bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ferrofluidic wavy Taylor vortices under alternating magnetic field
Authors: Altmeyer Sebastian A. 
Published: January 2023

Many natural and industrial flows are subject to time-dependent boundary conditions and temporal modulations (e.g. driving frequency), which significantly modify the dynamics compared with their static counterparts. The present problem addresses ferrofluidic wavy vortex flow in Taylor–Couette geometry, with the outer cylinder at rest in a spatially homogeneous magnetic field subject to an alternating modulation. Using a modified Niklas approximation, the effect of frequency modulation on nonlinear flow dynamics and appearing resonance phenomena are investigated in the context of either period doubling or inverse period doubling.This article is part of the theme issue ‘Taylor–Couette and related flows on the centennial of Taylor’s seminalPhilosophical Transactionspaper (part 1)’.
Experimental insights into elasto-inertial transitions in Taylor–Couette flows
Authors: Boulafentis T. , Lacassagne T. , Cagney N. , Balabani S. 
Published: January 2023

Since the seminal work of Taylor in 1923, Taylor–Couette (TC) flow has served as a paradigm to study hydrodynamic instabilities and bifurcation phenomena. Transitions of Newtonian TC flows to inertial turbulence have been extensively studied and are well understood, while in the past few years, there has been an increasing interest in TC flows of complex, viscoelastic fluids. The transitions to elastic turbulence (ET) or elasto-inertial turbulence (EIT) have revealed fascinating dynamics and flow states; depending on the rheological properties of the fluids, a broad spectrum of transitions has been reported, including rotating standing waves, flame patterns (FP), and diwhirls (DW). The nature of these transitions and the relationship between ET and EIT are not fully understood. In this review, we discuss experimental efforts on TC flows of viscoelastic fluids. We outline the experimental methods employed and the non-dimensional parameters of interest, followed by an overview of inertia, elasticity and elasto-inertia-driven transitions to turbulence and their modulation through shear thinning or particle suspensions. The published experimental data are collated, and a map of flow transitions to EIT as a function of the key fluid parameters is provided, alongside perspectives for the future work.This article is part of the theme issue 'Taylor–Couette and related flows on the centennial of Taylor’s seminalPhilosophical Transactionspaper (part 1)'.
Unified torque scaling in counter-rotating suspension Taylor–Couette flow
Authors: Alam Meheboob , Ghosh Manojit 
Published: January 2023

Torque measurements are reported for the Taylor–Couette flow of a neutrally buoyant non-colloidal suspension in the counter-rotation regime up to a particle volume fraction of

ϕ
=
0.2

. A unified scaling relation for the dimensionless torque (the pseudo-Nusselt number) of the form

Nu

ω
0

=
(

α
0

+

α
1

Ta

1

∗

α
2

)

Ta

(
0
)

k

μ
r

(
ϕ
)

n

is shown to hold over a range of Taylor numbers

Ta

c
1

≤

Ta

≤

10
6

that covers primary, secondary and tertiary bifurcating states; here,

Ta

1
∗

=

Ta

(
ϕ
)

/

Ta

c
1

(
ϕ
)

is the reduced Taylor number,

Ta

c
1

is the critical Taylor number at primary bifurcation and

μ
r

(
ϕ
)
=
μ
(
ϕ
)

/

μ
(
0
)

is the relative viscosity of the suspension. Possible effects of flow transitions and inhomogeneous distribution of particles on torque scaling are discussed.

This article is part of the theme issue ‘Taylor–Couette and related flows on the centennial of Taylor’s seminal
Philosophical Transactions
paper (part 1)’.
The Effects of 6 Weeks of Resistance Training on the Gut Microbiome and Cardiometabolic Health in Young Adults with Overweight and Obesity
Authors: Cullen John M.A. , Shahzad Shahim , Kanaley Jill A. , Ericsson Aaron C. , Dhillon Jaapna 
Published: January 2023

