gebhart/patrepeval huggingface dataset:
Efficient sparse coding algorithms (2007)

Sparse coding provides a class of algorithms for finding succinct representations of stimuli; given only unlabeled input data, it discovers basis functions that capture higher-level features in the data. However, finding sparse codes remains a very difficult computational problem. In this paper, we present efficient sparse coding algorithms that are based on iteratively solving two convex optimization problems: an L1-regularized least squares problem and an L2-constrained least squares problem. We propose novel algorithms to solve both of these optimization problems. Our algorithms result in a significant speedup for sparse coding, allowing us to learn larger sparse codes than possible with previously described algorithms. We apply these algorithms to natural images and demonstrate that the inferred sparse codes exhibit end-stopping and non-classical receptive field surround suppression and, therefore, may provide a partial explanation for these two phenomena in V1 neurons.
Some Properties of Time Varying Networks (1960)

In this paper, the general theory of reactance amplifiers is exemplified, with attention centered on three aspects. 1. Why may gain be obtained from a nonlinear reactance and not from a nonlinear resistance? 2. Where there is gain and feedback, the possibility of oscillation exists. But the situation is more complex than it is with vacuum tube amplifiers because the feedback path is through the modulator so that an external impedance at one frequency may be reflected as an impedance at another frequency. 3. The particular case of three frequencies, e.g., p, g, p-q, is calculated for large signals. The phenomena of regeneration and oscillation, with subharmonic oscillation as a special case, are studied and illuminated.
Potential Mechanisms for Cancer Resistance in Elephants and Comparative Cellular Response to DNA Damage in Humans (2015)

Compared with other mammalian species, elephants appeared to have a lower-than-expected rate of cancer, potentially related to multiple copies of TP53. Compared with human cells, elephant cells demonstrated increased apoptotic response following DNA damage. These findings, if replicated, could represent an evolutionary-based approach for understanding mechanisms related to cancer suppression.
ON NEW MOMENT ESTIMATION OF PARAMETERS OF THE GENERALIZED GAMMA DISTRIBUTION USING IT’S CHARACTERIZATION (2006)

In this paper, the three estimators for three parameters of the generalized gamma distribution are proposed by using its characterization, and shown to be more convenient and more efficient than the maximum likelihood estimator for small samples. Furthermore, the estimators for the parameter of its special distribution such as gamma and Weibull distributions which are the most important in the reliability field and survival analysis are obtained.
HDAC expression and activity is upregulated in diseased lupus-prone mice (2015)

Prior studies have shown that pan-HDAC inhibition can decrease disease in lupus mice; however, the mechanisms(s) remain to be elucidated. MRL/MpJ-Fas(lpr) (MRL/lpr) mice develop a lupus-like disease characterized by anti-dsDNA production, lymphoproliferation, and immune complex-mediated glomerulonephritis. Early- and late-disease (12 and 20weeks-of-age respectively) female MRL/lpr mice were compared to age-matched, healthy C57BL/6 mice for HDAC expression and activity in bone marrow (BM) B cells, splenic B and T cells, and glomerular cells. We found that HDAC6 was significantly overexpressed in B cells, splenic T cells and glomerular cells, whereas HDAC9 expression was significantly increased in splenic T cells, BM B cells and glomerular cells. Due to the overexpression of HDAC6, we tested whether treatment with a selective HDAC6 inhibitor (ACY-738) or a pan-HDAC inhibitor (TsA) would decrease HDAC activity. ACY-738 significantly reduced cytoplasmic HDAC activity whereas TsA significantly decreased both nuclear and cytoplasmic HDAC activity. In vitro studies in mesangial cells showed that ACY-738 increased α-tubulin and Hsp90 acetylation resulting in decreased nuclear activation of NF-κB. Treatment of pre-B cells with ACY-738 decreased the Bcl-2:Bax ratio leading to a pro-apoptotic environment. These results suggest that increased HDAC6 expression and activity contribute to SLE pathogenesis, and isoform-selective HDAC inhibitors may prove beneficial in the treatment of SLE by acetylating key signaling and transcription factors in inflammation and cell activation.
A New HTLV-III/LAV Protein Encoded by a Gene Found in Cytopathic Retroviruses (1986)

