gebhart/patrepeval huggingface dataset:
Quantitative multiplexed analysis of ErbB family coexpression for primary breast cancer prognosis in a large retrospective cohort (2009)

This work shows that the combined analysis of protein expression improved prognostic classification, and that multiplexed models were superior to any single-marker-based method for prediction of 10-year survival. These methods illustrate a protein-based, multiplexed approach that could more accurately identify patients for targeted therapies.
Micro tensile-test of silicon film having different crystallographic orientations (2002)

Uniaxial tensile testing of a single-crystal silicon film was carried out on a silicon chip. A tensile testing system was integrated on a silicon chip. A process for fabricating a test chip containing a specimen whose tensile axis has an arbitrary orientation was developed. The mechanical properties, such as elastic modulus and fracture strain, of silicon films having different orientations of <100>, <110>, and <111>, are tested and compared.
Material Selection/Fabrication Issues for Thermoplastic Fiber Placement (1995)

The Manufacture of Advanced Composite Submarine Structures (MACSS) program is part of the Advanced Research Projects Agency (ARPA) Maritime Systems Technology Office, Advanced Submarine Technology (AST) program. The program is developing the material product forms, processes, and equipment for automated fabrication of lowcost composite submarine structures. These developments will be demonstrated through fabrication and delivery of subscale and fullscale components of the Composite Dry Deck Shelter (CDDS). This paper will discuss the McDonnell Douglas Aerospace (MDA) thermoplastic fiber placement process, material selection, and machine that make fabrication of largescale submarine structures possible.
Induction of Heme Oxygenase 1 by Nitrosative Stress (2002)

Nitric oxide and S-nitrosothiols modulate a variety of important physiological activities. In vascular cells, agents that release NO and donate nitrosonium cation (NO(+)), such as S-nitrosoglutathione, are potent inducers of the antioxidant protein heme oxygenase 1 (HO-1) (Foresti, R., Clark, J. E., Green, C. J., and Motterlini, R. (1997) J. Biol. Chem. 272, 18411-18417; Motterlini, R., Foresti, R., Bassi, R., Calabrese, V., Clark, J. E., and Green, C. J. (2000) J. Biol. Chem. 275, 13613-13620). Here, we report that Angeli's salt (AS) (0.25-2 mm), a compound that releases nitroxyl anion (NO(-)) at physiological pH, induces HO-1 mRNA and protein expression in a concentration- and time-dependent manner, resulting in increased heme oxygenase activity in rat H9c2 cells. A time course analysis revealed that NO(-)-mediated HO-1 expression is transient and gradually disappears within 24 h, in accordance with the short half-life of AS at 37 degrees C (t(12) = 2.3 min). Interestingly, multiple additions of AS at lower concentrations (50 or 100 microm) over a period of time still promoted a significant increase in heme oxygenase activity. Experiments performed using a NO scavenger and the NO electrode confirmed that NO(-), not NO, is the species involved in HO-1 induction by AS; however, the effect on heme oxygenase activity can be amplified by accelerating the rate of NO(-) oxidation. N-Acetylcysteine almost completely abolished AS-mediated induction of HO-1, whereas a glutathione synthesis inhibitor (buthionine sulfoximine) significantly decreased heme oxygenase activation by AS, indicating that sulfydryl groups are crucial targets in the regulation of HO-1 expression by NO(-). We conclude that NO(-), in analogy with other reactive nitrogen species, is a potent inducer of heme oxygenase activity and HO-1 protein expression. These findings indicate that heme oxygenase can act both as a sensor to and target of redox-based mechanisms involving NO and extend our knowledge on the biological function of HO-1 in response to nitrosative stress.
Data storage and scheduling of the large-scale terrain (2007)

Based on the terrain walkthrough system of rendering multi-pipe scene,division storage of terrain data and strategy of dynamical scheduling are studied and a reasonable method of terrain data organization and scheduling is designed,which shortens the initialization time and enhances the frame rate,so that the display smoothness and continuity of the large-scale scene walkthrough system are realized.
Tuning the Excited-State Properties of Platinum(II) Diimine Dithiolate Complexes (1996)

