gebhart/patrepeval huggingface dataset:
Mass spectrometric kinetic analysis of human tyrosylprotein sulfotransferase-1 and -2 (2008)

Protein tyrosine O-sulfation, a widespread post-translational modification, is mediated by two Golgi enzymes, tyrosylprotein sulfotransferase-1 and -2. These enzymes catalyze the transfer of sulfate from the universal sulfate donor 3'-phosphoadenosine-5'-phosphosulfate (PAPS) to the hydroxyl group of tyrosine residues to form tyrosine O-sulfate ester and PAP. More than 60 proteins have been identified to be tyrosine sulfated including several G protein-coupled receptors, such as CC-chemokine receptor 8 (CCR8) that is implicated in allergic inflammation, asthma, and atherogenesis. However, the kinetic properties of purified tyrosylprotein sulfotransferase (TPST)-1 and -2 have not been previously reported. Moreover, currently there is no available quantitative TPST assay that can directly monitor individual sulfation of a series of tyrosine residues, which is present in most known substrates. We chose an MS-approach to address this limitation. In this study, a liquid chromatography electrospray ionisation mass spectrometry (LC/ESI-MS)-based TPST assay was developed to determine the kinetic parameters of individual TPSTs and a mixture of both isozymes using CCR8 peptides as substrates that have three tyrosine residues in series. Our method can differentiate between mono- and disulfated products, and our results show that the K(m,app) for the monosulfated substrate was 5-fold less than the nonsulfated substrate. The development of this method is the initial step in the investigation of kinetic parameters of the sequential tyrosine sulfation of chemokine receptors by TPSTs and in determining its catalytic mechanism.
Moving Diabetes Management From Clinic to Community: Development of a Prototype Based on Automated Voice Messaging (1997)

The purpose of this study is twofold. First, it provides a review of the literature supporting the development of a new service to help patients with diabetes and their providers manage their care. This service, automated voice messaging (AVM) with nurse follow-up, allows for systematic and intensive patient monitoring and diabetes education as well as a means of focusing clinical resources where they are most needed. Second, it provides a description of a prototype AVM-based diabetes management service that has been developed as part of two ongoing, randomized, controlled trials to test the efficacy of AVM care for patients with Type 2 diabetes. Preliminary findings from implementing this service in two large public healthcare systems suggest that AVM-supported care is feasible, desirable by clinicians and patients with diabetes, and may identify serious health problems that otherwise would go unnoted through standard means of clinic-based patient care.
Tetrahedral mesh generation and optimization based on centroidal Voronoi tessellations (2003)

Abstract The centroidal Voronoi tessellation based Delaunay triangulation (CVDT) provides an optimal distribution of generating points with respect to a given density function and accordingly generates a high‐quality mesh. In this paper, we discuss algorithms for the construction of the constrained CVDT from an initial Delaunay tetrahedral mesh of a three‐dimensional domain. By establishing an appropriate relationship between the density function and the specified sizing field and applying the Lloyd's iteration, the constrained CVDT mesh is obtained as a natural global optimization of the initial mesh. Simple local operations such as edges/faces flippings are also used to further improve the CVDT mesh. Several complex meshing examples and their element quality statistics are presented to demonstrate the effectiveness and efficiency of the proposed mesh generation and optimization method. Copyright © 2003 John Wiley & Sons, Ltd.
Survivin expression and its correlation with cell proliferation and prognosis in epithelial ovarian tumors (2002)

