gebhart/patrepeval huggingface dataset:
Neural networks for robust image feature classification: a comparative study (2002)

We propose a simple and powerful feature extractor using neural networks. This feature extractor is trained to detect features such as lines, corners, junctions in images. Different feature models are generated based on discontinuity in intensity values and the orientation of the boundary in the pixel neighborhood. Locating feature points in the image is carried out in two steps by considering an n/spl times/n window as a processing unit. At the first step, a covariance technique is used to calculate rotation-invariant descriptors, which represent discontinuities for edge types. At the second step, a multilayer feedforward neural network, trained with the invariant feature descriptors, is used to classify the centre pixel into one of the possible features. Experimental results using the proposed method are compared with Marr-Hildreth edge operator results to show the effectiveness of the proposed method.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Single-Cell Analysis of SMN Reveals Its Broader Role in Neuromuscular Disease (2017)

The mechanism underlying selective motor neuron (MN) death remains an essential question in the MN disease field. The MN disease spinal muscular atrophy (SMA) is attributable to reduced levels of the ubiquitous protein SMN. Here, we report that SMN levels are widely variable in MNs within a single genetic background and that this heterogeneity is seen not only in SMA MNs but also in MNs derived from controls and amyotrophic lateral sclerosis (ALS) patients. Furthermore, cells with low SMN are more susceptible to cell death. These findings raise the important clinical implication that some SMN-elevating therapeutics might be effective in MN diseases besides SMA. Supporting this, we found that increasing SMN across all MN populations using an Nedd8-activating enzyme inhibitor promotes survival in both SMA and ALS-derived MNs. Altogether, our work demonstrates that examination of human neurons at the single-cell level can reveal alternative strategies to be explored in the treatment of degenerative diseases.
Distilling the Knowledge of Specialist Deep Neural Networks in Acoustic Scene Classification (2019)

Different acoustic scenes that share common properties are one of the main obstacles that hinder successful acoustic scene classification. Top two most confusing pairs of acoustic scenes, 'airportshopping mall' and 'metro-tram' have occupied more than half of the total misclassified audio segments, demonstrating the need for consideration of these pairs. In this study, we exploited two specialist models in addition to a baseline model and applied the knowledge distillation framework from those three models into a single deep neural network. A specialist model refers to a model that concentrates on discriminating a pair of two similar scenes. We hypothesized that knowledge distillation from multiple specialist models and a pre-trained baseline model into a single model could gather the superiority of each specialist model and achieve similar effect to an ensemble of these models. In the results of the Detection and Classification of Acoustic Scenes and Events 2019 challenge, the distilled single model showed a classification accuracy of 81.2 %, equivalent to the performance of an ensemble of the baseline and two specialist models.
Silicon-on-insulator bipolar transistors (1983)

Thin-film lateral n-p-n bipolar transistors (BJT) have been fabricated in moving melt zone recrystallized silicon on a 0.5-µm silicon dioxide substrate thermally grown on bulk silicon. Current-voltage characteristics of devices with different base widths (5 and 10 µm) have been analyzed. The use of a metal gate over oxide covering the base region has allowed the devices to be operated as n-channel MOSFET's as well thus surface effects on device characteristics have been investigated under varying gate-bias voltages. Maximum dc current gain values of 2.5 were achieved with a 5-µm base width and values around 0.5 with a 10-µm base width. Higher gain values were impeded by onset of high-level injection which occurred at low currents because of light base doping of these devices.
Antibody penetration into living cells. I. Intranuclear immunoglobulin in peripheral blood mononuclear cells in mixed connective tissue disease and systemic lupus erythematosus. (1979)

