gebhart/patrepeval huggingface dataset:
Immunochemical studies on the interaction between staphylococcal protein A and gamma-G globulin. (1970)

Reactivity with staphylococcal protein A is a characteristic of IgG-1, -2 and -4 molecules. Human myeloma globulins of these types either precipitate with protein A or are capable of inhibiting such precipitation. In the present study chemical modifications of human myeloma globulins showed distinct effects on the reactivity with protein A. Carbamylation changed a precipitin reaction to one of inhibition. Acetylation rendered myeloma globulins completely non-reactive with protein A. Quantitative precipitin curves for the reaction between normal human γG or various myeloma globulins and staphylococcal protein A revealed marked quantitative differences with varying amounts of soluble complexes formed. Analytical ultracentrifugation of γG preparations with and without protein A revealed similar differences. No intermediate sized complexes were detected. Our results confirm a previous hypothesis that precipitation in this system is a secondary reaction after the primary combination between protein A and the Fc site on human γG globulin. Ultracentrifugational data also indicated that protein A may be univalent, structurally or functionally, in its reaction with γG.
STEROID 5α-REDUCTASE: TWO GENES/TWO ENZYMES (1994)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Building high-level features using large scale unsupervised learning (2013)

We consider the problem of building high-level, class-specific feature detectors from only unlabeled data. For example, is it possible to learn a face detector using only unlabeled images? To answer this, we train a deep sparse autoencoder on a large dataset of images (the model has 1 billion connections, the dataset has 10 million 200×200 pixel images downloaded from the Internet). We train this network using model parallelism and asynchronous SGD on a cluster with 1,000 machines (16,000 cores) for three days. Contrary to what appears to be a widely-held intuition, our experimental results reveal that it is possible to train a face detector without having to label images as containing a face or not. Control experiments show that this feature detector is robust not only to translation but also to scaling and out-of-plane rotation. We also find that the same network is sensitive to other high-level concepts such as cat faces and human bodies. Starting from these learned features, we trained our network to recognize 22,000 object categories from ImageNet and achieve a leap of 70% relative improvement over the previous state-of-the-art.
The kinase haspin is required for mitotic histone H3 Thr 3 phosphorylation and normal metaphase chromosome alignment (2005)

Post-translational modifications of conserved N-terminal tail residues in histones regulate many aspects of chromosome activity. Thr 3 of histone H3 is highly conserved, but the significance of its phosphorylation is unclear, and the identity of the corresponding kinase unknown. Immunostaining with phospho-specific antibodies in mammalian cells reveals mitotic phosphorylation of H3 Thr 3 in prophase and its dephosphorylation during anaphase. Furthermore we find that haspin, a member of a distinctive group of protein kinases present in diverse eukaryotes, phosphorylates H3 at Thr 3 in vitro. Importantly, depletion of haspin by RNA interference reveals that this kinase is required for H3 Thr 3 phosphorylation in mitotic cells. In addition to its chromosomal association, haspin is found at the centrosomes and spindle during mitosis. Haspin RNA interference causes misalignment of metaphase chromosomes, and overexpression delays progression through early mitosis. This work reveals a new kinase involved in composing the histone code and adds haspin to the select group of kinases that integrate regulation of chromosome and spindle function during mitosis and meiosis.
A vector Taylor series approach for environment-independent speech recognition (2002)

In this paper we introduce a new analytical approach to environment compensation for speech recognition. Previous attempts at solving analytically the problem of noisy speech recognition have either used an overly-simplified mathematical description of the effects of noise on the statistics of speech or they have relied on the availability of large environment-specific adaptation sets. Some of the previous methods required the use of adaptation data that consists of simultaneously-recorded or "stereo" recordings of clean and degraded speech. In this work we introduce the use of a vector Taylor series (VTS) expansion to characterize efficiently and accurately the effects on speech statistics of unknown additive noise and unknown linear filtering in a transmission channel. The VTS approach is computationally efficient. It can be applied either to the incoming speech feature vectors, or to the statistics representing these vectors. In the first case the speech is compensated and then recognized; in the second case HMM statistics are modified using the VTS formulation. Both approaches use only the actual speech segment being recognized to compute the parameters required for environmental compensation. We evaluate the performance of two implementations of VTS algorithms using the CMU SPHINX-II system on the 100-word alphanumeric CENSUS database and on the 1993 5000-word ARPA Wall Street Journal database. Artificial white Gaussian noise is added to both databases. The VTS approaches provide significant improvements in recognition accuracy compared to previous algorithms.
Speaker adaptation through vector quantization (2005)

