gebhart/patrepeval huggingface dataset:
A method for producing monoclonal antibodies to human T-cell-receptor beta-chain variable regions. (1993)

Study of the T-cell repertoire in humans has been hampered by the lack of monoclonal antibodies (mAbs) to the T-cell receptor (TCR) variable region (V) gene products. We describe a method for producing mAbs to the human TCR beta-chain V (V beta) gene products in which mice were immunized with a rat basophil cell line (RBL-2H3) transfected with the extracellular domain of the TCR heterodimer fused to the lambda chain of CD3. These cells acted as excellent immunogens for raising anti-TCR mAb and also formed the basis of a rapid screening assay. We generated mAbs against V beta protein of the TCR, showed that these mAbs stained approximately 1% of peripheral blood T cells, and further showed that the mAbs could stimulate proliferation of these T cells. We then characterized the mAbs by amplifying TCR cDNA derived from mAb-stimulated cells and sequencing the beta chain. All clones sequenced used the V beta 7.1 chain, proving conclusively that the mAbs generated were specific for V beta 7.1 subfamily. This method generates mAbs to human TCR V beta proteins efficiently and might allow production of a complete panel of mAbs directed against human TCR V beta proteins.
Protein binding of acetylsalicylic acid and salicylic acid in porcine and human serum. (1995)

As part of a pilot project establishing a porcine model for aspirin overdose, the percentage protein binding of acetylsalicylate (ASA) and salicylate (SA) in porcine and human sera was evaluated in vitro over a range of concentrations. Serum from 2 pigs and 4 humans were spiked with ASA concentrations of 0.5-100 mg/dL and SA concentrations of 1-120 mg/dL. Protein binding for each concentration of ASA and SA was determined using radiolabeled drug and ultrafiltration with the Centrifree micropartition system. The percentage protein binding for ASA in pig and human sera were similarly low (< 50%) for all concentrations evaluated. Percentage protein binding for SA for pig and human sera were high (approximately 90% and 80%) at low therapeutic concentrations, but then declined to approximately 30% at higher toxic concentrations (120 mg/dL). The protein binding of ASA and SA over a range of concentrations was similar for porcine and human sera.
β-Glycerophosphate Accelerates Calcification in Cultured Bovine Vascular Smooth Muscle Cells (1995)

Calcification is a common feature of advanced atherosclerotic lesions and is being reemphasized as a clinically significant element of vascular disease. However, the scarcity of in vitro models of vascular calcification preclude studying its molecular and cellular mechanism. In the present study, we describe an in vitro calcification in which diffuse calcification can be induced by culturing bovine vascular smooth muscle cells (BVSMC) in the presence of beta-glycerophosphate, ascorbic acid, and insulin in a manner analogous to in vitro mineralization by osteoblasts. Calcification was confirmed by von Kossa staining and 45Ca accumulation. Factor analysis revealed that beta-glycerophosphate is the most important factor for this calcification process, suggesting that alkaline phosphatase (ALP) may be involved. As predicted, high levels of ALP expression were detected by ALP assay and Northern blot analysis. Functional significance of ALP was confirmed by demonstrating that levamisole, a specific inhibitor of ALP, inhibited BVSMC calcification in a dose-dependent manner. Bisphosphonates such as etidronate and pamidronate potently inhibited BVSMC calcification, suggesting that hydroxyapatite formation may be involved. Importantly, expression of osteopontin mRNA was dramatically increased in calcified BVSMC compared with uncalcified control cells. These data suggest that beta-glycerophosphate can induce diffuse calcification by an ALP-dependent mechanism and that this in vitro calcification system is useful for analyzing the molecular and cellular mechanisms of vascular calcification.
High-Affinity Interactions of Tumor Necrosis Factor Receptor-Associated Factors (TRAFs) and CD40 Require TRAF Trimerization and CD40 Multimerization (1999)

Signaling by some TNF receptor family members, including CD40, is mediated by TNF receptor-associated factors (TRAFs) that interact with receptor cytoplasmic domains following ligand-induced receptor oligomerization. Here we have defined the oligomeric structure of recombinant TRAF domains that directly interact with CD40 and quantitated the affinities of TRAF2 and TRAF3 for CD40. Biochemical and biophysical analyses demonstrated that TRAF domains of TRAF1, TRAF2, TRAF3, and TRAF6 formed homo-trimers in solution. N-terminal deletions of TRAF2 and TRAF3 defined minimal amino acid sequences necessary for trimer formation and indicated that the coiled coil TRAF-N region is required for trimerization. Consistent with the idea that TRAF trimerization is required for high-affinity interactions with CD40, monomeric TRAF-C domains bound to CD40 significantly weaker than trimeric TRAFs. In surface plasmon resonance studies, a hierarchy of affinity of trimeric TRAFs for trimeric CD40 was found to be TRAF2 > TRAF3 >> TRAF1 and TRAF6. CD40 trimerization was demonstrated to be sufficient for optimal NF-kappaB and p38 mitogen activated protein kinase activation through wild-type CD40. In contrast, a higher degree of CD40 multimerization was necessary for maximal signaling in a cell line expressing a mutated CD40 (T254A) that signaled only through TRAF6. The affinities of TRAF proteins for oligomerized receptors as well as different requirements for degree of receptor multimerization appear to contribute to the selectivity of TRAF recruitment to receptor cytoplasmic domains.
Layer Normalization (2016)

