gebhart/patrepeval huggingface dataset:
A Liquid Chromatography-Mass Spectrometry-based Approach to Characterize the Substrate Specificity of Mammalian Heparanase (2014)

Extracellular heparanase activity releases growth factors and angiogenic factors from heparan sulfate (HS) storage sites and alters the integrity of the extracellular matrix. These activities lead to a loss of normal cell matrix adherent junctions and correlate with invasive cellular phenotypes. Elevated expression of heparanase is associated with several human cancers and with vascular remodeling. Heparanase cleaves only a limited fraction of glucuronidic linkages in HS. There have been few investigations of the functional consequences of heparanase activity, largely due to the heterogeneity and complexity of HS. Here, we report a liquid chromatography-mass spectrometry (LC-MS)-based approach to profile the terminal structures created by heparanase digestion and reconstruct the heparanase cleavage sites from the products. Using this method, we demonstrate that heparanase cleaves at the non-reducing side of highly sulfated HS domains, exposing cryptic growth factor binding sites. This cleavage pattern is observed in HS from several tissue sources, regardless of overall sulfation degree, indicating a common recognition pattern. We further demonstrate that heparanase cleavage of HS chains leads to increased ability to support FGF2-dependent cell proliferation. These results suggest a new mechanism to explain how heparanase might potentiate the uncontrolled cell proliferation associated with cancer through its ability to activate nascent growth factor-promoting domains within HS.
Leishmania major possesses a unique HemG-type protoporphyrinogen IX oxidase (2014)

Leishmania major was proposed to either utilize haem from its host or partially synthesize the tetrapyrrole from host provided precursors. However, only indirect evidence was available for this partial late haem biosynthetic pathway. Here, we demonstrate that the LMJF_06_1280 gene of L. major encodes a HemG-type PPO (protoporphyrinogen IX oxidase) catalysing the oxidation of protoporphyrinogen IX to protoporphyrin IX. Interestingly, trypanosomatids are currently the only known eukaryotes possessing HemG-type enzymes. The LMJF_06_1280 gene forms a potential transcriptional unit with LMJF_06_1270 encoding CPO (coproporphyrinogen III oxidase) and with LMJF_06_1290 for a cytochrome b5. In vivo function of the L. major hemG gene was shown by the functional complementation of the Escherichia coli ΔhemG strain LG285. Restored haem formation in E. coli was observed using HPLC analyses. Purified recombinant L. major HemG revealed PPO activity in vitro using different ubiquinones and triphenyltetrazolium as electron acceptors. FMN was identified as the L. major HemG cofactor. Active site residues were found to be essential for HemG catalysis. These data in combination with the solved crystal structures of L. major CPO and the physiological proof of a ferrochelatase activity provide clear-cut evidence for a partial haem biosynthetic pathway in L. major.
The STEM Interpreting Teaching Model for Undergraduate English Interpreting Majors (2016)

The intensification of the world economic integration and the expansion of the domestic exchanges with foreign countries skyrocket the demand of interpreters in China, which is unlikely to be fully satisfied at present just because the training of interpreters is mainly included under the MTI programs. For this reason, it is of great significance to explore the feasibility of training interpreters at undergraduate level. Based on the review of the current domestic demands of interpreters in China, this paper sets out to introduce the “Stage-featured, Teacher and Expert-operated Multidimensional (STEM, for short) Interpreting Teaching Model" that was developed during the research and experiment in the undergraduate interpreting program in Sias International College, with the hope of providing experience for other similar study in this field.
Living at the Frontiers of Life: Extremophiles in Chile and Their Potential for Bioremediation (2018)

