gebhart/patrepeval huggingface dataset:
Simplification of unstructured tetrahedral meshes by point sampling (2005)

Tetrahedral meshes are widely used in scientific computing for representing three-dimensional scalar, vector, and tensor fields. The size and complexity of some of these meshes can limit the performance of many visualization algorithms, making it hard to achieve interactive visualization. The use of simplified models is one way to enable the real-time exploration of these datasets. In this paper, we propose a novel technique for simplifying large unstructured meshes. Most current techniques simplify the geometry of the mesh using edge collapses. Our technique simplifies an underlying scalar field directly by segmenting the original scalar field into two pieces: the boundary of the original domain and the interior samples of the scalar field. We then simplify each piece separately, taking into account proper error bounds. Finally, we combine the simplified domain boundary and scalar field into a complete, simplified mesh that can be visualized with standard unstructured-data visualization tools. Our technique is much faster than edge-collapse-based simplification approaches. Furthermore, it is particularly suitable for aggressive simplification. Experiments show that isosurfaces and volume renderings of meshes produced by our technique have few noticeable visual artifacts.
Evaluating the Effect of Using Micronized Barite on the Properties of Water-Based Drilling Fluids (2019)

Solids sag and formation damage are serious problems encountered while drilling with barite-weighted drilling fluids. The objective of this study is to investigate the effect of reducing barite particle size on rheological properties, fluid stability, and filter cake removal. Barite samples with different particle sizes were prepared using sieve analysis and ball milling technique. Micronized barite (8 μm) showed a moderate stability with zeta potential measurements for a pH range greater than 8. Solubility tests showed good enhancement in barite removal as the particle size was reduced, with a difference of around 11 g/L between the largest size (75-106 μm) and the micronized size of barite. HPHT filtration test results confirmed the solubility results with 5 wt.% enhancement in filter cake removal efficiency as barite particle size was reduced to micronized size. [Received: December 4, 2017; Accepted: December 17, 2018]
Enhanced repair of meniscal hoop structure injuries using an aligned electrospun nanofibrous scaffold combined with a mesenchymal stem cell-derived tissue engineered construct (2018)

Damage to the meniscal hoop structure results in loss of biomechanical function, which potentially leads to the extrusion of the meniscus from the weight bearing area. However, there have been no established, effective treatments for such injuries. The purpose of this study was to investigate the applicability of cell-seeded nanofibrous scaffolds to repair the damaged meniscal hoop structure along with the prevention of subsequent cartilage degeneration using a rabbit model. Meniscal radial defects (5 mm width) in the medial meniscus were treated by wrapping and suturing with either an aligned electrospun nanofibrous scaffold alone or a scaffold combined with a tissue engineered construct (TEC) derived from synovial mesenchymal stem cells (MSCs), with the scaffold fiber direction matching that of the meniscal circumferential fibers. The MSC-based TEC-combined nanofibrous scaffolds contributed significantly to the prevention of meniscal extrusion and exerted a chondroprotective effect, compared with either scaffold alone or the untreated control groups. Also, meniscal defects treated with such TEC-combined nanofibrous scaffolds were consistently repaired with a fibrocartilaginous tissue. In this study, we have demonstrated the feasibility of a combined TEC-nanofibrous scaffold to repair the meniscal hoop structure, and prevent the progression to cartilage degeneration, as a potential tissue engineering method.
SYSTEMIC ADMINISTRATION OF SIRNA TARGETING P53 PROTECTS KIDNEYS FROM ISCHEMIA-REPERFUSION INJURY IN EXPERIMENTAL RAT KIDNEY TRANSPLANTATION MODEL (2009)

