bluuebunny/crossref_metadata_2025_split huggingface dataset:
Poroelastic and Viscoelastic Hallmarks in the Response of Porous and Transversely Isotropic Beams to Harmonic Excitation
Authors: Su Xing , Mehrabian Amin 
Published: June 2024

Abstract
A general solution to harmonic excitation of beam-shaped specimens made from porous, fluid-saturated, transversely isotropic, and viscoelastic materials is developed and presented. The solution draws from Biot's theory of dynamic poroviscoelasticity and adopts a modification of Timoshenko beam model to account for the moment due to pore fluid pressure. Closed-form expressions for transverse displacement and rotation angle of the beam are obtained for the case of three-point bending experiments. Solutions for Rayleigh and Euler–Bernoulli beam models are recovered as special cases. Implications for possible characterization through relevant dynamic mechanical analysis testing are discussed for materials which exhibit certain anisotropy in both the mechanical and flow properties. Three timescale groups shape the dynamic response of the vibrating beam. These timescales pertain to energy dissipation rate within the solid phase, viscous flow of the pore fluid, as well as the natural frequencies of the test specimen. The interplay of a varying excitation frequency with the described timescales is shown to enable simultaneous characterization of the viscoelastic and poroelastic parameters of the specimen constitutive behavior through the obtained dynamic moduli and loss angles of beam vibrations.
Ultrasound in bone fracture diagnosis – a comparative meta-analysis and systematic review
Authors: Matschiner Eric , Serban Oana , Fodor Daniela , Blaivas Michael , Horn Rudolf , Koch Jonas , Jakobi Marie-Lise , Grevelding Lara , Osterwalder Joseph , Srivastava David , Dietrich Christoph Frank 
Published: June 2024

Aim: This meta-analysis evaluates the diagnostic accuracy of ultrasound (US) for bone fractures over the past 47 years, comparing it to established imaging standards.Material and methods: We adhered to PRISMA 2020 guidelines to search Medline, EMBASE, and the Cochrane Library using tailored search strategies. The primary outcome, US diagnostic performance, was analyzed across various subgroups including clinical relevance, patient age, and anatomical considerations. The QUADAS-2 tool was employed to assess study quality and minimize bias.Results: From 5,107 initially identified studies, 75 met the inclusion criteria, encompassing 7,769 participants and 3,575 diagnosed fractures. The majority of studies were prospective (79%) and compared US primarily with plain radiography (76%) and CT scans (19%). Of these, 61 studies were amenable to systematic analysis, revealing US to have a sensitivity and specificity of 91% (95% CI: 90%-92%) and 91.3% (95% CI: 90.5%-92.1%), respectively. Likelihood ratios were favorable, with a positive value of 9.955 and a negative value of 0.087, and an odds ratio of 132.67. The area under the curve stood at 0.9715, indicating high diagnostic accuracy despite significant heterogeneity (I²=81.3% for sensitivity, 89.3% for specificity).Conclusion: The evidence supports US as a highly accurate diagnostic tool for bone fractures, rivalling standard imaging methods like CT and radiography. Its notable diagnostic efficacy, combined with advantages in reducing pain, wait times, and radiation exposure, advocates for its broader application. Further validation in large-scale, randomized trials is essential to integrate US more fully into clinical guidelines for fracture management.
What’s Your Poison? Is Sitting Always Health Hindering and Moving Always Health Promoting?
Authors: Straker Leon , Lund Rasmussen Charlotte , Gupta Nidhi , Holtermann Andreas 
Published: June 2024

The clear public messaging from international health authorities is that individuals should “sit less and move more.” While it is acknowledged that this guidance needs to be tailored to the age of people and also to their health, and abilities, the guidance is not tailored to their current level of physical behaviors. This opinion piece aims to highlight that although people with excessive sitting and insufficient moderate-to-vigorous physical activity should sit more and move less, for other people their health would be promoted by sitting more and moving less. Thus, physical behaviors are not always “poison” or “medicine,” but rather the health impact of changes in physical behaviors depends on people’s initial levels. Policy, research, and practice implications of this realization are presented. Only tailoring messaging to age and health status could be far from optimal for people with very different current levels of physical behaviors. Policy, research, and practice will be enhanced when the potential for physical behaviors to be either health hindering or health promoting is adequately considered.
Development of a logic regression-based approach for the discovery of host- and niche-informative biomarkers in
Escherichia coli
and their application for microbial source tracking
Authors: Yu Daniel , Andersson-Li Martin , Maes Sharon , Andersson-Li Lili , Neumann Norman F. , Odlare Monica , Jonsson Anders 
Published: June 2024