ABSTRACTINTRODUCTIONObesity is a known risk factor for the development of insulin resistance and other cardiometabolic disorders. Recently, the gut microbiome has been associated with obesity and subsequent health complications. Exercise has been regularly utilized as a therapeutic intervention to treat obesity and its associated comorbidities. This study examined the effects of a 6-week resistance training exercise program (RT) on the diversity, composition, and metabolic pathways of the gut microbiome.METHODSSedentary young adults (age 18-35 years) with overweight and obesity (BMI 25-45 kg/m2) were recruited to participate in this randomized controlled trial. Participants were randomized to RT (n=16), a 6-week resistance training program (3 days/week), or control (CT) (n=16), a non-exercising control. Main outcomes of the study included gut microbiome measures (taxa abundances, diversity, and predicted function) and cardiometabolic outcomes (blood pressure (BP) and glucoregulation).RESULTSIncreased abundances ofRoseburia, a short chain fatty acid (SCFA) producer and predicted starch and sucrose metabolism pathway were observed over 6 weeks (W6) with RT in comparison to CT (group × week, p<0.05, q<0.25). RT also induced higher abundance of microbial flagellar assembly, a pathway involved in cell motility, at W6 compared to CT (group × week, p<0.05, q<0.25). Moreover, RT resulted in higher QUICKI and lower diastolic BP at W6 compared to CT (BL-adjusted p<0.05).CONCLUSIONThis study provides preliminary evidence that resistance training increases abundance of selected SCFA producers and microbial pathways and improves cardiometabolic health. Additionally, the associations of cardiometabolic indicators with the microbial community structure warrants further investigation.
Omicron BA.1 breakthrough infection drives long-term remodeling of the memory B cell repertoire in vaccinated individuals
Authors: Sokal Aurélien , Barba-Spaeth Giovanna , Hunault Lise , Fernández Ignacio , Broketa Matteo , Meola Annalisa , Fourati Slim , Azzaoui Imane , Vandenberghe Alexis , Lagouge-Roussey Pauline , Broutin Manon , Roeser Anais , Bouvier-Alias Magali , Crickx Etienne , Languille Laetitia , Fournier Morgane , Michel Marc , Godeau Bertrand , Gallien Sébastien , Melica Giovanna , Nguyen Yann , Canoui-Poitrine Florence , Noizat-Pirenne France , Megret Jérôme , Pawlotsky Jean-Michel , Fillatreau Simon , Reynaud Claude-Agnès , Weill Jean-Claude , Rey Félix A. , Bruhns Pierre , Mahévas Matthieu , Chappert Pascal 
Published: January 2023

SummaryHow infection by a viral variant showing antigenic drift impacts a preformed mature human memory B cell (MBC) repertoire remains an open question. Here, we studied the MBC response up to 6 months after Omicron BA.1 breakthrough infection in individuals previously vaccinated with three doses of mRNA vaccine. Longitudinal analysis, using single-cell multi-omics and functional analysis of monoclonal antibodies from RBD-specific MBCs, revealed that a BA.1 breakthrough infection mostly recruited pre-existing cross-reactive MBCs with limitedde novoresponse against BA.1-restricted epitopes. Reorganization of clonal hierarchy and new rounds of germinal center reaction, however, combined to maintain diversity and induce progressive maturation of the MBC repertoire against common Hu-1 and BA.1, but not BA.5-restricted, SARS-CoV-2 Spike RBD epitopes. Such remodeling was further associated with marked improvement in overall neutralizing breadth and potency. These findings have fundamental implications for the design of future vaccination booster strategies.
MOTIFS IN SARS-COV-2 EVOLUTION
Authors: Barrett Christopher , Bura Andrei C. , He Qijun , Huang Fenix W. , Li Thomas J. X. , Reidys Christian M. 
Published: January 2023

AbstractWe present a novel framework enhancing the prediction of whether novel lineage poses the threat of eventually dominating the viral population. The framework is based purely on genomic sequence data, without requiring prior established biological analysis. Its building blocks are sets of co-evolving sites in the alignment (motifs), identified via co-evolutionary signals. The collection of such motifs forms a relational structure over the polymorphic sites. Motifs are constructed using distances quantifying the co-evolutionary coupling of pairs and manifest as co-evolving clusters of sites. We present an approach to genomic surveillance based on this notion of relational structure. Our system will issue an alert regarding a lineage, based on its contribution to drastic changes in the relational structure. We then conduct a comprehensive retrospective analysis of the COVID-19 pandemic based on SARS-CoV-2 genomic sequence data in GISAID from October 2020 to September 2022, across 21 lineages and 27 countries with weekly resolution. We investigate the performance of this surveillance system in terms of its accuracy, timeliness and robustness. Lastly, we study how well each lineage is classified by such a system.
Poles apart: the structure and composition of the bird community in bamboo in the Eastern Himalaya
Authors: Srinivasan Sidharth , Biswakarma Aman , Pradhan D.K. , Rai Shambu , Srinivasan Umesh 
Published: January 2023

