key packets have not arrived in IEEE 802.11a, and 8 packets have not arrived in IEEE 802.11p; at 8.0000 s, 38 key packets have not arrived in IEEE802.11a, and 6 packets have not arrived in IEEE802.11p. Comparing the performance of IEEE 802.11a and IEEE 802.11p, the study concluded that the use of the 802.11p protocol in urban mobile environments can improve reliability and reduce average packet latency.
Identification of epidermal growth factor receptor-tyrosine kinase inhibitor targeting the VP1 pocket of human rhinovirus
Authors: Miah Masum , Davis Andrew M. , Hannoun Charles , Said Joanna S. , Fitzek Martina , Preston Marian , Smith Dave , Uwamariya Colores , Kärmander Ambjörn , Lundbäck Thomas , Bergström Tomas , Trybala Edward 
Published: February 2024

ABSTRACT

Screening a library of 1,200 preselected kinase inhibitors for anti-human rhinovirus 2 (HRV-2) activity in HeLa cells identified a class of epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKI) as effective virus blockers. These were based on the 4-anilinoquinazoline-7-oxypiperidine scaffold, with the most potent representative AZ5385 inhibiting the virus with EC
50
of 0.35 µM. Several structurally related analogs confirmed activity in the low µM range, while interestingly, other TKIs targeting EGFR lacked anti-HRV-2 activity. To further probe this lack of association between antiviral activity and EGFR inhibition, we stained infected cells with antibodies specific for activated EGFR (Y1068) and did not observe a dependency on EGFR-TK activity. Instead, consecutive passages of HRV-2 in HeLa cells in the presence of a compound and subsequent nucleotide sequence analysis of resistant viral variants identified the S181T and T210A alterations in the major capsid VP1 protein, with both residues located in the vicinity of a known hydrophobic pocket on the viral capsid. Further characterization of the antiviral effects of AZ5385 showed a modest virus-inactivating (virucidal) activity, while anti-HRV-2 activity was still evident when the inhibitor was added as late as 10 h post infection. The RNA copy/infectivity ratio of HRV-2 propagated in AZ5385 presence was substantially higher than that of control HRV indicating that the compound preferentially targeted HRV progeny virions during their maturation in infected cells. Besides HRV, the compound showed anti-respiratory syncytial virus activity, which warrants its further studies as a candidate compound against viral respiratory infections.
Calpain-2 mediates SARS-CoV-2 entry via regulating ACE2 levels
Authors: Zeng Qiru , Antia Avan , Casorla-Perez Luis Alberto , Puray-Chavez Maritza , Kutluay Sebla B. , Ciorba Matthew A. , Ding Siyuan 
Published: February 2024

ABSTRACT

Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, much effort has been dedicated to identifying effective antivirals against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A number of calpain inhibitors show excellent antiviral activities against SARS-CoV-2 by targeting the viral main protease (M
pro
), which plays an essential role in processing viral polyproteins. In this study, we found that calpain inhibitors potently inhibited the infection of a chimeric vesicular stomatitis virus (VSV) encoding the SARS-CoV-2 spike protein but not M
pro
. In contrast, calpain inhibitors did not exhibit antiviral activities toward the wild-type VSV with its native glycoprotein. Genetic knockout of calpain-2 by CRISPR/Cas9 conferred resistance of the host cells to the chimeric VSV-SARS-CoV-2 virus and a clinical isolate of wild-type SARS-CoV-2. Mechanistically, calpain-2 facilitates SARS-CoV-2 spike protein-mediated cell attachment by positively regulating the cell surface levels of ACE2. These results highlight an M
pro
-independent pathway targeted by calpain inhibitors for efficient viral inhibition. We also identify calpain-2 as a novel host factor and a potential therapeutic target responsible for SARS-CoV-2 infection at the entry step.

IMPORTANCE
Many efforts in small-molecule screens have been made to counter SARS-CoV-2 infection by targeting the viral main protease, the major element that processes viral proteins after translation. Here, we discovered that calpain inhibitors further block SARS-CoV-2 infection in a main protease-independent manner. We identified the host cysteine protease calpain-2 as an important positive regulator of the cell surface levels of SARS-CoV-2 cellular receptor ACE2 and, thus, a facilitator of viral infection. By either pharmacological inhibition or genetic knockout of calpain-2, the SARS-CoV-2 binding to host cells is blocked and viral infection is decreased. Our findings highlight a novel mechanism of ACE2 regulation, which presents a potential new therapeutic target. Since calpain inhibitors also potently interfere with the viral main protease, our data also provide a mechanistic understanding of the potential use of calpain inhibitors as dual inhibitors (entry and replication) in the clinical setting of COVID-19 diseases. Our findings bring mechanistic insights into the cellular process of SARS-CoV-2 entry and offer a novel explanation to the mechanism of activities of calpain inhibitors.
Batf3-dependent orchestration of the robust Th1 responses and fungal control during cryptococcal infection, the role of cDC1
Authors: Xu Jintao , Hissong Rylan , Bareis Rachel , Creech Arianna , Goughenour Kristie D. , Freeman Christine M. , Olszewski Michal A. 
Published: February 2024

