bluuebunny/crossref_metadata_2025_split huggingface dataset:
Koo‐Kleinstreuer‐Li magneto‐nanofluid model for non‐Newtonian micropolar fluid through porous channel
Authors: Lone Showkat Ahmad , Bilal Muhammad , Mehmood Yasir , Sajid Tanveer , Nadeem Muhammad 
Published: May 2024

AbstractThe primary concern of writing this article is to study the rheological properties of the micropolar non‐Newtonian nanofluid flowing through the porous medium along with magnetic field effects. In it, the outer boundary of the sheet is heated by applying an external heat source. The insertion of aluminum oxide nanoparticles in water turned it into a nanofluid. Together with the viscous dissipation phenomena, adding a magnetic field has another effect known as a Joule heating impact that is considered in the energy equation. To investigate the impact of viscosity and thermal conductivity on flow patterns, we considered the Koo‐Kleinstreuer‐Li model. A generalized Proudman‐Johnson equation is obtained by using similarity transformation on Navier‐Stokes equations. The well‐known classical shooting method is used to get the numerical solution to the said problem. Graphical results are portrayed for variant rheological parameters lke power law index, Reynolds number, volume fraction, Prandtl number, expansion ratio, and Hartmann number on the velocity and temperature of nanofluids.
Cattaneo–Christov heat and mass flux model and thermal enhancement in three‐dimensional MHD Jeffrey hybrid nanofluid flow over a bi‐directional stretching sheet with convective boundary conditions
Authors: Hussain Zawar , Ayaz Muhammad , Islam Saeed 
Published: May 2024

AbstractInspired by the progressive relaxation characteristics of the Jeffrey model and its applied advantages in the rheological modeling of various dynamic fluids, the current study is focused to investigate the heat and mass transfer of magnetohydrodynamic (MHD) Jeffrey hybrid nanofluid flow over bi‐directional stretching sheet with convective boundary conditions. Additionally, the Cattaneo–Christov model of heat and mass flux is employed to take into consideration the time relaxation effects. The energy and concentration equation are taken into account to explore the effects of thermophoresis and Brownian motion. Homotopy analysis method (HAM) is employed for the solution of the current problem. Solution methodology is verified by comparing present results with those already published in open literature. The physical aspects of obtained graphical and numerical results are explained in detail to justify acquired trends. From the investigation, it is inferred that the magnetic and viscoelastic factors have a reducing influence on the flow profile along primary and secondary directions, while the stretching parameter has an increasing behavior on the flow profile in the secondary direction. Furthermore, the Brownian motion, magnetic parameter, and thermophoretic parameter have an escalating behavior on thermal distribution; however, the Brownian motion has a declining consequence on the concentration profile. The larger Biot number heightens the thermal and concentration distributions.
Constructing a Comprehensive Discourse
Authors: Ghaly Mohammed 
Published: May 2024

AbstractChapter two constructs a comprehensive ethical framework to facilitate the analysis of intricate bioethical issues like incidental findings (IFs) in genomics. Drawing from both secular and Islamic traditions, it synthesizes Robert Veatch's multi-layered approach to bioethics and the recommendation by Muslim ethicists to engage diverse scholarly disciplines. The “Theoretical Level” section explores Islamic metaethics rooted in theology and legal theory, centering on aligning human actions with God’s will to achieve benefit and avert harm. It examines the process of religio-ethical reasoning (ijtihād) employed by Muslim scholars to discern divine guidance on novel issues. The “Practical Level” section outlines the fivefold classification scheme for categorizing human acts based on their moral value within the Islamic tradition: prohibited, obligatory, reprehensible, recommended, and permissible. Distinct from secular schemes, this classification’s theological foundations, definitions, and moral dimensions are elucidated. Bridging theory and practice, the chapter proposes utilizing this fivefold scheme as a nuanced tool to evaluate the ethical management of IFs. It advocates a dynamic approach, acknowledging how evolving scientific understanding may shift the categorization of specific IFs over time. The chapter lays the groundwork for the subsequent analysis, where representative cases illustrating each ethical category are examined through the synthesized Islamic ethical lens, fostering constructive dialogue between religious and secular bioethical discourses on this complex issue.
Dynamic changes in RNA m6A and 5 hmC influence gene expression programs during macrophage differentiation and polarisation
Authors: Pinello Natalia , Song Renhua , Lee Quintin , Calonne Emilie , Duan Kun-Long , Wong Emilie , Tieng Jessica , Mehravar Majid , Rong Bowen , Lan Fei , Roediger Ben , Ma Cheng-Jie , Yuan Bi-Feng , Rasko John E. J. , Larance Mark , Ye Dan , Fuks François , Wong Justin J.-L. 
Published: May 2024

