bluuebunny/crossref_metadata_2025 huggingface dataset:
The Tensile Strength of Brittle Diamond Lattice Structure With Material Dispersion
Authors: Zhang Xiaoyu , Zhao Zeang , Duan Shengyu , Lei Hongshuai , Fang Daining
Published: March 2024

This work investigates the effect of material dispersion on the tensile strength of brittle diamond lattice structures. In actual lattice structures fabricated by additive manufacturing, the dispersion of strength comes from microscale defect, geometric deviation, and manufacture-induced anisotropy. The weakening of ultimate failure strength due to material dispersion cannot be predicted by most existing theoretical models, because they assume homogeneous and determinate mechanical properties of the lattice structure. In this paper, we employ a diamond lattice structure made from brittle material as a typical example, and its tensile behavior is numerically investigated by incorporating the Gaussian distribution of strut strength. Inspired by the simulation results, a stochastic theoretical model is developed to predict the deformation and failure of diamond lattice structure with material dispersion. This model captures the fact that weaker struts break first even if the whole structure can still bear the load. With the continuous increase of stress, these broken struts accumulate into continuous cracks, and ultimate failure occurs when the energy release rate of the initiated crack surpasses the fracture toughness of the lattice structure. This research supplements stochastic features into classical theories and improves the understanding of potential strengthening and toughening designs for lattice structures.
Ultrasonography and clinical findings of angiomyofibroblastoma in the right inguinal region
Authors: Zhang Xiaowei , Xu Tingting , Ying Jiajia
Published: March 2024

.
The utility of ultrasound for the diagnosis and treatment of primary and metastatic melanoma – a remaining oncological challenge
Authors: Badea Radu , Crisan Maria
Published: March 2024

.
Reconceptualising faculty development for the future
Authors: Kumar Koshila , King Svetlana , Kette Gillian
Published: March 2024

Faculty development (FD) helps to build educational expertise and capacity among those involved in health professional education (HPE). Informal FD encompasses the learning that health professionals, educators and researchers do outside of formal structures and includes learning through everyday work. This paper reframes learning through work using situativity theory and presents three principles for optimising it: cultivating a learning mindset, leveraging social conditions for learning and (re-)negotiating a social contract.
Based on this theorisation, we propose the term embedded FD in acknowledgement that learning through work arises in the complex interactions between individuals, groups and their environments. Implications of this reframing include shifting the focus onto helping individuals, groups and organisations develop effectivities to navigate social structures and systems for the purpose of learning, and redefining what success might look like. This reconceptualisation can help health professionals, educators, researchers and organisations optimise embedded FD to meet the educational opportunities and challenges of the next 50 years.
Walking backwards into the future of health professional practice
Authors: Wilson Hamish , O'Hagan Lucy , Williamson Martyn
Published: March 2024

Health professional education needs to be designed so that future practitioners are well equipped for clinical and professional challenges. While the biomedical model has enabled major biological advances in all health professions, its inherent presuppositions have prevented progress in many of the more complex issues within healthcare, examples being health inequities, somatisation, chronic pain and student/clinician burnout. We suggest that students learn about the scientific origins and tacit assumptions of the biomedical model, such as reductionism, biological plausibility and clinical objectivity. Critical reflection, including interprofessional discussion, can enable students to explore its strengths and limitations. Although biomedicine will remain the dominant paradigm in both training and clinical practice, other “ways of seeing” may be helpful, including biopsychosocial and Indigenous models. Complexity sciences now provide additional understandings of human physiology and socio-cultural processes within healthcare and could also be taught explicitly as core curricula. Student-selected components may enable faculty to pilot educational initiatives in relation to specific professional challenges, which could then be further developed for all students. Critical reflection and teaching innovation are core values of the Australian and New Zealand Association of Health Professional Educators (ANZAHPE). “Walking backwards into the future” in healthcare education means identifying and critiquing our taken-for-granted assumptions, then providing future clinicians with broader frameworks and skills to respond more effectively to persistent challenges in healthcare.
Partnerships in health care: Delivering a just-in-time professional development intervention as an effective crisis response
Authors: El Ali Mandy , Leathwick Sandra , Jacob Alycia , Jacob Elisabeth
Published: March 2024

Partnership between a government health department, a tertiary education provider and healthcare professionals is effective in providing professional development in response to a crisis in the form of just-in-time education. In 2020 and 2021, this type of partnership supported nurses and nurse educators in clinical settings when resources were stretched. The partnership fostered the provision of evidence-based practice. As a result of this partnership, nurse participants of a massive open online course demonstrated improved knowledge and confidence when caring for patients presenting with COVID-19.
Comparability of 24-hr Activity Cycle Outputs From ActiGraph Counts Generated in ActiLife and RStudio
Authors: Montoye Alexander H.K. , Clevenger Kimberly A. , Boudreaux Benjamin D. , Schmidt Michael D.
Published: March 2024