ABSTRACT

While type I conventional dendritic cells (cDC1s) are vital for generating adaptive immunity against intracellular pathogens and tumors, their role in defense against fungal pathogen
Cryptococcus neoformans
remains unclear. We investigated the role of the cDC1 subset in a fungus-restricting mouse model of cryptococcal infection. The cDC1 subset displayed a unique transcriptional signature with highly upregulated T-cell recruitment, polarization, and activation pathways compared to other DC subsets. Using Batf3
−/−
mice, which lack the cDC1 population, our results support that Batf3-dependent cDC1s are pivotal for the development of the effective immune response against cryptococcal infection, particularly within the lung and brain. Deficiency in Batf3 cDC1 led to diminished CD4 accumulation and decreased IFNγ production across multiple organs, supporting that cDC1s are a major driver of potent Th1 responses during cryptococcal infection. Consistently, mice lacking Batf3-cDC1 demonstrated markedly diminished fungicidal activity and weaker containment of the fungal pathogen. In conclusion, Batf3-dependent cDC1 can function as a linchpin in mounting Th1 response, ensuring effective fungal control during cryptococcal infection. Harnessing cDC1 pathways may present a promising strategy for interventions against this pathogen.

IMPORTANCE

Cryptococcus neoformans
causes severe meningoencephalitis, accounting for an estimated 200,000 deaths each year. Central to mounting an effective defense against these infections is T-cell-mediated immunity, which is orchestrated by dendritic cells (DCs). The knowledge about the role of specific DC subsets in shaping anti-cryptococcal immunity is limited. Here, we demonstrate that Batf3 cDC1s are important drivers of protective Th1 CD4 T-cell responses required for clearance of cryptococcal infection. Deficiency of Batf3 cDC1 in the infected mice leads to significantly reduced Th1 response and exacerbated fungal growth to the point where depleting the remaining CD4 T cells no longer affects fungal burden. Unveiling this pivotal role of cDC1 in antifungal defense is likely to be important for the development of vaccines and therapies against life-threatening fungal pathogens.
Evolutionary trade-off between heat shock resistance, growth at high temperature, and virulence expression in
Salmonella
Typhimurium
Authors: Berdejo Daniel , Mortier Julien , Cambré Alexander , Sobota Malgorzata , Van Eyken Ronald , Kim Tom Dongmin , Vanoirbeek Kristof , García Gonzalo Diego , Pagán Rafael , Diard Médéric , Aertsen Abram 
Published: February 2024

ABSTRACT

Understanding the evolutionary dynamics of foodborne pathogens throughout our food production chain is of utmost importance. In this study, we reveal that
Salmonella
Typhimurium can readily and reproducibly acquire vastly increased heat shock resistance upon repeated exposure to heat shock. Counterintuitively, this boost in heat shock resistance was invariantly acquired through loss-of-function mutations in the
dnaJ
gene, encoding a heat shock protein that acts as a molecular co-chaperone of DnaK and enables its role in protein folding and disaggregation. As a trade-off, however, the acquisition of heat shock resistance inevitably led to attenuated growth at 37°C and higher temperatures. Interestingly, loss of DnaJ also downregulated the activity of the master virulence regulator HilD, thereby lowering the fraction of virulence-expressing cells within the population and attenuating virulence in mice. By connecting heat shock resistance evolution to attenuation of HilD activity, our results confirm the complex interplay between stress resistance and virulence in
Salmonella
Typhimurium.

