gebhart/patrepeval huggingface dataset:
Microvesicular Steatosis of the Liver (1990)

The term "microvesicular steatosis of the liver" refers to a variant form of hepatic fat accumulation whose histologic features contrast with the much more common macrovesicular steatosis. Microvesicular steatosis of the liver was originally described in association with conditions who share a number of biochemical and a limited number of clinical features: acute fatty liver of pregnancy, Reye's syndrome, Jamaican vomiting sickness, sodium valproate toxicity, high-dose tetracycline toxicity and certain congenital defects of urea cycle enzymes; they were thought to constitute an entity of "microvesicular fat diseases". In recent years the disease has been described in a wide variety of conditions: alcoholism, toxicity of several medications, delta hepatitis in South America and Central Africa, sudden childhood death, congenital defects of fatty acid beta oxidation, cholesterol ester storage disease, Wolman disease and Alpers syndrome. Not much is known regarding the pathogenesis of microvesicular steatosis but in many instances the primary defect could be a mitochondrial lesion, and inhibition of the mitochondrial beta oxidation of fatty acids has been the most frequently implicated defect. The different conditions associated with microvesicular steatosis are heterogenous in many aspects. Maintaining the concept of "microvesicular fat diseases" as a unique entity seems no longer justified.
Double search self‐healing algorithm and its characteristics (1994)

Abstract The requirements of today's communication networks are changing rapidly with the introduction of highcapacity transmission links and the increased amount of data traffic, thus fast restoration from failures is of increasing importance. To meet this requirement, self‐healing algorithms, which are distributed algorithms based on autonomous control at each node, are discussed. The conventional self‐healing algorithms called single‐search self‐healing algorithms have the following problems: (1) the self‐healing process for bidirectional path failure has not been investigated; and (2) a large search area is affected by restoration messages. To solve these problems, this paper proposes and evaluates the restoration characteristics of a new self‐healing algorithm called the “double‐search self‐healing algorithm.” The results indicate that the proposed algorithm can restore foiled bidirectional paths faster and find alternate paths more effectively man conventional self‐healing algorithms. To evaluate the restoration characteristics, an SDH network model based on existing telephone network data in Japan also is constructed.
Inflammation and Taste Disorders (2009)

Taste disorders, including taste distortion and taste loss, negatively impact general health and quality of life. To understand the underlying molecular and cellular mechanisms, we set out to identify inflammation-related molecules in taste tissue and to assess their role in the development of taste dysfunctions. We found that 10 out of 12 mammalian Toll-like receptors (TLRs), type I and II interferon (IFN) receptors, and their downstream signaling components are present in taste tissue. Some TLRs appear to be selectively or more abundantly expressed in taste buds than in nongustatory lingual epithelium. Immunohistochemistry with antibodies against TLRs 1, 2, 3, 4, 6, and 7 confirmed the presence of these receptor proteins in taste bud cells, of which TLRs 2, 3, and 4 are expressed in the gustducin-expressing type II taste bud cells. Administration of TLR ligands, lipopolysaccharide, and double-stranded RNA polyinosinic:polycytidylic acid, which mimics bacterial or viral infection, activates the IFN signaling pathways, upregulates the expression of IFN-inducible genes, and downregulates the expression of c-fos in taste buds. Finally, systemic administration of IFNs augments apoptosis of taste bud cells in mice. Taken together, these data suggest that TLR and IFN pathways function collaboratively in recognizing pathogens and mediating inflammatory responses in taste tissue. This process, however, may interfere with normal taste transduction and taste bud cell turnover and contributes to the development of taste disorders.
Electrochemical Behavior of Monolayer and Bilayer Graphene (2011)

