bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring Wedge and Bulk Viscous Dissipation in Droplets Moving on Inclined Surfaces by Means of Direct Numerical Simulations
Authors: Bodziony Francisco , Li Xiaomei , Yin Mariana , Berger Rüdiger , Butt Hans-Jürgen , Marschall Holger 
Published: August 2023

Abstract
The motion of droplets on inclined surfaces is a ubiquitous phenomenon, yet the underlying dissipative mechanisms remain poorly understood. Employing direct numerical simulations, we investigate water and water-glycerol (85% wt.) droplets (∼25 μL) moving on smooth surfaces, with contact angles of around 90º, at varying inclinations. Our focus is on elucidating the role of wedge and bulk viscous dissipation in the droplets. We observe that, for fast-moving droplets, both mechanisms contribute comparably, while the wedge dissipation dominates in slow-moving cases. Comparisons with existing estimates reveal the inadequacy of previous predictions in capturing the contributions of wedge and bulk dissipation forces in fast-moving droplets. Furthermore, we demonstrate that droplets with identical sliding velocities can exhibit disparate viscous dissipation forces due to variations in internal fluid dynamics.
A Study of Cubic B-Spline Based Three Numerical Algorithms for Solving Nonlinear Reaction-diffusion Equations
Authors: Mittal R. C. , Rohila Rajni 
Published: August 2023

Abstract
In this work, three numerical methods using B-splines have been proposed and numerical solutions of nonlinear time dependent reaction diffusion equations have been obtained. We call the methods as Method I, Method II and Method III. Method I is based on modified cubic B-spline differential quadrature method while Method II and III are based on the colloca-tion of cubic B-spline functions. In Method II, we discretize time derivative by Crank Nicolson scheme and use B-spline functions for spatial derivatives while in Method III , we use modified B-spline functions for spatial variables and derivatives so that it gives a system of ordinary differential equations which is solved by SSP-RK43 method, a method that needs low storage space resulting in less accumulation of computational errors. If we compare three schemes in terms of complexity of implementation, Method I is more straightforward than II and III that evaluates the solution directly rather than computation of time dependent coefficients of B-splines. Considering all aspects involved in the three methods, we conclude that differential quadrature method is better than other two collocation based methods in the numerical experiments carried out.
Microglia/macrophages are ultrastructurally altered by their proximity to spinal cord injury in adult female mice
Authors: St-Pierre Marie-Kim , Ibáñez Fernando González , Kroner Antje , Tremblay Marie-Ève 
Published: August 2023

Abstract
Traumatic spinal cord injury can cause immediate physical damage to the spinal cord and result in severe neurological deficits. The primary, mechanical tissue damage triggers a variety of secondary damage mechanisms at the injury site which significantly contribute to a larger lesion size and increased functional damage. Inflammatory mechanisms which directly involve both microglia (MG) and monocyte-derived macrophages (MDM) play important roles in the post-injury processes including inflammation and debris clearing. In the current study, we investigated changes in the structure and function of MG/MDM in the injured spinal cord of adult female mice, seven days after a thoracic contusion SCI. With the use of chip mapping scanning electron microscopy, which allows to image large samples at the nanoscale, we performed an ultrastructural comparison of MG/MDM located near the lesion versus adjacent regions to provide novel insights into the mechanisms at play post-injury. We found that MG/MDM located near the lesion had more mitochondria overall, including mitochondria with and without morphological alterations, and had a higher proportion of altered mitochondria. MG/MDM near the lesion also showed an increased number of phagosomes, including phagosomes containing myelin and partially-digested materials. MG/MDM near the injury interacted differently with the spinal cord parenchyma, as shown by their reduced number of direct contacts with synaptic elements, axon terminals and dendritic spines. In this study, we characterized the ultrastructural changes of MG/MDM in response to spinal cord tissue damage in mice, uncovering changes in phagocytic activity, mitochondrial ultrastructure, and inter-cellular interactions within the spinal cord parenchyma.
Subject-specific one-dimensional fluid dynamics model of chronic thromboembolic pulmonary hypertension
Authors: Kachabi Amirreza , Colebank Mitchel J. , Chesler Naomi 
Published: August 2023