Survivin is a new member of the inhibitors of apoptosis proteins (IAP) family, selectively overexpressed in common human cancers but not in normal adult tissues, and associated with aggressiveness of the disease and unfavorable outcomes. Recent study also found that survivin expression is associated with cell proliferation. In order to gain insight into the role of survivin in ovarian tumors, we investigated the expression of survivin in a group of epithelial ovarian tumors, and examined the relationship of its expression with cell proliferation and clinical outcome. Immunohistochemical analysis was performed in 103 cases of epithelial ovarian tumors. Twenty-six of the 103 cases were evaluated by Western blot analysis. The results showed that survivin overexpression was detected in 21.2% (7 of 33) of benign tumors, 47.8% (11 of 23) of borderline tumors, and 51.1% (24 of 47) of ovarian carcinomas. The positive ratio was significantly higher in malignant or borderline tumors than in benign tumors, and the overexpression of survivin was significantly correlated with the size of residual disease. A positive correlation between survivin expression and proliferative activity of tumor cell measured by PCNA index was found. Kaplan-Meier analysis demonstrated that the patients with survivin overexpression have a short overall survival. These findings suggest that survivin overexpression may play a pivotal role in the progression of ovarian tumors and may provide an important prognostic implication for epithelial ovarian carcinomas.
A New Method for Leak Detection in Gas Pipelines (2015)

Two types of approaches -- physical inspection and mathematical-model simulation -- are used to identify a leak in a gas pipeline. The former method can result in an accurate detection of the location and the size of the leak, but comes with the expense of production shutdown and the high cost/long time to run the physical detection, which is very crucial in long-distance gas pipeline. The latter approach detects a gas leak by solving the governing equations, thus leading to quick evaluation at much lower costs, but with higher uncertainties. Our literature review indicates that a simple, practical, and reliable method to detect a gas leak under the conditions of unknown inlet or outlet gas rate, or unknown inlet or outlet pressure, is highly desirable. In this study, we develop single and multiple rate test methods to detect leaks in a gas pipeline. By conducting multiple rate tests, the location and size of leaks can be detected. The new method can be applied under the conditions of no inlet or outlet rate available or no inlet or outlet pressure available. Because these conditions are not uncommon in gas-pipeline transportation, our method provides a quick and low-computational-cost approach to detect leaks corresponding to different scenarios.
Platinum Group Organometallics Based on 'Pincer' Ligands: Sensors, Switchs and Catalys (2001)

Since the first reports in the late 1970s on transition metal complexes containing pincer-type ligands - named after the particular coordination mode of these ligands - these systems have attracted increasing interest owing to the unusual properties of the metal centers imparted by the pincer ligand. Typically, such a ligand comprises an anionic aryl ring which is ortho,ortho-disubstituted with heteroatom substituents, for example, CH2NR2, CH2PR2 or CH2SR, which generally coordinate to the metal center, and therefore support the M-C bond. This commonly results in a terdentate and meridional coordination mode consisting of two metallacycles which share the M-C bond. Detailed studies of the formation and the properties of a large variety of pincers containing platinum group metal complexes have provided direct access to both a fundamental understanding of a variety of reactions in organometallic chemistry and to a range of new applications of these complexes. The discovery of alkane dehydrogenation catalysts, the mechanistic elucidation of fundamental transformations (for example, C-C bond activation), the construction of the first metallodendrimers for sustainable homogeneous catalysis, and the engineering of crystalline switches for materials processing represent only a few of the many highlights which have emanated from these numerous investigations. This review discusses the synthetic methodologies that are currently available for the preparation of platinum group metal complexes containing pincer ligands and especially emphasizes different applications that have been realized in materials science such as the development and engineering of sensors, switches, and catalysts.
Josephson Arbitrary Waveform System with Optoelectronic Drive (2017)

Quantum-accurate arbitrary voltage waveforms have been generated using electrical pulse driven Josephson junction arrays (JJAs) by several groups [1, 2]. An alternative method is to use optoelectronic components to convert the electrical pulse drive into an optical signal which is subsequently converted by a photodiode into an electrical drive signal connected directly to the JJA. This optoelectronic pulse drive system has several advantages. Due to the electrical isolation between electrical pulse drive and JJA, it is possible to connect several arrays in series without the requirement for complex electrical compensation circuits. This allows larger output voltages to be realized. An optoelectronic drive also offers the ability to easily tune pulse height, via continuous optical attenuation, allowing the drive signal to be tuned to the middle of the JJA constant voltage step giving optimum operation margins. We here present an optoelectronic pulse drive which forms part of a system incorporating a JJA and delta sigma feedback loop [3] for quantum-accurate digitization of arbitrary voltage waveforms. Results showing the generation of quantum-accurate voltages synchronized to the feedback loop master clock are presented.
Critical Review of Techniques and Methodologies for Characterization of Emulsion Stability (2007)