AbstractBamboos (Poaceae: Bambuseae) are a unique and diverse group of plants (> 1500 species) that are found in tropical and subtropical regions of the world. Various birds, mammals, and insects use bamboo either directly or indirectly, and some species are obligate bamboo specialists. For instance, several species of Neotropical birds are found in bamboo alone. However, the mechanisms underlying dependence on/associations with bamboo are almost entirely unknown. We studied bird communities in bamboo and rainforest across two seasons in the Eastern Himalaya, where we explored a possible mechanism for bird associations with bamboo – dietary resource specialization. We calculated use of bamboo versus rainforest by bird species and described the structure and composition of the bird and arthropod communities in both habitats and seasons. We provide the first systematic evidence of bamboo specialist bird species from the Eastern Himalaya. Although the species richness of birds and arthropods in both habitats and seasons did not vary starkly, we found that the composition of bird and arthropod communities in both habitats and both seasons to be distinct. Interestingly, we found arthropod communities in different substrates of bamboo to also be distinct. Bird specialization in bamboo in the Eastern Himalaya could be because of their dietary specialization to the unique arthropods found in bamboo. The results from this study emphasise the importance of bamboo in the Eastern Himalaya and provide baseline information that might aid in conservation.
demuxmix: Demultiplexing oligonucleotide-barcoded single-cell RNA sequencing data with regression mixture models
Authors: Klein Hans-Ulrich 
Published: January 2023

AbstractMotivationDroplet-based single-cell RNA sequencing (scRNA-seq) is widely used in biomedical research to interrogate the transcriptomes of single cells on a large scale. Pooling and processing cells from different samples together can reduce costs and batch effects. In order to pool cells, cells are often first labeled with hashtag oligonucleotides (HTOs). These HTOs are sequenced along with the cells’ RNA in the droplets and are subsequently used to computationally assign each droplet to its sample of origin, which is referred to as demultiplexing. Accurate demultiplexing is crucial and can be challenging due to background HTOs, low-quality cells/cell debris, and multiplets.ResultsA new demultiplexing method, demuxmix, based on negative binomial regression mixture models is introduced. The method implements two significant improvements. First, demuxmix’s probabilistic classification framework provides error probabilities for droplet assignments that can be used to discard uncertain droplets and inform about the quality of the HTO data and the demultiplexing success. Second, demuxmix utilizes the positive association between detected genes in the RNA library and HTO counts to explain parts of the variance in the HTO data resulting in improved droplet assignments. The improved performance of demuxmix compared to existing demultiplexing methods is assessed on real and simulated data. Finally, the feasibility of accurately demultiplexing experimental designs where non-labeled cells are pooled with labeled cells is demonstrated.AvailabilityR/Bioconductor package demuxmix (https://doi.org/doi:10.18129/B9.bioc.demuxmix)
ChromDL: A Next-Generation Regulatory DNA Classifier
Authors: Hill Christopher , Hudaiberdiev Sanjarbek , Ovcharenko Ivan 
Published: January 2023

AbstractMotivationPredicting the regulatory function of non-coding DNA using only the DNA sequence continues to be a major challenge in genomics. With the advent of improved optimization algorithms, faster GPU speeds, and more intricate machine learning libraries, hybrid convolutional and recurrent neural network architectures can be constructed and applied to extract crucial information from non-coding DNA.ResultsUsing a comparative analysis of the performance of thousands of Deep Learning (DL) architectures, we developed ChromDL, a neural network architecture combining bidirectional gated recurrent units (BiGRU), convolutional neural networks (CNNs), and bidirectional long short-term memory units (BiLSTM), which significantly improves upon a range of prediction metrics compared to its predecessors in transcription factor binding site (TFBS), histone modification (HM), and DNase-I hypersensitive site (DHS) detection. Combined with a secondary model, it can be utilized for accurate classification of gene regulatory elements. The model can also detect weak transcription factor (TF) binding with higher accuracy as compared to previously developed methods and has the potential to accurately delineate TF binding motif specificities.AvailabilityThe ChromDL source code can be found athttps://github.com/chrishil1/ChromDL.
Delivering mRNAs to mouse tissues using the SEND system
Authors: Ohtsuka Masato , Imafuku Jurai , Hori Shuho , Kurosaki Aki , Nakamura Ayaka , Nakahara Tsubasa , Yahata Takashi , Bhat Kolari , Papastefan Steven T , Nakagawa So , Quadros Rolen M , Miura Hiromi , Gurumurthy Channabasavaiah B 
Published: January 2023

