gebhart/patrepeval huggingface dataset:
Serum autoantibodies as biomarkers for early cancer detection (2009)

Autoantibodies against autologous tumor-associated antigens have been detected in the asymptomatic stage of cancer and can thus serve as biomarkers for early cancer diagnosis. Moreover, because autoantibodies are found in sera, they can be screened easily using a noninvasive approach. Consequently, many studies have been initiated to identify novel autoantibodies relevant to various cancer types. To facilitate autoantibody discovery, approaches that allow the simultaneous identification of multiple autoantibodies are preferred. Five such techniques--SEREX, phage display, protein microarray, SERPA and MAPPing--are discussed here. In the second part of this review, we discussed autoantibodies found in the five most common cancers (lung, breast, colorectal, stomach and liver). The discovery of panels of tumor-associated antigens and autoantibody signatures with high sensitivity and specificity would aid in the development of diagnostics, prognostics and therapeutics for cancer patients.
Graph Neural Network-Based Anomaly Detection in Multivariate Time Series (2021)

Given high-dimensional time series data (e.g., sensor data), how can we detect anomalous events, such as system faults and attacks? More challengingly, how can we do this in a way that captures complex inter-sensor relationships, and detects and explains anomalies which deviate from these relationships? Recently, deep learning approaches have enabled improvements in anomaly detection in high-dimensional datasets; however, existing methods do not explicitly learn the structure of existing relationships between variables, or use them to predict the expected behavior of time series. Our approach combines a structure learning approach with graph neural networks, additionally using attention weights to provide explainability for the detected anomalies. Experiments on two real-world sensor datasets with ground truth anomalies show that our method detects anomalies more accurately than baseline approaches, accurately captures correlations between sensors, and allows users to deduce the root cause of a detected anomaly.
Growth Factor Signaling Induces Metastasis Genes in Transformed Cells: Molecular Connection between Akt Kinase and Osteopontin in Breast Cancer (2003)

Malignant tumors are characterized by excessive growth, immortalization, and metastatic spread, whereas benign tumors do not express gene products that mediate invasion. The molecular basis for this difference is incompletely understood. We have screened signal transduction molecules associated with the epidermal growth factor (EGF) receptor and have identified constitutive phosphorylation, indicative of activation, of Akt kinase in MT2994 breast cancer cells. In contrast, cells of the benign breast epithelial cell lines Comma-D and FSK-7 are immortalized through pathways that are independent of the EGF-phosphatidylinositol 3-kinase-Akt kinase cascade, but this is not associated with invasiveness. Transfection of constitutively active Akt kinase causes accelerated cell division and osteopontin expression. Conversely, dominant-negative Akt kinase slows cell cycle progression and suppresses osteopontin expression. The manipulation of osteopontin expression in this setting by transfection of the gene or its antisense does not affect the growth rate of the cells but alters cell motility and anchorage independence. Therefore, Akt kinase activates two distinct genetic programs: the program of growth and survival, which is independent of osteopontin expression, and the program of invasiveness and anchorage independence, which is mediated by osteopontin. These studies define Akt kinase as a molecular bridge between cell cycle progression and dissemination.
Characterization of the interaction between α2-macroglobulin and fibroblast growth factor-2: the role of hydrophobic interactions (2003)

Basic fibroblast growth factor (FGF-2) is important in development, wound healing and angiogenesis. The human plasma proteinase inhibitor alpha2-macroglobulin (alpha2M) binds to and regulates the biological activity of various growth factors, including FGF-2. FGF-2 binds specifically and saturably to native alpha2M and conformationally modified alpha2M (alpha2M*); however, the KD for FGF-2 binding to alpha2M* is 10-fold lower. This study investigates the biochemical nature of the interaction between FGF-2 and alpha2M* and localizes a possible FGF-2 binding site in the alpha2M subunit. FGF-2 binding to alpha2M* was not affected by shifts in pH between 6.5 and 10; however, increasing temperature decreased the KD for this interaction. The binding affinity of FGF-2 for alpha2M* also increased with increasing ionic strength. These results are consistent with the hypothesis that hydrophobic interactions predominate in promoting FGF-2 association with alpha2M*. Consistent with this hypothesis, FGF-2 bound to a glutathione S-transferase fusion protein containing amino acids 591-774 of the alpha2M subunit (FP3) and to a hydrophobic 16-amino-acid peptide (amino acids 718-733) within FP3. Specific binding of FGF-2 to the 16-amino-acid peptide was inhibited by excess transforming growth factor-beta1. When the 16-amino-acid peptide was chemically modified to neutralize the only two charged amino acids, FGF-2-binding activity was unaffected, supporting the predominant role of hydrophobic interactions. FGF-2 presentation to signalling receptors is influenced by growth factor binding to heparan sulphate proteoglycans (HSPGs), which is electrostatic in nature. Our results demonstrate that the interactions of FGF-2 with alpha2M* and HSPGs are biochemically distinct, suggesting that different FGF-2 sequences are involved.
Influence of LY 300164, an AMPA/kainate receptor antagonist upon the anticonvulsant action of antiepileptic drugs against aminophylline-induced seizures in mice. (2004)