Two series of Pt(diimine)(dithiolate) complexes have been prepared in order to investigate the effects of molecular design on the excited-state properties of this chromophore. The first series comprises Pt(dbbpy)(dithiolate) complexes where dbbpy = 4,4‘-di-tert-butyl-2,2‘-bipyridine and the dithiolates are 1-(tert-butylcarboxy)-1-cyanoethylene-2,2-dithiolate (tbcda), 1-diethylphosphonate-1-cyanoethylene-2,2-dithiolate (cpdt), 6,7-dimethyl-quinoxaline-2,3-dithiolate (dmqdt), maleonitriledithiolate (mnt), and toluene-3,4-dithiolate (tdt). The second series comprises Pt(diimine)(tdt) complexes where the diimines are 3,4,7,8-tetramethyl-1,10-phenanthroline (tmphen), 4,4‘-di-tert-butyl-2,2‘-bipyridine (dbbpy), 4,4‘-dimethyl-2,2‘-bipyridine (dmbpy), 2,2‘-bipyridine (bpy), 1,10-phenanthroline (phen), 5-chloro-1,10-phenanthroline (Cl-phen), 4,4‘-dichloro-2,2‘-bipyridine (Cl2bpy), and 4,4‘-bis(ethoxycarbonyl)-2,2‘-bipyridine (EC-bpy). All of the compounds display solvatochromic absorption bands and solution luminescence, which are attributed to a common charge-transfer-to-diimine excited state. The excited-state energies can be tuned by approximately 1 eV through ligand variation. Solution lifetimes range from 1 ns to over 1000 ns and Φem range from 6.4 × 10-3 to less than 10-5 in CH2Cl2. Based on these data, the nonradiative and radiative decay rate constants have been calculated. For the Pt(diimine)(tdt) series, the nonradiative decay rate constants increase exponentially with decreasing energy, in agreement with the Energy Gap Law, while those for the Pt(dbbpy)(dithiolate) complexes do not exhibit a similar correlation. Excited-state redox potentials have been estimated for all of the complexes from spectroscopic and electrochemical data. The ability to tune the driving force for bimolecular excited-state electron-transfer reactions has been demonstrated for eight of the complexes using reductive and oxidative quenching experiments.
Rapid Subfunctionalization Accompanied by Prolonged and Substantial Neofunctionalization in Duplicate Gene Evolution (2005)

Gene duplication is the primary source of new genes. Duplicate genes that are stably preserved in genomes usually have divergent functions. The general rules governing the functional divergence, however, are not well understood and are controversial. The neofunctionalization (NF) hypothesis asserts that after duplication one daughter gene retains the ancestral function while the other acquires new functions. In contrast, the subfunctionalization (SF) hypothesis argues that duplicate genes experience degenerate mutations that reduce their joint levels and patterns of activity to that of the single ancestral gene. We here show that neither NF nor SF alone adequately explains the genome-wide patterns of yeast protein interaction and human gene expression for duplicate genes. Instead, our analysis reveals rapid SF, accompanied by prolonged and substantial NF in a large proportion of duplicate genes, suggesting a new model termed subneofunctionalization (SNF). Our results demonstrate that enormous numbers of new functions have originated via gene duplication.
Fat cell adrenergic receptors and the control of white and brown fat cell function (1993)

Five adrenoceptor subtypes are involved in the adrenergic regulation of white and brown fat cell function. The effects on cAMP production and cAMP-related cellular responses are mediated through the control of adenylyl cyclase activity by the stimulatory beta 1-, beta 2-, and beta 3-adrenergic receptors and the inhibitory alpha 2-adrenoceptors. Activation of alpha 1-adrenoceptors stimulates phosphoinositidase C activity leading to inositol 1,4,5-triphosphate and diacylglycerol formation with a consequent mobilization of intracellular Ca2+ stores and protein kinase C activation which trigger cell responsiveness. The balance between the various adrenoceptor subtypes is the point of regulation that determines the final effect of physiological amines on adipocytes in vitro and in vivo. Large species-specific differences exist in brown and white fat cell adrenoceptor distribution and in their relative importance in the control of the fat cell. Functional beta 3-adrenoceptors coexist with beta 1- and beta 2-adrenoceptors in a number of fat cells; they are weakly active in guinea pig, primate, and human fat cells. Physiological hormones and transmitters operate, in fact, through differential recruitment of all these multiple alpha- and beta-adrenoceptors on the basis of their relative affinity for the different subtypes. The affinity of the beta 3-adrenoceptor for catecholamines is less than that of the classical beta 1- and beta 2-adrenoceptors. Conversely, epinephrine and norepinephrine have a higher affinity for the alpha 2-adrenoceptors than for beta 1-, 2-, or 3-adrenoceptors. Antagonistic actions exist between alpha 2- and beta-adrenoceptor-mediated effects in white fat cells while positive cooperation has been revealed between alpha 1- and beta-adrenoceptors in brown fat cells. Homologous down-regulation of beta 1- and beta 2-adrenoceptors is observed after administration of physiological amines and beta-agonists. Conversely, beta 3- and alpha 2-adrenoceptors are much more resistant to agonist-induced desensitization and down-regulation. Heterologous regulation of beta-adrenoceptors was reported with glucocorticoids while sex-steroid hormones were shown to regulate alpha 2-adrenoceptor expression (androgens) and to alter adenylyl cyclase activity (estrogens).
Spectrum and Prevalence of Fungi Infecting Deep Tissues of Lower-Limb Wounds in Patients with Type 2 Diabetes (2010)