The efficient development and production of high quality emulsion-based products depends on knowledge of their physicochemical properties and stability. A wide variety of different analytical techniques and methodologies have been developed to characterize the properties of food emulsions. The purpose of this review article is to provide a critical overview of the most important properties of emulsions that are of interest to the food industry, the type of analytical techniques that are available to measure these properties, and the experimental protocols that have been developed to characterize the stability of food emulsions. Recommendations are made about the most suitable analytical techniques and experimental protocols needed to characterize the stability and properties of food emulsions.
HYDRAULIC TRANSPORT OF COAL IN PIPES WITH DRAG REDUCING ADDITIVES† (1986)

The aim of the investigations was to determine the drag reduction produced by polymer additives in the hydraulic transport of coal. As no systematic results were available in the literature, experiments were undertaken using a wide range of flow velocities and polymer concentrations (up to 440 ppm) to obtain a clear picture about the processes involved. Special attention was paid to the effects of polymer degradation. The experiments were carried out on two different facilities for hydraulic transport with pipe diameters of 40 and 250 mm Two criteria were used for selecting the polymer with the most favourable properties. It was to produce the largest possible amount of drag reduction and have the greatest stability against degradation. Six different types of polymers were investigated. Experiments were undertaken to establish the dependence of drag reduction on the polymer concentration for the polymer showing the best results according to the above-mentioned criteria. It was found that the drag reduction on coal-watei mixtures containing polymer was less than in “pure” polymer solutions (not containing any solid particles). Furthermore, for both coal-water mixtures and “pure” polymer solutions there was always found to be a polymer concentration at which drag reduction reached a maximum and this concentration was higher for the coal-water mixtures. The value of drag reduction increased as the flow velocity was increased. In the polymer degradation experiments the decrease in drag reduction as a consequence of polymer degradation was stronger when the polymer concentration was lower for both the coal-water mixtures and the “pure” polymer solutions. Experiments of longer duration showed that even after several hours of transport in the facility, there was still considerable drag reduction. Finally, it was found that for coal-water mixtures polymer degradation was greater at higher flow velocities.
Plasmacytoid Dendritic Cells Delineate Immunogenicity of Influenza Vaccine Subtypes (2010)

A variety of different vaccine types are available for H1N1 influenza A virus infections; however, their immunological mechanisms of action remain unclear. Here, we show that plasmacytoid dendritic cells (pDCs) and type I interferon (IFN)-mediated signaling delineate the immunogenicity of live attenuated virus, inactivated whole-virus (WV), and split-virus vaccines. Although Toll-like receptor 7 acted as the adjuvant receptor for the immunogenicity of both live virus and WV vaccines, the requirement for type I IFN production by pDCs for the immunogenicity of the vaccines was restricted to WV. A split vaccine commonly used in humans failed to immunize naïve mice, but a pDC-activating adjuvant could restore immunogenicity. In blood from human adults, however, split vaccine alone could recall memory T cell responses, underscoring the importance of this adjuvant pathway for primary, but not secondary, vaccination.
Lentiviral vectors with a defective integrase allow efficient and sustained transgene expression <i>in vitro</i> and <i>in vivo</i> (2006)

Lentivirus-derived vectors are among the most promising viral vectors for gene therapy currently available, but their use in clinical practice is limited by the associated risk of insertional mutagenesis. We have overcome this problem by developing a nonintegrative lentiviral vector derived from HIV type 1 with a class 1 integrase (IN) mutation (replacement of the 262RRK motif by AAH). We generated and characterized HIV type 1 vectors carrying this deficient enzyme and expressing the GFP or neomycin phosphotransferase transgene (NEO) under control of the immediate early promoter of human CMV. These mutant vectors efficiently transduced dividing cell lines and nondividing neural primary cultures in vitro. After transduction, transient GFP fluorescence was observed in dividing cells, whereas long-term GFP fluorescence was observed in nondividing cells, consistent with the viral genome remaining episomal. Moreover, G418 selection of cells transduced with vectors expressing the NEO gene showed that residual integration activity was lower than that of the intact IN by a factor of 500-1,250. These nonintegrative vectors were also efficient in vivo, allowing GFP expression in mouse brain cells after the stereotactic injection of IN-deficient vector particles. Thus, we have developed a generation of lentiviral vectors with a nonintegrative phenotype of great potential value for secure viral gene transfer in clinical applications.
Spatial orientation of the angular vestibulo-ocular reflex (1999)