Data from ActiGraph accelerometers have long been imported into ActiLife software, where the company’s proprietary “activity counts” were generated in order to understand physical behavior metrics. In 2022, ActiGraph released an open-source method to generate activity counts from any raw, triaxial accelerometer data using Python, which has been translated into RStudio packages. However, it is unclear if outcomes are comparable when generated in ActiLife and RStudio. Therefore, the authors’ technical note systematically compared activity counts and related physical behavior metrics generated from ActiGraph accelerometer data using ActiLife or available packages in RStudio and provides example code to ease implementation of such analyses in RStudio. In addition to comparing triaxial activity counts, physical behavior outputs (sleep, sedentary behavior, light-intensity physical activity, and moderate- to vigorous-intensity physical activity) were compared using multiple nonwear algorithms, epochs, cut points, sleep scoring algorithms, and accelerometer placement sites. Activity counts and physical behavior outcomes were largely the same between ActiLife and the tested packages in RStudio. However, peculiarities in the application of nonwear algorithms to the first and last portions of a data file (that occurred on partial, first or last days of data collection), differences in rounding, and handling of counts values on the borderline of activity intensities resulted in small but inconsequential differences in some files. The hope is that researchers and both hardware and software manufacturers continue to push efforts toward transparency in data analysis and interpretation, which will enhance comparability across devices and studies and help to advance fields examining links between physical behavior and health.
Accelerometer and Survey Assessed Physical Activity in Children With Epilepsy: A Case-Controlled Study
Authors: Idowu Joan , Pearson Natalie , Meades Collette , Cross J. Helen , Muggeridge Amy , Lakhanpaul Monica , Robinson Kerry , Sherar Lauren B. , Reilly Colin
Published: March 2024

Purpose: Anecdotal evidence suggests that children with epilepsy (CWE) are limited in the frequency of their daily physical activity (PA). However, there is limited research utilizing device-based measures of PA. We compared levels of PA and sedentary behavior in CWE (11–15 y) and age- and gender-matched healthy controls. Method: Participants (n = 60 CWE [25 males, 35 females] and n = 49 controls [25 males, 24 females]) wore a Actigraph accelerometer (GT3X or GT3X+) for 7 consecutive days during waking hours and self-reported their PA and sedentary behaviors. CWE were compared with control children on time spent in different intensities of PA and on self-reported PA and sedentary behavior. Factors associated with PA were analyzed using linear regression. Results: CWE spent less time in accelerometer assessed light (189.15 vs 215.01 min/d, P < .05) and vigorous PA (35.14 vs 44.28 min/d, P < .05) on weekdays compared with controls. There were no significant differences between CWE and control participants in accelerometer assessed time spent sedentary or time spent in PA on weekends. Among CWE, older children engaged in more reported sedentary behavior and younger children spent more time in most domains of PA (P < .05). Furthermore, CWE reported less PA than controls (P = .006). Sixteen percent of controls met World Health Organization PA guidelines compared with 10% of CWE. There was a positive relationship between accelerometer assessed PA and quality of life for CWE. Conclusion: CWE spent less time in light and moderate to vigorous PA on weekdays. Further research is needed to understand reasons for these differences.
Discovery and characterization of noncanonical E2-conjugating enzymes
Authors: Abdul Rehman Syed Arif , Cazzaniga Chiara , Di Nisio Elena , Antico Odetta , Knebel Axel , Johnson Clare , Şahin Alp T. , Ibrahim Peter E. G. F. , Lamoliatte Frederic , Negri Rodolfo , Muqit Miratul M K , De Cesare Virginia
Published: March 2024

E2-conjugating enzymes (E2s) play a central role in the enzymatic cascade that leads to the attachment of ubiquitin to a substrate. This process, termed ubiquitylation, is required to maintain cellular homeostasis and affects almost all cellular process. By interacting with multiple E3 ligases, E2s dictate the ubiquitylation landscape within the cell. Since its discovery, ubiquitylation has been regarded as a posttranslational modification that specifically targets lysine side chains (canonical ubiquitylation). We used Matrix-Assisted Laser Desorption/Ionization-Time Of Flight Mass Spectrometry to identify and characterize a family of E2s that are instead able to conjugate ubiquitin to serine and/or threonine. We used structural modeling and prediction tools to identify the key activity determinants that these E2s use to interact with ubiquitin as well as their substrates. Our results unveil the missing E2s necessary for noncanonical ubiquitylation, underscoring the adaptability and versatility of ubiquitin modifications.
Cardiac tissue model of immune-induced dysfunction reveals the role of free mitochondrial DNA and the therapeutic effects of exosomes
Authors: Lu Rick Xing Ze , Rafatian Naimeh , Zhao Yimu , Wagner Karl T. , Beroncal Erika L. , Li Bo , Lee Carol , Chen Jingan , Churcher Eryn , Vosoughi Daniel , Liu Chuan , Wang Ying , Baker Andrew , Trahtemberg Uriel , Li Bowen , Pierro Agostino , Andreazza Ana C. , dos Santos Claudia C. , Radisic Milica
Published: March 2024