The prevalence rate and spectrum of fungi infecting deep tissues of diabetic lower-limb wounds (DLWs) have not been previously studied. Five hundred eighteen (382 male and 136 female) consecutive patients with type 2 diabetes hospitalized due to infected lower-limb wounds were enlisted in this study. Deep tissue (approximately 0.5- x 0.5-cm size) taken perioperatively from the wound bed was cultured for fungi. Fungi was found in 27.2% (141/518) of the study population. Candida parapsilosis (25.5%), Candida tropicalis (22.7%), Trichosporon asahii (12.8%), Candida albicans (10.6%), and Aspergillus species (5.0%) were the most predominant fungal isolates. Of the fungal isolates, 17.7% were resistant to itraconazole, 6.9% were resistant to amphotericin B, 6.9% were resistant to voriconazole, 3.9% were resistant to fluconazole, and 1.5% were resistant to flucytosine. Of the population, 79.7% (413/518) had bacterial infection in deep tissue. The predominant isolates were Enterococcus faecalis (14.1%), Staphylococcus aureus (12.2%), and Pseudomonas aeruginosa (10.8%). Mixed fungal and bacterial infections were seen in 21.4% of patients, while 5.8% had only fungal infection and 58.3% had only bacterial infections. Another 14.5% had neither bacteria nor fungi in the deep tissue. Patients with higher glycosylated hemoglobin levels had significantly more fungal infections. Our study reveals that deep-seated fungal infections are high in DLWs. In the context of delayed wound healing and amputation rates due to DLWs, it is important to study the pathogenicity of fungi in deep tissues of DLWs and their possible contribution to delayed wound healing. The role of antifungal agents in wound management needs to be evaluated further.
Osthol Ameliorates Kidney Damage and Metabolic Syndrome Induced by a High-Fat/High-Sugar Diet (2021)

Excessive intake of fructose results in metabolic syndrome (MS) and kidney damage, partly mediated by its metabolism by fructokinase-C or ketohexokinase-C (KHK-C). Osthol has antioxidant properties, is capable of regulating adipogenesis, and inhibits KHK-C activity. Here, we examined the potential protective role of osthol in the development of kidney disease induced by a Western (high-fat/high-sugar) diet. Control rats fed with a high-fat/high-sugar diet were compared with two groups that also received two different doses of osthol (30 mg/kg/d or 40 mg/kg/d body weight BW). A fourth group served as a normal control and received regular chow. At the end of the follow-up, kidney function, metabolic markers, oxidative stress, and lipogenic enzymes were evaluated. The Western diet induced MS (hypertension, hyperglycemia, hypertriglyceridemia, obesity, hyperuricemia), a fall in the glomerular filtration rate, renal tubular damage, and increased oxidative stress in the kidney cortex, with increased expression of lipogenic enzymes and increased kidney KHK expression. Osthol treatment prevented the development of MS and ameliorated kidney damage by inhibiting KHK activity, preventing oxidative stress via nuclear factor erythroid 2-related factor (Nrf2) activation, and reducing renal lipotoxicity. These data suggest that the nutraceutical osthol might be an ancillary therapy to slow the progression of MS and kidney damage induced by a Western diet.
Promoter methylation status of p15 and p21 genes in HPP-CFCs of bone marrow of patients with psoriasis (2009)