LY 300164 [7-acetyl-3-(4-aminophenyl)-8,9-dihydro-8-methyl-7H-1,3-dioxazolo[4,5-h][2,3]-benzodiazepine], a novel AMPA/kainate receptor antagonist, administered intraperitoneally protected mice against aminophylline-induced seizures. At doses up to 0.5 mg/kg, which did not significantly affect the convulsant activity of aminophylline, it potentiated the protective activity of diazepam. On the other hand, LY 300164 used at the lowest protective dose of 1.0 mg/kg enhanced anticonvulsant activity of all antiepileptic drugs tested in this seizure model. However, LY 300164 neither alone nor combined with antiepileptic drugs, reduced aminophylline-induced mortality.
Novel carbon nanotube FET design with tunable polarity (2005)

Based on a novel device concept, we have fabricated high-performance carbon nanotube transistors exhibiting pure n- and p-type behavior, tunable by electrostatic and/or chemical doping, with excellent off-state performance and the smallest inverse subthreshold slope (63 mV/dec) reported to date. This is achieved by combined electrostatic and chemical doping profiles along the nanotube channel. The device design allows for aggressive oxide thickness scaling while maintaining the desired device characteristics.
An Antigenic Analysis of Lactobacillus Acidophilus (1962)

Journal Article An Antigenic Analysis of Lactobacillus Acidophilus Get access Constantine Efthymiou, Constantine Efthymiou From the Department of Microbiology, University of Maryland, College Park, Maryland Search for other works by this author on: Oxford Academic PubMed Google Scholar P. Arne Hansen P. Arne Hansen From the Department of Microbiology, University of Maryland, College Park, Maryland Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 110, Issue 3, May 1962, Pages 258–267, https://doi.org/10.1093/infdis/110.3.258 Published: 01 May 1962 Article history Received: 18 December 1961 Published: 01 May 1962
Characterization of Swine Infertility and Respiratory Syndrome (SIRS) Virus (Isolate ATCC VR-2332) (1992)

The characterization of an isolate of swine infertility and respiratory syndrome (SIRS) virus (ATCC VR-2332) is reported. A commercial cell line (CL2621) was used for the propagation of the virus for all assays. Laboratory studies indicate that this isolate is a fastidious, nonhemagglutinating, enveloped RNA virus. Cesium chloride-purified virions visualized by electron microscopy were spherical particles with an average diameter of 62 nm (range: 48-83 nm) and a 25-30 nm core surrounded by an envelope. Virus replication was restricted to the cytoplasm, as demonstrated by immunofluorescence. The virus did not react serologically with antisera to several common porcine viruses or with antisera to known viruses in the alphavirus, rubivirus, pestivirus, and ungrouped lactic dehydrogenase virus genera of the Togaviridae. However, convalescent sow sera and rabbit hyperimmune sera neutralized the SIRS virus at titers of 1:256 and 1:512, respectively. The virus was stable at 4 and -70 C, but was labile at 37 and 56 C. The properties of this isolate of SIRS virus resemble those of the family Togaviridae but do not match the described genera.
The Effects of Standard Anthracycline-Based Chemotherapy on Soluble ICAM-1 and Vascular Endothelial Growth Factor Levels in Breast Cancer (2004)

The findings support prior studies suggesting that sICAM-1 levels derive from sources other than endothelial cells. In addition, whereas the more immediate effect of chemotherapy is to reduce sICAM-1 and VEGF, continued treatment may lead to significant elevations.
A PDMS / PAPER HYBRID MICROFLUIDIC DEVICE INTEGRATED WITH GRAPHENE OXIDE-BASED NANO-BIOSENSORS FOR MULTIPLEXED PATHOGEN DETECTION (2013)