During vestibular nystagmus, optokinetic nystagmus (OKN), and optokinetic afternystagmus (OKAN), the axis of eye rotation tends to align with the vector sum of linear accelerations acting on the head. This includes gravitational acceleration and the linear accelerations generated by translation and centrifugation. We define the summed vector of gravitational and linear accelerations as gravito-inertial acceleration (GIA) and designate the phenomenon of alignment as spatial orientation of the angular vestibuloocular reflex (aVOR). On the basis of studies in the monkey, we postulated that the spatial orientation of the aVOR is dependent on the slow (velocity storage) component of the aVOR, not on the short latency, compensatory aVOR component, which is in head-fixed coordinates. Experiments in which velocity storage was abolished by midline medullary section support this postulate. The velocity storage component of the aVOR is likely to be generated in the vestibular nuclei, and its spatial orientation was shown to be controlled through the nodulus and uvula of the vestibulocerebellum. Separate regions of the nodulus/uvula appear to affect the horizontal and vertical/torsional components of the response differently. Velocity storage is weaker in humans than in monkeys, but responds in a similar fashion in both species. We postulate that spatial orientation of the aVOR plays an important role in aligning gaze with the GIA and in maintaining balance during angular locomotion.
Wnt signaling in breast cancer: biological mechanisms, challenges and opportunities (2020)

Wnt signaling is a highly conserved signaling pathway that plays a critical role in controlling embryonic and organ development, as well as cancer progression. Genome-wide sequencing and gene expression profile analyses have demonstrated that Wnt signaling is involved mainly in the processes of breast cancer proliferation and metastasis. The most recent studies have indicated that Wnt signaling is also crucial in breast cancer immune microenvironment regulation, stemness maintenance, therapeutic resistance, phenotype shaping, etc. Wnt/β-Catenin, Wnt-planar cell polarity (PCP), and Wnt-Ca<sup>2+</sup> signaling are three well-established Wnt signaling pathways that share overlapping components and play different roles in breast cancer progression. In this review, we summarize the main findings concerning the relationship between Wnt signaling and breast cancer and provide an overview of existing mechanisms, challenges, and potential opportunities for advancing the therapy and diagnosis of breast cancer.
The final common pathway of cancer. (1990)

The «final common pathway of cancer» has been known for many years to result in clinical aberrations including (a) organ failure, (b) cachexia, and (c) death. These clinical effects result from the biological characteristics of cancer which include (a) growth of cells and masses without control, (b) invasiveness, (c) metastasis, and (d) nucleolar pleomorphism
An IkappaBalpha inhibitor causes leukemia cell death through a p38 MAP kinase-dependent, NF-kappaB-independent mechanism. (2001)

Treatment of U937 cells with an IkappaBalpha phosphorylation inhibitor, Bay 11-7085, induced a rapid phosphorylation of p38 mitogen-activated protein (MAP) kinase, significant apoptosis, extensive necrosis, and a weak phosphorylation of MAP kinase kinase. Bay 11-7085 had no effect on the basal levels of phosphorylated IkappaBalpha but completely inhibited phorbol 12-myristate 13-acetate-induced phosphorylation of IkappaBalpha. Although Bay 11-7085 prevented phorbol 12-myristate 13-acetate-induced NF-kappaB nuclear translocation, SN50, a specific inhibitor of nuclear translocation and function of NF-kappaB, did not induce any significant nuclear/DNA fragmentation, caspase 3 activation, or cell death. The p38 MAP kinase-specific inhibitor, SB203580, completely inhibited the phosphorylation of p38 MAP kinase and significantly decreased Bay 11-7085-induced apoptosis. In contrast, the MAP kinase kinase-specific inhibitor PD98059 had no effect on Bay 11-7085-induced apoptosis. Caspase-specific inhibitor, z-Val-Ala-Asp-fluoromethyl ketone prevented Bay 11-7085-induced activation of caspase 3 but was not able to block Bay 11-7085-induced phosphorylation of p38 MAP kinase. These data suggest that Bay 11-7085 induces apoptosis through a p38 MAP kinase-dependent, NF-kappaB-independent mechanism.
Blast furnace slag slurries may have limits for oil field use (1994)