AbstractmRNAs produced in a cell are almost always translated within the same cell. Some mRNAs are transported to other cells of the organism through processes involving membrane nanotubes or extracellular vesicles. A recent report describes a surprising new phenomenon of encapsulating mRNAs inside virus-like particles (VLPs) to deliver them to other cells in a process that was named SEND (Selective Endogenous eNcapsidation for cellular Delivery). Although the seminal work demonstrates the SEND process in cultured cells, it is unknown whether this phenomenon occursin vivo. Here, we demonstrate the SEND process in living organisms using specially designed genetically engineered mouse models. Our proof of principle study lays a foundation for the SEND-VLP system to potentially be used as a gene therapy tool to deliver therapeutically important mRNAs to tissues.
Autotrophic adaptive laboratory evolution of the acetogenClostridium autoethanogenumdelivers the gas-fermenting strain LAbrini with superior growth, products, and robustness
Authors: Ingelman Henri , Heffernan James K. , Harris Audrey , Brown Steven D. , Shaikh Kurshedaktar Majibullah , Saqib Asfand Yar , Pinheiro Marina J. , de Lima Lorena Azevedo , Martinez Karen Rodriguez , Gonzalez-Garcia Ricardo A. , Hawkins Grant , Daleiden Jim , Tran Loan , Zeleznik Hunter , Jensen Rasmus O. , Reynoso Vinicio , Schindel Heidi , Jänes Jürgen , Simpson Séan D. , Köpke Michael , Marcellin Esteban , Valgepea Kaspar 
Published: January 2023

ABSTRACTMicrobes able to convert gaseous one-carbon (C1) waste feedstocks are increasingly important to transition to the sustainable production of renewable chemicals and fuels. Acetogens are interesting biocatalysts since gas fermentation usingClostridium autoethanogenumhas already been commercialised. However, most acetogen strains need complex nutrients, display slow growth, and are not robust for routine bioreactor fermentations. In this work, we used three different and independent adaptive laboratory evolution (ALE) strategies to evolve the wild-typeC. autoethanogenumto grow faster, without yeast extract and to be robust in operating continuous bioreactor cultures. Multiple evolved strains with improved phenotypes were isolated on a minimal medium with one strain, named “LAbrini” (LT1), exhibiting superior performance regarding the maximum specific growth rate, product profile, and robustness in continuous cultures. Whole-genome sequencing of the evolved strains identified 25 mutations. Of particular interest are two genes that acquired seven different mutations across the three ALE strategies, potentially as a result of convergent evolution. Reverse genetic engineering of sporulation-related mutations in genes CLAU_3129 (spo0A) and CLAU_1957 recovered all three superior features of our ALE strains through triggering significant proteomic rearrangements. This work provides a robustC. autoethanogenumstrain to accelerate phenotyping and genetic engineering and to better understand acetogen metabolism, which we named “LAbrini”.
Dopamine promotesKlebsiella quasivariicolaproliferation and inflammatory response in the presence of macrophages
Authors: Li Xiang , Cheng Lin , Liu Xueyang , Wang Xiaoli , Li Rui , Fan Shao , Yan Qiulong , Ma Tonghui , Ma Yufang , Kang Jian 
Published: January 2023