Vector quantization (VQ) is a technique that reduces the computation amount and memory size drastically. In this paper, speaker adaptation algorithms through VQ are proposed in order to improve speaker-independent recognition. The speaker adaptation algorithms use VQ codebooks of a reference speaker and an input speaker. Speaker adaptation is performed by substituting vectors in the codebook of a reference speaker for vectors of the input speaker's codebook, or vice versa. To confirm the effectiveness of these algorithms, word recognition experiments are carried out using the IBM office correspondence task uttered by 11 speakers. The total number of words is 1174 for each speaker, and the number of different words is 422. The average word recognition rate using different speaker's reference through speaker adaptation is 80.9%, and the rate within the second choice is 92.0%.
Ocimum sanctum induces apoptosis in A549 lung cancer cells and suppresses the in vivo growth of lewis lung carcinoma cells (2009)

Although Ocimum sanctum has been used extensively for its medicinal values in India and China, its antitumor activity against human nonsmall cell lung carcinoma (NSCLC) A549 cells has not been investigated until now. Therefore, the antitumor mechanism of ethanol extracts of Ocimum sanctum (EEOS) was elucidated in A549 cells in vitro and the Lewis lung carcinoma (LLC) animal model. EEOS exerted cytotoxicity against A549 cells, increased the sub-G1 population and exhibited apoptotic bodies in A549 cells. Furthermore, EEOS cleaved poly(ADP-ribose)polymerase (PARP), released cytochrome C into cytosol and simultaneously activated caspase-9 and -3 proteins. Also, EEOS increased the ratio of proapoptotic protein Bax/antiapoptotic protein Bcl-2 and inhibited the phosphorylation of Akt and extracellular signal regulated kinase (ERK) in A549 cancer cells. In addition, it was found that EEOS can suppress the growth of LLC inoculated onto C57BL/6 mice in a dose-dependent manner. Overall, these results demonstrate that EEOS induces apoptosis in A549 cells via a mitochondria caspase dependent pathway and inhibits the in vivo growth of LLC, suggesting that EEOS can be applied to lung carcinoma as a chemopreventive candidate.
Direct electrophoretic detection of the allelic state of single DNA molecules in human sperm by using the polymerase chain reaction. (1990)

We have developed a procedure that allows the detection of polymerase chain reaction (PCR) products derived from a single target DNA molecule in a human sperm without using radioactive probes. With this method, three genetic loci present in a single sperm can be amplified simultaneously. The amplification procedure is specific as well as efficient and permits detection of the PCR product by ethidium bromide staining after polyacrylamide gel electrophoresis. When allele-specific PCR primers that differ in length are used, the size of the PCR products of different alleles also vary in length, allowing the allelic state at each locus to be determined electrophoretically. Studies on individual sperm by using this procedure should facilitate the measurement of genetic recombination in humans over small physical distances. The ability to directly analyze the allelic state of PCR products from one cell rapidly and simply will also be useful for the prenatal diagnosis of genetic disease, especially in the analysis of single blastomeres taken from in vitro fertilized eggs prior to implantation.
Near-Field Optics: Microscopy, Spectroscopy, and Surface Modification Beyond the Diffraction Limit (1992)

The near-field optical interaction between a sharp probe and a sample of interest can be exploited to image, spectroscopically probe, or modify surfaces at a resolution (down to approximately 12 nm) inaccessible by traditional far-field techniques. Many of the attractive features of conventional optics are retained, including noninvasiveness, reliability, and low cost. In addition, most optical contrast mechanisms can be extended to the near-field regime, resulting in a technique of considerable versatility. This versatility is demonstrated by several examples, such as the imaging of nanometric-scale features in mammalian tissue sections and the creation of ultrasmall, magneto-optic domains having implications for highdensity data storage. Although the technique may find uses in many diverse fields, two of the most exciting possibilities are localized optical spectroscopy of semiconductors and the fluorescence imaging of living cells.
Developing Monolithic Nanoporous Gold with Hierarchical Bicontinuity Using Colloidal Bijels (2014)