ABSTRACT

Microbial source tracking leverages a wide range of approaches designed to trace the origins of fecal contamination in aquatic environments. Although source tracking methods are typically employed within the laboratory setting, computational techniques can be leveraged to advance microbial source tracking methodology. Herein, we present a logic regression-based supervised learning approach for the discovery of source-informative genetic markers within intergenic regions across the
Escherichia coli
genome that can be used for source tracking. With just single intergenic loci, logic regression was able to identify highly source-specific (i.e., exceeding 97.00%) biomarkers for a wide range of host and niche sources, with sensitivities reaching as high as 30.00%–50.00% for certain source categories, including pig, sheep, mouse, and wastewater, depending on the specific intergenic locus analyzed. Restricting the source range to reflect the most prominent zoonotic sources of
E. coli
transmission (i.e., bovine, chicken, human, and pig) allowed for the generation of informative biomarkers for all host categories, with specificities of at least 90.00% and sensitivities between 12.50% and 70.00%, using the sequence data from key intergenic regions, including
emrKY–evgAS
,
ibsB–(mdtABCD-baeSR), ompC–rcsDB,
and
yedS–yedR
, that appear to be involved in antibiotic resistance. Remarkably, we were able to use this approach to classify 48 out of 113 river water
E. coli
isolates collected in Northwestern Sweden as either beaver, human, or reindeer in origin with a high degree of consensus—thus highlighting the potential of logic regression modeling as a novel approach for augmenting current source tracking efforts.

IMPORTANCE

The presence of microbial contaminants, particularly from fecal sources, within water poses a serious risk to public health. The health and economic burden of waterborne pathogens can be substantial—as such, the ability to detect and identify the sources of fecal contamination in environmental waters is crucial for the control of waterborne diseases. This can be accomplished through microbial source tracking, which involves the use of various laboratory techniques to trace the origins of microbial pollution in the environment. Building on current source tracking methodology, we describe a novel workflow that uses logic regression, a supervised machine learning method, to discover genetic markers in
Escherichia coli
, a common fecal indicator bacterium, that can be used for source tracking efforts. Importantly, our research provides an example of how the rise in prominence of machine learning algorithms can be applied to improve upon current microbial source tracking methodology.
Role of the intestinal microbiota in contributing to weight disorders and associated comorbidities
Authors: Van Hul Matthias , Neyrinck Audrey M. , Everard Amandine , Abot Anne , Bindels Laure B. , Delzenne Nathalie M. , Knauf Claude , Cani Patrice D. 
Published: June 2024

SUMMARY
The gut microbiota is a major factor contributing to the regulation of energy homeostasis and has been linked to both excessive body weight and accumulation of fat mass (i.e., overweight, obesity) or body weight loss, weakness, muscle atrophy, and fat depletion (i.e., cachexia). These syndromes are characterized by multiple metabolic dysfunctions including abnormal regulation of food reward and intake, energy storage, and low-grade inflammation. Given the increasing worldwide prevalence of obesity, cachexia, and associated metabolic disorders, novel therapeutic strategies are needed. Among the different mechanisms explaining how the gut microbiota is capable of influencing host metabolism and energy balance, numerous studies have investigated the complex interactions existing between nutrition, gut microbes, and their metabolites. In this review, we discuss how gut microbes and different microbiota-derived metabolites regulate host metabolism. We describe the role of the gut barrier function in the onset of inflammation in this context. We explore the importance of the gut-to-brain axis in the regulation of energy homeostasis and glucose metabolism but also the key role played by the liver. Finally, we present specific key examples of how using targeted approaches such as prebiotics and probiotics might affect specific metabolites, their signaling pathways, and their interactions with the host and reflect on the challenges to move from bench to bedside.
Adherence and metal-ion acquisition gene expression increases during infection with
Treponema phagedenis
strains from bovine digital dermatitis
Authors: Scott Colton , Dias Angelica P. , De Buck Jeroen 
Published: June 2024