We have developed a polydimethylsiloxane (PDMS)/paper hybrid microfluidic system integrated with aptamerfunctionalized graphene oxide (GO) nano-biosensors for one-step multiplexed pathogen detection. The paper substrate used in this hybrid microfluidic system facilitated the integration of nano-biosensors on the chip, and avoided complicated surface treatment and aptamer probe immobilization in a PDMS or glass-only microfluidic system. Lactobacillus acidophilus was first used as a bacterium model to develop the microfluidic platform, with a limit of detection of 11.0 cfu/mL obtained. We have further successfully extended this method to multiplexed detection of two infectious pathogens-Staphylococcus aureus and Salmonella enterica.
Long-term exposure to abnormal glucose levels alters drug metabolism pathways and insulin sensitivity in primary human hepatocytes (2016)

Hyperglycemia in type 2 diabetes mellitus has been linked to non-alcoholic fatty liver disease, which can progress to inflammation, fibrosis/cirrhosis, and hepatocellular carcinoma. Understanding how chronic hyperglycemia affects primary human hepatocytes (PHHs) can facilitate the development of therapeutics for these diseases. Conversely, elucidating the effects of hypoglycemia on PHHs may provide insights into how the liver adapts to fasting, adverse diabetes drug reactions, and cancer. In contrast to declining PHH monocultures, micropatterned co-cultures (MPCCs) of PHHs and 3T3-J2 murine embryonic fibroblasts maintain insulin-sensitive glucose metabolism for several weeks. Here, we exposed MPCCs to hypo-, normo- and hyperglycemic culture media for ~3 weeks. While albumin and urea secretion were not affected by glucose level, hypoglycemic MPCCs upregulated CYP3A4 enzyme activity as compared to other glycemic states. In contrast, hyperglycemic MPCCs displayed significant hepatic lipid accumulation in the presence of insulin, while also showing decreased sensitivity to insulin-mediated inhibition of glucose output relative to a normoglycemic control. In conclusion, we show for the first time that PHHs exposed to hypo- and hyperglycemia can remain highly functional, but display increased CYP3A4 activity and selective insulin resistance, respectively. In the future, MPCCs under glycemic states can aid in novel drug discovery and mechanistic investigations.
Assessment of dyssynchrony in patients with severe heart failure by nuclear imaging: paradise lost and regained or lost and gone forever? (2005)

Cardiac resynchronization therapy, based on biventricular and/or left ventricular preexcitation, is a recently introduced therapeutic option for patients with severe heart failure and intraventricular conduction disturbances. The invasive nature and expense of resynchronization therapy has highlighted the need to prospectively identify optimal candidates, because of the poor correlation of QRS duration with patient response. Scintigraphy and positron emission tomography made it possible the research investigation of the pathophysiological consequences of cardiac conduction disturbances on myocardial contraction, metabolism, and perfusion. Increasing evidence shows that nuclear imaging techniques allow a comprehensive evaluation of the candidates to resynchronization. In fact, phase analysis of equilibrium radionuclide angiography enables a simple, quick and reliable measurement of both of inter- and intraventricular mechanical dyssynchrony, affording an optimal predictive accuracy of the response. In addition, being scintigraphic data highly reproducible, they are suitable for sequential longitudinal follow-up of the ventricular performance and mechanical dyssynchrony in patients implanted with devices.
100 GHz-spaced 8 × 43 Gbit/s DWDM unrepeateredtransmission over 163 km using duobinary-carrier-suppressed return-to-zero format (2001)

A novel modulation format, the duobinary carrier-suppressed return-to-zero format, is proposed; its bandwidth is less than 100 GHz at 43 Gbit/s. 100 GHz-spaced DWDM unrepeatered transmission is demonstrated over 163 km at +10 dBm/channel with a crosstalk penalty under 1 dB.
Retracted: Characterization of enhanced antibacterial effects of novel silver nanoparticles (2007)