IMPORTANCE

Bacterial pathogens such as
Salmonella
Typhimurium are equipped with both stress response and virulence features in order to navigate across a variety of complex inhospitable environments that range from food-processing plants up to the gastrointestinal tract of its animal host. In this context, however, it remains obscure whether and how adaptation to one environment would obstruct fitness in another. In this study, we reveal that severe heat stress counterintuitively, but invariantly, led to the selection of
S.
Typhimurium mutants that are compromised in the activity of the DnaJ heat shock protein. While these mutants obtained massively increased heat resistance, their virulence became greatly attenuated. Our observations, therefore, reveal a delicate balance between optimal tuning of stress response and virulence features in bacterial pathogens.
Active pH regulation facilitates
Bacillus subtilis
biofilm development in a minimally buffered environment
Authors: Tran Peter , Lander Stephen M. , Prindle Arthur 
Published: February 2024

ABSTRACT

Biofilms provide individual bacteria with many advantages, yet dense cellular proliferation can also create intrinsic metabolic challenges including excessive acidification. Because such pH stress can be masked in buffered laboratory media—such as MSgg commonly used to study
Bacillus subtilis
biofilms—it is not always clear how such biofilms cope with minimally buffered natural environments. Here, we report how
B. subtilis
biofilms overcome this intrinsic metabolic challenge through an active pH regulation mechanism. Specifically, we find that these biofilms can modulate their extracellular pH to the preferred neutrophile range, even when starting from acidic and alkaline initial conditions, while planktonic cells cannot. We associate this behavior with dynamic interplay between acetate and acetoin biosynthesis and show that this mechanism is required to buffer against biofilm acidification. Furthermore, we find that buffering-deficient biofilms exhibit dysregulated biofilm development when grown in minimally buffered conditions. Our findings reveal an active pH regulation mechanism in
B. subtilis
biofilms that could lead to new targets to control unwanted biofilm growth.

IMPORTANCE

pH is known to influence microbial growth and community dynamics in multiple bacterial species and environmental contexts. Furthermore, in many bacterial species, rapid cellular proliferation demands the use of overflow metabolism, which can often result in excessive acidification. However, in the case of bacterial communities known as biofilms, these acidification challenges can be masked when buffered laboratory media are employed to stabilize the pH environment for optimal growth. Our study reveals that
B. subtilis
biofilms use an active pH regulation mechanism to mitigate both growth-associated acidification and external pH challenges. This discovery provides new opportunities for understanding microbial communities and could lead to new methods for controlling biofilm growth outside of buffered laboratory conditions.
Nanobody-mediated neutralization of candidalysin prevents epithelial damage and inflammatory responses that drive vulvovaginal candidiasis pathogenesis
Authors: Valentine Marisa , Rudolph Paul , Dietschmann Axel , Tsavou Antzela , Mogavero Selene , Lee Sejeong , Priest Emily L. , Zhurgenbayeva Gaukhar , Jablonowski Nadja , Timme Sandra , Eggeling Christian , Allert Stefanie , Dolk Edward , Naglik Julian R. , Figge Marc T. , Gresnigt Mark S. , Hube Bernhard 
Published: February 2024

ABSTRACT

Candida albicans
can cause mucosal infections in humans. This includes oropharyngeal candidiasis, which is commonly observed in human immunodeficiency virus infected patients, and vulvovaginal candidiasis (VVC), which is the most frequent manifestation of candidiasis. Epithelial cell invasion by
C. albicans
hyphae is accompanied by the secretion of candidalysin, a peptide toxin that causes epithelial cell cytotoxicity. During vaginal infections, candidalysin-driven tissue damage triggers epithelial signaling pathways, leading to hyperinflammatory responses and immunopathology, a hallmark of VVC. Therefore, we proposed blocking candidalysin activity using nanobodies to reduce epithelial damage and inflammation as a therapeutic strategy for VVC. Anti-candidalysin nanobodies were confirmed to localize around epithelial-invading
C. albicans
hyphae, even within the invasion pocket where candidalysin is secreted. The nanobodies reduced candidalysin-induced damage to epithelial cells and downstream proinflammatory responses. Accordingly, the nanobodies also decreased neutrophil activation and recruitment.
In silico
mathematical modeling enabled the quantification of epithelial damage caused by candidalysin under various nanobody dosing strategies. Thus, nanobody-mediated neutralization of candidalysin offers a novel therapeutic approach to block immunopathogenic events during VVC and alleviate symptoms.

IMPORTANCE

Worldwide, vaginal infections caused by
Candida albicans
(VVC) annually affect millions of women, with symptoms significantly impacting quality of life. Current treatments are based on anti-fungals and probiotics that target the fungus. However, in some cases, infections are recurrent, called recurrent VVC, which often fails to respond to treatment. Vaginal mucosal tissue damage caused by the
C. albicans
peptide toxin candidalysin is a key driver in the induction of hyperinflammatory responses that fail to clear the infection and contribute to immunopathology and disease severity. In this pre-clinical evaluation, we show that nanobody-mediated candidalysin neutralization reduces tissue damage and thereby limits inflammation. Implementation of candidalysin-neutralizing nanobodies may prove an attractive strategy to alleviate symptoms in complicated VVC cases.
Toxoplasma
and
Plasmodium
associate with host Arfs during infection
Authors: Schroeder Erin A. , Toro-Moreno Maria , Raphemot Rene , Sylvester Kayla , Colón Isabel C. , Derbyshire Emily R. 
Published: February 2024