Despite tremendous progress in the development of mature heart-on-a-chip models, human cell–based models of myocardial inflammation are lacking. Here, we bioengineered a vascularized heart-on-a-chip with circulating immune cells to model severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)–induced acute myocarditis. We observed hallmarks of coronavirus disease (COVID-19)–induced myocardial inflammation, as the presence of immune cells augmented the secretion of proinflammatory cytokines, triggered progressive impairment of contractile function, and altered intracellular calcium transients. An elevation of circulating cell-free mitochondrial DNA (ccf-mtDNA) was measured first in the heart-on-a-chip and then validated in COVID-19 patients with low left ventricular ejection fraction, demonstrating that mitochondrial damage is an important pathophysiological hallmark of inflammation-induced cardiac dysfunction. Leveraging this platform in the context of SARS-CoV-2–induced myocardial inflammation, we established that administration of endothelial cell–derived exosomes effectively rescued the contractile deficit, normalized calcium handling, elevated the contraction force, and reduced the ccf-mtDNA and cytokine release via Toll-like receptor–nuclear factor κB signaling axis.
No replication of direct neuronal activity–related (DIANA) fMRI in anesthetized mice
Authors: Choi Sang-Han , Im Geun Ho , Choi Sangcheon , Yu Xin , Bandettini Peter A. , Menon Ravi S. , Kim Seong-Gi
Published: March 2024

Direct imaging of neuronal activity (DIANA) by functional magnetic resonance imaging (fMRI) could be a revolutionary approach for advancing systems neuroscience research. To independently replicate this observation, we performed fMRI experiments in anesthetized mice. The blood oxygenation level–dependent (BOLD) response to whisker stimulation was reliably detected in the primary barrel cortex before and after DIANA experiments; however, no DIANA–like fMRI peak was observed in individual animals’ data with the 50 to 300 trials. Extensively averaged data involving 1050 trials in six mice showed a flat baseline and no detectable neuronal activity–like fMRI peak. However, spurious, nonreplicable peaks were found when using a small number of trials, and artifactual peaks were detected when some outlier-like trials were excluded. Further, no detectable DIANA peak was observed in the BOLD-responding thalamus from the selected trials with the neuronal activity–like reference function in the barrel cortex. Thus, we were unable to replicate the previously reported results without data preselection.
Compounding effects in flood drivers challenge estimates of extreme river floods
Authors: Jiang Shijie , Tarasova Larisa , Yu Guo , Zscheischler Jakob
Published: March 2024

Estimating river flood risks under climate change is challenging, largely due to the interacting and combined influences of various flood-generating drivers. However, a more detailed quantitative analysis of such compounding effects and the implications of their interplay remains underexplored on a large scale. Here, we use explainable machine learning to disentangle compounding effects between drivers and quantify their importance for different flood magnitudes across thousands of catchments worldwide. Our findings demonstrate the ubiquity of compounding effects in many floods. Their importance often increases with flood magnitude, but the strength of this increase varies on the basis of catchment conditions. Traditional flood analysis might underestimate extreme flood hazards in catchments where the contribution of compounding effects strongly varies with flood magnitude. Overall, our study highlights the need to carefully incorporate compounding effects in flood risk assessment to improve estimates of extreme floods.
Human-robot facial coexpression
Authors: Hu Yuhang , Chen Boyuan , Lin Jiong , Wang Yunzhe , Wang Yingke , Mehlman Cameron , Lipson Hod
Published: March 2024

Large language models are enabling rapid progress in robotic verbal communication, but nonverbal communication is not keeping pace. Physical humanoid robots struggle to express and communicate using facial movement, relying primarily on voice. The challenge is twofold: First, the actuation of an expressively versatile robotic face is mechanically challenging. A second challenge is knowing what expression to generate so that the robot appears natural, timely, and genuine. Here, we propose that both barriers can be alleviated by training a robot to anticipate future facial expressions and execute them simultaneously with a human. Whereas delayed facial mimicry looks disingenuous, facial coexpression feels more genuine because it requires correct inference of the human’s emotional state for timely execution. We found that a robot can learn to predict a forthcoming smile about 839 milliseconds before the human smiles and, using a learned inverse kinematic facial self-model, coexpress the smile simultaneously with the human. We demonstrated this ability using a robot face comprising 26 degrees of freedom. We believe that the ability to coexpress simultaneous facial expressions could improve human-robot interaction.
A fictional history of robotics features forgotten real-world robots
Authors: Murphy Robin R.
Published: March 2024

The science-fiction movie
The Creator
uses six real-world robots from the 1950s and 1960s to show progress in AI.
Comparison of the immunogenicity and protective efficacy of ACAM2000, MVA, and vectored subunit vaccines for Mpox in rhesus macaques
Authors: Jacob-Dolan Catherine , Ty Darren , Hope David , McMahan Katherine , Liu Jinyan , Powers Olivia C. , Cotter Catherine A. , Sciacca Michela , Wu Cindy , Borducchi Erica , Bouffard Emily , Richter Hannah , Velasco Jason , Teow Elyse , Boursiquot Mona , Cook Anthony , Feliciano Karen , Yalley-Ogunro Jake , Seaman Michael S. , Pessiant Laurent , Lewis Mark G. , Andersen Hanne , Moss Bernard , Barouch Dan H.
Published: March 2024