AbstractRNA modifications are essential for the establishment of cellular identity. Although increasing evidence indicates that RNA modifications regulate the innate immune response, their role in monocyte-to-macrophage differentiation and polarisation is unclear. While m6A has been widely studied, other RNA modifications, including 5 hmC, remain poorly characterised. We profiled m6A and 5 hmC epitranscriptomes, transcriptomes, translatomes and proteomes of monocytes and macrophages at rest and pro- and anti-inflammatory states. Transcriptome-wide mapping of m6A and 5 hmC reveals enrichment of m6A and/or 5 hmC on specific categories of transcripts essential for macrophage differentiation. Our analyses indicate that m6A and 5 hmC modifications are present in transcripts with critical functions in pro- and anti-inflammatory macrophages. Notably, we also discover the co-occurrence of m6A and 5 hmC on alternatively-spliced isoforms and/or opposing ends of the untranslated regions (UTR) of mRNAs with key roles in macrophage biology. In specific examples, RNA 5 hmC controls the decay of transcripts independently of m6A. This study provides (i) a comprehensive dataset to interrogate the role of RNA modifications in a plastic system (ii) a resource for exploring different layers of gene expression regulation in the context of human monocyte-to-macrophage differentiation and polarisation, (iii) new insights into RNA modifications as central regulators of effector cells in innate immunity.
CD200R activation on naïve T cells by B cells induces suppressive activity of T cells via IL-24
Authors: Chu Kuan-Hua , Chiang Bor-Luen 
Published: May 2024

AbstractCD200 is an anti-inflammatory protein that facilitates signal transduction through its receptor, CD200R, in cells, resulting in immune response suppression. This includes reducing M1-like macrophages, enhancing M2-like macrophages, inhibiting NK cell cytotoxicity, and downregulating CTL responses. Activation of CD200R has been found to modulate dendritic cells, leading to the induction or enhancement of Treg cells expressing Foxp3. However, the precise mechanisms behind this process are still unclear. Our previous study demonstrated that B cells in Peyer’s patches can induce Treg cells, so-called Treg-of-B (P) cells, through STAT6 phosphorylation. This study aimed to investigate the role of CD200 in Treg-of-B (P) cell generation. To clarify the mechanisms, we used wild-type, STAT6 deficient, and IL-24 deficient T cells to generate Treg-of-B (P) cells, and antagonist antibodies (anti-CD200 and anti-IL-20RB), an agonist anti-CD200R antibody, CD39 inhibitors (ARL67156 and POM-1), a STAT6 inhibitor (AS1517499), and soluble IL-20RB were also applied. Our findings revealed that Peyer’s patch B cells expressed CD200 to activate the CD200R on T cells and initiate the process of Treg-of-B (P) cells generation. CD200 and CD200R interaction triggers the phosphorylation of STAT6, which regulated the expression of CD200R, CD39, and IL-24 in T cells. CD39 regulated the expression of IL-24, which sustained the expression of CD223 and IL-10 and maintained the cell viability. In summary, the generation of Treg-of-B (P) cells by Peyer’s patch B cells was through the CD200R-STAT6-CD39-IL-24 axis pathway.
Circulating tumour cells predict recurrences and survival in head and neck squamous cell carcinoma patients
Authors: Zhang Xi , Weeramange Chameera Ekanayake , Hughes Brett G. M. , Vasani Sarju , Liu Zhen Yu , Warkiani Majid , Hartel Gunter , Ladwa Rahul , Thiery Jean Paul , Kenny Liz , Breik Omar , Punyadeera Chamindie 
Published: May 2024