We have shown recently (Alarcón-Segovia, Ruíz-Argüelles & Fishbein, 1978) that an IgG anti-RNP antibody obtained from a patient with mixed connective tissue disease (MCTD) can penetrate viable mononuclear cells (MNC) from normal donors via their Fc receptors. Live MNC from twelve MCTD patients incubated with goat anti-Ig antibody had intranuclear antibody with a speckled pattern in a mean of 5.5% of all MNC and 57.3% of all Fc receptor-bearing MNC. We found intranuclear immunoglobulins in all twelve patients with MCTD which were present only in cells with Fc receptors. Only three out of twenty-one patients with systemic lupus erythematosus (SLE) were found to have intranuclear antibody in a mean of 17.2% of their Fc receptor-bearing cells. Further experiments with MNC from SLE patients revealed a partial blocking of penetration of antibody via Fc receptors. MNC from ten scleroderma, ten rheumatoid arthritis patients and eleven normal controls did not have intranuclear immunoglobulin. In vivo penetration of autoantibodies into Fc receptor-bearing cells in MCTD, and probably in SLE as well, may represent an important pathogenetic mechanism.
Purification, Properties, Sequencing, and Cloning of a Lipoprotein-Associated, Serine-Dependent Phospholipase Involved in the Oxidative Modification of Low-Density Lipoproteins (1996)

A novel LDL-associated phospholipase A2 (LDL-PLA2) has been purified to homogeneity from human LDL obtained from plasma apheresis. This enzyme has activity toward both oxidized phosphatidylcholine and platelet activating factor (PAF). A simple purification procedure involving detergent solubilization and affinity and ion exchange chromatography has been devised. Vmax and Km for the purified enzyme are 170 micromol.min-1.mg-1 and 12 micromol/L, respectively. Extensive peptide sequence from LDL-PLA2 facilitated identification of an expressed sequence tag partial cDNA. This has led to cloning and expression of active protein in baculovirus. A lipase motif is also evident from sequence information, indicating that the enzyme is serine dependent. Inhibition by diethyl p-nitrophenyl phosphate and 3,4-dichloroisocoumarin and insensitivity to EDTA, Ca2+, and sulfhydryl reagents confirm that the enzyme is indeed a serine-dependent hydrolase. The protein is extensively glycosylated, and the glycosylation site has been identified. Antibodies to this LDL-PLA2 have been raised and used to show that this enzyme is responsible for >95% of the phospholipase activity associated with LDL. Inhibition of LDL-PLA2 before oxidation of LDL reduces both lysophosphatidylcholine content and monocyte chemoattractant ability of the resulting oxidized LDL. Lysophosphatidylcholine production and monocyte chemoattractant ability can be restored by addition of physiological quantities of pure LDL-PLA2.
TILLING. Traditional Mutagenesis Meets Functional Genomics (2004)

Most of the genes of an organism are known from sequence, but most of the phenotypes are obscure. Thus, reverse genetics has become an important goal for many biologists. However, reverse-genetic methodologies are not similarly applicable to all organisms. In the general strategy for reverse genetics that we call TILLING (for Targeting Induced Local Lesions in Genomes), traditional chemical mutagenesis is followed by high-throughput screening for point mutations. TILLING promises to be generally applicable. Furthermore, because TILLING does not involve transgenic modifications, it is attractive not only for functional genomics but also for agricultural applications. Here, we present an overview of the status of TILLING methodology, including Ecotilling, which entails detection of natural variation. We describe public TILLING efforts in Arabidopsis and other organisms, including maize (Zea mays) and zebrafish. We conclude that TILLING, a technology developed in plants, is rapidly being adopted in other systems.
Electronic structure of nanometer-scale GaAs whiskers (2002)

We report a theoretical study of the electronic structure of GaAs nanowhiskers, grown in the [111] direction with hexagonal cross section, based on a tight binding approach. It is shown that the band structure of the GaAs nanowhiskers shifts from a direct band gap to an indirect band gap when the lateral size of the nanowhiskers becomes smaller than a certain value. The effective masses of the electrons and holes are shown to increase with decreasing the nanowhisker lateral size. It is also shown that the light-hole states appear to be at the top of the valence bands. The electrical and optical properties of the nanowhiskers are discussed in terms of the results of the calculations.
The stabilization of proteins by sucrose. (1981)