The 2022–2023 mpox outbreak triggered vaccination efforts using smallpox vaccines that were approved for mpox, including modified vaccinia Ankara (MVA; JYNNEOS), which is a safer alternative to live replicating vaccinia virus (ACAM2000). Here, we compare the immunogenicity and protective efficacy of JYNNEOS by the subcutaneous or intradermal routes, ACAM2000 by the percutaneous route, and subunit Ad35 vector–based L1R/B5R or L1R/B5R/A27L/A33R vaccines by the intramuscular route in rhesus macaques. All vaccines provided robust protection against high-dose intravenous mpox virus challenge with the current outbreak strain, with ACAM2000 providing near complete protection and JYNNEOS and Ad35 vaccines providing robust but incomplete protection. Protection correlated with neutralizing antibody responses as well as L1R/M1R- and B5R/B6R-specific binding antibody responses, although additional immune responses likely also contributed to protection. This study demonstrates the protective efficacy of multiple vaccine platforms against mpox virus challenge, including both current clinical vaccines and vectored subunit vaccines.
Accelerating therapeutics development during a pandemic: population pharmacokinetics of the long-acting antibody combination AZD7442 (tixagevimab/cilgavimab) in the prophylaxis and treatment of COVID-19
Authors: Clegg Lindsay E. , Stepanov Oleg , Schmidt Henning , Tang Weifeng , Zhang Huixia , Webber Chris , Cohen Taylor S. , Esser Mark T. , Någård Mats
Published: March 2024

AZD7442 is a combination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-neutralizing antibodies, tixagevimab and cilgavimab, developed for pre-exposure prophylaxis (PrEP) and treatment of coronavirus disease 2019 (COVID-19). Using data from eight clinical trials, we describe a population pharmacokinetic (popPK) model of AZD7442 and show how modeling of “interim” data accelerated decision-making during the COVID-19 pandemic. The final model was a two-compartmental distribution model with first-order absorption and elimination, including standard allometric exponents for the effect of body weight on clearance and volume. Other covariates included were as follows: sex, age >65 years, body mass index ≥30 kg/m
2
, and diabetes on absorption rate; diabetes on clearance; Black race on central volume; and intramuscular (IM) injection site on bioavailability. Simulations indicated that IM injection site and body weight had > 20% effects on AZD7442 exposure, but no covariates were considered to have a clinically relevant impact requiring dose adjustment. The pharmacokinetics of AZD7442, cilgavimab, and tixagevimab were comparable and followed linear kinetics with extended half-lives (median 78.6 days for AZD7442), affording prolonged protection against susceptible SARS-CoV-2 variants. Comparison of popPK simulations based on “interim data” with a target concentration based on 80% viral inhibition and assuming 1.81% partitioning into the nasal lining fluid supported a decision to double the PrEP dosage from 300 mg to 600 mg to prolong protection against Omicron variants. Serum AZD7442 concentrations in adolescents weighing 40–95 kg were predicted to be only marginally different from those observed in adults, supporting authorization for use in adolescents before clinical data were available. In these cases, popPK modeling enabled accelerated clinical decision-making.
Triazole resistance in
Aspergillus fumigatu
s isolated from a tomato production environment exposed to propiconazole
Authors: M. Jimenez Madrid Alejandra , Paul Raees A. , Rotondo Francesca , Deblais Loic , Rajashekara Gireesh , Miller Sally A. , Ivey Melanie L. Lewis
Published: March 2024

The emergence of azole-resistant
Aspergillus fumigatus
(AR
Af
) across the world is an important public health concern. We sought to determine if propiconazole, a demethylase inhibitor (DMI) fungicide, exerted a selective pressure for AR
Af
in a tomato production environment following multiple exposures to the fungicide. A tomato field trial was established in 2019 and propiconazole was applied weekly until harvest. Soil, leaf, and fruit (when present) samples were collected at baseline and after each propiconazole application.
A. fumigatus
isolates (
n
, 178) were recovered and 173 were tested for susceptibility to itraconazole, posaconazole, voriconazole, and propiconazole in accordance with CLSI M38 guidelines. All the isolates were susceptible to medical triazoles and the propiconazole MIC ranged from 0.25 to 8 mg/L. A linear regression model was fitted that showed no longitudinal increment in the log
2
-fold azole MIC of the isolates collected after each propiconazole exposure compared to the baseline isolates. AsperGenius real-time multiplex assay ruled out TR34/L98H and TR46/Y121F/T289A
cyp
51A resistance markers in these isolates. Sequencing of a subset of isolates (
n
, 46) demonstrated widespread presence of F46Y/M172V/E427K and F46Y/M172V/N248T/D255E/E427K
cyp
51A mutations previously associated with reduced susceptibility to triazoles.

IMPORTANCE

The agricultural use of azole fungicides to control plant diseases has been implicated as a major contributor to ARAf infections in humans. Our study did not reveal imposition of selection pressure for ARAf in a vegetable production system. However, more surveillance studies for ARAf in food crop production and other environments are warranted in understanding this public and One Health issue.
Glycine betaine metabolism is enabled in
Methylorubrum extorquens
PA1 by alterations to dimethylglycine dehydrogenase
Authors: Hying Zachary T. , Miller Tyler J. , Loh Chin Yi , Bazurto Jannell V.
Published: March 2024