Training state-of-the-art, deep neural networks is computationally expensive. One way to reduce the training time is to normalize the activities of the neurons. A recently introduced technique called batch normalization uses the distribution of the summed input to a neuron over a mini-batch of training cases to compute a mean and variance which are then used to normalize the summed input to that neuron on each training case. This significantly reduces the training time in feed-forward neural networks. However, the effect of batch normalization is dependent on the mini-batch size and it is not obvious how to apply it to recurrent neural networks. In this paper, we transpose batch normalization into layer normalization by computing the mean and variance used for normalization from all of the summed inputs to the neurons in a layer on a single training case. Like batch normalization, we also give each neuron its own adaptive bias and gain which are applied after the normalization but before the non-linearity. Unlike batch normalization, layer normalization performs exactly the same computation at training and test times. It is also straightforward to apply to recurrent neural networks by computing the normalization statistics separately at each time step. Layer normalization is very effective at stabilizing the hidden state dynamics in recurrent networks. Empirically, we show that layer normalization can substantially reduce the training time compared with previously published techniques.
TheRole ofSuppressors ofCytokineSignaling(SOCS) Proteins inRegulation of theImmuneResponse (2004)

Cytokines are an integral component of the adaptive and innate immune responses. The signaling pathways triggered by the engagement of cytokines with their specific cell surface receptors have been extensively studied and have provided a profound understanding of the intracellular machinery that translates exposure of cells to cytokine to a coordinated biological response. It has also become clear that cells have evolved sophisticated mechanisms to prevent excessive responses to cytokines. In this review we focus on the suppressors of cytokine signaling (SOCS) family of cytoplasmic proteins that completes a negative feedback loop to attenuate signal transduction from cytokines that act through the janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway. SOCS proteins inhibit components of the cytokine signaling cascade via direct binding or by preventing access to the signaling complex. The SOCS proteins also appear to target signal transducers for proteasomal destruction. Analyses of genetically modified mice in which SOCS proteins are overexpressed or deleted have established that this family of negative regulators has indispensable roles in regulating cytokine responses in cells of the immune system as well as other tissues. Emerging evidence also suggests that disruption of SOCS expression or activity is associated with several immune and inflammatory diseases, raising the prospect that manipulation of SOCS activity may provide a novel future therapeutic strategy in the management of immunological disorders.
Time Course and Diagnostic Accuracy of Glial and Neuronal Blood Biomarkers GFAP and UCH-L1 in a Large Cohort of Trauma Patients With and Without Mild Traumatic Brain Injury (2016)

GFAP performed consistently in detecting MMTBI, CT lesions, and neurosurgical intervention across 7 days. UCH-L1 performed best in the early postinjury period.
Biochemical Characterization of Soybean Protein Consisting of Different Subunits of Glycinin (1997)

Soybean isogenic lines having different glycinin subunit compositions are now being bred. To compare the characteristics of the genetically improved soybean proteins, total protein and purified glycinin proteins were investigated in this study. The absence of subunit(s) resulted in marked changes in the proportion of glycinin to β-conglycinin. When the pH of the total protein and glycinin solution was changed and NaCl was added to the solution, glycinin consisting of only group I subunits and β-conglycinin are highly soluble compared to the A5A4B3 or A3B4 subunit at a NaCl concentration lower than 0.05 M at pH 5.5. Ultracentrifuge analysis showed that the glycinin containing all subunits was able to assemble to form the 11S structure. That consisting of group I subunits formed a uniform 7S structure. Decreasing glycinin/β-conglycinin ratios and structural changes caused by a lack of glycinin subunit(s) are thus expected to influence the food-processing properties of soybeans. Keywords: Soybean; glycinin; mutant; subunit composition
Towards people detection from fused time-of-flight and thermal infrared images (2014)