The DNA of the HTLV-III/LAV group of retroviruses contains certain additional open reading frames that are not found in typical avian or mammalian retroviruses. The role of these sequences in encoding for gene products that may be related to pathogenesis remains to be resolved. An open reading frame whose 5' end overlaps with the pol gene, but is unrelated to the env gene, has been observed in HTLV-III/LAV and visna virus, both cytopathic mammalian retroviruses. Evidence presented here shows that this open reading frame is a bona fide coding sequence of HTLV-III/LAV and that its product, a protein with a molecular weight of 23,000, induces antibody production in the natural course of infection.
Ball Grid Array Technology (1994)

Introduction to BGA technology ceramic substrates for BGA packages BT substrates for BGA packages PCBs for BGA ceramic BGA packages ceramic BGA multichip carrier modules plastic BGA packages plastic BGA multichip carrier modules plastic BGA assembly thermal and electrical management of plastic BGA reliability of plastic BGA assembly inspection of BGA assembly BGA tests and sockets infrastructure to support BGA manufacturing.
A Model of Obstructive Sleep Apnea in Normal Humans: Role of the Upper Airway (2000)

We determined whether upper airway obstruction in normal individuals with intact reflexes could produce the syndrome of obstructive sleep apnea. Upper airway obstruction was produced in 12 normal individuals by lowering nasal pressure to -10 cm H(2)O during sleep. Full night polysomnography was performed during two consecutive nights of sleep with subatmospheric nasal pressure and compared with control nights before and after the negative pressure nights. We found that the application of negative pressure was associated with the development of recurrent obstructive apneas (non-REM-disordered breathing rate, 32.6 +/- 34.8 and 37.8 +/- 29.1 events/h during each of two negative pressure nights; p < 0.001) that were associated with oxyhemoglobin desaturation, arousals from sleep, and alterations in sleep stage distribution. Moreover, the median daytime sleep latency after two nights of sleep with subatmospheric pressure fell from 6.9 +/- 1.1 to 3.4 +/- 0.6 min, and rose significantly again to 8.1 +/- 1.5 min (p < 0.03) after the control night following subatmospheric pressure nights. Our findings suggest that a decrease in the pharyngeal transmural pressure alone is a sufficient condition for the production of the sleep apnea syndrome in normal individuals.
Mild Cognitive Impairment: A Systematic Review (2007)

MCI is a nosological entity proposed as an intermediate state between normal aging and dementia. The syndrome can be divided into two broad subtypes: amnestic MCI (aMCI) characterized by reduced memory, and non-amnestic MCI (naMCI) in which other cognitive functions rather than memory are mostly impaired. aMCI seems to represent an early stage of AD, while the outcomes of the naMCI subtypes appear more heterogeneous--including vascular dementia, frontotemporal dementia or dementia with Lewy bodies--but this aspect is still under debate. MCI in fact represents a condition with multiple sources of heterogeneity, including clinical presentation, etiology, and prognosis. To improve classification and prognosis, there is a need for more sensitive instruments specifically developed for MCI as well as for more reliable methods to determine its progression or improvement. Current clinical criteria for MCI should be updated to include restriction in complex ADL; also the diagnostic and prognostic role of behavioral symptoms and motor dysfunctions should be better defined. A multidisciplinary diagnostic approach including biological and neuroimaging techniques may probably represent the best option to predict the conversion from MCI to dementia. In this review we discuss the most recent aspects related to the epidemiological, clinical, neuropathological, neuroimaging, biochemical and therapeutic aspects of MCI, with specific attention to possible markers of conversion to dementia.
Six epitopes reacting with human cytotoxic CD8+ T cells in the central region of the HIV-1 NEF protein (1991)