Abstract
Chronic thromboembolic pulmonary hypertension (CTEPH) develops due to the accumulation of blood clots in the lung vasculature that obstruct flow and increase pressure. The mechanobiological factors that drive progression of CTEPH are not understood, in part because mechanical and hemodynamic changes in the pulmonary vasculature due to CTEPH are not easily measurable. Using previously published hemodynamic measurements and imaging from a large animal model of CTEPH, we developed a subject-specific one-dimensional (1D) computational fluid dynamic (CFD) models to investigate the impact of CTEPH on pulmonary artery stiffening, time averaged wall shear stress (TAWSS), and oscillatory shear index (OSI). Our results demonstrate that CTEPH increases pulmonary artery wall stiffness and decreases TAWSS in extralobar (main, right and left pulmonary arteries) and intralobar vessels. Moreover, CTEPH increases the percentage of the intralobar arterial network with both low TAWSS and high OSI. This subject-specific experimental-computational framework shows potential as a predictor of the impact of CTEPH on pulmonary arterial hemodynamics and pulmonary vascular mechanics. By leveraging advanced modeling techniques and calibrated model parameters, we predict spatial distributions of flow and pressure, from which we can compute potential physiomarkers of disease progression, including the combination of low mean wall shear stress with high oscillation. Ultimately, this approach can lead to more spatially targeted interventions that address the needs of individual CTEPH patients.
Analysis of Antimicrobial resistance gene in Staphylococcus aureus by Gene Networking using Cytoscape
Authors: E Santhosh M , Selvam Prasanna Kumar , Vasudevan Karthick 
Published: August 2023

Abstract
Antibiotic resistance One of the major global issues of this century is AMR among microorganisms, which is still a challenge for mankind. It's crucial to understand the genes responsible for AMR and how those genes create resistance in order to solve this issue effectively. Staphylococcus aureus, which has AMR genes imparting resistance against numerous antibiotics, was the main subject of our investigation. We performed a phylogenetic study to examine the gene network's evolutionary history. To increase our understanding, a gene interaction network with 46 functional partners was built from String Database and Cytoscape and examined. Clustering analysis revealed one cluster (C1) that was linked to a multidrug resistance mechanism. According to Cluego's enrichment analysis, 20 genes are significantly involved in biological processes, as are 14 genes in cellular components and 16 genes in molecular functions. RpoB, RpoC, FusA, RplI, and RpsL had the most interactions by Cytohubba when the degree and closeness of the network were studied, according to the analysis of the gene interaction network. Understanding the molecular basis of AMR requires analysis of the enriched pathways and Gene Ontologies (GO). The suggested study may also help researchers find new ways to battle the multi-drug resistance of Staphylococcus aureus.
Unraveling the Radiative Properties of the Interstellar Medium: The First 3D Map of the Interstellar Dust Temperature
Authors: Zelko Ioana , Finkbeiner Douglas , Lee Albert , Green Gregory 
Published: August 2023

Abstract
Despite making up only 1% of the mass of the interstellar medium, dust has an outsize impact on the evolution of galaxies. Dust absorbs and scatters a substantial fraction of the ultraviolet and optical light produced in a galaxy, re-radiating it in the infrared. It influences the formation and evolution of stars and planetary systems. It also serves as an astrophysical probe, providing information about magnetic field structure and the radiation field, but only if we understand its properties in 3D. Recent years have brought rapid progress in mapping dust density in 3D [1, 2, 4, 5, 45], but attempts to derive its temperature and other optical properties have been few. Here, we present the first comprehensive large-scale, three-dimensional map of dust temperature in the Milky Way. We show that this methodology has enough precision to discern temperature differences with 3σ significance along the line of sight. Star formation regions are clearly observable in the map. This technique and the resulting 3D dust temperature map open up new areas of research into models of galactic magnetic field in 3D, polarization maps, cosmological foreground analysis, cosmic ray propagation for dark matter searches, correlations with star forming regions and other data catalogs.
Anatomical, physical and mechanical characterization of the wood of three eucalyptus species: E. camaldulensis Dehn, E. cladocalyx and E. gomphocephala
Authors: TAZROUT Mansour , BENOTMANE Benamar 
Published: August 2023