Results of a study on the electrochemical properties of exfoliated single and multilayer graphene flakes are presented. Graphene flakes were deposited on silicon/silicon oxide wafers to enable fast and accurate characterization by optical microscopy and Raman spectroscopy. Conductive silver paint and silver wires were used to fabricate contacts; epoxy resin was employed as a masking coating in order to expose a stable, well-defined area of graphene. Both multilayer and monolayer graphene microelectrodes showed quasi-reversible behavior during voltammetric measurements in potassium ferricyanide. However, the standard heterogeneous charge transfer rate constant, k°, was estimated to be higher for monolayer graphene flakes.
How does yeast respond to pressure? (2005)

The brewing and baking yeast Saccharomyces cerevisiae has been used as a model for stress response studies of eukaryotic cells. In this review we focus on the effect of high hydrostatic pressure (HHP) on S. cerevisiae. HHP exerts a broad effect on yeast cells characteristic of common stresses, mainly associated with protein alteration and lipid bilayer phase transition. Like most stresses, pressure induces cell cycle arrest. Below 50 MPa (500 atm) yeast cell morphology is unaffected whereas above 220 MPa wild-type cells are killed. S. cerevisiae cells can acquire barotolerance if they are pretreated with a sublethal stress due to temperature, ethanol, hydrogen peroxide, or pressure. Nevertheless, pressure only leads to protection against severe stress if, after pressure pretreatment, the cells are also re-incubated at room pressure. We attribute this effect to the inhibition of the protein synthesis apparatus under HHP. The global genome expression analysis of S. cerevisiae cells submitted to HHP revealed a stress response profile. The majority of the up-regulated genes are involved in stress defense and carbohydrate metabolism while most repressed genes belong to the cell cycle progression and protein synthesis categories. However, the signaling pathway involved in the pressure response is still to be elucidated. Nitric oxide, a signaling molecule involved in the regulation of a large number of cellular functions, confers baroprotection. Furthermore, S. cerevisiae cells in the early exponential phase submitted to 50-MPa pressure show induction of the expression level of the nitric oxide synthase inducible isoform. As pressure becomes an important biotechnological tool, studies concerning this kind of stress in microorganisms are imperative.
Genome-wide protective response used by group A Streptococcus to evade destruction by human polymorphonuclear leukocytes (2003)

Group A Streptococcus (GAS) evades polymorphonuclear leukocyte (PMN) phagocytosis and killing to cause human disease, including pharyngitis and necrotizing fasciitis (flesh-eating syndrome). We show that GAS genes differentially regulated during phagocytic interaction with human PMNs comprise a global pathogen-protective response to innate immunity. GAS prophage genes and genes involved in virulence, oxidative stress, cell wall biosynthesis, and gene regulation were up-regulated during PMN phagocytosis. Genes encoding novel secreted proteins were up-regulated, and the proteins were produced during human GAS infections. We discovered an essential role for the Ihk-Irr two-component regulatory system in evading PMN-mediated killing and promoting host-cell lysis, processes that would facilitate GAS pathogenesis. Importantly, the irr gene was highly expressed during human GAS pharyngitis. We conclude that a complex pathogen genetic program circumvents human innate immunity to promote disease. The gene regulatory program revealed by our studies identifies previously undescribed potential vaccine antigens and targets for therapeutic interventions designed to control GAS infections.
Small-molecule-based identification of dynamic assembly of E2F–pocket protein–histone deacetylase complex for telomerase regulation in human cells (2004)

Activation of telomerase is crucial for cells to gain immortality. Most normal human somatic cells have a limited proliferative life span, and expression of the rate-limiting telomerase catalytic subunit, known as human telomerase reverse transcriptase (hTERT), has been believed to be tightly repressed. This model of hTERT regulation is challenged by the recent identification of the induction of hTERT in normal cycling human fibroblasts during their transit through S phase. Here we show the small-molecule-based identification of the assembly and disassembly of E2F-pocket protein-histone deacetylase (HDAC) complex as a key mechanistic basis for the repression and activation of hTERT in normal human cells. A cell-based chemical screen was used to identify a small molecule, CGK1026, that derepresses hTERT expression. CGK1026 inhibits the recruitment of HDAC into E2F-pocket protein complexes assembled on the hTERT promoter. Chromatin immunoprecipitation analysis reveals dynamic alterations in hTERT promoter occupancy by E2F and pocket proteins according to the cell cycle-dependent regulation of hTERT. Dominant-negative or protein-knockout strategies to disrupt the assembly of E2F-pocket protein-HDAC complex derepress hTERT and telomerase activity. Taken together with the results on the regulatory function of these complexes in cellular senescence and tumorigenesis, our findings suggest that dynamic assembly of E2F-pocket protein-HDAC complex plays a central role in the regulation of hTERT in a variety of proliferative conditions (e.g., normal cycling, senescent, and tumor cells).
Colloidal Gels Assembled via a Temporary Interfacial Scaffold (2009)