In order to identify the target epitopes recognized by specific CTL in the NEF protein of HIV-1, 33 peptides derived from the HIV-BRU sequence were tested with NEF-specific CTL generated from HIV-seropositive donors. Six different epitopes were identified and several points were remarkable: 1) They were all located in two regions of the central part of the NEF protein corresponding to residues 73 to 94 and 113 to 147, respectively. 2) The CTL issued from a single donor could recognize several peptides of the NEF protein. 3) Some of these peptides could be recognized in association with at least two or three different HLA class I molecules. 4) Two different overlapping epitopes were present in a relatively short sequence of 15 amino acids. These results suggest that multiple epitopes corresponding to different HLA restrictions could coexist in a relatively small region of the NEF protein. The implications of these results in vaccine strategies using synthetic peptides bearing CTL epitopes are discussed.
Brain Natriuretic Peptide Enhances Renal Actions of Furosemide and Suppresses Furosemide-Induced Aldosterone Activation in Experimental Heart Failure (2004)

Fs+BNP has more profound diuretic and natriuretic responses than Fs alone and also increases GFR without activation of aldosterone. Coadministration of BNP and loop diuretic is effective in maximizing natriuresis and diuresis while preserving renal function and inhibiting activation of aldosterone.
Electrowetting-Based Microfluidics for Analysis of Peptides and Proteins by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (2004)

A new technique for preparing samples for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is reported. The technique relies on electrowetting-on-dielectric (EWOD) to move droplets containing proteins or peptides and matrix to specific locations on an array of electrodes for analysis. Standard MALDI-MS reagents, analytes, concentrations, and recipes are demonstrated to be compatible with the technique. Mass spectra are comparable to those collected by conventional methods. Nonspecific adsorption of analytes to device surfaces is demonstrated to be negligible. The results suggest that EWOD may be a useful tool for automating sample preparation for high-throughput proteomics and other applications of MALDI-MS.
Function of PI3Kγ in Thymocyte Development, T Cell Activation, and Neutrophil Migration (2000)

Phosphoinositide 3-kinases (PI3Ks) regulate fundamental cellular responses such as proliferation, apoptosis, cell motility, and adhesion. Viable gene-targeted mice lacking the p110 catalytic subunit of PI3Kgamma were generated. We show that PI3Kgamma controls thymocyte survival and activation of mature T cells but has no role in the development or function of B cells. PI3Kgamma-deficient neutrophils exhibited severe defects in migration and respiratory burst in response to heterotrimeric GTP-binding protein (G protein)-coupled receptor (GPCR) agonists and chemotactic agents. PI3Kgamma links GPCR stimulation to the formation of phosphatidylinositol 3,4,5-triphosphate and the activation of protein kinase B, ribosomal protein S6 kinase, and extracellular signal-regulated kinases 1 and 2. Thus, PI3Kgamma regulates thymocyte development, T cell activation, neutrophil migration, and the oxidative burst.
Fragile X Mental Retardation Protein: Nucleocytoplasmic Shuttling and Association with Somatodendritic Ribosomes (1997)

Fragile X syndrome, a leading cause of inherited mental retardation, is attributable to the unstable expansion of a CGG-repeat within the FMR1 gene that results in the absence of the encoded protein. The fragile X mental retardation protein (FMRP) is a ribosome-associated RNA-binding protein of uncertain function that contains nuclear localization and export signals. We show here detailed cellular localization studies using both biochemical and immunocytochemical approaches. FMRP was highly expressed in neurons but not glia throughout the rat brain, as detected by light microscopy. Although certain structures, such as hippocampus, revealed a strong signal, the regional variation in staining intensity appeared to be related to neuron size and density. In human cell lines and mouse brain, FMRP co-fractionated primarily with polysomes and rough endoplasmic reticulum. Ultrastructural studies in rat brain revealed high levels of FMRP immunoreactivity in neuronal perikarya, where it is concentrated in regions rich in ribosomes, particularly near or between rough endoplasmic reticulum cisternae. Immunogold studies also provided evidence of nucleocytoplasmic shuttling of FMRP, which was localized in neuronal nucleoplasm and within nuclear pores. Moreover, labeling was observed in large- and small-caliber dendrites, in dendritic branch points, at the origins of spine necks, and in spine heads, all known locations of neuronal polysomes. Dendritic localization, which was confirmed by co-fractionation of FMRP with synaptosomal ribosomes, suggests a possible role of FMRP in the translation of proteins involved in dendritic structure or function and relevant for the mental retardation occurring in fragile X syndrome.
Control of a Family of Phosphatase Regulatory Genes ( phr ) by the Alternate Sigma Factor Sigma-H of Bacillus subtilis (2001)