Thorough testing, economic evaluations, and environmental evaluations of blast furnace slag slurries revealed that replacing Portland cement with slag slurries may compromise essential properties in a cementing operation. The use of blast furnace slag (BFS) slurries should be analyzed on a per case basis for oil well cementing operations. BFS slurry technology may be a viable mud solidification process, but the slurries are not cement and should not be considered as such. Several slurries using field and laboratory prepared drilling fluids solidified with blast furnace slag were investigated to determine thickening time, compressive strength, free water, and other pertinent properties. The tests included an evaluation of the expansion of the set material and shear bond, as well as rheological compatibility studies of the finished slurries with the base muds. These additional tests are critical in the potential application of this process under field conditions.
Parkinsonism following bilateral lesions of the globus pallidus: performance on a variety of motor tasks shows similarities with Parkinson's disease (2005)

In general, the present results were similar to those reported previously in patients with PD. This provides further indirect evidence that the output of globus pallidus is of major importance in abnormal motor function in PD. The possible similarities of the functional status of GP in PD and our case are discussed.
Model-based brightness constraints: on direct estimation of structure and motion (2002)

We describe a new direct method for estimating structure and motion from image intensities of multiple views. We extend the direct methods of B.K.P. Horn and E.J. Weldon (1988) to three views. Adding the third view enables us to solve for motion, and compute a dense depth map of the scene, directly from image spatio-temporal derivatives in a linear manner without first having to find point correspondences or complete optical flow. We describe the advantages and limitations of this method which are then verified with experiments using real images.
A Genetically Encoded aza-Michael Acceptor for Covalent Cross-Linking of Protein–Receptor Complexes (2014)

Selective covalent bond formation at a protein-protein interface potentially can be achieved by genetically introducing into a protein an appropriately "tuned" electrophilic unnatural amino acid that reacts with a native nucleophilic residue in its cognate receptor upon complex formation. We have evolved orthogonal aminoacyl-tRNA synthetase/tRNACUA pairs that genetically encode three aza-Michael acceptor amino acids, N(ε)-acryloyl-(S)-lysine (AcrK, 1), p-acrylamido-(S)-phenylalanine (AcrF, 2), and p-vinylsulfonamido-(S)-phenylalanine (VSF, 3), in response to the amber stop codon in Escherichia coli. Using an αErbB2 Fab-ErbB2 antibody-receptor pair as an example, we demonstrate covalent bond formation between an αErbB2-VSF mutant and a specific surface lysine ε-amino group of ErbB2, leading to near quantitative cross-linking to either purified ErbB2 in vitro or to native cellular ErbB2 at physiological pH. This efficient biocompatible reaction may be useful for creating novel cell biological probes, diagnostics, or therapeutics that selectively and irreversibly bind a target protein in vitro or in living cells.
A reliable multicast session protocol for collaborative continuous-feed applications (1997)

This paper presents a reliable multicast session protocol for collaborative continuous-feed applications. The protocol supports NxN group multicast communications at the session layer and runs on the top of existing reliable transport protocols (e.g., TCP). It does not assume multicast support at the network layer. The protocol is portable as a network-layer-independent library that is suitable for both LAN and WAN environments. It multiplexes messages from different nodes into transport packets to reduce the transport-layer processing requirements per message. It requires only two transport-level connections per node, irrespective of the multicast group size, to reduce the processing requirements of acknowledgements and retransmissions per node. Analytical studies show that the protocol yields higher throughput than general sender-initiated and receiver-initiated reliable multicast transport protocols.