Low nutrient availability is a key characteristic of the phyllosphere (the aerial surface of plants). Phyllospheric bacteria utilize a wide array of carbon sources generated by plant hosts. Glycine betaine (GB) is a plant-derived compound that can be metabolized by certain members of the phyllosphere microbiota. Metabolism of glycine betaine generates formaldehyde, an intermediate of methylotrophic metabolism, leading us to investigate how the ubiquitous plant colonizing bacterium
Methylorubrum extorquens
PA1 might metabolize GB encountered in its native environment.
M. extorquens
PA1 cannot utilize GB as a sole carbon source. Through suppressor mutation analysis, we show that
M. extorquens
PA1 encodes a conserved GB utilization pathway that can be activated by single point mutations conferring GB utilization as a carbon source. We identified the gene cluster encoding the GB catabolic enzymes and found that gene expression was induced in the presence of GB. We show that utilization of GB is conserved among representative
Methylobacterium
species and generates the one-carbon metabolism intermediate formaldehyde, which
M. extorquens
utilizes as a source of energy. Our results support a model where suppressor mutations in
Mext_3745
or
ftsH
(
Mext_4840
) prevent the degradation of the dimethylglycine dehydrogenase subunit DgcB by the membrane integral protease FtsH, conferring the ability to utilize GB by either (i) restoring stable membrane topology of DgcB or (ii) decreasing FtsH protease activity, respectively. Both mutations alleviate the bottleneck at the second step of GB degradation catalyzed by DgcAB.

IMPORTANCE

Overcoming low nutrient availability is a challenge many bacteria encounter in the environment. Facultative methylotrophs are able to utilize one-carbon and multi-carbon compounds as carbon and energy sources. The utilization of plant-derived glycine betaine (GB) represents a possible source of multi-carbon and one-carbon substrates. The metabolism of glycine betaine produces formaldehyde and glycine, which may be used simultaneously by facultative methylotrophs. However, the genes required for the utilization of GB in the ubiquitous plant-associated bacterium
Methylorubrum extorquens
have yet to be identified or described. Our work identifies and validates the genes required for glycine betaine metabolism in
M. extorquens
and shows that it directly intersects with methylotrophic metabolism through the production of formaldehyde.
Continuous planting of euhalophyte
Suaeda salsa
enhances microbial diversity and multifunctionality of saline soil
Authors: Zhao Shuai , Liu Xu , Banerjee Samiran , Hartmann Martin , Peng Bin , Elvers Rylie , Zhao Zhen-Yong , Zhou Na , Liu Jun-Jie , Wang Baozhan , Tian Chang-Yan , Jiang Jiandong , Lian Teng-Xiang
Published: March 2024

Halophyte-based remediation emerges as a novel strategy for ameliorating saline soils, offering a sustainable alternative to conventional leaching methods. While bioremediation is recognized for its ability to energize soil fertility and structure, the complex interplays among plant traits, soil functions, and soil microbial diversity remain greatly unknown. Here, we conducted a 5-year field experiment involving the continuous cultivation of the annual halophyte
Suaeda salsa
in saline soils to explore soil microbial diversity and their relationships with plant traits and soil functions. Our findings demonstrate that a decline in soil salinity corresponded with increases in the biomass and seed yield of
S. salsa
, which sustained a consistent seed oil content of approximately 22% across various salinity levels. Significantly, prolonged cultivation of halophytes substantially augmented soil microbial diversity, particularly from the third year of cultivation. Moreover, we identified positive associations between soil multifunctionality, seed yield, and taxonomic richness within a pivotal microbial network module. Soils enriched with taxa from this module showed enhanced multifunctionality and greater seed yields, correlating with the presence of functional genes implicated in nitrogen fixation and nitrification. Genomic analysis suggests that these taxa have elevated gene copy numbers of crucial functional genes related to nutrient cycling. Overall, our study emphasizes that the continuous cultivation of
S. salsa
enhances soil microbial diversity and recovers soil multifunctionality, expanding the understanding of plant-soil-microbe feedback in bioremediation.

IMPORTANCE

The restoration of saline soils utilizing euhalophytes offers a viable alternative to conventional irrigation techniques for salt abatement and soil quality enhancement. The ongoing cultivation of the annual
Suaeda salsa
and its associated plant traits, soil microbial diversity, and functionalities are, however, largely underexplored. Our investigation sheds light on these dynamics, revealing that cultivation of
S. salsa
sustains robust plant productivity while fostering soil microbial diversity and multifunctionality. Notably, the links between enhanced soil multifunctionality, increased seed yield, and network-dependent taxa were found, emphasizing the importance of key microbial taxa linked with functional genes vital to nitrogen fixation and nitrification. These findings introduce a novel understanding of the role of soil microbes in bioremediation and advance our knowledge of the ecological processes that are vital for the rehabilitation of saline environments.
Signaling through the
Salmonella
PbgA-LapB regulatory complex activates LpxC proteolysis and limits lipopolysaccharide biogenesis during stationary-phase growth
Authors: Mettlach Joshua A. , Cian Melina B. , Chakraborty Medha , Dalebroux Zachary D.
Published: March 2024

