bluuebunny/crossref_metadata_2025 huggingface dataset:
Patient‐reported difficulty in activities of daily living and corresponding muscle weakness in elderly patients undergoing haemodialysis
Authors: Matsufuji Shota , Shoji Tetsuo , Lee Suhye , Hoshio Atsuhiro , Tanaka Ruri , Fujimoto Koji , Watanuki Hiroaki , Nishimura Mari , Tsujimoto Yoshihiro , Morioka Tomoaki , Mori Katsuhito , Emoto Masanori
Published: February 2024

Aim

Patients undergoing haemodialysis have reduced muscle strength and impaired activities of daily living (ADL). We examined possible relationship between difficult ADL and corresponding muscle weakness in elderly haemodialysis patients.

Methods

This was a single‐centre, cross‐sectional study. Patient‐reported ADL difficulty was examined using a questionnaire in six ADL using upper limbs (eating, grooming and dressing) and lower limbs (bathing, toileting and locomotion). We measured six muscle strengths by dynamometers of shoulder flexion, shoulder abduction, elbow flexion, handgrip, hip abduction and knee extension. The muscle strength with the lowest Z‐score was considered as the weakest muscle strength for the patient.

Results

The six scores of ADL difficulty were all inversely associated with the six muscle strengths in the 81 total participants of whom 71 individuals (87.7%) had any ADL difficulty. Among the six measurements of muscle strength, handgrip strength showed the highest associations with all ADL difficulties. In 25 patients who perceived that the most difficult ADL was an activity using upper limbs, the common weakest muscle strengths were the hip abduction, handgrip and elbow flexion. In 44 patients who perceived that the most difficult ADL was an activity using lower limbs, knee extension was the most prevalent weakest muscle strength.

Conclusion

This study suggested preferential relationship between the most difficult ADL and corresponding muscle weakness in elderly haemodialysis patients. This finding may be useful in prevention and treatment.

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Weight reduction and the risk of gallbladder and biliary disease: A systematic review and meta‐analysis of randomized clinical trials
Authors: Yang Wenjia , Wu Han , Cai Xiaoling , Lin Chu , Luo Yingying , Hu Suiyuan , Li Zonglin , Jiao Ruoyang , Bai Shuzhen , Liu Geling , Yang Xiaolin , Ji Linong
Published: February 2024

In this meta‐analysis, we aim to evaluate the risk of gallbladder and biliary disease of weight management strategies and investigate the association between weight reduction and risk of gallbladder or biliary disease. Randomized controlled trials (RCTs) with a duration of at least 12 weeks that compare antiobesity medications (AOMs) with placebo or bariatric surgery with less intensive weight management strategy were concluded. Weight management strategy was associated with a significant increased risk of gallbladder or biliary disease (OR 1.361, 95% CI 1.147 to 1.614, P < 0.001, I2 = 3.5%), cholelithiasis, cholecystitis, and cholecystectomy compared with placebo or controls. The increased risk of gallbladder or biliary disease was observed both in pharmacotherapies subgroup and bariatric surgery subgroup. With regards of specific pharmacotherapies, an increased risk of gallbladder or biliary disease was observed in trials with glucagon‐like peptide 1 receptor agonist (GLP‐1 RA) treatments. In addition, trials with indication of obesity and overweight treatment and trials with higher doses showed significant higher risk of gallbladder or biliary disease compared with placebo or controls. In conclusion, weight management strategy was associated with an increased risk of gallbladder or biliary disease when compared with placebo or control groups.
The impact of perinatal and at birth risk factors on the progression from preschool wheezing to adolescent asthma
Authors: Gallagher Claire , Batra Mehak , Malamardi Sowmya Nagappa , Erbas Bircan
Published: February 2024