Psoriasis is an inflammatory disease related to dysfunctional immunity. The dysfunctional immunity may influence the haematopoietic microenvironment or haematopoiesis in psoriasis. However, direct evidence is lacking. Our objective was to investigate the proliferation of hematopoietic cells from psoriatic patients and any link between the promoter methylation status of p15 and p21 genes and the colony formation ability of high proliferative potential colony-forming cells (HPP-CFCs). Marrow mononuclear cells were isolated from the bone marrow of psoriatic patients and normal controls by density gradient centrifugalization. Colony forming assays of HPP-CFCs were performed in vitro in methylcellulose semi-solid culture medium. mRNA expression and the promoter methylation status of p15 and p21 genes in HPP-CFCs were studied by semi-quantitative RT-PCR and methylation-specific PCR respectively. In methycellulose semi-solid culture system, the colony count of HPP-CFCs in bone marrow of psoriatic patients was significantly less than that of normal controls. Moreover, significantly lower positive frequencies of promoter methylation and higher transcription levels for p15 and p21 genes were observed in psoriasis in comparison to normal volunteers. The lower promoter methylation of p15 and p21 genes may be an important mechanism for the dysfunctional growth regulation pathways in HPP-CFCs in psoriasis.
Issues in data stream management (2003)

Traditional databases store sets of relatively static records with no pre-defined notion of time, unless timestamp attributes are explicitly added. While this model adequately represents commercial catalogues or repositories of personal information, many current and emerging applications require support for on-line analysis of rapidly changing data streams. Limitations of traditional DBMSs in supporting streaming applications have been recognized, prompting research to augment existing technologies and build new systems to manage streaming data. The purpose of this paper is to review recent work in data stream management systems, with an emphasis on application requirements, data models, continuous query languages, and query evaluation.
Regulating Intracellular Antiviral Defense and Permissiveness to Hepatitis C Virus RNA Replication through a Cellular RNA Helicase, RIG-I (2005)

ABSTRACT Virus-responsive signaling pathways that induce alpha/beta interferon production and engage intracellular immune defenses influence the outcome of many viral infections. The processes that trigger these defenses and their effect upon host permissiveness for specific viral pathogens are not well understood. We show that structured hepatitis C virus (HCV) genomic RNA activates interferon regulatory factor 3 (IRF3), thereby inducing interferon in cultured cells. This response is absent in cells selected for permissiveness for HCV RNA replication. Studies including genetic complementation revealed that permissiveness is due to mutational inactivation of RIG-I, an interferon-inducible cellular DExD/H box RNA helicase. Its helicase domain binds HCV RNA and transduces the activation signal for IRF3 by its caspase recruiting domain homolog. RIG-I is thus a pathogen receptor that regulates cellular permissiveness to HCV replication and, as an interferon-responsive gene, may play a key role in interferon-based therapies for the treatment of HCV infection.
Detection of endogenous macrophage colony-stimulating factor (M-CSF) in human blood. (1989)

We have detected endogenous human macrophage colony-stimulating factor (M-CSF) in blood of normal individuals, using a novel RIA that accurately measures M-CSF concentrations as low as 60 U/ml (1.2 ng/ml) in the presence of serum proteins. The RIA uses an antibody to highly purified recombinant human M-CSF and is calibrated to a mouse bone marrow colony-forming assay. Ten samples of normal human blood plasma contained an average 118 +/- 9 U/ml of M-CSF, and similar concentrations were detected in serum prepared from the same individuals. RIA-positive samples contained biologically active M-CSF, as determined in a colony assay performed on mouse bone marrow cells. The M-CSF biological activity was removed by specific immune precipitation and inhibited by addition of M-CSF antibody. Physical characterization of plasma M-CSF was done by immunoblotting after partial purification on controlled pore glass and immunoaffinity chromatography. The major reduced protein species of plasma M-CSF had an apparent molecular weight of about 24 kd, and minor species of 30, 45, and 60-70 kd were also present. The RIA results on ten normal individuals suggest that endogenous circulating M-CSF is present at a low but detectable concentration. This RIA can be used to measure M-CSF in clinical samples that contain serum proteins and other growth factors that may interfere with accurate bioassay determinations.
Megakaryocyte Potentiation Factor Cleaved from Mesothelin Precursor Is a Useful Tumor Marker in the Serum of Patients with Mesothelioma (2006)

Using new mAbs to MPF, we showed that MPF is secreted by several mesothelioma cell lines and is frequently elevated in the blood of patients with mesothelioma. Measurement of MPF may be useful in following the response of mesothelioma to treatment.
ALTERATIONS OF MACROPHAGE FUNCTIONS BY MEDIATORS FROM LYMPHOCYTES (1971)