You have accessJournal of Urology1 Apr 2009SYSTEMIC ADMINISTRATION OF SIRNA TARGETING P53 PROTECTS KIDNEYS FROM ISCHEMIA-REPERFUSION INJURY IN EXPERIMENTAL RAT KIDNEY TRANSPLANTATION MODEL Ryoichi Imamura, Yoshitaka Isaka, Ruben M Sandoval, Yoichi Kakuta, Toyofumi Abe, Masayoshi Okumi, Naotsugu Ichimaru, Shingo Takada, Kiyomi Matsumiya, Bruce A Molitoris, Akihiko Okuyama, and Shiro Takahara Ryoichi ImamuraRyoichi Imamura More articles by this author , Yoshitaka IsakaYoshitaka Isaka More articles by this author , Ruben M SandovalRuben M Sandoval More articles by this author , Yoichi KakutaYoichi Kakuta More articles by this author , Toyofumi AbeToyofumi Abe More articles by this author , Masayoshi OkumiMasayoshi Okumi More articles by this author , Naotsugu IchimaruNaotsugu Ichimaru More articles by this author , Shingo TakadaShingo Takada More articles by this author , Kiyomi MatsumiyaKiyomi Matsumiya More articles by this author , Bruce A MolitorisBruce A Molitoris More articles by this author , Akihiko OkuyamaAkihiko Okuyama More articles by this author , and Shiro TakaharaShiro Takahara More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(09)62075-9AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "SYSTEMIC ADMINISTRATION OF SIRNA TARGETING P53 PROTECTS KIDNEYS FROM ISCHEMIA-REPERFUSION INJURY IN EXPERIMENTAL RAT KIDNEY TRANSPLANTATION MODEL." The Journal of Urology, 181(4S), p. 743 © 2009 by American Urological AssociationFiguresReferencesRelatedDetails Volume 181Issue 4SApril 2009Page: 743 Advertisement Copyright & Permissions© 2009 by American Urological AssociationMetrics Author Information Ryoichi Imamura More articles by this author Yoshitaka Isaka More articles by this author Ruben M Sandoval More articles by this author Yoichi Kakuta More articles by this author Toyofumi Abe More articles by this author Masayoshi Okumi More articles by this author Naotsugu Ichimaru More articles by this author Shingo Takada More articles by this author Kiyomi Matsumiya More articles by this author Bruce A Molitoris More articles by this author Akihiko Okuyama More articles by this author Shiro Takahara More articles by this author Expand All Advertisement PDF downloadLoading ...
Architectural and protocol structure for composite DVB-RCS/IEEE 802.16 platforms (2006)

In this paper a new hybrid network solution relying on synergy between a IEEE 802.16-based networks (commonly known as a WiMAX networks) and digital video broadcasting-return channel satellite (DVB-RCS) networks is presented. The novelty of the architecture proposed is that of employing DVB-RCS domains as a backhaul for content delivery to IEEE 802.16 domains. It goes on to analyse key implementation issues concerning IEEE 802.16/DVB-RCS hybrid platforms, providing innovative and efficient solutions to problems like functional network entities definition and their connectivity, protocol stack specifications, QoS control and mobility management over heterogeneous routes.
Laser Based Angle-Resolved Photoemission, the Sudden Approximation, and Quasiparticle-Like Spectral Peaks inBi2Sr2CaCu2O8+δ (2006)

A new low photon energy regime of angle-resolved photoemission spectroscopy is accessed with lasers and used to study the high T(C) superconductor Bi2Sr2CaCu2O(8+delta). The low energy increases bulk sensitivity, reduces background, and improves resolution. With this we observe spectral peaks which are sharp on the scale of their binding energy--the clearest evidence yet for quasiparticles in the normal state. Crucial aspects of the data such as the dispersion, superconducting gaps, and the bosonic coupling kink are found to be robust to a possible breakdown of the sudden approximation.
Segmental Dynamics and Density Fluctuations in Polymer Networks during Chemical Vitrification (1999)

Molecular dynamics of network-forming reactive polymers were examined as a function of the advancement of chemical reaction as the materials structure undergoes a transition from liquid to amorphous solid. The accompanying changes in the segmental relaxation time (α process) are a signature of the materials state (within the liquid to amorphous solid spectrum of physical properties). Both broad-band dielectric relaxation spectroscopy (DRS), which probes the α process via dipolar reorientational mobility, and dynamic light scattering (DLS), which probes the α process via density fluctuations, were used to monitor the system under reaction conditions in the reaction bath (to our knowledge, the first study of its kind). An excellent agreement was found between DRS and DLS for the α process characteristic parameters: relaxation time and KWW, the stretched exponential parameter (characterizing the relaxation breadth). That dipole dynamics exhibit the same α relaxation characteristics as time dependent density fluctuations, suggests that the rotational motion observed in a DRS measurement is directly controlled by the behavior of the density domains. It was concluded that the broadening of the α process is due to a general phenomenon: the micro/nanoscale heterogeneous nature of glass formers. The results of the study are discussed in terms of cooperative and local relaxation modes in the growing network.
Metabolic Surgery in the Treatment Algorithm for Type 2 Diabetes: A Joint Statement by International Diabetes Organizations (2016)