The interactions between proteins and solvent components have been investigated for the sucrose/water system. Thermodynamic and kinetic measurements of the thermal unfolding of alpha-chymotrypsin, chymotrypsinogen, and ribonuclease were performed as a function of sucrose concentration. The alteration in protein-solvent interactions in the presence of sucrose was also studied by density measurements and analyzed by multicomponent thermodynamic theory. Sucrose does not induce a conformational change in three proteins studied, although it does induce a small change in the circular dichroism spectrum of ribonuclease. The enthalpy of thermal unfolding shows little dependence on the concentration of sucrose, while the apparent activation energy of the unfolding process is increased by the addition of sucrose. The results from the protein-solvent interaction study indicate that sucrose is preferentially excluded from the protein domain, increasing the free energy of the system. Thermodynamically this leads to protein stabilization since the unfolded state of the protein becomes thermodynamically even less favorable in the presence of sucrose. The exclusion of sucrose from the protein domain seems to be related to the higher cohesive force of the sucrose water solvent system since all the experimental observations can be correlated with the effect of sucrose on the surface tension of water.
Circulating Levels of Secretory Type II Phospholipase A 2 Predict Coronary Events in Patients with Coronary Artery Disease (1999)

Background-The circulating levels of secretory nonpancreatic type II phospholipase A(2) (sPLA(2)) are increased in various chronic inflammatory diseases and the increase in the levels correlates with the disease severity. sPLA(2) may possibly play a role in atherogenesis and is highly expressed in atherosclerotic arterial walls that are known to have inflammatory features. Thus, this study prospectively examined whether circulating levels of sPLA(2) may have a significant risk and prognostic values in patients with coronary artery disease (CAD). Methods and Results-Plasma levels of sPLA(2) were measured in 142 patients with CAD and in 93 control subjects by a radioimmunoassay. The sPLA(2) levels had a significant and positive relations with serum levels of C-reactive protein, a marker of systemic inflammation, and with the number of the traditional coronary risk factors associated with individuals. Multivariate logistic regression analysis showed that higher levels of sPLA(2) (>246 ng/dL; 75th percentile of sPLA(2) distribution in controls) were a significant and independent risk factor for the presence of CAD. In multivariate Cox hazard analysis, the higher levels of sPLA(2) were a significant predictor of developing coronary events (ie, coronary revascularization, myocardial infarction, coronary death) during a 2-year follow-up period in patients with CAD independent of other risk factors, including CRP levels, an established inflammatory predictor. Conclusions-The increase in circulating levels of sPLA(2) is a significant risk factor for the presence of CAD and predicts clinical coronary events independent of other risk factors in patients with CAD; these results may reflect possible relation of sPLA(2) levels with inflammatory activity in atherosclerotic arteries.
A brief history of automatic control (1996)

The author looks at the history of automatic control in four main periods as follows: early control up to 1900; the pre-classical period 1900-1940; the classical period 1935-1960; and modem control post 1955. This article is concerned with the first three of the above; other articles in this issue deal with the more recent period.
Burst Spinal Cord Stimulation (2010)

The authors present a new method of spinal cord stimulation using bursts that suppress neuropathic pain without the mandatory paresthesia. Pain suppression seems as good as or potentially better than that achieved with the currently used stimulation. Average follow-up after nearly 2 years (20.5 months) suggests that this stimulation design is stable.
Sampling rate scalable lossless audio coding (2003)

This paper proposes a lossless audio coding scheme with hierarchical sampling rate scalability. A single bit stream contains hierarchical information that can generate waveforms ranging from a 96 kHz with 24 bit amplitude resolution through lower sampling/resolution lossless waveforms to highly compressed lossy ones created using an MPEG-4 audio coder. This bit stream structure enables a dynamic rate control and a hierarchical multicasting based on a simple priority control of the IP packet. These functions will be useful for high quality archiving, broadband streaming for various types of networks and terminal equipments.
Interference with p53 protein inhibits hematopoietic and muscle differentiation. (1996)