A family of 11 phosphatases can help to modulate the activity of response regulator proteins in Bacillus subtilis. Downstream of seven of the rap (phosphatase) genes are phr genes, encoding secreted peptides that function as phosphatase regulators. By using fusions to lacZ and primer extension analysis, we found that six of the seven phr genes are controlled by the alternate sigma factor sigma-H. These results expand the potential of sigma-H to contribute to the output of several response regulators by controlling expression of inhibitors of phosphatases.
Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties (2010)

aCGH analysis identified dozens of mutations in each strain analyzed. The resolution was at the level of single nucleotide mutation. High-density aCGH is a powerful tool for genome-wide analysis of organisms with small genomes e.g. fungi, especially in studies where a large set of interesting strains is analyzed.
The GATA factor Serpent is required for the onset of the humoral immune response in Drosophila embryos (2001)

Innate immunity in Drosophila is characterized by the inducible expression of antimicrobial peptides. We have investigated the development and regulation of immune responsiveness in Drosophila embryos after infection. Immune competence, as monitored by the induction of Cecropin A1-lacZ constructs, was observed first in the embryonic yolk. This observation suggests that the yolk plays an important role in the humoral immune response of the developing embryo by synthesizing antimicrobial peptides. Around midembryogenesis, the response in the yolk was diminished. Simultaneously, Cecropin expression became inducible in a large number of cells in the epidermis, demonstrating that late-stage embryos can synthesize their own antibiotics in the epidermis. This production likely serves to provide the hatching larva with an active antimicrobial barrier and protection against systemic infections. Cecropin expression in the yolk required the presence of a GATA site in the promoter as well as the involvement of the GATA-binding transcription factor Serpent (dGATAb). In contrast, neither the GATA site nor Serpent were necessary for Cecropin expression in the epidermis. Thus, the inducible immune responses in the yolk and in the epidermis can be uncoupled and call for distinct sets of transcription factors. Our data suggest that Serpent is involved in the distinction between a systemic response in the yolk/fat body and a local immune response in epithelial cells. In addition, the present study shows that signal transduction pathways controlling innate and epithelial defense reactions can be dissected genetically in Drosophila embryos.
SIGNALING PATHWAYS IN INTESTINAL DEVELOPMENT AND CANCER (2004)

The study of the epithelium of the adult mammalian intestine touches upon many modern aspects of biology. The epithelium is in a constant dialogue with the underlying mesenchyme to control stem cell activity, proliferation in transit-amplifying compartments, lineage commitment, terminal differentiation and, ultimately, cell death. There are spatially distinct compartments dedicated to each of these events. The Wnt, TGF-beta, BMP, Notch, and Par polarity pathways are the major players in homeostatic control of the adult epithelium. Several hereditary cancer syndromes deregulate these same signaling cascades through mutational (in)activation. Moreover, these mutations often also occur in sporadic tumors. Thus symmetry exists between the roles that these signaling pathways play in physiology and in cancer of the intestine. This is particularly evident for the Wnt/APC pathway, for which the mammalian intestine has become one of the most-studied paradigms. Here, we integrate recent knowledge of the molecular inner workings of the prototype signaling cascades with their specific roles in intestinal epithelial homeostasis and in neoplastic transformation of the epithelium.
Characterization of nascent HDL particles and microparticles formed by ABCA1-mediated efflux of cellular lipids to apoA-I (2006)