Salmonella enterica
serovar Typhimurium (
S
. Typhimurium) controls lipopolysaccharide (LPS) biosynthesis by regulating proteolysis of LpxC, the rate-limiting enzyme and target of preclinical antibiotics. PbgA/YejM/LapC regulates LpxC levels and controls outer membrane (OM) LPS composition at the log-to-stationary phase transition. Suppressor substitutions in
L
PS
a
ssembly
p
rotein
B
(LapB/YciM) rescue the LPS and OM integrity defects of
pbgA
-mutant
S
. Typhimurium. We hypothesized that PbgA regulates LpxC proteolysis by controlling LapB’s ability to bind LpxC as a function of the growth phase. According to existing models, when nutrients are abundant, PbgA binds and restricts LapB from interacting with LpxC and FtsH, which limits LpxC proteolysis. However, when nutrients are limited, there is debate whether LapB dissociates from PbgA to bind LpxC and FtsH to enhance degradation. We sought to examine these models and investigate how the structure of LapB enables salmonellae to control LpxC proteolysis and LPS biosynthesis. Salmonellae increase LapB levels during the stationary phase to promote LpxC degradation, which limits lipid A-core production and increases their survival. The deletion of
lapB
, resulting in unregulated lipid A-core production and LpxC overabundance, leads to bacterial growth retardation. Tetratricopeptide repeats near the cytosol-inner membrane interface are sufficient for LapB to bind LpxC, and remarkably, LapB and PbgA interact in both growth phases, yet LpxC only associates with LapB in the stationary phase. Our findings support that PbgA-LapB exists as a constitutive complex in
S
. Typhimurium, which differentially binds LpxC to control LpxC proteolysis and limit lipid A-core biosynthesis in response to changes in the environment.

IMPORTANCE

Antimicrobial resistance has been a costly setback for human health and agriculture. Continued pursuit of new antibiotics and targets is imperative, and an improved understanding of existing ones is necessary. LpxC is an essential target of preclinical trial antibiotics that can eliminate multidrug-resistant Gram-negative bacterial infections. LapB is a natural LpxC inhibitor that targets LpxC for degradation and limits lipopolysaccharide production in Enterobacteriaceae. Contrary to some studies, findings herein support that LapB remains in complex instead of dissociating from its presumed negative regulator, PbgA/YejM/LapC, under conditions where LpxC proteolysis is enhanced. Advanced comprehension of this critical protein-lipid signaling network will lead to future development and refinement of small molecules that can specifically interfere.
Bile-induced biofilm formation in
Bacteroides thetaiotaomicron
requires magnesium efflux by an RND pump
Authors: Lopes Anne-Aurélie , Vendrell-Fernández Sol , Deschamps Julien , Georgeault Sonia , Cokelaer Thomas , Briandet Romain , Ghigo Jean-Marc
Published: March 2024

Bacteroides thetaiotaomicron
is a prominent member of the human gut microbiota contributing to nutrient exchange, gut function, and maturation of the host’s immune system. This obligate anaerobe symbiont can adopt a biofilm lifestyle, and it was recently shown that
B. thetaiotaomicron
biofilm formation is promoted by the presence of bile. This process also requires a
B. thetaiotaomicron
extracellular DNase, which is not, however, regulated by bile. Here, we showed that bile induces the expression of several Resistance-Nodulation-Division (RND) efflux pumps and that inhibiting their activity with a global competitive efflux inhibitor impaired bile-dependent biofilm formation. We then showed that, among the bile-induced RND-efflux pumps, only the tripartite BT3337-BT3338-BT3339 pump, re-named BipABC [for Bile Induced Pump A (
BT3337
), B (
BT3338
), and C (
BT3339
)], is required for biofilm formation. We demonstrated that BipABC is involved in the efflux of magnesium to the biofilm extracellular matrix, which leads to a decrease of extracellular DNA concentration. The release of magnesium in the biofilm matrix also impacts biofilm structure, potentially by modifying the electrostatic repulsion forces within the matrix, reducing interbacterial distance and allowing bacteria to interact more closely and form denser biofilms. Our study therefore, identified a new molecular determinant of
B. thetaiotaomicron
biofilm formation in response to bile salts and provides a better understanding on how an intestinal chemical cue regulates biofilm formation in a major gut symbiont.

IMPORTANCE

Bacteroides thetaiotaomicron
is a prominent member of the human gut microbiota able to degrade dietary and host polysaccharides, altogether contributing to nutrient exchange, gut function, and maturation of the host’s immune system. This obligate anaerobe symbiont can adopt a biofilm community lifestyle, providing protection against environmental factors that might, in turn, protect the host from dysbiosis and dysbiosis-related diseases. It was recently shown that
B. thetaiotaomicron
exposure to intestinal bile promotes biofilm formation. Here, we reveal that a specific
B. thetaiotaomicron
membrane efflux pump is induced in response to bile, leading to the release of magnesium ions, potentially reducing electrostatic repulsion forces between components of the biofilm matrix. This leads to a reduction of interbacterial distance and strengthens the biofilm structure. Our study, therefore, provides a better understanding of how bile promotes biofilm formation in a major gut symbiont, potentially promoting microbiota resilience to stress and dysbiosis events.
Hsp90, a team player in protein quality control and the stress response in bacteria
Authors: Wickramaratne Anushka C. , Wickner Sue , Kravats Andrea N.
Published: March 2024