Abstract. Obtaining accurate 3d descriptions in the thermal infrared (TIR) is a quite challenging task due to the low geometric resolutions of TIR cameras and the low number of strong features in TIR images. Combining the radiometric information of the thermal infrared with 3d data from another sensor is able to overcome most of the limitations in the 3d geometric accuracy. In case of dynamic scenes with moving objects or a moving sensor system, a combination with RGB cameras of Time-of-Flight (TOF) cameras is suitable. As a TOF camera is an active sensor in the near infrared (NIR) and the thermal infrared camera captures the radiation emitted by the objects in the observed scene, the combination of these two sensors for close range applications is independent from external illumination or textures in the scene. This article is focused on the fusion of data acquired both with a time-of-flight (TOF) camera and a thermal infrared (TIR) camera. As the radiometric behaviour of many objects differs between the near infrared used by the TOF camera and the thermal infrared spectrum, a direct co-registration with feature points in both intensity images leads to a high number of outliers. A fully automatic workflow of the geometric calibration of both cameras and the relative orientation of the camera system with one calibration pattern usable for both spectral bands is presented. Based on the relative orientation, a fusion of the TOF depth image and the TIR image is used for scene segmentation and people detection. An adaptive histogram based depth level segmentation of the 3d point cloud is combined with a thermal intensity based segmentation. The feasibility of the proposed method is demonstrated in an experimental setup with different geometric and radiometric influences that show the benefit of the combination of TOF intensity and depth images and thermal infrared images.
The 2007 LabROSA Cover Song Detection System (2007)

We describe our cover song detection system, as submitted to the MIREX 2007 Cover Song Detection evaluation. The system is developed from our 2006 MIREX system, which was the best-performing entry in last year's evaluation. Using the new "covers80" dataset of 80 pairs of songs and covers, we improve the overall detection from 42.5% to 67.5% through a collection of minor modifications relating to correlation normalization, tempo tracking, and temporal filtering of the beat-synchronous chroma representation.
IgA nephropathy: an update (2004)

Purpose of review The elution of nephrectomy specimens from patients with IgA nephropathy yields IgA1 with galactose-deficient glycans in the hinge region. In this review, we summarize recent advances in our understanding of the role of the aberrant immunoglobulin in the pathogenesis of this form of glomerulonephritis. In the absence of a disease-specific therapy, we discuss current therapeutic approaches. Recent findings Galactose-deficient IgA1 forms macromolecular complexes that bind to mesangial cells and stimulate them to proliferate, synthesize various cytokines and chemokines, and secrete extracellular matrix proteins. Whereas progress has been made in understanding the glycosylation pathways of IgA1 O-linked glycans and binding galactose-deficient IgA1-complexes to mesangial cells, there is still no IgA nephropathy-specific therapy. The current approach to suppress the effects of angiotensin II, by angiotensin-converting enzyme inhibitors, angiotensin II receptor type 1 blockers, or both, as a cornerstone of the therapy of IgA nephropathy has been strengthened by recent studies. Treatment with glucocorticoids, cyclophosphamide, or both, may be appropriate for a subset of IgA nephropathy patients. Summary A better understanding of the mechanisms underlying the synthesis of galactose-deficient IgA1, the formation of circulating immune complexes, and interactions with mesangial cells will provide further insights into the pathogenetic mechanisms that culminate in the glomerular and interstitial damage of IgA nephropathy, and could identify novel therapeutic targets in the prevention and management of this renal disease.
Super resolution of discrete arrivals in a cellular geolocation system (2000)

A method to determine a cellular subscriber's location which utilizes the digital mode of the IS-54-B air-interface standard, and subsequently the IS-1 3 6 air-interface standard, is presented.Time-of-arrival (TOA) estimates are made by correlating the cellular mobile's transmit burst message; either normal mc or shortened bursts, with the cellular mobile's assigned time-slot synchronization word.The resolution of the time estimates are firher improved by employing super-resolution processing, which helps mitigate multipath effects incurred by the mobile radio channel.The polynomial variant of Schmidt's MUSIC algorithm, root-MUSIC, is utilized in the processing method.The super-resolved TOA values are used in conventional multilateration algorithms to obtain two-dimensional position estimates.An overview of super-resolution processing by previous researchers at the University of Calgary is provided.Computer simulations are conducted on wideband signals, including indoor channel measurements, and airinterface signaling used for the North American digital cellular system.
In vivo properties of an IgG3-IL-2 fusion protein. A general strategy for immune potentiation (1996)