The nascent HDL created by ABCA1-mediated efflux of cellular phospholipid (PL) and free (unesterified) cholesterol (FC) to apolipoprotein A-I (apoA-I) has not been defined. To address this issue, we characterized the lipid particles released when J774 mouse macrophages and human skin fibroblasts in which ABCA1 is activated are incubated with human apoA-I. In both cases, three types of nascent HDL containing two, three, or four molecules of apoA-I per particle are formed. With J774 cells, the predominant species have hydrodynamic diameters of approximately 9 and 12 nm. These discoidal HDL particles have different FC contents and PL compositions, and the presence of acidic PL causes them to exhibit alpha-electrophoretic mobility. These results are consistent with ABCA1 located in more than one membrane microenvironment being responsible for the production of the heterogeneous HDL. Activation of ABCA1 also leads to the release of apoA-I-free plasma membrane vesicles (microparticles). These larger, spherical particles released from J774 cells have the same PL composition as the 12 nm HDL and contain CD14 and ganglioside, consistent with their origin being plasma membrane raft domains. The various HDL particles and microparticles are created concurrently, and there is no precursor-product relationship between them. Importantly, a large fraction of the cellular FC effluxed from these cells by ABCA1 is located in microparticles. Collectively, these results show that the products of the apoA-I/ABCA1 interaction include discoidal HDL particles containing different numbers of apoA-I molecules. The cellular PLs and cholesterol incorporated into these nascent HDL particles originate from different cell membrane domains.
Fabrication and characterisation of polypropylene nanofibres by melt electrospinning and meltblowing (2012)

This research achieved uniform nanofibres of polypropylene (PP) in melt electrospinning by using additives such as sodium oleate (SO) and sodium chloride (NaCl), which increased the electrical conductivity of the polymer melt. The average fibre diameters achieved by the use of pure polymers of 100, 300, 1000 and 2000 melt flow index (MFI) were in the range of 3.01-14.19 µm. The optimal amount of SO and NaCl were 7% and 5%, respectively for the fabrication of nanofibres from 1000 and 2000 MFI PP. The lowest average fibre diameters (achieved from 2000 MFI PP) were 0.371 ± 0.106 µm and 0.310 ± 0.102 µm corresponding to the optimum conditions of SO and NaCl, respectively. This research established the fact that there is no effect of the die shape on the cross-sectional shape of the meltelectrospun fibres. <br><br>This study also demonstrated the scope of fabricating nanofibres by meltblowing with the injection of various fluids such as air, nitrogen (N<sub>2</sub>) and water. The use of water worked better in terms of fibre morphology as compared to air and N<sub>2</sub> for the fabrication of nanofibres. The lowest fibre diameter of 0.438 µm was achieved from the 300 MFI PP with water. <br><br>This study also established the fact that the molecular weight was the predominant factor governing the fibre diameter in melt electrospinning. In contrast, the molecular weight was not the predominant factor governing the fibre diameter in meltblowing. The effective collector distances for nanofibre fabrication in the case of melt electrospinning were lower compared to the meltblowing. The polymer feed rate was substantially lower in the case of melt electrospinning (i.e. 0.64 g/hr) compared to meltblowing (i.e. 80 g/hr).<br><br>The results of energy dispersive x-ray (EDX) and Fourier transform infrared (FTIR) studies established the presence of additives in the melt electrospun fibres. Similar FTIR and NMR spectra of the polymer and the fibres indicated that there was no chemical change of the fibres fabricated by the application of various fluids and high temperature during meltblowing. The melting points of the fibres fabricated in melt electrospinning and meltblowing shifted to lower values compared to the initial polymer. This change was due to the thermal degradation caused by the high temperature during melt electrospinning and meltblowing. <br><br>The degree of thermal degradation was higher in the case of meltblowing. X-ray diffraction (XRD) studies showed that all the fibres fabricated by melt electrospinning and meltblowing contained low degree of crystallinity. The crystallinity, tensile strength and modulous of the meltblown fibres were increased with annealing. The fibres fabricated by melt electrospinning and meltblowing showed high values of contact angle indicating the hydrophobic nature. The additives SO, PEG and NaCl were washed away from the fibres fabricated by melt electrospinning. Hence, this research has achieved the goal of fabricating nanofibres and added new knowledge to the field of nanofibres.<br>
Matrix metalloproteinases and aggrecanases cleave aggrecan in different zones of normal cartilage but colocalize in the development of osteoarthritic lesions in STR/ort mice (2001)

MMP- and aggrecanase-generated neoepitopes map predominantly to different regions in normal murine tibial cartilage. However, both groups of enzymes generate increased amounts of neoepitopes in pericellular and interterritorial matrix adjacent to histopathologic lesions of OA. Aggrecan degradation and the development of OA appear to be independent of sex hormone status in this model.