Abstract

Eucalyptus represents the second largest tree plantation in Algeria after Aleppo pine. However, the valorisation of its wood as lumber and wood products remains unsatisfactory. This study investigates the anatomical, physical and mechanical properties of three eucalyptus wood species (E. camaldulensis Dehn, E. cladocalyx, and E. gomphocephala), which are 35 years old. The obtained results showed that the wood of E. gomphocephala and E. cladocalyxare classified in the high-density category, while the wood of E. camaldulensis is in the medium-density category. The E. cladocalyxwood exhibits strong shrinkage in the volumetric, radial, and tangential directions. Whereas the wood of E. camaldulensis and E. gomphocephalapossesses strong volumetric shrinkage, and mean radial and tangential shrinkages. The wood of E. cladocalyx has lower average values for fiber length, fiber width, lumen diameter, and cell wall thickness, while E. camaldulensis wood exhibits higher average values for both fiber length and lumen diameter, and E. gomphocephala wood has greater average values for both fiber width and cell wall thickness. Moreover, the E. cladocalyxwood possesses the greatest bending strength and hardness, and the lowest modulus of elasticity in flexure and compression strength. Whereas, E. camaldulensis wood has the highest compression strength, and E. gomphocephala wood has the highest modulus of elasticity in bending. In addition, the bending strength, compressive strength, and hardness correlate positively with the wood density at 12% moisture content for three eucalyptus species. There are significant differences (P < 0.05) between the average values of the measured parameters for wood of three eucalyptus species. The results of this study can be used in the field of paper industry, timber structures, and industry of furniture and wood.
A rapid point-of-care population-scale dipstick assay to identify and differentiate SARS-CoV-2 variants in COVID-19-positive patients
Authors: Paul Deepjyoti , Verma Jyoti , Kumar Shakti , Talukdar Daizee , Jana Pradipta , Narendrakumar Lekshmi , Kumar Roshan , Tanwar Subhash , Gosain Mudita , Karmakar Sonali Porey , Pareek Madhu , Mani Shailendra , Chaudhuri Susmita , Kshetrapal Pallavi , Wadhwa Nitya , Bhatnagar Shinjini , Garg Pramod Kumar , Das Bhabatosh 
Published: August 2023

Abstract

Delta and Omicron variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are remarkably contagious, and have been recognized as variants of concern (VOC). The acquisition of spontaneous substitutions or insertion–deletion mutations (indels) in the spike protein-encoding gene substantially increases the binding affinity of the receptor binding domain (RBD)-hACE2 complex and upsurges the transmission of both variants. In this study, we analyzed thousands of genome sequences representing 30 different SARS-CoV-2 variants and identified the Delta and Omicron variants specific nucleic acid signatures in the spike gene. Based on the variant-specific nucleic acid sequences, we synthesized different oligos and optimized a multiplex PCR (mPCR) assay that can identify and differentiate the Delta and Omicron variants of SARS-CoV-2. We further extended our work on this mPCR and translated it into a dipstick assay by adding a tag linker sequence to the 5’ end of the forward primer and biotin to the 3’ end of the oligos. Streptavidin-coated latex beads and the dipstick imprinted with a probe for the tag linker sequence in the test strips were used for the detection assay. Our dipstick-based assay, developed as a rapid point-of-care test for identifying and differentiating SARS-CoV-2 variants has the potential to be used in low-resource settings and scaled up to the population level.
Structure-Informed Protein Language Models are Robust Predictors for Variant Effects
Authors: Sun Yuanfei , Shen Yang 
Published: August 2023