Although additional studies are needed to further demonstrate long-term benefits, there is sufficient clinical and mechanistic evidence to support inclusion of metabolic surgery among antidiabetes interventions for people with T2D and obesity. To date, the DSS-II guidelines have been formally endorsed by 45 worldwide medical and scientific societies. Health care regulators should introduce appropriate reimbursement policies.
A Pilot Study of Rituximab in Immune-Mediated Inner Ear Disease (2010)

Immune-mediated inner ear disease (IMED) is a cause of rapidly progressive auditory dysfunction. Patients are often responsive to high-dose corticosteroids and the disease is believed to be mediated by an antibody to inner ear proteins. To date, no therapies have proven effective as corticosteroid-sparing agents. Rituximab is a monoclonal antibody that depletes B cells, resulting in a reduction in autoantibody production. For that reason, rituximab was evaluated in a small pilot study in patients with IMED to see if there was a signal suggesting benefit. In all, 5/7 patients met the primary endpoint of an improvement in pure tone average (500-3000 Hz) by 10 dB in at least one ear, or an improvement in word identification score by at least 12% at 24 weeks, both relative to screening precorticosteroid values after 1 course of treatment. No significant adverse events were reported. The results of this study suggest further evaluation of rituximab as a treatment for IMED is indicated.
DISC1 regulates N-methyl-D-aspartate receptor dynamics: abnormalities induced by a Disc1 mutation modelling a translocation linked to major mental illness (2018)

The neuromodulatory gene DISC1 is disrupted by a t(1;11) translocation that is highly penetrant for schizophrenia and affective disorders, but how this translocation affects DISC1 function is incompletely understood. N-methyl-D-aspartate receptors (NMDAR) play a central role in synaptic plasticity and cognition, and are implicated in the pathophysiology of schizophrenia through genetic and functional studies. We show that the NMDAR subunit GluN2B complexes with DISC1-associated trafficking factor TRAK1, while DISC1 interacts with the GluN1 subunit and regulates dendritic NMDAR motility in cultured mouse neurons. Moreover, in the first mutant mouse that models DISC1 disruption by the translocation, the pool of NMDAR transport vesicles and surface/synaptic NMDAR expression are increased. Since NMDAR cell surface/synaptic expression is tightly regulated to ensure correct function, these changes in the mutant mouse are likely to affect NMDAR signalling and synaptic plasticity. Consistent with these observations, RNASeq analysis of the translocation carrier-derived human neurons indicates abnormalities of excitatory synapses and vesicle dynamics. RNASeq analysis of the human neurons also identifies many differentially expressed genes previously highlighted as putative schizophrenia and/or depression risk factors through large-scale genome-wide association and copy number variant studies, indicating that the translocation triggers common disease pathways that are shared with unrelated psychiatric patients. Altogether, our findings suggest that translocation-induced disease mechanisms are likely to be relevant to mental illness in general, and that such disease mechanisms include altered NMDAR dynamics and excitatory synapse function. This could contribute to the cognitive disorders displayed by translocation carriers.
Tactile Whole-Field Imaging Sensor on Photoelasticity (2007)

The paper describes a whole-field imaging sensor developed on the principles of photoelasticity. The sensor produces colored fringe patterns when load is applied on the contacting surface. These fringes can be analyzed using conventional photoelastic techniques, however, as the loading in the present case is not conventional some new strategies need to be devised to analyze the load imprint. The loading is unconventional in the sense that low modulus photoelastic material is deformed under vertical load in the direction of light travel to induce the photoelastic effect. The paper discusses the efficacy of both RGB calibration and phase shifting techniques in sensing applications. The characteristics of fringe patterns obtained under vertical and shear loads have been studied and the results obtained under these conditions are discussed with their limitations specifically when this is applied for sensing applications. Finally a case study has been conducted to analyze a foot image and conclusions drawn from this have been presented.
Analysis of Blood Stem Cell Activity and Cystatin Gene Expression in a Mouse Model Presenting a Chromosomal Deletion Encompassing Csta and Stfa2l1 (2009)