AbstractPatients with head and neck squamous cell carcinoma (HNSCC) are at a high risk of developing recurrence and secondary cancers. This study evaluates the prognostic and surveillance utilities of circulating tumour cells (CTCs) in HNSCC. A total of 154 HNSCC patients were recruited and followed up for 4.5 years. Blood samples were collected at baseline and follow-up. CTCs were isolated using a spiral microfluid device. Recurrence and death due to cancer were assessed during the follow-up period. In patients with HNSCC, the presence of CTCs at baseline was a predictor of recurrence (OR = 8.40, p < 0.0001) and death (OR= ∞, p < 0.0001). Patients with CTCs at baseline had poor survival outcomes (p < 0.0001). Additionally, our study found that patients with CTCs in a follow-up appointment were 2.5 times more likely to experience recurrence or death from HNSCC (p < 0.05) prior to their next clinical visit. Our study highlights the prognostic and monitoring utilities of CTCs’ in HNSCC patients. Early identification of CTCs facilitates precise risk assessment, guiding treatment choices and ultimately enhancing patient outcomes.
Effects of beam power and feed rate in the process of cutting fresh wood with a CO2 laser on water contact angle on the cut surface
Authors: Maciak Adam , Aniszewska Monika , Zychowicz Witold , Zowczak Włodzimierz , Danielewski Hubert 
Published: May 2024

AbstractThe paper describes a study on the effects of beam power and feed rate in the process of cutting fresh wood with a CO2 laser on water contact angle on the cut surface. The study involved several broadleaved tree species (oak, birch, alder, plum, and apple tree) and one coniferous species (pine). Samples were cut with a Trumpf TLC1005 laser equipped with a TruFlow 6000 CO2 resonator at a wavelength of 10.6 μm at three power output settings (1 kW, 2 kW, and 3 kW) and one feed rate (0.4 m∙min− 1). Contact angle was measured by pipetting a drop of distilled water on the wood surface and recording the process with a camera. Subsequently, images of the drop were analyzed over one minute at 10 s intervals to determine changes in contact angle for each of the cases examined. It was not possible to measure the contact angle on saw-cut samples as the water was immediately absorbed, while water drops placed on laser-cut samples remained on the surface for over 60 s, with the contact angle decreasing over time for the examined species from an average of 90° to 40°. The higher beam power settings (2 or 3 kW) were found to be preferable for the hardwood species (oak, birch, alder, and apple tree). In turn, in the case of the softwood species (pine), the laser power output did not matter, as both at the low (1 kW) and high (3 kW) settings the drop did not spread over the surface quickly. Finally, the optimum beam power for plum tree wood was found to be 1 kW.
Heterogeneity of glycaemic phenotypes in type 1 diabetes
Authors: Fagherazzi Guy , Aguayo Gloria A. , Zhang Lu , Hanaire Hélène , Picard Sylvie , Sablone Laura , Vergès Bruno , Hamamouche Naïma , Detournay Bruno , Joubert Michael , Delemer Brigitte , Guilhem Isabelle , Vambergue Anne , Gourdy Pierre , Hadjadj Samy , Velayoudom Fritz-Line , Guerci Bruno , Larger Etienne , Jeandidier Nathalie , Gautier Jean-François , Renard Eric , Potier Louis , Benhamou Pierre-Yves , Sola Agnès , Bordier Lyse , Bismuth Elise , Prévost Gaëtan , Kessler Laurence , Cosson Emmanuel , Riveline Jean-Pierre ,   on behalf of the SFDT1 study team
Published: May 2024

Abstract
Aims/hypothesis
Our study aims to uncover glycaemic phenotype heterogeneity in type 1 diabetes.

Methods
In the Study of the French-speaking Society of Type 1 Diabetes (SFDT1), we characterised glycaemic heterogeneity thanks to a set of complementary metrics: HbA1c, time in range (TIR), time below range (TBR), CV, Gold score and glycaemia risk index (GRI). Applying the Discriminative Dimensionality Reduction with Trees (DDRTree) algorithm, we created a phenotypic tree, i.e. a 2D visual mapping. We also carried out a clustering analysis for comparison.