Asthma is a global health concern affecting millions of children and adolescents. This review focuses on the possible factors that are associated with the transition from preschool wheezing to childhood asthma and highlights the significance of early‐life environmental exposures during pregnancy and the first 6 months of life in shaping allergies and asthma. We observed a scarcity of studies investigating this subgroup, with most focusing on wheezing trajectories. We undertook a thorough investigation of diverse perinatal exposures that have the potential to impact this transition. These factors include maternal asthma, smoking during pregnancy, diet, prepregnancy weight, infant birthweight, gestational age, and breastfeeding. Although limited, studies do suggest that maternal asthma increases the likelihood of preschool wheeze in offspring that persists through childhood with potential asthma progression. Findings concerning other perinatal exposures remain inconsistent. Further research is needed to identify asthma progression risk factors and assess perinatal exposure effects.
Growing or reproducing? Assessing the existence of a trade‐off in the globose cactus Gymnocalycium monvillei
Authors: Lorenzati M. A. , Aliscioni N. L. , Delbón N. E. , Gurvich D. E.
Published: February 2024

Resource allocation in plants is a fundamental aspect of life history theory. In Cactaceae, the specific trade‐off between sexual reproduction and vegetative growth has still not been studied. The aim of this work was to assess if there is a trade‐off between growth and reproduction, and to analyse whether both growth and allocation to reproduction depend on size of the individual.

In this study, we used Gymnocalycium monvillei, a globose cactus endemic to the mountains of central Argentina, as a model species. Specifically, we analysed the relationship of growth (percentage increase in diameter) and size of individuals (diameter) to seed production, seed mass, germination, and mean germination time. To relativize the effect of size on seed production, two variables were calculated: the ratio of seed production to plant size (RSPS), and the ratio of total seed mass to plant size (RSMS).

We found that both seed production and total seed mass were significantly related to cactus size. However, growth was not related to seed mass or to seed production, even when they were relativized. Germination and mean germination time were not related to plant size or growth.

In the studied species, a slow‐growing globose cactus, we did not find a trade‐off between growth and reproduction.
Investigating the relationship between gender equality and citizen trust: Evidence from Latin America
Authors: Lee Yunsoo , Ottervik Mattias
Published: February 2024

Objectives

Previous research has shown a relationship between social and economic equality and trust, but the relationship between gender equality and trust has received relatively little attention. This study addresses that lacuna and analyzes the relationship between gender equality and political trust as well as social trust.

Methods

Using the 2015 Latinobarómetro, we test the relationship between two types of gender equality, labor gender equality and overall gender equality, and two types of trust, political trust and social trust in a series of regressions.

Results

The results show that gender equality is positively associated with social and political trust. In particular, the magnitude of association of labor gender equality with social trust is greater than that of overall gender equality. Also, the magnitude of association of overall gender equality with political trust is greater than that of labor gender equality.

Conclusions

Our article contributes to the literature by demonstrating that overall gender equality and labor gender equality have varying association with trust depending on types of trust.
More than the Second Amendment: Liberal gun owners, citizenship, and emancipatory democracy in the United States
Authors: Hubbert Jennifer , Eaton Hannah
Published: February 2024

Objective

This study seeks to understand how liberal gun owners configure the rights and responsibilities of ethical gun citizenship in the face of a dominant public narratives that rejects guns as markers of liberal belonging.

Methods

This study employs a qualitative, textual analysis approach to explore the narratives of liberal gun owners participating in online discussions of mass shootings and contentious political elections.

Results

The results show how liberal gun owners, in these online forums, advocated for an emancipatory democracy that largely prioritized the collective over the individual, demanded an accountable government, and was radical in its insistence on the importance of accessibility and meaningful participation, thus configuring social belonging and commensurability as central to formal citizenship.

Conclusion

The results suggest that how one formulates the values of citizenship is linked to how one practices the politics of democracy. Highlighting the greater range of possibilities for the alignment of guns and citizenship may thus offer some hope to the rancor of contemporary partisan politics as liberal gun owners seek to normalize a democracy that brings individual and collective identities and needs into its culture and practice.
Spatiotemporal stacking method with daily‐cycle restrictions for reconstructing missing hourly PM2.5 records
Authors: Chen Chuanfa , Li Kunyu
Published: February 2024