Abstract

Predicting protein variant effects through machine learning is often challenged by the scarcity of experimentally measured effect labels. Recently, protein language models (pLMs) emerge as zero-shot predictors without the need of effect labels, by modeling the evolutionary distribution of functional protein sequences. However, biological contexts important to variant effects are implicitly modeled and effectively marginalized. By assessing the sequence awareness and the structure awareness of pLMs, we find that their improvements often correlate with better variant effect prediction but their tradeoff can present a barrier as observed in over-finetuning to specific family sequences. We introduce a framework of structure-informed pLMs (SI-pLMs) to inject protein structural contexts purposely and controllably, by extending masked sequence denoising in conventional pLMs to cross-modality denoising. Our SI-pLMs are applicable to revising any sequence-only pLMs through model architecture and training objectives. They do not require structure data as model inputs for variant effect prediction and only use structures as context provider and model regularizer during training. Numerical results over deep mutagenesis scanning benchmarks show that our SI-pLMs, despite relatively compact sizes, are robustly top performers against competing methods including other pLMs, regardless of the target protein family's evolutionary information content or the tendency to overfitting / over-finetuning. Learned distributions in structural contexts could enhance sequence distributions in predicting variant effects. Ablation studies reveal major contributing factors and analyses of sequence embeddings provide further insights. The data and scripts are available at https://github.com/Stephen2526/Structure-informed_PLM.git
Agroforestry Contributions to Ecosystem Services in Southeast Asia: a Systematic Review
Authors: Ahmadzai Mujib Rahman , Ismail Mohd Hasmadi , Zaki Pakhriazad Hassan , Bawon Paiman , Magiman Mohd. Maulana 
Published: August 2023

Abstract

This systematic review examines the current state of knowledge and research trends in agroforestry in the South Asian region. The study analyzed 150 scholarly publications on agroforestry techniques and their ecological, financial, and community benefits. The results show that the proportion of agroforestry-associated papers focusing on the South Asian region is rapidly increasing, but it remains tiny in comparison to the literature on the topic worldwide. The most frequently studied agroforestry systems are schemes focused on simultaneous implementation, such as planted agriculture combined with tree administration and species/natural management sanctuaries combined with genetic diversity/gene pool processes. In comparison to the West, where silvopastoral technologies are widely used, South Asia has paid less attention to agrosilvopastoral and silvopastoral systems. Ultimately, the study identified and highlighted the types, volumes, and characteristics of agroforestry and ecological facilities research in South Asia. The findings suggest that agroforestry is a crucial strategy for improving the ecological, financial, and community benefits of a region's social-ecological systems.
Health-related quality of life and factors associated with depression among people with oculocutaneous albinism in Jinja , Uganda
Authors: Gaylord INENA WA INENA 
Published: August 2023

Abstract
Background
Depression is among the common psychiatric disorders with high prevalence in the general population across the world. Studies carried out on specific populations have shown that this prevalence is higher in vulnerable populations including people living with albinism. Despite the fact that several aspects linked with it have been found among people with oculocuteneous albinism in the Busoga region, data have remained unclear locally. Limited information is available regarding prevalence of depression, its associated factors and health related quality of life in the study area.The main objective of the present study was to determine the health related quality of life and factors associated with depression among people with oculocutaneous albinism in Jinja,Uanda.
Methods
A cross-sectional design was used to capture data from a study sample size of 384 adults
living with oculocutaneous albinism who were involved in completion of the screening tests for depression Hopkins Symptom Checklist-25(HSCL-25).The summation of scores for depression were averaged and the probable depression determined for each participant using a cut-off of 1.75. Logistic regression analyses were used to examine associations between depression and associated factors. Dermatology life quality index (DLQI) was used to assess the health related quality of life.The DLQI was calculated by the summation of the score of each question resulting in a maximum of 30 and a minimumof 0.The higher was the score,the more quality of life was impaired.
Results
The analyses revealed that the prevalence of depression among people with oculocutaneous albinism in jinja city stands at 65.4 %. The risk of depression was significantly associated with age (AOR = 1.059, 95% CI = 1.020–1.100, P = 0.003), history of diabetes mellitus (AOR = 12.030, 95% CI = 1.117–12.961, P = 0.040) and taking chronically medication (AOR = 6.583, 95% CI = 1.618–26.782, P = 0.008).Family support (AOR = 0.505, 95% CI = 0.286–0.892, P = 0.019) and marital status (AOR = 0.505, 95% CI = 0.286–0.892, P = 0.019) were significantly protective factors.The mean Dermatology Life Quality Index scores was 14.55.Oculocutaneous albinism had no effect on the quality of life of only 5.7% of the participants. On the remaining 95% affected participants, 48.7% were largely affected.
Conclusions
These findings show that the estimated prevalence of depression among people with oculocutaneous albinism in the study area is high and worrying and oculocutaneous albinism highly impacts negatively the quality of life of people with oculocutaneous albinism. Strategies targeted at early interventions and ultimately depression prevention need urgent attention in order to reduce risk factors of the disease and improve the health related quality of life of People with oculocutaneous albinism in the study area.
SVision-pro: comparative sequence-to-image representation and instance segmentation for de novo and somatic structural variant discovery
Authors: Ye Kai , Wang Songbo , Lin Jiadong , Jia Peng , Xu Tun , Meng DeYu 
Published: August 2023