The involvement of p53 protein in cell differentiation has been recently suggested by some observations made with tumor cells and the correlation found between differentiation and increased levels of p53. However, the effect of p53 on differentiation is in apparent contrast with the normal development of p53-null mice. To test directly whether p53 has a function in cell differentiation, we interfered with the endogenous wt-p53 protein of nontransformed cells of two different murine histotypes: 32D myeloid progenitors, and C2C12 myoblasts. A drastic inhibition of terminal differentiation into granulocytes or myotubes, respectively, was observed upon expression of dominant-negative p53 proteins. This inhibition did not alter the cell cycle withdrawal typical of terminal differentiation, nor p21(WAF1/CIP1) upregulation, indicating that interference with endogenous p53 directly affects cell differentiation, independently of the p53 activity on the cell cycle. We also found that the endogenous wt-p53 protein of C2C12 cells becomes transcriptionally active during myogenesis, and this activity is inhibited by p53 dominant-negative expression. Moreover, we found that p53 DNA-binding and transcriptional activities are both required to induce differentiation in p53-negative K562 cells. Taken together, these data strongly indicate that p53 is a regulator of cell differentiation and it exerts this role, at least in part, through its transcriptional activity.
A monoclonal antibody to the human epidermal growth factor receptor (1982)

A monoclonal antibody of the IgG class, EGFR1, has been isolated using cells of the epidermoid carcinoma line A431 as immunogen. The A431 antigen recognized by EGFR1 has an apparent molecular weight of approximately 175,000, is a cell-surface molecule which can be specifically cross-linked to EGF, exhibits an EGF-stimulated protein kinase activity, binds to EGFR1 in a number of human cell lines to a degree which parallels EGF binding, and shows EGF-dependent internalization in A431 cells and human fibroblasts. We therefore conclude that EGFR1 is directed against an antigenic site on the human EGF receptor. EGFR1 is not mitogenic for human fibroblasts and does not inhibit EGF binding under a variety of assay conditions. The characterization of EGFR1 has allowed the unambiguous assignment of the structural gene for the human EGF receptor to chromosome 7. Preliminary results suggest that a convenient method for isolating a range of anti-EGF receptor monoclonal antibodies can be developed, based on a hybridoma supernatant screening assay in which positive supernatants bind selectively to a human-mouse cell hybrid containing human chromosome 7.
The G protein‐coupled receptor BLR1 is involved in murine B cell differentiation and is also expressed in neuronal tissues (1993)

The BLR1 gene, isolated initially from Burkitt's lymphoma cells (Eur. J. Immunol. 1992. 22: 2795), encodes a G protein-coupled receptor with significant relationship to receptors for chemokines (IL-8, MIP-1 alpha) and neuropeptides. The murine homologue of human BLR1 was cloned and used to investigate its expression in vivo. blr1-specific transcripts are observed in secondary lymphatic organs and to a lesser extent in brain of adult mice but not in other tissues. RNA in situ hybridization localizes blr1 transcription to primary follicles and to the mantle zone of secondary follicles. SCID mice in which mature B cell development is severely impaired exhibit a strongly reduced level of blr1-specific RNA in the spleen. The analysis of murine lymphoid tumor cell lines representing distinct stages of the B cell lineage reveals elevated expression of blr1 in B cell lymphomas but not in pre-B lymphomas or plasmacytomas. Induction of differentiation of resting B cells by cytokines or mitogens down-regulates expression of blr1. RNA in situ hybridization using brain sections of adult mice detects blr1 transcription in the granule and Purkinje cell layer of the cerebellum. Interestingly, the blr1 gene is also expressed during late embryogenesis in fetal liver and brain. In view of the remarkable expression pattern in the B cell lineage we suggest that murine BLR1 may represent a cytokine/neuropeptide receptor exerting regulatory functions on recirculating mature B lymphocytes.
Array-based analog computation: principles, advantages and limitations (2002)

Analog implementations of neural networks and other computing architectures have gained increasing interest over the last decade. The field is at a critical juncture: continued interest will depend on the ability to demonstrate a clear advantage over digital solutions to problems of commercial interest. The neural network design group at SGS-Thomson Microelectronics has been working to explore the advantages and limitations of analog computation and implementations of neural network architectures. We are investigating 3 large-scale analog VLSI chips, all of which work on problems in image processing. The use of analog computing arrays, because of their efficiency and regularity, have formed the basis of most of our designs, while several different computing modes, including current, charge, and conductance have been explored. Another area in which we have focused is on the use of floating-gate flash-EEPROM devices for both non-volatile analog storage and computation. This paper will share insights into the lessons we have learned, the results we have achieved, and the limitations we have encountered. Particular emphasis will be made on two subjects: computational efficiency and equivalent precision of array-based analog computing circuits.
Free radical biology for medicine: learning from nonalcoholic fatty liver disease (2013)