The reliability of hourly PM2.5 data obtained from air quality monitoring stations is compromised as a result of the missing values, thereby impeding the thorough examination of crucial information. In this paper, we present a spatiotemporal (ST) stacking machine learning (ML) method with daily‐cycle restrictions for reconstructing missing hourly PM2.5 records. First, the ST neighbors for the target station with missing values are selected at a daily scale. Subsequently, the non‐null data within the ST neighbors undergo an iterative P‐BSHADE interpolation process for re‐interpolation. Next, a stacking ML model is constructed using the re‐interpolation values and several environmental factors associated with PM2.5 as the predictors, while the observed PM2.5 is taken as the independent variable. Finally, the missing values are reconstructed by inputting the predictors into the trained stacking model. The study utilized hourly PM2.5 data in the Beijing‐Tianjin‐Hebei region as a case study to assess the effectiveness of the proposed method, using daily missing ratios of 10%, 30%, and 50%, respectively. The accuracy of the proposed method was then compared to four contemporary ST interpolation methods. The results indicate that the proposed method exhibits superior performance compared to the classical methods. Specifically, it achieves a reduction in the average root mean square error and mean absolute error by at least 40.6% and 40.1%, respectively. Additionally, the proposed method demonstrates the successful recovery of extreme values in the hourly PM2.5 records, in contrast to the classical methods which often exhibit a tendency to overestimate low values and underestimate high values. Overall, the proposed method presents a viable and efficient approach to recover missing values in the hourly PM2.5 records that demonstrate evident daily periodic patterns.
The nuts and bolts of transplant infectious disease training
Authors: Harris Courtney E. , Kumar Rebecca N. , Haidar Ghady , La Hoz Ricardo M. , Gorsline Chelsea A.
Published: February 2024

The number of transplant infectious disease (TID) fellowship programs has expanded rapidly in the past 5 years, with the creation of many new programs and the expansion of training tracks and dedicated years as the demand for TID physicians grows drastically. This editorial focuses on major factors and complexities that programs should consider in TID fellowship creation, as well as highlighting examples of formative experiences, programmatic structure, and fellow resources that trainees can use to identify their desired career path in TID.

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Effect of Rim Seal Geometry on Rotationally-Driven Ingestion
Authors: Burden Shaun , Chew John W. , Gao Feng , Marxen Olaf
Published: February 2024

This study investigates turbine rim seal geometry effects within the rotationally-driven ingestion regime. Computations were performed with a wall-resolved unsteady Reynolds-averaged Navier–Stokes (URANS) model and a large-eddy simulation (LES) model including near-wall boundary layer modeling, that is, wall-modeled LES (WMLES). Use of simplified rim sealing models is proposed as an efficient method of ranking seal designs and investigating sensitivity to seal geometry. Four rim seal configurations, two chute seals, an axial seal and a radial seal which are representative of those used in gas turbines and in previous research were investigated. Furthermore, hybrid seals combining geometric characteristics from both the chute and radial seal were considered. Significant sensitivities of sealing performance to turbulence modeling are identified, but URANS and WMLES show similar trends in ranking of seal performance, and these are consistent with previous experimental work. The addition of an outer radial clearance section to a chute seal is effective in reducing ingestion levels.
Melting and Heat Transfer Characteristics of Phase Change Material: A Comparative Study on Wire Mesh Finned Structure and Other Fin Configurations
Authors: Uniyal Arun , Kumar Deepak , Prajapati Yogesh K.
Published: February 2024

In the present paper, a two-dimensional transient numerical study has been performed to investigate the influence of different fin designs on the melting and heat transfer characteristics of a phase change material (PCM), i.e., Paraffin wax, filled in square enclosures equipped with fin structures. Five distinct fin designs were examined: single rectangular, double rectangular, double triangular, double angled, and wire mesh. It is worth noting that all these fin designs have the equal heat transfer area. An isothermal heat source of temperature 350 K is provided at the left wall of the square enclosure and the remaining walls are assumed to be adiabatic. Six parameters were evaluated to determine the best fin configurations: melting time, enhancement ratio (ER), time savings, energy stored, mean power, and Nusselt number. The results show that all the fin designs outperformed as compared to model 1 (no fin configuration). Among the finned configurations, model 2 had the poorest performance, taking 1314 s to complete the melting, while model 6 had the most efficient fin design, with a melting time reduced by 67.53% compared to model 1. Model 6 also had the highest ER and mean power, i.e., 70.43% and 199.51%, respectively and as the melting process continued, the Nusselt number decreased. In addition to the above, we optimized the element size of the wire-mesh fin design using RSM methodology. This optimized design decreases the melting period by 70.04%. Overall, present study provides a comprehensive analysis of different finned configurations for improving the melting performance of the PCM in square enclosures and found wire-mesh fin design most appropriate and promising.
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