ABSTRACT

The apicomplexans
Toxoplasma gondii
and
Plasmodium
are intracellular parasites that reside within a host-derived compartment termed the parasitophorous vacuole (PV). During infection, the parasites must acquire critical host resources and transport them across their PV for development. However, the mechanism by which host resources are trafficked to and across the PV remains uncertain. Here, we investigated host ADP ribosylation factors (Arfs), a class of proteins involved in vesicular trafficking that may be exploited by
T. gondii
and
Plasmodium berghei
for nutrient acquisition. Using overexpressed Arf proteins coupled with immunofluorescence microscopy, we found that all Arfs were internalized into the
T. gondii
PV, with most vacuoles containing at least one punctum of Arf protein by the end of the lytic cycle. We further characterized Arf1, the most abundant Arf inside the
T. gondii
PV, and observed that active recycling between its GDP/GTP-bound state influenced Arf1 internalization independent of host guanine nucleotide exchange factors (GEFs). In addition, Arf1 colocalized with vesicle coat complexes and exogenous sphingolipids, suggesting a role in nutrient acquisition. While Arf1 and Arf4 were not observed inside the PV during
P. berghei
infection, our gene depletion studies showed that liver stage development and survival depended on the expression of Arf4 and the host GEF, GBF1. Collectively, these observations indicate that apicomplexans use distinct mechanisms to subvert the host vesicular trafficking network and efficiently replicate. The findings also pave the way for future studies to identify parasite proteins critical to host vesicle recruitment and the components of vesicle cargo.

IMPORTANCE

The parasites
Toxoplasma gondii
and
Plasmodium
live complex intracellular lifestyles where they must acquire essential host nutrients while avoiding recognition. Although previous work has sought to identify the specific nutrients scavenged by apicomplexans, the mechanisms by which host materials are transported to and across the parasite vacuole membrane are largely unknown. Here, we examined members of the host vesicular trafficking network to identify specific pathways subverted by
T. gondii
and
Plasmodium berghei
. Our results indicate that
T. gondii
selectively internalizes host Arfs, a class of proteins involved in intracellular trafficking. For
P. berghei
, host Arfs were restricted by the parasite’s vacuole membrane, but proteins involved in vesicular trafficking were identified as essential for liver stage development. A greater exploration into how and why apicomplexans subvert host vesicular trafficking could help identify targets for host-directed therapeutics.
Use of a combined antibacterial synergy approach and the ANNOgesic tool to identify novel targets within the gene networks of multidrug-resistant
Klebsiella pneumoniae
Authors: Lee Hyunsook , Yu Sung-Huan , Shim Jung Eun , Yong Dongeun 
Published: February 2024

ABSTRACT

Since the 1980s, the development of new drug classes for the treatment of multidrug-resistant
Klebsiella pneumoniae
has become limited, highlighting the urgent need for novel antibiotics. To address this challenge, this study aimed to explore the synergistic interactions between chemical compounds and representative antibiotics, such as carbapenem and colistin. The primary objective of this study was not only to mitigate the adverse impact of multidrug-resistant
K. pneumoniae
on public health but also to establish a sustainable balance among humans, animals, and the environment. Phenotypical measurements were conducted using the broth microdilution technique to determine the drug sensitivity of bacterial strains. Additionally, a genotypical approach was employed, involving traditional RNA sequencing analysis to identify differentially expressed genes and the computational ANNOgesic tool to detect noncoding RNAs. This study revealed the existence of various pathways and regulatory RNA elements that form a functional network. These pathways, characterized by the expression of specific genes, contribute to the combined treatment effect and bacterial survival strategies. The connections between pathways are facilitated by regulatory RNA elements that respond to environmental changes. These findings suggest an adaptive response of bacteria to harsh environmental conditions.

IMPORTANCE
Noncoding RNAs were identified as key players in post-transcriptional regulation. Moreover, this study predicted the presence of novel small regulatory RNAs that interact with target genes, as well as the involvement of riboswitches and RNA thermometers in conjunction with associated genes. These findings will contribute to the discovery of potential antimicrobial therapeutic candidates. Overall, this study offers valuable insights into the synergistic effects of chemical compounds and antibiotics, highlighting the role of regulatory RNA elements in bacterial response, and survival strategies. The identification of novel noncoding RNAs and their interactions with target genes, riboswitches, and RNA thermometers holds promise for the development of antimicrobial therapies.