Extremophiles are organisms capable of adjust, survive or thrive in hostile habitats that were previously thought to be adverse or lethal for life. Chile gathers a wide range of extreme environments: salars, geothermal springs, and geysers located at Altiplano and Atacama Desert, salars and cold mountains in Central Chile, and ice fields, cold lakes and fjords, and geothermal sites in Patagonia and Antarctica. The aims of this review are to describe extremophiles that inhabit main extreme biotopes in Chile, and their molecular and physiological capabilities that may be advantageous for bioremediation processes. After briefly describing the main ecological niches of extremophiles along Chilean territory, this review is focused on the microbial diversity and composition of these biotopes microbiomes. Extremophiles have been isolated in diverse zones in Chile that possess extreme conditions such as Altiplano, Atacama Desert, Central Chile, Patagonia, and Antarctica. Interesting extremophiles from Chile with potential biotechnological applications include thermophiles (e.g., <i>Methanofollis tationis</i> from Tatio Geyser), acidophiles (e.g., <i>Acidithiobacillus ferrooxidans, Leptospirillum ferriphilum</i> from Atacama Desert and Central Chile copper ores), halophiles (e.g., <i>Shewanella</i> sp. Asc-3 from Altiplano, <i>Streptomyces</i> sp. HKF-8 from Patagonia), alkaliphiles (<i>Exiguobacterium</i> sp. SH31 from Altiplano), xerotolerant bacteria (<i>S. atacamensis</i> from Atacama Desert), UV- and Gamma-resistant bacteria (<i>Deinococcus peraridilitoris</i> from Atacama Desert) and psychrophiles (e.g., <i>Pseudomonas putida</i> ATH-43 from Antarctica). The molecular and physiological properties of diverse extremophiles from Chile and their application in bioremediation or waste treatments are further discussed. Interestingly, the remarkable adaptative capabilities of extremophiles convert them into an attractive source of catalysts for bioremediation and industrial processes.
Recombinant Rabies Virus Overexpressing OX40-Ligand Enhances Humoral Immune Responses by Increasing T Follicular Helper Cells and Germinal Center B Cells (2020)

Rabies, caused by the rabies virus (RABV), remains a serious threat to public health in most countries. Development of a single-dose and efficacious rabies vaccine is the most important method to restrict rabies virus transmission. Costimulatory factor OX40-ligand (OX40L) plays a crucial role in the T cell-dependent humoral immune responses through T-B cell interaction. In this work, a recombinant RABV overexpressing mouse OX40L (LBNSE-OX40L) was constructed, and its effects on immunogenicity were evaluated in a mouse model. LBNSE-OX40L-immunized mice generated a larger number of T follicular helper (Tfh) cells, germinal center (GC) B cells, and plasma cells (PCs) than the parent virus LBNSE-immunized mice. Furthermore, LBNSE-OX40L induced significantly higher levels of virus-neutralizing antibodies (VNA) as early as seven days post immunization (dpi), which lasted for eight weeks, resulting in better protection for mice than LBNSE (a live-attenuated rabies vaccine strain). Taken together, our data in this study suggest that OX40L can be a novel and potential adjuvant to improve the induction of protective antibody responses post RABV immunization by triggering T cell-dependent humoral immune responses, and that LBNSE-OX40L can be developed as an efficacious and nonpathogenic vaccine for animals.
The design of ambisonics decoders for irregular speaker array conforming to subjective perception (2014)

An analysis of previously derived Ambisonics decoders shows that the mid-high frequency performance of these decoders has poor agreement with subjective perception, since the optimized decoder coefficients could not well meet the objectives developed by the energy vector, and the polar pattern of speaker feeds is suboptimal. In this paper, new objectives are added to fitness function for the optimal speaker response, and the sum of weighted rations genetic algorithm is applied to search a good set of decoder coefficients to meet all the objectives. The decoder of an example application of ITU-4.0 speaker array exhibits a significant improvement in localization performance at the rear of the listeners. In addition, the binaural evaluation demonstrates that the performance of the proposed decoder better conform to the subjective perception.
Three dimensional data manipulation and representation for accurate and realistic data visualization (2002)