The liquid-liquid phase separation of a binary solvent can be arrested by colloidal particles trapped at the interface [K. Stratford, Science 309, 2198 (2005)]. We show experimentally that the colloidal network so formed can remain stable after fully remixing the liquids, creating a new type of gel in which colloids in a single-phase solvent have locally planar coordination. We argue that this structure is likely maintained by primary-minimum Derjaguin-Landau-Verweg-Overbeek bonding of our charged colloids, created under strong compression by capillary forces. We present simulation evidence that the combination of a short-ranged attraction with a repulsive barrier can strongly stabilize such locally planar gels.
Taking Advantage of Multiple Scattering to Communicate with Time-Reversal Antennas (2003)

We present an experimental demonstration showing that, contrary to first intuition, the more scattering a mesoscopic medium is, the more information can be conveyed through it. We used a multiple input-multiple output configuration: a multichannel ultrasonic time-reversal antenna is used to transmit random series of bits simultaneously to different receivers which were only a few wavelengths apart. Whereas the transmission is free of error when multiple scattering occurs in the propagation medium, the error rate is huge in a homogeneous medium.
The Disulfide Bond Structure of Plasmodium Apical Membrane Antigen-1 (1996)

Apical membrane antigen-1 (AMA-1) of Plasmodium falciparum is one of the leading asexual blood stage antigens being considered for inclusion in a malaria vaccine. The ability of this molecule to induce a protective immune response has been shown to be dependent upon a conformation stabilized by disulfide bonds. In this study we have utilized the reversed-phase high performance liquid chromatography of dithiothreitol-reduced and nonreduced tryptic digests of Plasmodium chabaudi AMA-1 secreted from baculovirus-infected insect cells, in conjunction with N-terminal sequencing and electrospray-ionization mass spectrometry, to identify and assign disulfide-linked peptides. All 16 cysteine residues that are conserved in all known sequences of AMA-1 are incorporated into intramolecular disulfide bonds. Six of the eight bonds have been assigned unequivocally, whereas the two unassigned disulfide bonds connect two Cys-Xaa-Cys sequences separated by 14 residues. The eight disulfide bonds fall into three nonoverlapping groups that define three possible subdomains within the AMA-1 ectodomain. Although the pattern of disulfide bonds within subdomain III has not been fully elucidated, one of only two possible linkage patterns closely resembles the cystine knot motif found in growth factors. Sites of amino acid substitutions in AMA-1 that are well separated in the primary sequence are clustered by the disulfide bonds in subdomains II and III. These findings are consistent with the conclusion that these amino acid substitutions are defining conformational disulfide bond-dependent epitopes that are recognized by protective immune responses.
Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances (2009)

Array manufacturers originally designed single nucleotide polymorphism (SNP) arrays to genotype human DNA at thousands of SNPs across the genome simultaneously. In the decade since their initial development, the platform's applications have expanded to include the detection and characterization of copy number variation--whether somatic, inherited, or de novo--as well as loss-of-heterozygosity in cancer cells. The technology's impressive contributions to insights in population and molecular genetics have been fueled by advances in computational methodology, and indeed these insights and methodologies have spurred developments in the arrays themselves. This review describes the most commonly used SNP array platforms, surveys the computational methodologies used to convert the raw data into inferences at the DNA level, and details the broad range of applications. Although the long-term future of SNP arrays is unclear, cost considerations ensure their relevance for at least the next several years. Even as emerging technologies seem poised to take over for at least some applications, researchers working with these new sources of data are adopting the computational approaches originally developed for SNP arrays.
Mismatch between the 1997/1998 influenza vaccine and the major epidemic A(H3N2) virus strain as the cause of an inadequate vaccine-induced antibody response to this strain in the elderly (2000)