We report a universal platform for the synthesis of monolithic porous gold materials with hierarchical bicontinuous morphology and combined macro- and mesoporosity using a synergistic combination of nanocasting and chemical dealloying. This robust and accessible approach offers a new design paradigm for the parallel optimization of active surface area and mass transport in porous metal electrodes.
Fusions between dendritic cells and whole tumor cells as anticancer vaccines (2013)

Various strategies have been developed to deliver tumor-associated antigens (TAAs) to dendritic cells (DCs). Among these, the fusion of DCs and whole cancer cells can process a broad array of TAAs, including hitherto unidentified molecules, and present them in complex with MHC Class I and II molecules and in the context of co-stimulatory signals. DC-cancer cell fusions have been shown to stimulate potent antitumor immune responses in animal models. In early clinical trials, however, the antitumor effects of DC-cancer cell fusions are not as vigorous as in preclinical settings. This mini-review summarizes recent advances in anticancer vaccines based on DC-cancer cell fusions.
Preserving Mafa Expression in Diabetic Islet β-Cells Improves Glycemic Control in Vivo (2015)

The murine Mafa transcription factor is a key regulator of postnatal islet β-cell activity, affecting insulin transcription, insulin secretion, and β-cell mass. Human MAFA expression is also markedly decreased in islet β-cells of type 2 diabetes mellitus (T2DM) patients. Moreover, levels are profoundly reduced in db/db islet β-cells, a mouse model of T2DM. To examine the significance of this key islet β-cell-enriched protein to glycemic control under diabetic conditions, we generated transgenic mice that conditionally and specifically produced Mafa in db/db islet β-cells. Sustained expression of Mafa resulted in significantly lower plasma glucose levels, higher plasma insulin, and augmented islet β-cell mass. In addition, there was increased expression of insulin, Slc2a2, and newly identified Mafa-regulated genes involved in reducing β-cell stress, like Gsta1 and Gckr. Importantly, the levels of human GSTA1 were also compromised in T2DM islets. Collectively, these results illustrate how consequential the reduction in Mafa activity is to islet β-cell function under pathophysiological conditions.
Endothelin B Receptor Blockade Inhibits Dynamics of Cell Interactions and Communications in Melanoma Cell Progression (2004)

Phenotypic and genotypic analyses of cutaneous melanoma have identified the endothelin B receptor (ET(B)R) as tumor progression marker, thus representing a potential therapeutic target. Here, we demonstrate that activation of ET(B)R by endothelin-1 (ET-1) and ET-3 leads to loss of expression of the cell adhesion molecule E-cadherin and associated catenin proteins and gain of N-cadherin expression. Exposure of melanoma cells to ET-1 leads to a 60% inhibition in intercellular communication by inducing phosphorylation of gap junctional protein connexin 43. Additionally, activation of the ET(B)R pathway increases alpha(v)beta(3) and alpha(2)beta(1) integrin expression and matrix metalloproteinase (MMP)-2 and MMP-9, membrane type-1-MMP activation, and tissue inhibitor MMP-2 secretion. The ET(B)R pathway results into the downstream activation of focal adhesion kinase and extracellular signal-regulated kinase 1/2 signaling pathways, which lead to enhanced cell proliferation, adhesion, migration, and MMP-dependent invasion. The small molecule A-192621, an orally bioavailable nonpeptide ET(B)R antagonist, significantly inhibits melanoma growth in nude mice. These findings demonstrate that ET-1 and ET-3 through ET(B)R activation trigger signaling pathways involved in events associated with disruption of normal host-tumor interactions and progression of cutaneous melanoma. Pharmacological interruption of ET(B)R signaling may represent a novel therapeutic strategy in the treatment of this malignancy.
Predicting and Measuring the Perceived Texture of Car Paints (2012)