The cystatin protein superfamily is characterized by the presence of conserved sequences that display cysteine protease inhibitory activity (e.g., towards cathepsins). Type 1 and 2 cystatins are encoded by 25 genes of which 23 are grouped in 2 clusters localized on mouse chromosomes 16 and 2. The expression and essential roles of most of these genes in mouse development and hematopoiesis remain poorly characterized. In this study, we describe a set of quantitative real-time PCR assays and a global expression profile of cystatin genes in normal mouse tissues. Benefiting from our collection of DelES embryonic stem cell clones harboring large chromosomal deletions (to be reported elsewhere), we selected a clone in which a 95-kb region of chromosome 16 is missing (Del(16qB3Delta/+)). In this particular clone, 2 cystatin genes, namely Csta and Stfa2l1 are absent along with 2 other genes (Fam162a, Ccdc58) and associated intergenic regions. From this line, we established a new homozygous mutant mouse model (Del(16qB3Delta/16qB3Delta)) to assess the in vivo biological functions of the 2 deleted cystatins. Stfa2l1 gene expression is high in wild-type fetal liver, bone marrow, and spleen, while Csta is ubiquitously expressed. Homozygous Del(16qB3Delta/16qB3Delta) animals are phenotypically normal, fertile, and not overtly susceptible to spontaneous or irradiation-induced tumor formation. The hematopoietic stem and progenitor cell activity in these mutant mice are also normal. Interestingly, quantitative real-time PCR expression profiling reveals a marked increase in the expression levels of Stfa2l1/Csta phylogenetically-related genes (Stfa1, Stfa2, and Stfa3) in Del(16qB3Delta/16qB3Delta) hematopoietic tissues, suggesting that these candidate genes might be contributing to compensatory mechanisms. Overall, this study presents an optimized approach to globally monitor cystatin gene expression as well as a new mouse model deficient in Stfa2l1/Csta genes, expanding the available tools to dissect cystatin roles under normal and pathological conditions.
DNA Methylation in Health, Disease, and Cancer (2007)

The spatial arrangement and three-dimensional structure of DNA in the nucleus is controlled through the interdigitation of DNA binding proteins such as histones and their modifiers, the Polycomb-Trithorax proteins, and the DNA methyltransferase enzymes. DNA methylation forms the foundation of chromatin and is crucial to epigenetic gene regulation in mammals. Disease pathogenesis mediated through infectious agents, inflammation, aging, or genetic damage often involves changes in gene expression. In particular, cellular transformation coincides with multiple changes in chromatin architecture, many of which appear to affect genome integrity and gene expression. Infectious agents, such as viruses directly affect genome structure and induce methylation of particular sequences to suppress host immune responses. Hyperproliferative tissues such as those in the gastrointestinal tract and colon have been shown to gradually acquire aberrant promoter hypermethylation. Here we review recent findings on altered DNA methylation in human disease, with particular focus on cancer and the increasingly large number of genes subject to tumor-specific promoter hypermethylation and the possible role of aberrant methylation in tumor development.
Submarine Gel Electrophoresis Purification of a Small Molecule:  99.9998 Fluorescently Pure IMI2 (1998)

HPLC and related techniques failed to raise the fluorescence purity of a BODIPY−imidazole dye (IMI2) above 99.5%, based on assessment of dye purity by capillary electrophoresis with laser-induced fluorescence detection (CE-LIF). This difficulty was overcome by employing submarine gel electrophoresis, which raised the fluorescence purity level to about 99.9998%. This estimate of final dye purity was made by using immobilized metal affinity chromatography to selectively remove the dye from a sample that was then analyzed by CE-LIF as a 5000× more concentrated sample than the original. The amount of dye purified on a 87- × 67- × 10-mm (l × w × h) gel in a 40-min run was at the 0.5-mg level. The dye was recovered by soaking the sliced-out electrophoretic band in methanol. We are now in a position to employ this dye for labeling of trace phosphomonoester analytes without being hampered by dye impurities, by further developing methodology that we reported previously (Wang, P.; Giese, R. W. Anal. Chem. 1993, 65, 3518−3520). More generally, we conclude that submarine gel electrophoresis can be a convenient and useful separation technique for purifying small molecules.
Mollamides B and C, Cyclic Hexapeptides from the Indonesian Tunicate Didemnum molle (2008)