ABSTRACT

Digital dermatitis (DD) is an ulcerative foot lesion on the heel bulbs of dairy cattle. DD is a polymicrobial disease with no precise etiology, although
Treponema
spirochetes are found disproportionally abundant in diseased tissue. Within
Treponema,
several different species are found in DD; however, the species
Treponema phagedenis
is uniformly found in copious quantities and deep within the skin layers of the active, ulcerative stages of disease. The pathogenic mechanisms these bacteria use to persist in the skin and the precise role they play in the pathology of DD are widely unknown. To explore the pathogenesis and virulence of
Treponema phagedenis
, newly isolated strains of this species were investigated in a subcutaneous murine abscess model. In the first trial, a dosage study was conducted to compare the pathogenicity of different strains across three different treponemes per inoculum (TPI) doses based on abscess volumes. In the second trial, the expression levels of 11 putative virulence genes were obtained to gain insight into their involvement in pathogenesis. During the RT-qPCR analysis, it was determined that genes encoding for two metal-ion import lipoproteins and two adherence genes were found highly upregulated during infection. Conversely, two genes involved in motility and chemotaxis were found to not be significantly upregulated or utilized during infection. These results were supported by gene expression data from natural M2 lesions of dairy cattle. This gene expression analysis could highlight the preference in strategy for
T. phagedenis
to persist and adhere in the host rather than engage in motility and disseminate.
Proteolytic control of FixT by the Lon protease impacts FixLJ signaling in
Caulobacter crescentus
Authors: Yigit Kubra , Chien Peter 
Published: June 2024

ABSTRACT

Responding to changes in oxygen levels is critical for aerobic microbes. In
Caulobacter crescentus
, low oxygen is sensed by the FixL-FixJ two-component system which induces multiple genes, including those involved in heme biosynthesis, to accommodate microaerobic conditions. The FixLJ inhibitor FixT is also induced under low oxygen conditions and is degraded by the Lon protease when the oxygen levels are sufficient, which together provides negative feedback proposed to adjust FixLJ signaling thresholds during changing conditions. Here, we address whether degradation of FixT by the Lon protease contributes to phenotypic defects associated with loss of Lon. We find that ∆
lon
strains are deficient in FixLJ-dependent heme biosynthesis, consistent with elevated FixT levels as deletion of
fixT
suppresses this defect. Transcriptomics validate this result as, along with heme biosynthesis, there is diminished expression of many FixL-activated genes in ∆
lon
. However, stabilization of FixT in ∆
lo
n strains does not contribute to restoring any known Lon-related fitness defect, such as cell morphology defects or stress sensitivity. In fact, cells lacking both FixT and Lon are compromised in viability during growth in standard aerobic conditions. Our work highlights the complexity of protease-dependent regulation of transcription factors and explains the molecular basis of defective heme accumulation in Lon-deficient
Caulobacter
.

IMPORTANCE
The Lon protease shapes protein quality control, signaling pathways, and stress responses in many bacteria species. Loss of Lon often results in multiple phenotypic consequences. In this work, we found a connection between the Lon protease and deficiencies in heme accumulation that then led to our finding of a global change in gene expression due in part to degradation of a regulator of the hypoxic response. However, loss of degradation of this regulator did not explain other phenotypes associated with Lon deficiencies demonstrating the complex and multiple pathways that this highly conserved protease can impact.
In situ
fate of Chikungunya virus replication organelles
Authors: Girard Justine , Le Bihan Olivier , Lai-Kee-Him Joséphine , Girleanu Maria , Bernard Eric , Castellarin Cedric , Chee Matthew , Neyret Aymeric , Spehner Danièle , Holy Xavier , Favier Anne-Laure , Briant Laurence , Bron Patrick 
Published: June 2024