In the present study, we report the preparation of silver nanoparticles in the range of 10-15 nm with increased stability and enhanced anti-bacterial potency. The morphology of the nanoparticles was characterized by transmission electron microscopy. The antibacterial effect of silver nanoparticles used in this study was found to be far more potent than that described in the earlier reports. This effect was dose dependent and was more pronounced against gram-negative bacteria than gram-positive organisms. Although bacterial cell lysis could be one of the reasons for the observed antibacterial property, nanoparticles also modulated the phosphotyrosine profile of putative bacterial peptides, which could thus affect bacterial signal transduction and inhibit the growth of the organisms.
An amber mutation in the gene encoding the beta' subunit of Escherichia coli RNA polymerase (1982)

An Escherichia coli strain carrying an amber mutation (UAG) in rpoC, the gene encoding the beta prime subunit of RNA polymerase, was isolated after mutagenesis with nitrosoguanidine. The mutation was moved into an unmutagenized strain carrying the supD43,74 allele, which encodes a temperature-sensitive su1 amber suppressor, and sue alleles, which enhance the efficiency of the suppressor. In this background, beta prime is not synthesized at high temperature. Suppression of the mutation by the non-temperature-sensitive amber suppressor su1+ yields a protein which is functional at all temperatures examined (30, 37, and 42 degrees C).
Research on Dengue during World War II (1952)

Most of the basic and significant contributions to our knowledge of dengue prior to World War II were made by honored members of the medical depart ment of the U. S. Army. Ashburn and Craig (1) provided the evidence for the viral etiology of the disease. Siler, Hall and Hitchens (2) clearly established the period of infectivity of dengue patients for Aedes aegypti mosquitoes, the period required for the development of the virus in these mosquitoes before they could transmit the infection, as well as the very long period during which these mos quitoes were capable of transmitting dengue. Simmons, St. John and Rey
Local Environmental Policy Capacity: A Framework for Research (1998)

Environmental protection at the sub-state level varies substantially.This paper proposes a framework for explaining variation in local environmental policy outcomes.The analysis proceeds in three parts.The first part briefly reviews some of the literature on state and local policy variations, noting how researchers tend to overlook local policy patterns and that most studies focus exclusively on policy outputs as opposed to outcomes.Part two develops a concept of policy capacity that can fruitfully guide longitudinal and crosssectional studies of local environmental protection activities in the United States.Part three draws attention to local environmental policy outputs and outcomes in California as an illustrative example of the policy capacity framework, showing that environmental protection policies and collective actions vary substantially from county to county in ways that can be captured by the indicators of local policy capacity.
Fredericamycin A a new antitumor antibiotic. II. Biological properties. (1981)

Fredericamycin A is a novel antibiotic produced by a soil isolate of Streptomyces griseus (FCRC-48). In vitro, fredericamycin A exhibits antibacterial, antifungal, and cytotoxic activities. In vivo, fredericamycin A exhibits very good antitumor activity against P388 mouse leukemia as well as the CD8F mammary tumor and marginal activity against B16 melanoma. Fredericamycin A failed to demonstrate any interaction with DNA and inhibited protein and RNA synthesis preferentially to DNA synthesis in Bacillus subtilis and P388 cells.
Methane monooxygenase mutants ofMethylosinus trichosporiumconstructed by marker-exchange mutagenesis (1995)

Methylosinus trichosporium OB3b synthesizes a soluble cytoplasmic methane monooxygenase when grown in copper-depleted medium and a membrane-bound particulate methane monooxygenase under copper-replete conditions. The genes encoding the hydroxylase component of soluble methane monooxygenase, carried on a plasmid in Escherichia coli, were insertionally inactivated using a kanamycin cassette and transferred back into M. trichosporium by conjugation. Marker-exchange mutagenesis, via a double homologous recombination event, yielded a soluble methane monooxygenase-negative mutant which grew only on methane using the particulate methane monooxygenase during copper-replete growth conditions, thus proving that the two methane oxidation systems in this methanotroph are genetically distinct.
Processing of the Pre‐β‐amyloid Protein by Cathepsin d is Enhanced by a Familial Alzheimer's Disease Mutation (1994)