The success of influenza vaccination depends largely on the antigenic match between the influenza vaccine strains and the virus strains actually circulating during the season. In the past, this match has proved to be satisfactory in most seasons. In the 1997/1998 season, however, hemagglutination inhibition (HI) assays with ferret antisera indicated a considerable mismatch between the H3N2 vaccine component and the most prevalent epidemic influenza A(H3N2) virus. The results from antigenic analyses using pre- and postvaccination serum samples from volunteers of various ages, including residents of nursing homes who were more than 60 years of age, were in good agreement with the results obtained with ferret antisera. Homologous serum antibody responses to the H3N2 vaccine component as well as the cross-reactivity of the induced antibodies to the epidemic H3N2 strain, declined with increasing age of the vaccinees. As a consequence of these two effects, 84% of the vaccinees over 75 years of age did not develop HI antibody titers >/= 40 against the major H3N2 virus variant of 1997/1998, suggesting that they were not protected against infection with this virus variant. These findings support the current policy of the World Health Organization (WHO), which is to base worldwide influenza virus surveillance on results predominantly obtained by antigenic analyses of influenza virus isolates with ferret antisera in HI tests. If an antigenic mismatch is observed, the protective efficacy of the vaccine, especially for the elderly, may be insufficient. The observations also support the current policy to include the elderly in serologic efficacy trials.
Detection of Minimal Disease in Patients with Solid Tumors (1996)

The detection and elimination of minimal systemic disease in patients with solid tumors is one of the main current topics in clinical oncology. The present review focuses, therefore, on new diagnostic approaches to identify minimal disease in peripheral blood, bone marrow, and lymph nodes of patients with epithelial cancer as the major type of solid tumors in Western industrialized countries. These approaches may be used to improve tumor staging and monitoring of adjuvant therapies, as well as to detect tumor cell contamination in autologous stem cell grafts. Most investigators have developed either immunocytochemical assays with monoclonal antibodies to a variety of epithelial-specific cytoskeleton and membrane antigens or molecular methods based on the extensive amplification of a specific (c)DNA sequence by the polymerase-chain reaction (PCR). In immunocytochemical assays, antibodies to cytokeratins can be regarded as the most specific and sensitive probes to detect isolated epithelial tumor cells in bone marrow and blood. Molecular methods are based on the detection of either mutations in oncogenes and tumor suppressor genes (e.g., ki-ras and p53 genes) or the mRNA expression of tissue-specific and tumor-associated genes. mRNA species targeted in these assays encode cytokeratins, prostate-specific antigen, prostate-specific membrane antigen, carcinoembryonic antigen, and polymorphic-epithelial mucin. To introduce the available methods into clinical practice, standardized protocols need to be developed and validated in multi-center studies.
Algorithms for computing almost periodic steady-state response of nonlinear systems to multiple input frequencies (1981)

Two efficient algorithms are presented for obtaining steadystate solutions of nonlinear circuits and systems driven by two or more distinct frequency input signals. These algorithms are particularly useful in cases where the steady-state response is either not periodic, or is periodic but its period is too large for existing methods. The first algorithm is applicable to any circuit or system driven by any number <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p\geq 2</tex> of input frequencies. The second algorithm is restricted only to 2 input frequencies and is therefore significantly more efficient than the first algorithm. Both algorithms are formulated for systems described by an implicit system of nonlinear algebraic-differential equations, thereby obviating the need to write state equations. Numerous examples have been solved successfully using these two algorithms. A selection of some of these examples is given for illustrative purposes.
Toward Neurally-Inspired Computational Models of Narrative (Invited Talk) (2014)