In this paper, we describe new methods to predict and measure the perceived texture of car paints. Previously, we have shown that the perceived texture of car paints can best be described by two parameters, Glint impression and Diffuse coarseness. The actually perceived texture is a combination of these, depending mainly on the relative contributions of diffuse versus directional lighting. Commercially available instruments have been developed to accurately measure these texture parameters. As a next step, the paint industry requires a texture model that uses the paint composition as input and produces predicted values for the texture parameters as output. We describe two different types of texture models, which are based on either physical considerations or on a simple statistical approach. We compare the accuracy of the models with the visual accuracy of assessing texture.
Tissue Engineering, Morphogenesis, and Regeneration of the Periodontal Tissues By Bone Morphogenetic Proteins (1997)

Tissue engineering is the emerging field of science developing techniques for fabrication of new tissues for replacement based on principles of cell and developmental biology and biomaterials. Morphogenesis is the cascade of pattern formation and the attainment of form of the various organs and the organism as a whole. The periodontium consist of the periodontal ligament, cementum, and alveolar bone. Bone has considerable potential for regeneration and therefore is a prototypic model for tissue engineering. The three main ingredients for tissue engineering are regulatory signals, responding stem cells, and extracellular matrix. Recent advances in molecular biology of the bone morphogenetic proteins (BMPs) have set the stage for tissue engineering of bone and related tissues, including the periodontium. Bone-derived BMPs, with a collagenous matrix as carrier, induced cementum and alveolar bone regeneration in surgically created furcation defects in the primate. It is noteworthy that there was morphogenesis of periodontal ligament and a faithful insertion of Sharpey's fibers into cementum. In the same furcation model, recombinant human osteogenic protein-1 (rhOP-1, also known as BMP-7), in conjunction with the collagenous carrier, induced extensive cementogenesis with insertion of Sharpey's fibers into the newly formed cementum. The observation that BMPs induce cementogenesis and periodontal ligament formation indicates that these proteins may have multiple functions in vivo not limited to cartilage and bone induction. The rapid advances in the molecular biology of BMPs and their receptors bode well for novel strategies to engineer the regeneration of the periodontal tissues.
Interaction of a 59-kDa Connective Tissue Matrix Protein with Collagen I and Collagen II (1989)

We have studied binding to collagen of the 59-kDa protein present in most connective tissues. Collagen fibril formation, measured as increasing turbidity, was markedly retarded and reduced by the presence of small amounts of this protein. This was true for both collagen I and collagen II. The effect was also observed when pepsin-treated collagens were used, indicating that interaction with the telopeptides is not involved. The proportion of collagen precipitated in the assay was not or only marginally reduced. Thus, the altered optical properties indicate that structurally different fibrils are formed in the presence of the 59-kDa protein. The 59-kDa protein bound to collagen I or collagen II that had been insolubilized on polystyrene 96-well microtiter plates, as measured by enzyme-linked immunosorbent assay. Analogously, binding to the collagens was demonstrated for the PG-S2 low Mr proteoglycan, previously shown only to inhibit collagen fibrillogenesis. The two matrix components showed similar strength of binding, i.e. Kd 35 nM for the 59-kDa protein and 16 nM for PG-S2 at 20 degrees C. The results do not reveal if the collagen interaction site of the 59-kDa protein is different from that of PG-S2. Our observations do, however, suggest that the 59-kDa protein, as well as PG-S2, have functions related to the regulation of collagen organization in tissues.
Intestinal Epithelial Cell Differentiation Involves Activation of p38 Mitogen-activated Protein Kinase That Regulates the Homeobox Transcription Factor CDX2 (2001)