A realistic method of visualizing random depth maps of the human back is described. A realistic surface was created that can be used in the assessment of subjects with scoliosis. Methods are presented to remove the effects of noise and to create a realistic solid surface that can be viewed and manipulated in three dimensions. Automated techniques of triangulation, resampling, noise reduction and various screen representations are discussed. This work determines the best techniques for representing a back surface, with the criteria being: realism of presentation; and accuracy.
Gingiva-Derived Mesenchymal Stem Cell-Mediated Therapeutic Approach for Bone Tissue Regeneration (2011)

Up to now, the gingiva-derived mesenchymal stem cells (GMSCs) as a new postnatal stem cells have been isolated and characterized with multipotential differentiation capabilities in vitro. However, the in vivo efficacy of utilizing the GMSCs in bone regeneration remains obscure. First of all, we identified canonical MSCs in human gingival tissue, which possessed homogenous immunophenotype (CD34(-)CD45(-)CD29(+)CD105(+)CD90(+) STRO-1(+)) and had tri-lineage differentiation potential (osteoblasts, adipocytes, and chondrocytes). Next, we examined the efficacy of utilizing these stem cells in bone tissue regeneration; the enhanced green fluorescent protein-labeled GMSCs seeded on type I collagen gel were implanted into the mandibular defects as well as the critical-sized calvarial defects in Sprague Dawley rats. We first demonstrated that GMSCs could repair the mandibular wounds and calvarial defects at 2 months in rats postsurgical reconstruction. Histomorphological analysis and image of fluorescence microscope certified that new bone in the defect areas was derived from the transplanted GMSCs. Immunohistochemical analysis of green fluorescent protein, human collagen I, and osteopontin further confirmed our conclusion. The above results implied that mesenchymal stem cells derived from gingival tissue could be a novel source for stem cell-based therapy in bone reconstruction in clinical applications.
The Selective Values of Alleles in a Molecular Network Model Are Context Dependent (2004)

Classical quantitative genetics has applied linear modeling to the problem of mapping genotypic to phenotypic variation. Much of this theory was developed prior to the availability of molecular biology. The current understanding of the mechanisms of gene expression indicates the importance of nonlinear effects resulting from gene interactions. We provide a bridge between genetics and gene network theories by relating key concepts from quantitative genetics to the parameters, variables, and performance functions of genetic networks. We illustrate this methodology by simulating the genetic switch controlling galactose metabolism in yeast and its response to selection for a population of individuals. Results indicate that genes have heterogeneous contributions to phenotypes and that additive and nonadditive effects are context dependent. Early cycles of selection suggest strong additive effects attributed to some genes. Later cycles suggest the presence of strong context-dependent nonadditive effects that are conditional on the outcomes of earlier selection cycles. A single favorable allele cannot be consistently identified for most loci. These results highlight the complications that can arise with the presence of nonlinear effects associated with genes acting in networks when selection is conducted on a population of individuals segregating for the genes contributing to the network.
Abstract PO-065: SIWA318H, an advanced glycation end product (AGE) targeting antibody, is efficacious in a humanized mouse xenograft model for pancreatic cancer (2021)