Two new cyclic hexapeptides, mollamides B (1) and C (2), were isolated from the Indonesian tunicate Didemnum molle along with the known peptide keenamide A (3). The structures were established using 1D and 2D NMR experiments. The relative configuration of mollamide B at the thiazoline moiety was determined using molecular modeling coupled with NMR-derived restraints. Their absolute configuration was determined using Marfey's method. The new peptides have been evaluated for their antimicrobial, antimalarial, anticancer, anti-HIV-1, anti-Mtb, and anti-inflammatory activities. Keenamide A and mollamide B show cytotoxicity against several cancer cell lines.
Systematic optimization of a lead‐structure identities for a selective short peptide agonist for the human orphan receptor BRS‐3 (2002)

The orphan receptor, human bombesin receptor subtype 3 (BRS-3) was assigned to the G-protein coupled bombesin receptor family because of its high sequence homology with the neuromedin B receptor (NMB-R) and gastrin-releasing peptide receptor (GRP-R). Since its pharmacology is stiIl unknown, new highly potent and selective tool-substances are needed, that may be able to elucidate its possible role in obesity and cancer. We have performed structure activity relationship studies on the high affinity peptide agonists [D-Phe6,beta-Ala11,Phe13,Nle14]Bn(6-14) and [D-Phe6,Phe13]Bn(6-13)propylamide, using their ability to mobilize intracellular calcium in BRS-3 transfected CHOGa-16 cells combined with receptor binding studies. It was demonstrated that for [D-Phe,beta-Ala11,Phe13,Nle14]Bn(6-14) the side chains of the residues Trp8 and Phe13, and to a smaller extent beta-Ala11, are the important amino acid side chains for receptor activation and binding, however for [D-Phe6,Phe13]Bn(6-13) propylamide His12 seems to be more important than Phe13. C-and N-terminal deletions and amino acid substitutions allowed further understanding. It was demonstrated that substitution of His 12 by Tyr leads to a high selectivity towards GRP-R. Using the acquired information, a small tetrapeptide library was designed with compounds presenting Trp and Phe at varying stereochemistry and distances, which led to the discovery of the lead-structure H-D-Phe-Gln-D-Trp-Phe-NH2. Systematic SAR revealed the important structural features of this peptide, C-terminal optimization resulted in the highly active and selective BRS-3 agonist H-D-Phe-Gln-D-Trp-1-(2-phenylethyl)amide. In summary, the size of the peptide was reduced from 8 or 9 amino acids to a tripeptide for BRS-3.
Modelling of multiple, semantically-coupled flow-graphs (2008)

Various monitoring applications specifically in the process industry but not restricted to it need explorable models representing multiple flows and their properties. Most (plant) models share two characteristics: They mix structural and behavioral aspects and they are tailored for specific applications - either with respect to human interpretation or for easy automated treatment. The under-lying physics are however often rather shrouded. Thus the implicit assumptions and prerequisites in many cases are not obvious, making it difficult to add new software layers or to re-engineer. This paper discusses systems dealing with multiple, balanceable flows, which are semantically (i.e. usually physically) coupled, independently from their application domain. Specifically the various flow characteristics and their interaction are contrasted. By providing check-lists for these properties design decisions and their consequences are made explicit. The second part of this paper derives and discusses the graph representation in a general way. Starting off from several graphs (one per balanceable flow) finally one single hierarchically structured graph is derived. Additionally some aspects for implementations are discussed briefly.
Tender Coconut Classification using Decision Tree and Deep Learning Technique (2023)

A number of industry sectors such as Food & nutraceuticals, Pharma, Irrigation, Transport and Automobile use coconut and its parts for varied products. As different sectors make use of different type and parts of coconut, an automated separation of coconut Would aid in faster processing. Thus the major issue faced by these sectors is the automated sorting of coconut into different categories such as Non-Tender Coconut, Tender Whole coconut, Tender coconut cut With flesh and Without flesh. In this Work We have trained and tested a Decision Tree and DenseNet model to automatically classify coconut images into various categories. For Decision Tree 93% of accuracy Was obtained While the advanced Deep learning model, DenseNet, gave 100% accuracy. This showed that the Deep Learning models such as DenseNet perform better as compared to conventional machine learning algorithms such as Decision Tree.