Sensitized lymphocytes were incubated in vitro with the specific antigen Supernatants from these cultures were chromatographed on Sephadex G-100 columns. Supernatant fractions containing MIF, chemotactic factor, and lymphotoxin, but free of antigen and antibody, were incubated with normal peritoneal exudate macrophages. Macrophage adherence, phagocytosis, spreading, motility, and direct hexose monophosphate oxidation were enhanced, while protein synthesis was unaffected. Thus, antigen-stimulated lymphocytes secrete a factor or factors which enhance certain macrophage functions. Implications for models of cellular immunity and cellular hypersensitivity are discussed.
Drought- and salt-tolerant plants result from overexpression of the AVP1 H + -pump (2001)

Transgenic plants overexpressing the vacuolar H(+)-pyrophosphatase are much more resistant to high concentrations of NaCl and to water deprivation than the isogenic wild-type strains. These transgenic plants accumulate more Na(+) and K(+) in their leaf tissue than the wild type. Moreover, direct measurements on isolated vacuolar membrane vesicles derived from the AVP1 transgenic plants and from wild type demonstrate that the vesicles from the transgenic plants have enhanced cation uptake. The phenotypes of the AVP1 transgenic plants suggest that increasing the vacuolar proton gradient results in increased solute accumulation and water retention. Presumably, sequestration of cations in the vacuole reduces their toxic effects. Genetically engineered drought- and salt-tolerant plants could provide an avenue to the reclamation of farmlands lost to agriculture because of salinity and a lack of rainfall.
ARGININE-RICH PROTEINS OF POLYMORPHONUCLEAR LEUKOCYTE LYSOSOMES (1968)

The cationic antibacterial proteins of rabbit PMN lysosomes have been resolved into at least five subfractions. Each of these showed substantial selectivity in its antibacterial action against several pathogenic bacteria, including two smooth and two rough Escherichia coli strains, three Staphylococcus aureus strains, one S. albus, three proteus species and four different cultures of streptococcus. Each of the subfractions possesses a different electrophoretic mobility. Amino acid analyses of the three most cationic components revealed high contents of arginine consistent with their relative electrophoretic mobilities and very high arginine to lysine ratios. Aromatic amino acids were present in very low concentrations in these proteins and their light absorption at 2800 A was correspondingly weak. The evidence of antibacterial specificity, along with marked differences in the arginine-lysine ratios, shows that the cationic antibacterial components of rabbit PMN lysosomes are biologically and chemically heterogeneous.
Preparation, Characterization, and Clinical Implications of Human Decellularized Adipose Tissue Extracellular Matrix (hDAM): A Comprehensive Review (2015)

Fat grafting is commonly employed by plastic and reconstructive surgeons to address contour abnormalities and soft-tissue defects; however, because retention rates and thus volume filling effects are unpredictable, there is a search for new and innovative approaches. Initial studies on the use of human decellularized adipose tissue extracellular matrix (hDAM) show promise for its use not only in tissue engineering, but also in fat grafting. In this review, we examine and analyze the literature for the preparation, characterization, and use of hDAM and its derivatives in tissue engineering and plastic surgery applications. All studies reviewed involve physical, chemical, and/or biological treatment stages for the preparation of hDAM; however a distinction should be made between detergent and nondetergent-based processing, the latter of which appears to preserve the native integrity of the hDAM while most-efficiently achieving complete decellularization. Methods of hDAM characterization vary among groups and included simple and immunohistochemical staining, biochemical assays, 3-dimensional (3D) imaging, and mechano-stress testing, all of which are necessary to achieve a comprehensive description of this novel tissue. Finally, we examine the various preclinical models utilized to optimize hDAM performance, which primarily include the addition of adipose-derived stem cells or cross-linking agents. Overall, hDAM appears to be a promising adjunct in fat-grafting applications or even possibly as a stand-alone soft-tissue filler with off-the-shelf potential for commercial applications.
Shaping regularization in geophysical-estimation problems (2007)

Abstract Regularization is a required component of geophysical-estimation problems that operate with insufficient data. The goal of regularization is to impose additional constraints on the estimated model. I introduce shaping regularization, a general method for imposing constraints by explicit mapping of the estimated model to the space of admissible models. Shaping regularization is integrated in a conjugate-gradient algorithm for iterative least-squares estimation. It provides the advantage of better control on the estimated model in comparison with traditional regularization methods and, in some cases, leads to a faster iterative convergence. Simple data interpolation and seismic-velocity estimation examples illustrate the concept.