Reactive oxygen species, when released under controlled conditions and limited amounts, contribute to cellular proliferation, senescence, and survival by acting as signaling intermediates. In past decades there has been an epidemic diffusion of nonalcoholic fatty liver disease (NAFLD) that represents the result of the impairment of lipid metabolism, redox imbalance, and insulin resistance in the liver. To date, most studies and reviews have been focused on the molecular mechanisms by which fatty liver progresses to steatohepatitis, but the processes leading toward the development of hepatic steatosis in NAFLD are not fully understood yet. Several nuclear receptors, such as peroxisome proliferator-activated receptors (PPARs) α/γ/δ, PPARγ coactivators 1α and 1β, sterol-regulatory element-binding proteins, AMP-activated protein kinase, liver-X-receptors, and farnesoid-X-receptor, play key roles in the regulation of lipid homeostasis during the pathogenesis of NAFLD. These nuclear receptors may act as redox sensors and may modulate various metabolic pathways in response to specific molecules that act as ligands. It is conceivable that a redox-dependent modulation of lipid metabolism, nuclear receptor-mediated, could cause the development of hepatic steatosis and insulin resistance. Thus, this network may represent a potential therapeutic target for the treatment and prevention of hepatic steatosis and its progression to steatohepatitis. This review summarizes the redox-dependent factors that contribute to metabolism alterations in fatty liver with a focus on the redox control of nuclear receptors in normal liver as well as in NAFLD.
Differential distribution of glucocorticoid and estrogen receptor isoforms: localization of GRbeta and ERalpha in nucleoli and GRalpha and ERbeta in the mitochondria of human osteosarcoma SaOS-2 and hepatocarcinoma HepG2 cell lines. (2008)

The localization of glucocorticoid and estrogen receptors alpha (GRalpha, ERalpha) and beta (GRbeta, ERbeta) in osteosarcoma SaOS-2 and hepatocarcinoma HepG2 cells was studied by immunofluorescence labelling and confocal laser scanning microscopy, as well as by subcellular fractionation and immunoblotting of the proteins of the fractions with respective antibodies. In HepG2 and SaOS-2 cells GRbeta and ERalpha were localized mainly in the nucleus, particularly concentrated in nuclear structures, which on the basis of their staining with antibody against C23-nucleolin, were characterized as nucleoli. A faint, diffuse GRbeta and ERalpha staining was also observed in the cytoplasm. GRalpha and ERbeta were specifically enriched at the site of cell mitochondria, which were visualized by labelling with the vital dye CMX. Immunoblotting experiments corroborated the immunofluorescence labelling distribution of glucocorticoid and estrogen receptor isoforms in the cell lines studied. These findings support the concept of a direct action of steroid/thyroid hormones on mitochondrial functions by way of their cognate receptors and also suggest a direct involvement of GRbeta and ERalpha in nucleolar-related processes in HepG2 and SaOS-2 cells.
Nanoscale dysregulation of collagen structure-function disrupts mechano-homeostasis and mediates pulmonary fibrosis (2018)

Matrix stiffening with downstream activation of mechanosensitive pathways is strongly implicated in progressive fibrosis; however, pathologic changes in extracellular matrix (ECM) that initiate mechano-homeostasis dysregulation are not defined in human disease. By integrated multiscale biomechanical and biological analyses of idiopathic pulmonary fibrosis lung tissue, we identify that increased tissue stiffness is a function of dysregulated post-translational collagen cross-linking rather than any collagen concentration increase whilst at the nanometre-scale collagen fibrils are structurally and functionally abnormal with increased stiffness, reduced swelling ratio, and reduced diameter. In ex vivo and animal models of lung fibrosis, dual inhibition of lysyl oxidase-like (LOXL) 2 and LOXL3 was sufficient to normalise collagen fibrillogenesis, reduce tissue stiffness, and improve lung function in vivo. Thus, in human fibrosis, altered collagen architecture is a key determinant of abnormal ECM structure-function, and inhibition of pyridinoline cross-linking can maintain mechano-homeostasis to limit the self-sustaining effects of ECM on progressive fibrosis.