Results
We included 618 participants with type 1 diabetes (52.9% men, mean age 40.6 years [SD 14.1]). Our phenotypic tree identified seven glycaemic phenotypes. The 2D phenotypic tree comprised a main branch in the proximal region and glycaemic phenotypes in the distal areas. Dimension 1, the horizontal dimension, was positively associated with GRI (coefficient [95% CI]) (0.54 [0.52, 0.57]), HbA1c (0.39 [0.35, 0.42]), CV (0.24 [0.19, 0.28]) and TBR (0.11 [0.06, 0.15]), and negatively with TIR (−0.52 [−0.54, −0.49]). The vertical dimension was positively associated with TBR (0.41 [0.38, 0.44]), CV (0.40 [0.37, 0.43]), TIR (0.16 [0.12, 0.20]), Gold score (0.10 [0.06, 0.15]) and GRI (0.06 [0.02, 0.11]), and negatively with HbA1c (−0.21 [−0.25, −0.17]). Notably, socioeconomic factors, cardiovascular risk indicators, retinopathy and treatment strategy were significant determinants of glycaemic phenotype diversity. The phenotypic tree enabled more granularity than traditional clustering in revealing clinically relevant subgroups of people with type 1 diabetes.

Conclusions/interpretation
Our study advances the current understanding of the complex glycaemic profile in people with type 1 diabetes and suggests that strategies based on isolated glycaemic metrics might not capture the complexity of the glycaemic phenotypes in real life. Relying on these phenotypes could improve patient stratification in type 1 diabetes care and personalise disease management.

Graphical Abstract
Key points of statistics for clinically oriented research
Authors: Laky Brenda ,   AGA Research Committee
Published: May 2024

AbstractProcessing of research data is a crucial point in every scientific study. The basis of each statistical test is a clear research question and hypothesis. Then the scientist must consider which type of data are to be collected (nominal, ordinal, continuous). It is recommended that study-specific spreadsheets are developed before data collection, which consider the type of data being collected, how the data are to be analyzed, and which software will be used. Then, once the data have been gathered, tests for normality should be applied before proceeding with the specific statistical tests. This article provides a brief overview of common statistical tests based on fictional examples.
Testing for Granger causality in heterogeneous panels with cross-sectional dependence
Authors: Nazlioglu Saban , Karul Cagin 
Published: May 2024

AbstractThis paper proposes a panel Granger causality approach for heterogeneous panels with cross-sectional dependence. We define a panel VAR model with unobserved common factors and apply the PANIC procedure to obtain the de-factored data. We then estimate the lag augmented (LA)-VAR model for each cross section and construct the panel statistics based on the meta-analytic approach that combines the p-values of the individual statistics. The Monte Carlo simulations indicate that the combination tests show good size and power properties and appear suitable for the panels where cross sections may have different unit root or co-integration properties. We finally re-investigate Granger causality between export and economic growth in OECD countries. The results shed light on the importance of accounting for cross-sectional dependence within a factor model framework in determining direction of Granger causality for country-specific analysis. The results further reveal that export and economic growth do not cause each other in the majority of the European Union countries.
DESI-MSI-guided exploration of metabolic-phenotypic relationships reveals a correlation between PI 38:3 and proliferating cells in clear cell renal cell carcinoma via single-section co-registration of multimodal imaging
Authors: Zickuhr Greice M. , Um In Hwa , Laird Alexander , Harrison David J. , Dickson Alison L. 
Published: May 2024

AbstractA workflow has been evaluated that utilizes a single tissue section to obtain spatially co-registered, molecular, and phenotypical information suitable for AI-enabled image analysis. Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) was used to obtain molecular information followed by conventional histological staining and immunolabelling. The impact of varying DESI-MSI conditions (e.g., heated transfer line (HTL) temperature, scan rate, acquisition time) on the detection of small molecules and lipids as well as on tissue integrity crucial for integration into typical clinical pathology workflows was assessed in human kidney. Increasing the heated transfer line temperature from 150 to 450 °C resulted in a 1.8-fold enhancement in lipid signal at a scan rate of 10 scans/s, while preserving histological features. Moreover, increasing the acquisition speed to 30 scans/s yielded superior lipid signal when compared to 10 scans/s at 150 °C. Tissue morphology and protein epitopes remained intact allowing full histological assessment and further multiplex phenotyping by immunofluorescence (mIF) and immunohistochemistry (mIHC) of the same section. The successful integration of the workflow incorporating DESI-MSI, H&E, and immunolabelling on a single tissue section revealed an accumulation of ascorbic acid in regions of focal chronic inflammatory cell infiltrate within non-cancerous kidney tissue. Additionally, a strong positive correlation between PI 38:3 and proliferating cells was observed in clear cell renal cell carcinoma (ccRCC) showing the utility of this approach in uncovering molecular associations in disease pathology.
Graphical Abstract
Tandem gene duplication selected by activation of horizontally transferred gene in bacteria
Authors: Zhang Fangqing , Shi Xinxin , Xu Jian , Yuan Wen , Li Zhichao 
Published: May 2024