AbstractKlebsiella quasivariicolawas a novel strain ofKlebsiellaspecies and had potential pathogenicity. Our previously studies showed dopamine, one of the most commonly used rescue drugs for critically ill patients, had clear effects on the growth ofK. quasivariicolain culture medium, however, its effects on host immune system were ignored. Therefore, in consideration of the host immunity, the interactions ofK. quasivariicola, dopamine and macrophages were explored. In this study, RAW264.7 cells and C57/BL6 mice were infected withK. quasivariicola, and the bacterial growth in macrophage, the production of inflammatory cytokines and the pathological changes of mice lung were detected, in the absence or presence of dopamine. Our results showed dopamine inhibited theK. quasivariicolagrowth in medium, but promoted the bacterial growth whenK. quasivariicolawas co-cultured with macrophages; The expression of proinflammatory cytokines inK. quasivariicolainfected RAW 264.7 were increased, while a sharp rise was observed with the addition of dopamine; Infection ofK. quasivariicolato mice induced an inflammatory response and lung injury, which were exacerbated by dopamine administration. It can be concluded that dopamine administration resulted in a significantly increase ofK. quasivariicolaburdens in the presence of macrophage, consequently, aggravated the inflammatory response and inflammatory injury.ImportanceDopamine is one of the most commonly used rescue drugs for critically ill patients. Here we indicatedK. quasivariicolawas a potential pathogen of pulmonary infection, and dopamine significantly increased the proliferation ofK. quasivariicolawhen exposed to macrophage, subsequently result in severe inflammatory response and inflammatory injury. We also proposed anin vitromodel of microbes-drugs-host immune cells that could better mimicin vivoenvironment and more suitable for the studies of inhibitor screening. This fundamental work had contributed to the present understanding of the crosstalk between pathogen, dopamine and host immune cells. Furthermore, our data showed dopamine was one of the risk factors for patients withK. quasivariicolainfection, which provided a basis for clinical precision medicine.
The post-translational modification profile of TAR DNA-Binding Protein (TDP-43) in platelets of patients with Alzheimer’s disease: An exploratory study for blood-based biomarker development
Authors: Johnson Qwynton , Hadjian Mahan , Bah Alpha , Smith Sean , Kosa Edina , Agbas Abdulbaki 
Published: January 2023

AbstractThe assignment of blood-based biomarkers for neurodegenerative diseases is of great clinical value. Well-developed and validated blood-based biomarkers can serve in early diagnosis and prognosis as well as aid in patient screening when recruiting for clinical trials. We attempted to establish a portfolio for post-translationally modified TAR DNA/RNA-binding protein (TDP-43), a regulator of nuclear transcription, in platelet cytosol obtained from patients with Alzheimer’s disease (AD) comparing to age-matched healthy subjects and a disease control cohort. We aimed to identify the most prominent post-translational modifications of TDP-43 as an AD-relevant biomarker and to demonstrate that such an assessment can be performed in peripheral blood. We have isolated TDP-43 protein from human platelet cytosol utilizing an Immunoaffinity chromatography. The eluates were immunoprobed with a series of antibodies raised against post-translationally modified proteins. We employed a capillary electrophoretic immunoassay (CEI) to assess the phosphorylated TDP-43 profile. We observed that SUMOylation, phosphorylation, ubiquitination, and cysteine oxidation of TDP-43 are more prominent in platelet cytosol of AD patients as compared to control subjects. These studies will pave the way for identifying disease-specific TDP-43 derivatives that can be potential biomarkers for early diagnosis and the development of therapeutics.
Promote the “wow”: (mis)representation, perception and reception of media promotion on wheelchair rugby
Authors: Hu Tiao , Cottingham Michael , Shapiro Deborah , Lee Don 
Published: January 2023

PurposeThis phenomenological study aims to explore how media promote and should promote wheelchair rugby.Design/methodology/approachSemi-structured interviews were conducted with 31 athletes at National Wheelchair Rugby Championship. In using a reflective thematical analysis approach, three themes were identified – media coverage: the promise of an unknown quantity; the battle of inspiration and athleticism; and leverage marketing and promote the “wow”.FindingsLacking fair representation from media resulting in the perception and reception gap between the general public and spectators was identified and explained by most of the athletes. Besides urging increased coverage with a shifting focus on athleticism, the important role of marketing was highlighted.Originality/valueIn short, the “wow” factor of the sport is its aggressiveness which can be its bestselling feature and used by stakeholders for maximum impact when marketing wheelchair rugby.
Effect of limestone usage on tribological properties in copper and asbestos-free brake friction materials
Authors: Yavuz Hicri 
Published: January 2023

Purpose
This study aims to determine the braking performance of limestone as a filler in brake friction materials.

Design/methodology/approach
Samples containing limestone material (30-35-40%), which can be an alternative to brake friction material filler, were produced. The samples were weighed on precision scales, mixed homogeneously and produced using the hot molding method. The physical and tribological properties of the produced samples were determined, and their microscopic analyzes were made with scanning electron microscopy.

Findings
As the amount of limestone increased, the density of the samples decreased. The friction coefficient and wear rates were close to each other and within the optimum limits for all samples. Limestone materials can be used instead of barite materials studied in the literature on brake linings. Microcracks were observed only in samples containing 30% and 35% limestone in microscopic images.

Originality/value
In this study, the wear rate, coefficient of friction and microstructures on the friction surfaces of brake friction materials containing limestone were investigated. The usability of limestone as a filler in brake friction materials provides valuable information to researchers and industrial organizations in the brake friction material field.