ABSTRACT

Chikungunya virus (CHIKV) is a mosquito-borne pathogen responsible for an acute musculoskeletal disease in humans. Replication of the viral RNA genome occurs in specialized membranous replication organelles (ROs) or spherules, which contain the viral replication complex. Initially generated by RNA synthesis-associated plasma membrane deformation, alphavirus ROs are generally rapidly endocytosed to produce type I cytopathic vacuoles (CPV-I), from which nascent RNAs are extruded for cytoplasmic translation. By contrast, CHIKV ROs are poorly internalized, raising the question of their fate and functionality at the late stage of infection. Here, using
in situ
cryogenic-electron microscopy approaches, we investigate the outcome of CHIKV ROs and associated replication machinery in infected human cells. We evidence the late persistence of CHIKV ROs at the plasma membrane with a crowned protein complex at the spherule neck similar to the recently resolved replication complex. The unexpectedly heterogeneous and large diameter of these compartments suggests a continuous, dynamic growth of these organelles beyond the replication of a single RNA genome. Ultrastructural analysis of surrounding cytoplasmic regions supports that outgrown CHIKV ROs remain dynamically active in viral RNA synthesis and export to the cell cytosol for protein translation. Interestingly, rare ROs with a homogeneous diameter are also marginally internalized in CPV-I near honeycomb-like arrangements of unknown function, which are absent in uninfected controls, thereby suggesting a temporal regulation of this internalization. Altogether, this study sheds new light on the dynamic pattern of CHIKV ROs and associated viral replication at the interface with cell membranes in infected cells.

IMPORTANCE
The Chikungunya virus (CHIKV) is a positive-stranded RNA virus that requires specialized membranous replication organelles (ROs) for its genome replication. Our knowledge of this viral cycle stage is still incomplete, notably regarding the fate and functional dynamics of CHIKV ROs in infected cells. Here, we show that CHIKV ROs are maintained at the plasma membrane beyond the first viral cycle, continuing to grow and be dynamically active both in viral RNA replication and in its export to the cell cytosol, where translation occurs in proximity to ROs. This contrasts with the homogeneous diameter of ROs during internalization in cytoplasmic vacuoles, which are often associated with honeycomb-like arrangements of unknown function, suggesting a regulated mechanism. This study sheds new light on the dynamics and fate of CHIKV ROs in human cells and, consequently, on our understanding of the Chikungunya viral cycle.
The pseudogene GBP1P1 suppresses influenza A virus replication by acting as a protein decoy for DHX9
Authors: Yu Xiaohang , Tian Jiaxin , Wang Yihe , Su Ning , Luo Jinna , Duan Ming , Shi Ning 
Published: June 2024

ABSTRACT

Recently, substantial evidence has demonstrated that pseudogene-derived long noncoding RNAs (lncRNAs) as regulatory RNAs have been implicated in basic physiological processes and disease development through multiple modes of functional interaction with DNA, RNA, and proteins. Here, we report an important role for GBP1P1, the pseudogene of guanylate-binding protein 1, in regulating influenza A virus (IAV) replication in A549 cells. GBP1P1 was dramatically upregulated after IAV infection, which is controlled by JAK/STAT signaling. Functionally, ectopic expression of GBP1P1 in A549 cells resulted in significant suppression of IAV replication. Conversely, silencing GBP1P1 facilitated IAV replication and virus production, suggesting that GBP1P1 is one of the interferon-inducible antiviral effectors. Mechanistically, GBP1P1 is localized in the cytoplasm and functions as a sponge to trap DHX9 (DExH-box helicase 9), which subsequently restricts IAV replication. Together, these studies demonstrate that GBP1P1 plays an important role in antagonizing IAV replication.

IMPORTANCE
Long noncoding RNAs (lncRNAs) are extensively expressed in mammalian cells and play a crucial role as regulators in various biological processes. A growing body of evidence suggests that host-encoded lncRNAs are important regulators involved in host–virus interactions. Here, we define a novel function of GBP1P1 as a decoy to compete with viral mRNAs for DHX9 binding. We demonstrate that GBP1P1 induction by IAV is mediated by JAK/STAT activation. In addition, GBP1P1 has the ability to inhibit IAV replication. Importantly, we reveal that GBP1P1 acts as a decoy to bind and titrate DHX9 away from viral mRNAs, thereby attenuating virus production. This study provides new insight into the role of a previously uncharacterized GBP1P1, a pseudogene-derived lncRNA, in the host antiviral process and a further understanding of the complex GBP network.
Draft genome of carotenoid-producing endophytic
Pseudomonas
sp. 102515 from
Taxus chinensis
Authors: Fidan Ozkan 
Published: June 2024

