bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational Study of In-Phase and Anti-Phase Interactions of Fish in a Phalanx School
Authors: Guo Jiacheng , Dong Haibo 
Published: September 2024

Abstract
Biological studies have shown schooling behavior to benefit fish’s swimming performance. Particularly, side-by-side, or phalanx, formation, combined with the synchronization of undulation of the neighbors was shown to allow the group to sustain fast incoming flow. In this work the hydrodynamic interactions between neighbors in a phalanx school, through three-dimensional (3D) flow simulation. Trout-like computational models, composed of trunk (TK) and caudal fin (CF), are used with undulatory kinematics prescribed using a traveling-wave equation. An immersed-boundary method (IBM) direct numerical simulation (DNS) code is used. Three trout-like models are arranged in a dense phalanx formation so that the middle fish would interact strongly with both its neighbor. The undulation of all the fish are synchronized, with the middle fish undulating either in phase or completely out of phase with its two neighbors, to examine the hydrodynamic interaction in a phalanx school in both in-phase and anti-phase modes. Results show significantly enhanced thrust though at the cost of slightly increased power consumption through anti-phase interaction, which enhanced the 3D pressure fields and momentum of the flow around neighboring CF. The wake of each fish also interacted strongly, producing expanding vortex rings and enhanced wake jets.
Drag Reduction Through Boundary Layer Analysis on Flow Over Bi-Textured Thin Plates
Authors: Chandran K. Nandakumar , Jeong Yu Sin , S. Kumar Ranjith , Min June Kee , Ha Man Yeong 
Published: September 2024

Abstract
In the present work, laminar flow over one-dimensional bi-textured thin plates is numerically studied, focusing on the skin friction coefficient and its role in drag reduction for bio-mimetic, energy-efficient surfaces. Using the Finite Volume Method, the methodology is benchmarked against the Blasius solution and analyzes flow over anisotropic patterned plates, particularly variations in boundary layer thickness and skin friction due to alternating no-slip-perfect-slip patterns, starting with a no-slip pattern at the leading edge. The effect of increasing Reynolds numbers (1 × 105 &lt; Re &lt; 2 × 105) shows stepped boundary layer growth at pattern junctions, with up to 20% drag reduction at a Reynolds number of 1.3 × 105 compared to its classical no-slip boundary condition counterpart. The study also examines how changes in the shear-free area ratio and periodicity affect skin friction distribution, finding reduced drag with increased shear-free areas and increased effective drag-contributing length with more periods. For a shear-free area ratio value of 0.4 with 2 periods and for 4 periods with a shear-free area ratio value of 0.25 drag reduction to Blasius solution where found to be 15% and 12% respectively at Re = 1 × 105. Results, also suggest that the larger the number of periods on a textured plate the closer it behaves to the classical flat plate. This research suggests an alternative method for estimating average skin friction, moving away from traditional equivalent slip formulations to consider near-surface flow dynamics, providing insights crucial for designing drag-reducing fluid dynamic surfaces.
Investigating Unsteady Flow Physics Within Shock-Bubble Interactions
Authors: Ferguson Frederick , Niu Xinru , Feng Dehua 
Published: September 2024

Abstract
In efforts to elucidate the unsteady physics within shock-bubble interactions (SBI), two rectangular SBI problems were simulated with varying Atwood numbers. The problems of interest are: (a) the unsteady interaction of a Mach 1.17 planar shock wave with a square sulfur hexafluoride (SF6) bubble surrounded by air, and (b) the unsteady interaction of a Mach 1.21 planar shock wave with a square helium bubble surrounded by nitrogen. The expectations are to simulate the morphologies of these SBI fields, as the shock wave propagates throughout the media, and as the bubble is transported and deformed. In addition, plans are to quantitatively observe and document the complicated thermodynamic processes, such as, shock refraction, shock reflection and shock diffraction as they develop, interact and propagate through the field. In the cases of the problems investigated herein, at the edges of the rectangular bubble geometry, vortexes are expected to be induced due to shock compression, the generation of vorticity and the acceleration of the media. Numerous experiments have confirmed that this type of problems contain specific fundamental fluid physics that does not lend themselves to simulations without severe numerical challenges. Simulation challenges of great significance to this analysis are the evolution of known fluid instabilities, such as, the Kelvin-Helmholtz instability (KHI) and the Richtmyer-Meshkov Instability (RMI). The unsteady nature of the flow morphology was studied using the Integro-Differential Scheme (IDS) simulation tool. The IDS captured all known flow characteristics and their interactions. The SBI morphology derived from the IDS simulations closely matches the results obtained from experimental findings and the limited available CFD simulations.
Determination of the combined effect of grape seed extract and cold atmospheric plasma on foodborne pathogens and their environmental stress knockout mutants
Authors: Kitsiou Melina , Wantock Thomas , Sandison Gavin , Harle Thomas , Gutierrez-Merino Jorge , Klymenko Oleksiy V. , Karatzas Kimon Andreas , Velliou Eirini 
Published: September 2024