Heat shock protein 90 (Hsp90) participates in proteostasis by facilitating protein folding, activation, disaggregation, prevention of aggregation, degradation, and protection against degradation of various cellular proteins. It is highly conserved from bacteria to humans. In bacteria, protein remodeling by Hsp90 involves collaboration with the Hsp70 molecular chaperone and Hsp70 cochaperones. In eukaryotes, protein folding by Hsp90 is more complex and involves collaboration with many Hsp90 cochaperones as well as Hsp70 and Hsp70 cochaperones. This review focuses primarily on bacterial Hsp90 and highlights similarities and differences between bacterial and eukaryotic Hsp90. Seminal research findings that elucidate the structure and the mechanisms of protein folding, disaggregation, and reactivation promoted by Hsp90 are discussed. Understanding the mechanisms of bacterial Hsp90 will provide fundamental insight into the more complex eukaryotic chaperone systems.
Analyzing the safety of the parasiticide fungus
Mucor circinelloides
: first insights on its virulence profile and interactions with the avian gut microbial community
Authors: Lozano João , Cunha Eva , Almeida Cristina , Nunes Mónica , Dias Ricardo , Vicente Eduardo , Sebastião Daniela , Henriques Sérgio , Madeira de Carvalho Luís , Paz-Silva Adolfo , Oliveira Manuela
Published: March 2024

Parasiticide fungi are considered an accurate, sustainable, and safe solution for the biocontrol of animal gastrointestinal (GI) parasites. This research provides an initial characterization of the virulence of the native parasiticide fungus
Mucor circinelloides
(FMV-FR1) and an assessment of its impact on birds’ gut microbes. The genome of this fungus was sequenced to identify the genes coding for virulence factors. Also, this fungus was checked for the phenotypic expression of proteinase, lecithinase, DNase, gelatinase, hemolysin, and biofilm production. Finally, an
in vivo
trial was developed based on feeding
M. circinelloides
spores to laying hens and peacocks three times a week. Bird feces were collected for 3 months, with total genomic DNA being extracted and subjected to long-read 16S and 25S-28S sequencing. Genes coding for an iron permease (FTR1), iron receptors (FOB1 and FOB2), ADP-ribosylation factors (ARFs) (ARF2 and ARF6), and a GTPase (CDC42) were identified in this
M. circinelloides
genome. Also, this fungus was positive only for lecithinase activity. The field trial revealed a fecal microbiome dominated by Firmicutes and Proteobacteria in laying hens, and Firmicutes and Bacteroidetes in peacocks, whereas the fecal mycobiome of both bird species was mainly composed of Ascomycetes and Basidiomycetes fungi. Bacterial and fungal alpha-diversities did not differ between sampling time points after
M. circinelloides
administrations (
P
= 0.62 and
P
= 0.15, respectively). Although findings from this research suggest the lack of virulence of this
M. circinelloides
parasiticide isolate, more complementary
in vitro
and
in vivo
research is needed to conclude about the safety of its administration to birds, aiming at controlling their GI parasites.

IMPORTANCE

A previous study revealed that the native
Mucor circinelloides
isolate (FMV-FR1) can develop parasiticide activity toward coccidia oocysts, one of the most pathogenic GI parasites in birds. However, ensuring its safety for birds is of utmost importance, namely by studying its virulence profile and potential effect on commensal gut microbes. This initial study revealed that although this
M. circinelloides
isolate had genes coding for four types of virulence factors—iron permease, iron receptors, ADP-ribosylation factors, and GTPase—and only expressed phenotypically the enzyme lecithinase, the administration of its spores to laying hens and peacocks did not interfere with the abundances and diversities of their gut commensal bacteria and fungi. Although overall results suggest the lack of virulence of this
M. circinelloides
isolate, more complementary research is needed to conclude about the safety of its administration to birds in the scope of parasite biocontrol programs.
Open bypass revascularisation for endovascular-resistant transplant renal artery stenosis secondary to mechanical renal artery kinking
Authors: Koo Mei Ping Melody , Lahham Yahya
Published: March 2024

Transplant renal artery stenosis (TRAS) represents a significant vascular complication subsequent to renal transplantation. This pathology is associated with grave implications including graft dysfunction and mortality. Early identification and therapeutical intervention are imperative for preserving graft longevity and achieving optimal clinical outcomes. We detail the case of a male in his 20s, following renal transplantation, who encountered recurrent TRAS, aetiologically linked to mechanical arterial kinking. Initial management using endovascular techniques yielded insufficient resolution. Consequently, the persistence of endovascular-resistant stenosis necessitated a surgical bypass intervention using the great saphenous vein, granting a 2-year period devoid of restenosis. The existing literature emphasises the indispensability of discerning the appropriate juncture for transitioning from endovascular to surgical management in TRAS cases. The robustness and durability of bypass grafts present an efficacious therapeutical strategy in contemporaneous practice.
Online tools to predict individualised survival for primary oesophageal cancer patients with and without pathological complete response after neoadjuvant therapy followed by oesophagectomy: development and external validation of two independent nomograms
Authors: Cao Yuqin , Huang Binhao , Tang Han , Dong Dong , Shen Tianzheng , Chen Xiang , Feng Xijia , Zhang Jiahao , Shi Liqiang , Li Chengqiang , Jiao Heng , Tan Lijie , Zhang Jie , Li Hecheng , Zhang Yajie
Published: March 2024

Objective

This study aimed to develop and validate robust predictive models for patients with oesophageal cancer who achieved a pathological complete response (pCR) and those who did not (non-pCR) after neoadjuvant therapy and oesophagectomy.