Abstract
Long-read based de novo and somatic structural variant (SV) discovery remains challenging, necessitating genomic comparison between samples. Here, SVision-pro visually represents genome-to-genome-level sequencing differences and comparatively discoveries SV between genomes by a neural-network-based instance segmentation framework without prerequisite of SV inference models. SVision-pro outperforms state-of-the-art approaches, particularly in resolving complex SV (CSV), with low Mendelian error rates and high sensitivity of low-frequency SVs. Moreover, SVision-pro successfully discoveries 26 high-quality de novo SVs in six family datasets and retrieves eight somatic CSVs in normal-tumor-paired samples.
Mineral and crystal chemical study of pseudo-C2/mnon-metamict chevkinite-(Ce): An investigation into the intracrystalline distribution of LREE, HREE, and octahedral cations in samples from the Azores and Pakistan
Authors: Carbonin Susanna , Ridolfi Filippo , Renzulli Alberto , Belluso Elena , Nodari Luca , Liziero Federica , Capella Silvana 
Published: August 2023

AbstractThe cation distribution among the A, B, C, and D sites of 13 crystals of chevkinite-(Ce) by X-ray single-crystal diffraction and electron microprobe analyses is reported in this article. The general formula of chevkinite-(Ce) is A4BC2D2O8(Si2O7)2, where A = REE, Ca, Th, Sr; B = Fe, Mn, Mg; C = Fe, Ti, Nb, Zr, Mg, Al; and D = Ti. Ten crystals come from quartz-bearing syenite samples of Agua de Pau (Azores Islands), and three are euhedral chevkinite crystals of a quartz-bearing pegmatite from Tangir Valley, northwestern Pakistan. The real space group for these samples is P21/a, but the average structure in space group C2/m was used for structural refinement and further interpretation. Cation distribution was determined by minimization of the function fΣNσ2 that represents the sum of the squared numbers of standard deviation by which each expected quantity differs from the calculated one. Both X-ray diffraction and electron microprobe data were considered in minimization. Our results show that the two non-equivalent A sites are occupied dominantly by REE and Ca, distributed mainly as a function of their ionic size. Lanthanum enters only the 10-coordinated A2 site, whereas heavier and smaller REE enter only the 8-coordinated A1. Furthermore, comparison between bond valence sum and formal charge revealed highly stretched bonds for the A1 polyhedron, suggesting that bond lengths are too long for HREE. These findings can help better characterize the well-known ability of chevkinite to fractionate LREE from HREE. The Azores chevkinite is particularly enriched in Nb relative to its host rock. Our results show that Ti occupancy in the D sites can be as low as ca. 50% due to the presence of significant amounts of Nb, besides Fe and Zr. For two Azores crystals showing patchy zoning, a complex history of late-stage crystallization is inferred, with multiple events of Ca and REE enrichments. One of these crystals showed the best structure refinement, implying that late-magmatic to deuteric alteration stages did not affect its crystallinity. The CaO content of Azores chevkinites practically spans the entire chevkinite field in the chevkinite/perrierite CaO vs. FeO discrimination diagram. In addition, we identified possible structural stability limits that can be linked to the occupancy of the B site at high CaO, and of the C sites at high-FeO contents. The Pakistan chevkinites were also analyzed by Mössbauer spectroscopy. Only one Fe3+ component was identified, which occupies the C sites. Among the two ferrous doublets, the component with the highest isomeric shift value is Fe2+ entering the most distorted crystallographic site B, while the other, representative of a less distorted octahedral site, corresponds to Fe2+ entering the D sites.