ABSTRACT

The study aimed to explore the antimicrobial efficacy of grape seed extract (GSE) and cold atmospheric plasma (CAP) individually or in combination against
L. monocytogenes
and
E. coli
wild type (WT) and their isogenic mutants in environmental stress genes. More specifically, we examined the effects of 1% (wt/vol) GSE, 4 min of CAP treatment, and their combined effect on
L. monocytogenes
10403S WT and its isogenic mutants Δ
sigB
, Δ
gadD1
, Δ
gadD2
, Δ
gadD3,
as well as
E. coli
K12 and its isogenic mutants Δ
rpoS
, Δ
oxyR
, and Δ
dnaK
. In addition, the sequence of the combined treatments was tested. A synergistic effect was achieved for all
L. monocytogenes
strains when exposure to GSE was followed by CAP treatment. However, the same effect was observed against
E. coli
strains, only for the reversed treatment sequence. Additionally,
L. monocytogenes
Δ
sigB
was more sensitive to the individual GSE and the combined GSE/CAP treatment, whereas Δ
gadD2
was more sensitive to CAP
,
as compared to the rest of the mutants under study. Individual GSE exposure was unable to inhibit
E. coli
strains, and individual CAP treatment resulted in higher inactivation of
E. coli
in comparison to
L. monocytogenes
with the strain Δ
rpoS
appearing the most sensitive among all studied strains. Our findings provide a step toward a better understanding of the mechanisms playing a role in the tolerance/sensitivity of our model Gram-positive and Gram-negative bacteria toward GSE, CAP, and their combination. Therefore, our results contribute to the development of more effective and targeted antimicrobial strategies for sustainable decontamination.

IMPORTANCE
Alternative approaches to conventional sterilization are gaining interest from the food industry, driven by (i) the consumer demand for minimally processed products and (ii) the need for sustainable, environmentally friendly processing interventions. However, as such alternative approaches are milder than conventional heat sterilization, bacterial pathogens might not be entirely killed by them, which means that they could survive and grow, causing food contamination and health hazards. In this manuscript, we performed a systematic study of the impact of antimicrobials derived from fruit industry waste (grape seed extract) and cold atmospheric plasma on the inactivation/killing as well as the damage of bacterial pathogens and their genetically modified counterparts, for genes linked to the response to environmental stress. Our work provides insights into genes that could be responsible for the bacterial capability to resist/survive those novel treatments, therefore, contributing to the development of more effective and targeted antimicrobial strategies for sustainable decontamination.
Genomic analysis of conjugative and chromosomally integrated mobile genetic elements in oral streptococci
Authors: Lee Erica , Priutt Erin , Woods Seth , Quick Allison , King Shawn , McLellan Lisa K. , Shields Robert C. 
Published: September 2024

ABSTRACT

This study aimed to investigate the diversity of conjugative and chromosomally integrated mobile genetic elements (cciMGEs) within six oral streptococci species. cciMGEs, including integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs), are stably maintained on the host cell chromosome; however, under certain conditions, they are able to excise, form extrachromosomal circles, and transfer via a conjugation apparatus. Many cciMGEs encode “cargo” functions that aid survival in new niches and evolve new antimicrobial resistance or virulence properties, whereas others have been shown to influence host bacterial physiology. Here, using a workflow employing preexisting bioinformatics tools, we analyzed 551 genomes for the presence of cciMGEs across six common health- and disease-associated oral streptococci. We identified 486 cciMGEs, 173 of which were ICEs and 233 of which were IMEs. The cciMGEs were diverse in size, cargo genes, and relaxase types. We identified several novel relaxase proteins and a widespread IME carrying a small multidrug resistance transporter. Additionally, we provide evidence that several of the bioinformatically predicted cciMGEs encoded within various
Streptococcus mutans
strains are capable of excision and circularization, a critical step for cciMGE conjugative transfer. These findings highlight the significance and potential impact of MGEs in shaping the genetic landscape, pathogenicity, and antimicrobial resistance profiles of the oral microbiota.