Design

Clinicopathological data of 6517 primary oesophageal cancer patients who underwent neoadjuvant therapy and oesophagectomy were obtained from the National Cancer Database for the training cohort. An independent cohort of 444 Chinese patients served as the validation set. Two distinct multivariable Cox models of overall survival (OS) were constructed for pCR and non-pCR patients, respectively, and were presented using web-based dynamic nomograms (graphical representation of predicted OS based on the clinical characteristics that a patient could input into the website). The calibration plot, concordance index and decision curve analysis were employed to assess calibration, discrimination and clinical usefulness of the predictive models.

Results

In total, 13 and 15 variables were used to predict OS for pCR and non-pCR patients undergoing neoadjuvant therapy followed by oesophagectomy, respectively. Key predictors included demographic characteristics, pretreatment clinical stage, surgical approach, pathological information and postoperative treatments. The predictive models for pCR and non-pCR patients demonstrated good calibration and clinical utility, with acceptable discrimination that surpassed that of the current tumour, node, metastases staging system.

Conclusions

The web-based dynamic nomograms for pCR (https://predict-survival.shinyapps.io/pCR-eso/) and non-pCR patients (https://predict-survival.shinyapps.io/non-pCR-eso/) developed in this study can facilitate the calculation of OS probability for individual patients undergoing neoadjuvant therapy and radical oesophagectomy, aiding clinicians and patients in making personalised treatment decisions.
Laboratory investigation of peritoneal fluids: an updated practical approach based on the available evidence
Authors: Colombo Giulia , Aloisio Elena , Panteghini Mauro
Published: March 2024

Even though analysis of peritoneal fluids (PF) is often requested to medical laboratories for biochemical and morphological tests, there is still no mutual agreement on what the most appropriate way is to manage PF samples and which tests should be appropriately executed. In this update, we tried to identify the most useful tests for PF analysis to establish best practice indications. We performed a literature review and examined available guidelines to select the most appropriate tests by an evidence-based approach. Accordingly, the basic PF profile should include (1) serum to effusion albumin gradient and (2) automated cell counts with differential analysis. This profile allows to determine the PF nature, differentiating between ‘high-albumin gradient’ and ‘low-albumin gradient’ effusions, which helps to identify the pathophysiological process causing the ascites formation. Restricted to specific clinical situations, additional tests can be requested as follows: PF lactate dehydrogenase (LDH) and glucose, to exclude (LDH) or confirm (glucose) secondary bacterial peritonitis; PF total protein, to differentiate ascites of cardiac origin from other causes; PF (pancreatic) amylase, for the identification of pancreatic ascites; PF bilirubin, when a choleperitoneum is suspected; PF triglycerides, in differentiating chylous from pseudochylous ascites and PF creatinine, to detect intraperitoneal urinary leakage.
Benchmarking digital displays (monitors) for histological diagnoses: the nephropathology use case
Authors: Cazzaniga Giorgio , Mascadri Francesco , Marletta Stefano , Caputo Alessandro , Guidi Gabriele , Gambaro Giovanni , Eccher Albino , Dei Tos Angelo Paolo , Pagni Fabio , L'Imperio Vincenzo
Published: March 2024

Aim

The digital transformation of the pathology laboratory is being continuously sustained by the introduction of innovative technologies promoting whole slide image (WSI)-based primary diagnosis. Here, we proposed a real-life benchmark of a pathology-dedicated medical monitor for the primary diagnosis of renal biopsies, evaluating the concordance between the ‘traditional’ microscope and commercial monitors using WSI from different scanners.

Methods

The College of American Pathologists WSI validation guidelines were used on 60 consecutive renal biopsies from three scanners (Aperio, 3DHISTECH and Hamamatsu) using pathology-dedicated medical grade (MG), professional grade (PG) and consumer-off-the-shelf (COTS) monitors, comparing results with the microscope diagnosis after a 2-week washout period.

Results

MG monitor was faster (1090 vs 1159 vs 1181 min, delta of 6–8%, p<0.01), with slightly better performances on the detection of concurrent diseases compared with COTS (κ=1 vs 0.96, 95% CI=0.87 to 1), but equal concordance to the commercial monitors on main diagnosis (κ=1). Minor discrepancies were noted on specific scores/classifications, with MG and PG monitors closer to the reference report (r=0.98, 95% CI=0.83 to 1 vs 0.98, 95% CI=0.83 to 1 vs 0.91, 95% CI=0.76 to 1, κ=0.93, 95% CI=077 to 1 vs 0.93, 95% CI=0.77 to 1 vs 0.86, 95% CI=0.64 to 1, κ=1 vs 0.50, 95% CI=0 to 1 vs 0.50, 95% CI=0 to 1, for IgA, antineutrophilic cytoplasmic antibody and lupus nephritis, respectively). Streamlined Pipeline for Amyloid detection through congo red fluorescence Digital Analysis detected amyloidosis on both monitors (4 of 30, 13% cases), allowing detection of minimal interstitial deposits with slight overestimation of the Amyloid Score (average 6 vs 7).

Conclusions

The digital transformation needs careful assessment of the hardware component to support a smart and safe diagnostic process. Choosing the display for WSI is critical in the process and requires adequate planning.