ABSTRACT

Here, we report the draft genome sequence of endophytic
Pseudomonas
sp. 102515 isolated from
Taxus chinensis
collected from Logan, UT, USA. The genome is composed of 36 contigs and around 4.9 Mbp in size. The GC content is 66% with an
N
50
length of 918.9 kbp and
L
50
count of 2.
Group membership, not diet, structures the composition and functional potential of the gut microbiome in a wild primate
Authors: Finnegan Peter M. , Garber Paul A. , McKenney Anna C. , Bicca-Marques Júlio César , De la Fuente María Fernanda , Abreu Filipa , Souto Antonio , Schiel Nicola , Amato Katherine R. , Mallott Elizabeth K. 
Published: June 2024

ABSTRACT

The gut microbiome has the potential to buffer temporal variations in resource availability and consumption, which may play a key role in the ability of animals to adapt to a broad range of habitats. We investigated the temporal composition and function of the gut microbiomes of wild common marmosets (
Callithrix jacchus
) exploiting a hot, dry environment—Caatinga—in northeastern Brazil. We collected fecal samples during two time periods (July–August and February–March) for 2 years from marmosets belonging to eight social groups. We used 16S rRNA gene amplicon sequencing, metagenomic sequencing, and butyrate RT-qPCR to assess changes in the composition and potential function of their gut microbiomes. Additionally, we identified the plant, invertebrate, and vertebrate components of the marmosets’ diet via DNA metabarcoding. Invertebrate, but not plant or vertebrate, consumption varied across the year. However, gut microbiome composition and potential function did not markedly vary across study periods or as a function of diet composition. Instead, the gut microbiome differed markedly in both composition and potential function across marmosets residing in different social groups. We highlight the likely role of factors, such as behavior, residence, and environmental heterogeneity, in modulating the structure of the gut microbiome.

IMPORTANCE
In a highly socially cohesive and cooperative primate, group membership more strongly predicts gut microbiome composition and function than diet.
Exploring novel microbial metabolites and drugs for inhibiting
Clostridioides difficile
Authors: Abouelkhair Ahmed A. , Seleem Mohamed N. 
Published: June 2024

ABSTRACT

Clostridioides difficile
is an enteric pathogen that can cause a range of illnesses from mild diarrhea to pseudomembranous colitis and even death. This pathogen often takes advantage of microbial dysbiosis provoked by antibiotic use. With the increasing incidence and severity of infections, coupled with high recurrence rates, there is an urgent need to identify innovative therapies that can preserve the healthy state of the gut microbiota. In this study, we screened a microbial metabolite library against
C. difficile
. From a collection of 527 metabolites, we identified 18 compounds with no previously identified antimicrobial activity and metabolites that exhibited potent activity against
C. difficile
growth. Of these 18 hits, five drugs and three metabolites displayed the most potent anti-
C
.
difficile
activity and were subsequently assessed against 20 clinical isolates of
C. difficile
. These potent agents included ecteinascidin 770 (minimum inhibitory concentration against 50% of isolates [MIC
50
] ≤0.06 µg/mL); 8-hydroxyquinoline derivatives, such as broxyquinoline and choloroquinaldol (MIC
50
= 0.125 µg/mL); ionomycin calcium salt, carbadox, and robenidine hydrochloride (MIC
50
= 1 µg/mL); and dronedarone and milbemycin oxime (MIC
50
= 4 µg/mL). Unlike vancomycin and fidaxomicin, which are the standard-of-care anti-
C
.
difficile
antibiotics, most of these metabolites showed robust bactericidal activity within 2–8 h with minimal impact on the growth of representative members of the normal gut microbiota. These results suggest that the drugs and microbial metabolite scaffolds may offer alternative avenues to address unmet needs in
C. difficile
disease prevention and treatment.

IMPORTANCE

The most frequent infection associated with hospital settings is
Clostridioides difficile
, which can cause fatal diarrhea and severe colitis, toxic megacolon, sepsis, and leaky gut. Those who have taken antibiotics for other illnesses that affect the gut's healthy microbiota are more susceptible to
C. difficile
infection (CDI). Recently, some reports showed higher recurrence rates and resistance to anti-
C. difficile
, which may compromise the efficacy of CDI treatment. Our study is significant because it is anticipated to discover novel microbial metabolites and drugs with microbial origins that are safe for the intestinal flora, effective against
C. difficile
, and reduce the risk of recurrence associated with CDI.