IMPORTANCE
Oral streptococci are important players in the oral microbiome, influencing both health and disease states within dental bacterial communities. Evolutionary adaptation, shaped in a major part by the horizontal transfer of genes, is essential for their survival in the oral cavity and within new environments. Conjugation is a significant driver of horizontal gene transfer; however, there is limited information regarding this process in oral bacteria. This study utilizes publicly available genome sequences to identify conjugative and chromosomally integrated mobile genetic elements (cciMGEs) across several species of oral streptococci and presents the preliminary characterization of these elements. Our findings significantly enhance our understanding of the mobile genomic landscape of oral streptococci critical for human health, with valuable insights into how cciMGEs might influence the survival and pathogenesis of these bacteria in the oral microbiome.
Transmission potential of
Streptococcus pyogenes
during a controlled human infection trial of pharyngitis
Authors: Enkel Stephanie L. , Wong Bernadette , Hla Thel K. , Pickering Janessa , Barnett Timothy C. , Thomas Hannah M. M. , Lansbury Nina , Carapetis Jonathan R. , Osowicki Joshua , Steer Andrew , Manning Laurens , Bowen Asha C. 
Published: September 2024

ABSTRACT

Controlled human infection (CHI) models can provide insights into transmission of pathogens such as
Streptococcus pyogenes
(Strep A). As part of the Controlled Human Infection with Penicillin for
Streptococcus pyogenes
(CHIPS) trial, we explored the potential for transmission among participants deliberately infected with the Strep A emm75 strain. Three approaches to understanding transmission were employed: the use of agar settle plates to capture possible droplet or airborne spread of Strep A; measurement of distance droplets could spread during conversation; and environmental swabbing of high-touch items to detect Strep A on surfaces. Of the 60 (27%) CHIPS trial participants across five cohorts, 16 were enrolled in this sub-study; availability of study staff was the primary reason for selection. In total, 189 plates and 260 swabs were collected. Strep A was grown on one settle plate from a participant on the second day, using plates placed 30 cm away. This participant received the placebo dose of penicillin and had met the primary endpoint of pharyngitis. Whole-genome sequencing identified this to be the challenge strain. Strep A was not detected on any swabs. In this small sample of CHI participants, we did not find evidence of Strep A transmission by the airborne route or fomites, and just one instance of droplet spread while acutely symptomatic with streptococcal pharyngitis. Although these experiments provide evidence of minimal transmission within controlled clinical settings, greater efforts are required to explore Strep A transmission in naturalistic settings.

IMPORTANCE

Streptococcus pyogenes
remains a significant driver of morbidity and mortality, particularly in under-resourced settings. Understanding the transmission modalities of this pathogen is essential to ensuring the success of prevention methods. This proposed paper presents a nascent attempt to determine the transmission potential of
Streptococcus pyogenes
nested within a larger controlled human infection model.
Soil diazotrophs sustain nitrogen fixation under high nitrogen enrichment
via
adjustment of community composition
Authors: Zheng Mianhai , Xu Meichen , Zhang Jing , Liu Zhanfeng , Mo Jiangming 
Published: September 2024

ABSTRACT

Biological nitrogen (N) fixation, an important pathway of N, inputs from the atmosphere to Earth’s ecosystems, is well demonstrated to decline under N input. However, it remains unclear why N fixers sustain N fixation in many forests under high atmospheric N deposition. To address this knowledge gap, we analyzed the response of the diazotroph community to low N loads (short-term and low N addition; 3-year N addition at the rates of 25–50 kg N ha
−1
year
−1
) vs high loads (chronic and high N addition; 9-year N addition at the rate of 150 kg N ha
−1
year
−1
) in forest soils using high-throughput sequencing. Rates of N fixation decreased under low and high N loads (by 13%–27% and 10%–12%, respectively). Richness and alpha diversity (ACE and Chao1) of the soil diazotroph community decreased under low but not high N loads. Approximately 67.1%–74.4% of the
nifH
gene sequences at the OTU level overlapped between the control and low N loads, but only 52.0%–53.6% of those overlapped between the control and high N loads, indicating a larger shift of diazotroph community composition under high N loads. Low N loads increased soil NH
4
+
concentrations, which decreased diazotroph community richness, diversity, and N fixation rates, whereas the increased soil NH
4
+
concentrations under high N loads did not have negative impacts on the structure and function of the diazotroph community. These findings indicate that diazotrophs sustain N fixation under high N deposition
via
adjustment of their community composition in forest soils.