Abstract
Horizontal gene transfer occurs frequently in bacteria, but the mechanism driving activation and optimization of the expression of horizontally transferred genes (HTGs) in new recipient strains is not clear. Our previous study found that spontaneous tandem DNA duplication resulted in rapid activation of HTGs. Here, we took advantage of this finding to develop a novel technique for tandem gene duplication, named tandem gene duplication selected by activation of horizontally transferred gene in bacteria (TDAH), in which tandem duplication was selected by the activation of horizontally transferred selectable marker gene. TDAH construction does not contain any reported functional elements based on homologous or site-specific recombination and DNA amplification. TDAH only contains an essential selectable marker for copy number selection and 9-bp-microhomology border sequences for precise illegitimate recombination. One transformation and 3 days were enough to produce a high-copy strain, so its procedure is simple and fast. Without subsequent knockout of the endogenous recombination system, TDAH could also generate the relatively stable high-copy tandem duplication for plasmid-carried and genome-integrated DNA. TDAH also showed an excellent capacity for increase gene expression and worked well in different industrial bacteria. We also applied TDAH to select the optimal high copy number of ribA for vitamin B2 production in E. coli; the yield was improved by 3.5 times and remained stable even after 12 subcultures. TDAH is a useful tool for recombinant protein production and expression optimization of biosynthetic pathways.

Key points
• We develop a novel and efficient technique (TDAH) for tandem gene duplication in bacterium. TDAH is based on the mechanism of HTG rapid activation. TDAH does not contain any reported functional elements based on homologous recombination and DNA amplification. TDAH only contains an essential selectable marker for copy number selection, so its construction and procedure are very simple and fast.
• TDAH is the first reported selected and stable tandem-gene-duplication technique in which the selected high-copy plasmid-carried and genome-integrated DNA could remain stable without the subsequent knockout of recombination system.
• TDAH showed an excellent capacity for regulating gene expression and worked well in different industrial bacteria, indicating it is a useful tool for recombinant protein production and expression optimization of biosynthetic pathways.
• TDAH was applied to select the optimal high copy number of ribA for vitamin B2 production in E. coli; the yield was improved by 3.5-fold and remained stable even after 12 subcultures.
Flow-cytometry Assessment of DNA content and Immunophenotyping of Immune-cells in Lymph-node-specimens as a Potential Diagnostic Signature of Aggressiveness in B-Non-Hodgkin Lymphomas
Authors: Azoulay David , Tapuchi Tal , Ronen Ohad , Akria Luiza , Cohen Hector I. , Surio Celia , Chepa Svetlana Rodin , Eshel Elizabeth , Zarfati Moran , Stemer Galia , Horowitz Netanel A. 
Published: May 2024

AbstractFlow-cytometry (FC) is a powerful tool that can assist in lymphoma diagnosis in lymph node (LN) specimens. Although lymphoma diagnosis and classification are mainly based on tumor cell characteristics, surrounding cells are less employed in this process. We retrospectively investigated alterations in the ploidy status, proliferative cell fraction (PF) and the percentages of surrounding immune cells in 62 consecutive LN specimens with B-Cell Non-Hodgkin Lymphoma (B-NHL) that were submitted for FC evaluation between 2019–2022. Compared with indolent B-NHLs, aggressive B-NHLs show increased DNA aneuploidy and PF, increased monocytes, immature-granulocytes, mature granulocytes, CD8+ T-cells, Double-Negative-T-cells and Double-Positive-T-cells, and decreased total CD45+ cells, total lymphocytes, CD4+ T-cells and CD4/CD8 ratio. Receiver operating characteristic analysis determined PF > 6.8% and immature-granulocytes > 0.9% as optimal cutoffs with highest specificity and sensitivity in differentiating aggressive and indolent B-NHLs. These findings further strength the diagnostic value of DNA content analysis by FC and suggest the utilization of tumor surrounding immune cells in NHL diagnosis and classification.