In this report, we describe a strategy for enhancing the immunogenicity of a wide variety of Ags by linking them to IL-2 via an IgG3-IL-2 fusion protein with high affinity for a convenient hapten Ag, dansyl (DNS; N,N-dimethyl-1-aminonaphthalene-5-sulfonyl chloride). This fusion protein, anti-DNS-IgG3-IL-2, combines the functional characteristics of its constituents and has pharmacokinetic properties that are greatly improved over those of IL-2 and a previously described IgG1-IL-2 fusion. The molecule is intact and recoverable from the blood of mice hours after i.p. injection and reaches distant organs throughout the animal. The 7-h in vivo half-life of this molecule is much longer than that of IL-2, addressing a major obstacle in the application of IL-2 to human diseases, including cancer and AIDS. Additionally, the Ab's specificity for the hapten dansyl and the convenient chemistry of dansyl provide a means to link IL-2 to virtually any molecule of interest without the complexities and uncertainties of making IL-2 fusions with each molecule individually. Using hapten-conjugated-BSA (DNS-BSA) as a model Ag we show that the Ab response elicited by anti-DNS-IgG3-IL-2-bound DNS-BSA-Sepharose injected into mice is increased over that of DNS-BSA-Sepharose or anti-DNS-IgG3-bound DNS-BSA-Sepharose. Anti-DNS-IgG3-IL-2 also increased the Ab response to soluble DNS-BSA after a booster injection. This system should be useful in testing the ability of IL-2 to potentiate the immune response to Ag and in screening a large number of potential Ags for use in vaccines. The dramatically improved pharmacokinetics should also overcome one of the major difficulties in applying IL-2 to the treatment of human disease, its short half-life.
A Wrench-Shaped Synthetic Molecule that Modulates a Transcription Factor−Coactivator Interaction (2004)

Development of synthetic molecules that provide external control over the transcription of a given gene represents a challenge in medicinal and bioorganic chemistry. Here we report design and analysis of wrenchnolol, a wrench-shaped synthetic molecule that impairs the transcription of the Her2 oncogene by disrupting association of transcription factor ESX with its coactivator Sur-2. The "jaw" part of the compound mimics the alpha-helical interface of the activation domain of ESX, and the "handle" region accepts chemical modifications for a range of analysis. A water-soluble handle permitted NMR study in aqueous solution; a biotinylated handle verified the selectivity of the interaction, and a fluorescent handle confirmed the cell permeability of the compound. The case study of wrenchnolol foreshadows the promise and the challenge of targeting protein-protein interactions in the nucleus and may lead to the development of unique synthetic modulators of gene transcription.
Properties of the ribosome-inactivating proteins gelonin, Momordica charantia inhibitor, and dianthins (1982)

The amino acid and sugar compositions of four ribosome-inactivating proteins (gelonin, Momordica charantia inhibitor, dianthin 30 and dianthin 32) were determined. The proteins are all basic glycoproteins (pI greater than 8) containing mannose (more abundant in gelonin), glucose, xylose, fucose (absent from gelonin) and glucosamine. The ribosome-inactivating properties of the proteins examined are not modified by pretreatment with N-ethylmaleimide. Precipitating and inactivating antibodies can be raised against ribosome-inactivating proteins; a weak cross-reaction was observed only between dianthin 30 and dianthin 32.
StereoBrush (2011)

We introduce a novel workflow for stereoscopic 2D to 3D conversion in which the user "paints" depth onto a 2D image via sparse scribbles, instantaneously receiving intuitive 3D feedback. This workflow is enabled by the introduction of a discontinuous warping technique that creates stereoscopic pairs from sparse, possibly erroneous user input. Our method assumes a piecewise continuous depth representation, preserving visual continuity in most areas, while creating sharp depth discontinuities at important object boundaries. As opposed to prior work that relies strictly on a per pixel depth map, our scribbles are processed as soft constraints in a global solve and operate entirely on image domain disparity, allowing for relaxed input requirements. This formulation also allows us to simultaneously compute a disparity-and-content-aware stretching of background areas to automatically fill disoccluded regions with valid stereo information. We tightly integrate all steps of stereo content conversion into a single optimization framework, which can then be solved on a GPU at interactive rates. The instant feedback received while painting depth allows even untrained users to quickly create compelling 3D scenes from single-view footage.
Complexes of p21RAS with JUN N-terminal kinase and JUN proteins. (1995)

RAS gene-encoded p21 protein has been found to increase in vitro phosphorylation of JUN via its kinase, JUN N-terminal kinase (JNK). This effect is mediated by increased phosphorylation of JNK in the presence of wild-type and oncogenic (Val-12) p21 protein in a dose-dependent manner. Oncogenic p21 protein is more potent in mediating this effect than its normal counterpart. Both normal and oncogenic p21 proteins bind to purified JNK and to JNK that is present in cell extracts from transformed fibroblasts and melanoma cells. Oncogenic and normal p21 proteins have also been found to bind to bacterially expressed JUN protein. This binding is dose dependent, enhanced by the presence of GTP, and depends on the presence of the first 89 amino acids of JUN (the delta domain), as it does not occur with v-jun. While the ability of both normal and oncogenic p21 proteins to bind JNK is strongly inhibited by a p21 peptide corresponding to aa 96-110, and more weakly inhibited by the p21 peptide corresponding to aa 115-126, p21-JUN interaction is inhibited by peptides corresponding to aa 96-110 and, to a lesser degree, by peptides corresponding to aa 35-47. The results suggest that the p21 protein interacts specifically with both JNK and JUN proteins.