Abstract SIWA318H is a novel monoclonal antibody that selectively targets a biomarker (an advanced glycation end product) found on the surface of cells exhibiting a combination of: (a) an abnormally high level of aerobic glycolysis, a process known to be associated with initiation and progression of cancer as well as metastasis; and (b) oxidative stress. Cells with this biomarker are often dysfunctional and associated with aging, cancer, and infectious diseases. In this study, we evaluated the antitumor activity of SIWA318H in a humanized xenograft model for pancreatic cancer. SIWA318H was found to react to pancreatic cancer cells (PSN1) and cancer associated fibroblasts (CAF08) using immunofluorescent staining. SIWA318H also showed strong reactivity with tumor xenografts derived from patients with pancreatic cancer as demonstrated by immunohistochemistry. Humanized CD34+ NSG mice were injected subcutaneously with PSN1 pancreatic cancer tumor cells. Ten days later, mice were randomized and enrolled in one of the following groups (n=16/group): 1) IgG1 isotype control (20mg/kg, BIWx1 followed by 10 mg/kg, BIWx2); 2) high dose SIWA318H (20mg/kg, BIWx1 followed by 10 mg/kg, BIWx2); and 3) low dose SIWA318H (10 mg/kg, BIWx1 followed by 5mg/kg, BIWx2). Tumors in mice treated with SIWA318H grew significantly slower than those in mice treated with isotype control antibody (p&amp;lt;0.001). After 3 weeks of treatment with the high dose or the low dose of SIWA318H, the tumor growth was suppressed by 68.8% and 61.5%, respectively, when compared to the isotype antibody control (ANOVA p&amp;lt;0.002). Moreover, a significant increase in complete remission (CR) rate was observed in mice receiving high (60%, p&amp;lt;0.05) or low dose (77.8%, p&amp;lt;0.02) of SIWA318H treatment compared with the control mice (6.7%). No significant antibody treatment related weight loss in mice was observed. These results provide compelling evidence that SIWA318H is a promising novel therapeutic for pancreatic cancer. Additional studies to better understand the mechanism of action of this novel immunotherapy agent are underway. Citation Format: Ashley Jensen, Gabriela R. Rossi, Ruben Muñoz, Kimberly Brothers, Lewis Gruber, Misty Gruber, Haiyong Han. SIWA318H, an advanced glycation end product (AGE) targeting antibody, is efficacious in a humanized mouse xenograft model for pancreatic cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2021 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2021;81(22 Suppl):Abstract nr PO-065.
Correction: Microstructures of Poly(alkyl a-chloro-acrylate) Determined by I3C and 1H NMR (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleCorrection: Microstructures of Poly(alkyl a-chloro-acrylate) Determined by I3C and 1H NMRC Pathak, M Patni, G Babu, and James CheinCite this: Macromolecules 1986, 19, 10, 2672Publication Date (Print):October 1, 1986Publication History Published online29 December 2003Published inissue 1 October 1986https://pubs.acs.org/doi/10.1021/ma00164a601https://doi.org/10.1021/ma00164a601research-articleACS PublicationsRequest reuse permissionsArticle Views30Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Synthesis and Properties of Vermiculite-Reinforced Polyurethane Nanocomposites (2011)

Natural vermiculite was modified by cation exchange with long-chain quaternary alkylammonium salts and then dispersed in polyether-based polyols with different structures and ethylene oxide/propylene oxide ratios. The dispersions were evaluated by X-ray scattering and rheology. In all polyol dispersions tested, polyols were intercalated into the vermiculite interlayers. Also, significant shear thinning behavior was observed. A large interlayer spacing of ∼90 Å was achieved in one polyol suitable for polyurethane elastomer synthesis. In polyurethane made with this polyol, clay platelets were extensively intercalated or exfoliated. The composites showed a >270% increase in tensile modulus, >60% increase in tensile strength, and a 30% reduction in N(2) permeability with a loading of 5.3 wt % clay in polyurethane. Differential scanning calorimetry and dynamic mechanical analysis revealed that the nanoclay interacts with the polyurethane hard segments.
Medicine Tablet Authentication Using "Fingerprints" of Ink-Jet Printed Characters (2019)

Counterfeit drugs have been a serious problem causing damage to people's health over the world. Numerous anti-counterfeiting methods based on tagging have been proposed; however, they suffer from three major issues: (1) tagging is applicable only to packages, not tablets directly; (2) end-users, i.e., patients, cannot inspect the tags; (3) tagging incurs extra costs for manufacturers. This paper describes a new method that we propose for authenticating individual medicine tablets as-is by matching images of printed characters. The printed characters on individual tablets of the same medicine seem the same to human eyes, but each is characterized by tiny unique differences. The contributions of this paper are: (a) to reveal the uniqueness of the characters printed by an actual pharmaceutical-use machine and (b) to propose a practical system to identify individual tablets using image matching. Our system is useful for any patients who want to authenticate a medicine tablet at hand: it only requires a picture with a smartphone camera. Our system is also useful for medicine manufacturers, because the database can be constructed using the existing manufacturing process without incurring additional cost. Our image matching algorithm recognizes very detailed features of the images and is accurate and fast even for a large-scale database. In conducted experiments, 1,000 sample tablets were captured using the same optical setup as an actual medicine manufacturing machine. Obtained results showed that 100% accuracy in individual tablet authentication was achieved.
Synthesis and Characterization of (Aminotroponiminato)titanium(IV) Dialkyl Complexes:  Control of Reactivity by Ligand Design (1999)