The intracellular signaling pathways responsible for cell cycle arrest and differentiation along the crypt-villus axis of the human small intestine remain largely unknown. p38 mitogen-activated protein kinases (MAPKs) have recently emerged as key modulators of various vertebrate cell differentiation processes. In order to elucidate further the mechanism(s) responsible for the loss of proliferative potential once committed intestinal cells begin to differentiate, the role and regulation of p38 MAPK with regard to differentiation were analyzed in both intact epithelium as well as in well established intestinal cell models recapitulating the crypt-villus axis in vitro. Results show that phosphorylated and active forms of p38 were detected primarily in the nuclei of differentiated villus cells. Inhibition of p38 MAPK signaling by 2-20 microm SB203580 did not affect E2F-dependent transcriptional activity in subconfluent Caco-2/15 or HIEC cells. p38 MAPK activity dramatically increased as soon as Caco-2/15 cells reached confluence, whereas addition of SB203580 during differentiation of Caco-2/15 cells strongly attenuated sucrase-isomaltase gene and protein expression as well as protein expression of villin and alkaline phosphatase. The binding of CDX2 to the sucrase-isomaltase promoter and its transcriptional activity were significantly reduced by SB203580. Pull-down glutathione S-transferase and immunoprecipitation experiments demonstrated a direct interaction of CDX3 with p38. Finally, p38-dependent phosphorylation of CDX3 was observed in differentiating Caco-2/15 cells. Taken together, our results indicate that p38 MAPK may be involved in the regulation of CDX2/3 function and intestinal cell differentiation.
Brain basic fibroblast growth factor stimulates the proliferation of rat neuronal precursor cells in vitro (1987)

Neuronal cells from cerebral hemispheres of 13-day-old rat embryos were grown in a serum-free culture medium for 48 h, 4 or 8 days. The neuronal precursor cells proliferate for 5 days. The addition of bovine brain basic fibroblast growth factor stimulates their proliferation as determined by measurement of [125I]-iododeoxyuridine incorporation and by autoradiographic analysis after [3H]thymidine incorporation. The proliferating responsive cells were characterized as neurons by immunostaining against neurofilament proteins. Five other growth factors tested were without effect on the proliferative activity of these neuronal cells. The present results show that bFGF is mitogenic in vitro for rat neuronal precursor cells of the central nervous system.
Disease Detection by Ultrasensitive Quantification of Microdosed Synthetic Urinary Biomarkers (2014)

The delivery of exogenous agents can enable noninvasive disease monitoring, but existing low-dose approaches require complex infrastructure. In this paper, we describe a microdose-scale injectable formulation of nanoparticles that interrogate the activity of thrombin, a key regulator of clotting, and produce urinary reporters of disease state. We establish a customized single molecule detection assay that enables urinary discrimination of thromboembolic disease in mice using doses of the nanoparticulate diagnostic agents that fall under regulatory guidelines for "microdosing."
Serum hyaluronic acid is a useful marker of liver fibrosis in chronic hepatitis C virus infection (1998)

Patients with chronic hepatitis C virus (HCV) infection are often asymptomatic with few clinical signs of liver disease. Recognition of the presence of fibrosis or cirrhosis is difficult without liver biopsy, but with the availability of effective treatments, such as interferon, and the potential for progression to hepatoma in some cases, an accurate measure of the stage of disease is important. Serum hyaluronic acid (HA) has been identified as a potential marker of fibrosis or cirrhosis in other settings. In a prospective study in 130 chronic HCV carriers therefore, serum HA concentrations were compared with conventional liver function tests (including alanine aminotransferase (ALT), a-glutathione-S transferase (GST) and serum HCV RNA in order to determine which identified the stage of liver fibrosis as assessed by liver biopsy most accurately. The median HA concentrations according to the stage of fibrosis 0, 1 & 2, 3 and 4 & 5 were 17 g l-1 (range 5-37), 17 g l-1 (5-80), 30 g l-1 (10-105) and 350 g l-1 (20-800) respectively. The median HA concentration in stage 4 & 5 was significantly greater than in stages 0, 1 & 2 or 3. Serum HA concentration rose with age, but even when adjusted for age the median HA at stage 4 & 5 was greater than all other groups (95% CI of difference between the medians exceeded 0). Thus, serum HA gave a sensitivity and specificity for stage 4 & 5 fibrosis of 85% and 88% respectively, exceeding those for ALT or GST. In contrast, serum ALT or GST levels were not correlated with the stage of fibrosis although ALT was significantly greater in the cirrhotic group when compared to the group with no fibrosis (stage 0). There was no correlation between serum HA and either the grade of inflammatory changes or serum HCV RNA. These results suggest that serum hyaluronic acid is a useful marker of liver fibrosis in patients with chronic HCV infection. It could therefore be used to monitor patients at risk of progressive fibrosis, in controlled clinical trials, as a measure of response to antifibrotic therapy and in those in whom liver biopsy is difficult or contraindicated.