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

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.
Comparison between combined ultrasounds and magnetic resonance imaging in the differentiation of benign and malignant breast lesions: a cross-sectional study
Authors: Li Chaoxi , Wen Dehui , Lu Haiyong
Published: February 2024

Aim: To explore the performance of single or combined ultrasound (US) in diagnosing malignant breast lesions, and then compare the results with a magnetic resonance imaging (MRI) aspect.Material and methods: Patients’ demographics, tumor markers, and imaging examination were collected. Diagnostic models based on B-mode, color Doppler ultrasounds (CDU), strain elastography (SE), MRI, B-mode US + CDU, B-mode US + SE, and B-mode US + CDU + SE were developed using logistic regression analysis. The performance was assessed using the area under the curve (AUC) with 95% confidence intervals (CIs). Performance of MRI and B-mode US + CDU was compared using DeLong analysis.Results: For single imaging modality, MRI showed the best performance, with AUC of 0.938 (95%CI: 0.888-0.988). For combined US modalities, combination of B-mode US and CDU had the best performance, with AUC of 0.948 (95%CI: 0.877-1.000). There was no significant difference in the diagnostic performance between the combination of B-mode US and CDU and MRI (p>0.05).Conclusions: Our study found the performance of B-mode + CDU was comparable to MRI. Our findings suggested that the combination of B-mode US and CDU was recommended to diagnose malignant breast lesions in order to save time and expense and provide guidance to make decisions for a biopsy
Passion is not misconduct
Authors: Thorp H. Holden
Published: February 2024

University of Pennsylvania climate scientist Michael Mann was awarded more than $1 million in a lawsuit against bloggers who accused him of scientific misconduct in inflammatory terms, likening his treatment of data to what a noted child molester did to children. The verdict suggests that there are limits to which scientists working on politically sensitive topics can be falsely attacked. But the case also says something profound about the difference between matters of opinion and scientific interpretations that can be worked out through normal academic processes. Although Mann has expressed strong—and even intemperate—emotions and words in political discourse, the finding of the District of Columbia Superior Court boiled down to the fact that it is not an opinion that determines when scientific misconduct occurs but rather, misconduct can be established using known processes.
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

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

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

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

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

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

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

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

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.
Serial passage of PDCoV in cell culture reduces its pathogenicity and its damage of gut microbiota homeostasis in piglets
Authors: Zhang Yunfei , Si Lulu , Gao Junlong , Shu Xiangli , Qiu Congrui , Zhang Yue , Zu Shaopo , Hu Hui
Published: February 2024

Porcine deltacoronavirus (PDCoV) is an enteropathogenic coronavirus that mainly causes diarrhea in suckling piglets, and also has the potential for cross-species transmission. However, there are still no commercial vaccines available to prevent and control PDCoV infection. In this study, PDCoV strain HNZK-02 was serially propagated
in vitro
for up to 150 passages and the amino acid changes have mainly occurred in the S protein during serial passage which caused structure change. PDCoV HNZK-02-passage 5 (P5)-infected piglets exhibited acute and severe watery diarrhea, an obvious intestinal damage, while the piglets infected with PDCoV HNZK-02-P150 showed no obvious clinical signs, weak intestinal lesions, and lower viral loads in rectal swabs and various tissues. Compared with the PDCoV HNZK-02-P5 infection, HNZK-02-P150 infection resulted in a decrease in intestinal mucosal permeability and pro-inflammatory cytokines. Moreover, PDCoV HNZK-02-P5 infection had significantly reduced bacterial diversity and increased relative abundance of opportunistic pathogens, while PDCoV HNZK-02-P150 infection did not significantly affect the bacterial diversity, and the relative abundance of probiotics increased. Furthermore, the alterations of gut microbiota were closely related to the change of pro-inflammatory factor. Metagenomics prediction analysis demonstrated that HNZK-02-P150 modulated the tyrosine metabolism, Nucleotide-binding and oligomerization domain (NOD)-like receptor signaling pathway, and lipopolysaccharide biosynthesis, which coincided with lower inflammatory response and intestinal permeability in the piglets infected with HNZK-02-P150. In conclusion, the PDCoV HNZK-02 was successfully attenuated by serial passage
in vitro
, and the changes of S gene, metabolic function, and gut microbiota may contribute to the attenuation. The PDCoV HNZK-02-P150 may have the potential for developing live-attenuated vaccine.