The synthesis and structural characterization of titanium(IV) dialkyl complexes ligated by a new tetradentate C2-symmetric aminotroponiminate ligand are reported. Included are rare examples of thermally stable titanium diethyl and di-n-butyl complexes and an η2-imine complex.
supplemental figure legend from Combined Antitumor Therapy with Metronomic Topotecan and Hypoxia-Activated Prodrug, Evofosfamide, in Neuroblastoma and Rhabdomyosarcoma Preclinical Models (2023)

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Hearing and motorcycle helmets (1983)

This study evaluates the attenuation of the sound when using a motorcycle helmet, and measures the aerodynamically generated noise inside a helmet when driving. The possibility of detecting certain signals was judged when masking and attenuation effects were taken into consideration. It concludes that the risk of hearing damage is very limited, acoustic warning signals are audible only at low speed, the helmets don't put the wearers at a disadvantage compared with non-helmet situations, and further development of the aerodynamic design of motorcycle helmets is considered essential.
A video assisted approach for structural health monitoring of highway bridges under normal traffic (2006)

Structural condition assessment of highway bridges is traditionally performed by visual inspections or nondestructive evaluation techniques, which are either slow, unreliable or detects only local flaws. Instrumentation of bridges with accelerometers and other sensors, however, can provide real-time data useful for monitoring the global structural conditions of the bridges due to ambient and forced excitations. This paper reports a video-assisted approach for structural health monitoring of highway bridges, with results from field tests and subsequent offline parameter identification. The field tests were performed on a short-span instrumented bridge. Videos of vehicles passing by were captured, synchronized with data recordings from the accelerometers. For short-span highway bridges, vibration is predominantly due to traffic excitation. A stochastic model of traffic excitation on bridges is developed assuming that vehicles traversing a bridge (modeled as an elastic beam) form a sequence of Poisson process moving loads and that the contact force of a vehicle on the bridge deck can be converted to equivalent dynamic loads at the nodes of the beam elements. Basic information of vehicle types, arrival times and speeds are extracted from video images to develop a physics-based simulation model of the traffic excitation. This modeling approach aims at circumventing a difficulty in the system identification of bridge structural parameters. Current practice of system identification of bridge parameters is often based on the measured response (or system output) only, and knowledge of the input (traffic excitation) is either unknown or assumed, making it difficult to obtain an accurate assessment of the state of the bridge structures. Our model reveals that traffic excitation on bridges is spatially correlated, an important feature that is usually incorrectly ignored in most output-only methods. A recursive Bayesian filtering is formulated to monitor the evolution of the state of the bridge. The effectiveness and viability of this video-assisted approach are demonstrated by the field results.
Nonlinear optical phenomena in fullerene-doped liquid crystal films and fibers (1995)

In this presentation, we shall describe the mechanisms and dynamics of two newly observed phenomena in fullerene C<SUB>60</SUB> doped liquid crystal, namely, holographic grating formation in thin film structures and nonlinear pulsed propagation and optical limiting in isotropic liquid crystal cored fibers and fiber arrays. The unusually large photorefractive like nonlinearity of C<SUB>60</SUB> doped nematic film allows us to write permanent holographic gratings which can be electronically modulated. In fullerene-doped liquid crystalline cored fibers, we have observed greatly enhanced nonlinear optical transmission and propagation effects caused by nonlinear scattering, defocusing, increasing absorption and possibly other nonlinear processes. The resulting lower threshold and reduced interaction-length requirement enable one to design practical liquid crystal fiber arrays that could function as imaging faceplate as well as sensor protection devices.