IMPORTANCE

This study examined the changes in soil diazotroph community under different loads of simulated N deposition and analyzed its relationship with N fixation rates in in five forests using high-throughput sequencing. The magnitudes of N fixation rates reduced by low N loads were higher than those by high N loads. Low N loads decreased richness and diversity of diazotroph community, whereas diazotroph community structure remained stable under high N loads. Compared with low N loads, high N loads resulted in a less similarity and overlap of
nifH
gene sequences among the treatments and a larger adjustment of diazotroph community. Low N loads increased soil NH4+ concentrations, which decreased diazotroph community richness, diversity, and N fixation rates, whereas the increased soil NH4+ under high N loads did not have negative impacts on diazotroph community structure and N fixation. Based on these findings, it is urgently needed to incorporate the loads of N deposition and the composition of diazotroph community into terrestrial N-cycling models for accurate understanding of N inputs in forest ecosystems.
Assessment of Inhibition of the Growth of Breast and Colon Tumors when Blocking VEGFR-1 with Monoclonal Antibodies
Authors: Shtam T. A. , Demyanov A. V. , Garaeva L. A. , Emelianova S. S. , Nikitina A. V. , Putevich E. D. , Potyseva A. S. , Bidghieva M. S. , Volnitskiy A. V. , Kvanchiani V. V. , Solomina L. A. , Shabalin K. A. , Sergeeva E. V. , Trashkov A. P. , Sidorova Zh. Yu. , Zhahov A. V. , Burdakov V. S. , Verlov N. A. , Konevega A. L. 
Published: September 2024

AbstractVascular endothelial growth factor receptor-1 (VEGFR-1) plays a critical role in tumor-associated angiogenesis. VEGFR-1 is found on the surface of tumor cells and cells in the tumor microenvironment. Blocking this receptor leads to the suppression of proliferation and increased apoptosis of tumor cells, reduction of tumor vascularization, inhibition of the production of immunosuppressive cytokines by tumor-associated macrophages, and the suppression of tumor invasion and metastasis. The creation of monoclonal antibody drugs that block VEGFR-1 is an urgent task in the development of potential antitumor therapeutic drugs. Target molecules created on the basis of antibodies that bind to VEGFR-1 are a promising basis for the creation of theranostic radiopharmaceuticals for the diagnosis and treatment of malignant neoplasms. To study the therapeutic potential of VEGFR-1 inhibition in breast and colon cancers using antibodies, monoclonal antibodies against recombinant human VEGFR-1 protein are developed. The resulting monoclonal antibodies bind to the VEGFR-1 receptor on the cell surface and effectively inhibit the proliferation of breast and colon cancer cells in vitro, reduce the growth rate of the tumor node in vivo, and prolong the survival of tumor-inoculated mice.
Associations of occupational and leisure-time physical activity with all-cause mortality: an individual participant data meta-analysis
Authors: Coenen Pieter , Huysmans Maaike A , Holtermann Andreas , Troiano Richard P , Mork Paul Jarle , Krokstad Steinar , Clays Els , Cillekens Bart , De Bacquer Dirk , Aadahl Mette , Kårhus Line Lund , Sjøl Anette , Andersen Lars Bo , Kauhanen Jussi , Voutilainen Ari , Pulsford Richard M , Stamatakis Emmanuel , Goldbourt Uri , Peters Annette , Thorand Barbara , Rosengren Annika , Björck Lena , Sprow Kyle , Franzon Kristin , Rodriguez-Barranco Miguel , Luján-Barroso Leila , Knutsson Anders , Alfredsson Lars , Bahls Martin , Ittermann Till , Kluttig Alexander , Hassan Lamiaa , Wanner Miriam , Bopp Matthias , Marott Jacob Louis , Schnohr Peter , Nordestgaard Børge Grønne , Dalene Knut Eirik , Ekelund Ulf , Clausen Johan , Jensen Magnus Thorsten , Petersen Christina Bjørk , Krause Niklas , Twisk Jos , Mechelen Willem van , van der Beek Allard J 
Published: September 2024