In the spirit of the neuroscience theme of this year's meeting, I will describe a set of cognitive and neurophysiological phenomena that are important for the processing of narrative text at the discourse level. Text processing depends on sequential structure in language and also in the events that language describes. Semantic representations of events capture perceptual and motor properties of described situations, leveraging previous lived experience. Although a large number of neural systems are involved in processing narrative text, a constrained subset of systems are selectively engaged by discourse-level processing. To bring these phenomena together, I will present a simple neurally-inspired computational model of visual event processing that may provide a helpful analogy for some features of language processing.
Specific binding of basic fibroblast growth factor to basement membrane‐like structures and to purified heparan sulfate proteoglycan of the EHS tumor (1988)

The binding of iodinated basic fibroblast growth factor (bFGF) to low-density heparan sulfate proteoglycan purified from the Engelbreth Holm Swarm (EHS) sarcoma was investigated using different techniques. The tumor clearly contained bFGF, the level being comparable to that found in other tissues such as human or bovine brain. 125I bFGF strongly bound to the basement membrane-like matrix of EHS frozen sections as revealed by autoradiography. Iodinated bFGF bound to purified heparan sulfate proteoglycan but not to laminin or collagen type IV, three components isolated from the same tumor. In contrast, acidic fibroblast growth factor (aFGF) displayed negligible binding to heparan sulfate proteoglycan. Binding of bFGF to frozen sections and to purified proteoglycan could be strongly inhibited by heparin and was displaced by an excess of unlabeled factor and completely suppressed after heparitinase and heparinase treatments. Binding was a function of the salt concentration and was abolished at 0.6 M NaCl. Scatchard analysis indicated the affinity site had a Kd of about 30 nM, a value 10-15 higher than that recently reported by Moscatelli (J. Cell. Physiol., 131:123-130, 1987) in the case of the low-affinity binding sites present on the surface of baby hamster kidney (BHK) cells.
Studies on the Expression of Endothelin, Its Receptor Subtypes, and Converting Enzymes in Lung Cancer and in Human Bronchial Epithelium (2000)

Lung cancer, particularly small cell lung cancer (SCLC), is characterized by production of numerous peptides and their resulting clinical syndromes. Such peptides can act as autocrine growth factors for these tumors. In this study, we investigated the role of endothelin (ET)-1 in lung cancer. Using reverse transcription/polymerase chain reaction (RT-PCR), enzyme-linked immunosorbent assay, and immunocytochemistry, we screened a panel of lung cancer cell lines for ET-1, its receptors, and endothelin converting enzyme-1 (ECE-1), which generates the active form of ET-1. ET-1 messenger RNA was expressed in five of seven SCLC, four of four non-small cell lung cancer (NSCLC), and human bronchial epithelial (HBE) cells. The intracellular isoform of ECE-1, important in processing ET-1 if an autocrine growth loop is to function, was downregulated in the lung cancer cell lines as compared with expression of the extracellular isoform. Endothelin A receptor (ETAR), which mediates the mitogenic effects of ET-1 in prostate and ovarian cancer, was upregulated in HBE cells compared with expression in three of seven SCLC and two of four NSCLC cell lines. Endothelin B receptor (ETBR) was more widespread, being expressed in seven of seven SCLC, four of four NSCLC, and the HBE cells. We used flow cytometry to measure mobilization of intracellular calcium as a functional assay for the ETAR. These data concurred with the RT-PCR results, indicating that the ETAR was downregulated or was involved in an alternative signal transduction pathway in lung cancer, and no evidence of functional receptor mediating an autocrine growth loop was found. From our study, the data do not support the putative functional autocrine growth role of ET-1 in lung cancer. We propose instead that ET-1 may act as a paracrine growth factor for surrounding epithelial and endothelial cells via alternative pathways, promoting angiogenesis and stromal growth.