IMPORTANCE

Porcine deltacoronavirus (PDCoV) is an enteropathogen causing severe diarrhea, dehydration, and death in nursing piglets, devastating great economic losses for the global swine industry, and has cross-species transmission and zoonotic potential. There are currently no approved treatments or vaccines available for PDCoV. In addition, gut microbiota has an important relationship with the development of many diseases. Here, the PDCoV virulent HNZK-02 strain was successfully attenuated by serial passage on cell cultures, and the pathogenesis and effects on the gut microbiota composition and metabolic function of the PDCoV HNZK-02-P5 and P150 strains were investigated in piglets. We also found the genetic changes in the S protein during passage
in vitro
and the gut microbiota may contribute to the pathogenesis of PDCoV, while their interaction molecular mechanism would need to be explored further.
Accurate detection of influenza A virus by use of a novel cross-priming isothermal amplification-based point-of-care assay
Authors: Deng Jiankai , Zhu Hongji , An Shu , Huang Hao , Wang Ruizhi , Chen Yaoming , Chen Peisong , Yu Xuegao
Published: February 2024

Influenza virus is known to cause respiratory tract infections of varying severity in individuals of all ages. The EasyNAT Rapid Flu assay is a newly developed
in vitro
diagnostic test that employs cross-priming isothermal amplification (CPA) to detect and differentiate influenza A and B viruses in human nasopharyngeal (NP) swabs. The aim of this study is to determine the performance characteristics of the EasyNAT Rapid Flu assay for rapid detection of influenza virus. The limit of detection (LOD) and cross-reactivity of the EasyNAT Rapid Flu assay were assessed. The clinical performance of the assay was evaluated using NP swab samples that were tested with real-time reverse-transcription polymerase chain reaction (RT-PCR) and Xpert Xpress Flu/RSV assay. The LOD for the detection of influenza A and B using the EasyNAT Rapid Flu assay was found to be 500 copies/mL. Furthermore, the assay exhibited no cross-reactivity with other common respiratory viruses tested. For the 114 NP swab samples tested for influenza A using both the EasyNAT Rapid Flu assay and real-time RT-PCR, the two assays demonstrated a high level of agreement (
κ
= 0.963,
P
< 0.001), with a positive percentage agreement (PPA) of 97.7% and a negative percentage agreement (NPA) of 98.6%. Similarly, for the 43 NP swab samples tested for influenza A and B using both the EasyNAT Rapid Flu assay and Xpert Xpress Flu/RSV assay, the two assays showed a high level of agreement (
κ
= 0.933,
P
< 0.001), with the overall rate of agreement (ORA) of 97.7% for influenza A and 100% for influenza B. The EasyNAT Rapid Flu assay demonstrates excellent performance in the detection of influenza A, highlighted by its strong agreement with RT-PCR-based assays.

IMPORTANCE

The newly developed EasyNAT Rapid Flu assay is an innovative cross-priming isothermal amplification-based method designed for detecting influenza A and B viruses at point-of-care settings. This study aims to thoroughly assess the analytical and clinical performance of the assay, offering valuable insights into its potential advantages and limitations. The findings of this research hold significant implications for clinical practice.