ObjectiveHealth effects of different physical activity domains (ie, during leisure time, work and transport) are generally considered positive. UsingActive Worker consortiumdata, we assessed independent associations of occupational and leisure-time physical activity (OPA and LTPA) with all-cause mortality.DesignTwo-stage individual participant data meta-analysis.Data sourcePublished and unpublished cohort study data.Eligibility criteriaWorking participants aged 18–65 years.MethodsAfter data harmonisation, we assessed associations of OPA and LTPA with all-cause mortality. In stage 1, we analysed data from each study separately using Cox survival regression, and in stage 2, we pooled individual study findings with random-effects modelling.ResultsIn 22 studies with up to 590 497 participants from 11 countries, during a mean follow-up of 23.1 (SD: 6.8) years, 99 743 (16%) participants died. Adjusted for LTPA, body mass index, age, smoking and education level, summary (ie, stage 2) hazard ration (HRs) and 95% confidence interval (95% CI) for low, moderate and high OPA among men (n=2 96 134) were 1.01 (0.99 to 1.03), 1.05 (1.01 to 1.10) and 1.12 (1.03 to 1.23), respectively. For women (n=2 94 364), HRs (95% CI) were 0.98 (0.92 to 1.04), 0.96 (0.92 to 1.00) and 0.97 (0.86 to 1.10), respectively. In contrast, higher levels of LTPA were inversely associated with mortality for both genders. For example, for women HR for low, moderate and high compared with sedentary LTPA were 0.85 (0.81 to 0.89), 0.78 (0.74 to 0.81) and 0.75 (0.65 to 0.88), respectively. Effects were attenuated when adjusting for income (although data on income were available from only 9 and 6 studies, for men and women, respectively).ConclusionOur findings indicate that OPA may not result in the same beneficial health effects as LTPA.
Protocol for the effectiveness of multimonth refill of antituberculosis drugs (MORAD) on treatment success among people with drug-susceptible tuberculosis in rural eastern Uganda: a non-inferiority randomised trial
Authors: Izudi Jonathan , Bajunirwe Francis , Cattamanchi Adithya 
Published: September 2024

IntroductionMultimonth dispensing of antituberculosis (TB) drugs reduces frequent visits and costs associated with longer travel distances to a TB clinic. We will evaluate the effectiveness of multimonth dispensing of anti-TB drugs on treatment success in individuals with drug-susceptible TB in rural eastern Uganda, and explore its relevance and appropriateness from the stakeholders’ perspectives.Methods and analysisIn this open-label, non-inferiority, individually randomised trial, we will randomise 260 participants to either the intervention (multimonth dispensing of anti-TB drugs) or control arm (routine care) and follow-up for 6 months. Intervention participants will receive monthly anti-TB refills for 2 months then a 2-month refill for 4 months, totalling four visits. Control participants will receive routine care comprising biweekly anti-TB refills for 2 months and monthly refills for 6 months, totalling eight visits. The primary outcome will be treatment success (treatment completion or cure) at month 6. Secondary outcomes will include adherence to anti-TB treatment over 6 months measured by self-report and pill counts, and sputum smear conversion at months 2 and 6 defined as a change in sputum smear status from positive to negative among bacteriologically confirmed individuals. Data will be analysed using a generalised linear mixed model at a 5% significance level, reported as a risk difference with a 95% CI. A formative qualitative study will be conducted among stakeholders at the national, district and health facility levels and people with TB including their treatment supporters to inform the intervention’s relevance, appropriateness and implementation. Qualitative data gathered through focus group discussions and in-depth and key informant interviews will be transcribed and analysed using content analysis.Ethics and disseminationThe Infectious Diseases Institute Research Ethics Committee and the Uganda National Council for Science and Technology approved the protocol. Findings will be disseminated to all stakeholders through presentations, synthesised reports and manuscript publication.Trial registration numberPACTR202403586718783.