A major pre-beta-amyloid protein695 (APP695) processing activity from Alzheimer's disease brain extracts was identified and found to be indistinguishable from the activity of cathepsin D.APP695 processing activity cleaved APP695 into a series of fragments that reacted on immunoblots to a monoclonal antibody (C286.8a) against beta-amyloid-(1-7)-peptide and cleaved N-dansyl-APP-(591-601)-amide at the Glu-Val and Met-Asp bonds. Fragments of 5.5 kDa and 10-12 kDa were formed from the cleavage of APP695 by cathepsin D at the Glu593-Val594 bond, and had the same N-terminus as a minor form of beta-amyloid released by cells. The Lys595-->Asn and Met596-->Leu substitutions found in a pedigree of familial Alzheimer's disease, increased the cathepsin D-catalyzed rate of accumulation of 5.5 kDa and 10-12 kDa C286.8a-reactive fragments 5-10fold. This substitution also increased the rate of N-dansyl-APP-(591-601)-amide cleavage at the Xaa-Asp bond by up to 41-fold. These observations suggest a role of cathepsin D in beta-amyloid formation under certain circumstances.
Solid phase DNA sequencing using the biotin-avidin system (1988)

A novel method for solid-phase DNA sequencing is described. A plasmid vector, pRIT27, has been designed to allow directional immobilization of double stranded plasmid to avidin agarose. The strategy involves enzymatic incorporation of 11-bio-dUTP into the plasmid and strand specific elution using alkali. The immobilized single stranded DNA is used as template for sequencing reactions and the resulting labelled oligonucleotides are eluted by alkali. The affinity gel containing the immobilized template is consecutively used for the four different dideoxy-nucleotide reactions. The solid-phase technique can be used for both primer specific or extension specific labelling. The possibility to use the system in automated DNA sequencing is discussed.
The vaccinia virus B9R protein is a 6 kDa intracellular protein that is non-essential for virus replication and virulence (2002)

Vaccinia virus (VV) strain Western Reserve gene B9R is shown to encode an intracellular 6 kDa protein that is expressed late during the infectious cycle. In vitro transcription and translation produced two polypeptides in the presence of microsomal membranes, but only the larger protein in the absence of membranes. The smaller protein sedimented with microsomes during centrifugation, suggesting it was inserted into the lipid membrane or into the microsomal lumen via the N-terminal hydrophobic signal sequence that was subsequently cleaved proteolytically. A VV mutant lacking B9R was constructed and found to replicate normally in cell culture and two in vivo models.
PD-1 on dendritic cells impedes innate immunity against bacterial infection (2009)

Programmed death one (PD-1) is an inducible molecule belonging to the immunoglobulin superfamily. It is expressed on activated T and B lymphocytes and plays pivotal roles in the negative regulation of adaptive immune responses. We report here an unexpected finding: that PD-1 could also be induced on splenic dendritic cells (DCs) by various inflammatory stimuli. Adoptive transfer of PD-1-deficient DCs demonstrates their superior capacity to wild-type DCs in innate protection of mice against lethal infection by Listeria monocytogenes. Furthermore, PD-1-deficient mice are also more resistant to the infection than wild-type controls, even in the absence of T and B cells, accompanied by elevated production of DC-derived interleukin-12 and tumor necrosis factor-alpha. Our results reveal a novel role of PD-1 in the negative regulation of DC function during innate immune response.
Migration of human monocytes in response to vascular endothelial growth factor (VEGF) is mediated via the VEGF receptor flt-1 (1996)

Treatment of human monocytes with vascular endothelial growth factor (VEGF) isolated from tumor cell supernatants was reported to induce monocyte activation and migration. In this study we show that recombinant human VEGF165, and VEGF121 had a maximal effect on human monocyte migration at 65 to 250 pmol/L. Chemotactic activity of VEGF165 was inhibited by a specific antiserum against VEGF, by heat treatment of VEGF165, and by protein kinase inhibitors. In addition, we could show that VEGF-stimulated monocyte migration is mediated by a pertussis toxin-sensitive GTP-binding protein. Placenta growth factor (PlGF152), a heparin-binding growth factor related to VEGF, was also chemotactic for monocytes at concentrations between 2.5 and 25 pmol/L. In accordance with these findings, human monocytes showed specific and saturable binding for 125I-VEGF165 (half-maximal binding at 1 to 1.5 nmol/L). Using Northern blot analysis, we further could show that human monocytes express only the gene for the VEGF receptor type, flt-1, but not for the second known VEGF receptor, KDR. Resting monocytes expressed low levels of flt-1 gene only. Brief exposure (2 to 4 hours) of human monocytes to lipopolysaccharide, a prototypic monocyte activator, led to a significant upregulation of the flt-1 mRNA level. The results presented here suggest that monocyte chemotaxis in response to VEGF and most likely to PlGF152 is mediated by flt-1 and thus show a possible function for the VEGF-receptor flt-1.