gebhart/patrepeval huggingface dataset:
Use of Collateral Text in Image Interpretation (1994)

Our research explores the interaction of textual and photographic information in document understanding. Specifically, we have been working on a computational model whereby textual captions are used as collateral information in the interpretation of the corresponding photographs. The final understanding of the picture and caption reflects a consolidation of the information obtained from each of the two sources and can thus be used in intelligent information retrieval tasks. The problem of performing general-purpose vision without a priori knowledge is very difficult at best. The concept of using collateral information in scene understanding has been explored in systems that use general scene context in the task of object identification. The work described here extends this notion by incorporating picture specific information. A multi-stage system PICTION which uses captions to identify humans in an accompanying photograph is described. 1 Introduction Our research has focused on devel...
Identification and characterization of human GRID2IP gene and rat Grid2ip gene in silico (2003)

Formin-homology proteins are implicated in the cell polarity control through the assembly of specific actin structures. FMNL1/KW-13/FMNL, FMNL2/KIAA1902/FHOD2, FMNL3/KIAA2014, DAAM1, DAAM2, DIAPH1 and DIAPH2 are Formin-homology proteins with the FDD domain, while Fmn1, Fmn2, FHOD1 and Grid2ip/Delphilin are Formin-homology proteins without the FDD domain. Mouse Grid2ip links glutamate receptor delta2 subunit with actin cytoskeleton and various signaling molecules. Here, we identified and characterized human GRID2IP gene as well as rat Grid2ip gene by using bioinformatics. Human GRID2IP gene was identified within human genome sequence CTD-2195F21 (AC072052.6). Human GRID2IP gene, consisting of 21 exons, was mapped to human chromosome 7p22.1. Rat Grid2ip gene, consisting of 21 exons, was identified within rat genome sequence CH230-82F18 (AC126572.3). Human GRID2IP (1020 aa) showed 91.7% total-amino-acid identity with rat Grid2ip (1024 aa), and 92.7% total-amino-acid identity with mouse Grid2ip. Human GRID2IP protein was found to consist of PDZ domain (codon 94-166), GRCAH domain (codon 204-269), FH1 domain (codon 559-621), and FH2 domain (codon 640-1005). GRCAH domain identified in this study was conserved among mammalian GRID2IP orthologs and mammalian CIP98/KIAA1526 orthologs. This is the first report on comprehensive characterization of human GRID2IP gene as well as on identification of GRCAH domain.
Cells expressing the DG42 gene from early Xenopus embryos synthesize hyaluronan. (1996)

DG42 is one of the main mRNAs expressed during gastrulation in embryos of Xenopus laevis. Here we demonstrate that cells expressing this mRNA synthesize hyaluronan. The cloned DG42 cDNA was expressed in rabbit kidney (RK13) and human osteosarcoma (tk-) cells using a vaccinia virus system. Lysates prepared from infected cells were incubated in the presence of UDP-N-acetylglucosamine and UDP-[14C]glucuronic acid. This yielded a glycosaminoglycan with a molecular mass of about 200,000 Da. Formation of this product was only observed in the presence of both substrates. The glycosaminoglycan could be digested with testicular hyaluronidase and with Streptomyces hyaluronate lyase but not with Serratia chitinase. Hyaluronan synthase activity could also be detected in homogenates of early Xenopus embryos, and the activity was found to correlate with the expression of DG42 mRNA at different stages of development. Synthesis of hyaluronan is thus an early event after midblastula transition, indicating its importance for the ensuing cell movements in the developing embryo. Our results are at variance with a recent report (Semino, C. E. & Robbins, P. W. (1995) Proc. Natl. Acad. Sci. USA 92, 3498-3501) that DG42 codes for an enzyme that catalyzes the synthesis of chitin-like oligosaccharides.
Development of anaplastic lymphoma kinase (ALK) small‐molecule inhibitors for cancer therapy (2007)

Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase (RTK) involved in the genesis of several human cancers; indeed, ALK was initially identified in constitutively activated and oncogenic fusion forms--the most common being nucleophosmin (NPM)-ALK--in a non-Hodgkin's lymphoma (NHL) known as anaplastic large-cell lymphoma (ALCL) and subsequent studies identified ALK fusions in the human sarcomas called inflammatory myofibroblastic tumors (IMTs). In addition, two recent reports have suggested that the ALK fusion, TPM4-ALK, may be involved in the genesis of a subset of esophageal squamous cell carcinomas. While the cause-effect relationship between ALK fusions and malignancies such as ALCL and IMT is very well established, more circumstantial links implicate the involvement of the full-length, normal ALK receptor in the genesis of additional malignancies including glioblastoma, neuroblastoma, breast cancer, and others; in these instances, ALK is believed to foster tumorigenesis following activation by autocrine and/or paracrine growth loops involving the reported ALK ligands, pleiotrophin (PTN) and midkine (MK). There are no currently available ALK small-molecule inhibitors approved for clinical cancer therapy; however, recognition of the variety of malignancies in which ALK may play a causative role has recently begun to prompt developmental efforts in this area. This review provides a succinct summary of normal ALK biology, the confirmed and putative roles of ALK fusions and the full-length ALK receptor in the development of human cancers, and efforts to target ALK using small-molecule kinase inhibitors.
Comparison of the virologic and immunologic responses of volunteers to live avian-human influenza A H3N2 reassortant virus vaccines derived from two different avian influenza virus donors (1989)

We compared the abilities of the six internal RNA segments of two avian influenza viruses, A/Mallard/Alberta/88/76 (H3N8) and A/Mallard/NY/6750/78 (H2N2), to confer attenuation on wild-type human influenza A/Bethesda/1/85 (H3N2) virus in seronegative adult volunteers. Live avian-human influenza A reassortant virus vaccines derived from either avian virus parent were comparable in the following properties: safety, infectivity, immunogenicity, and genetic stability. Since the avian influenza A/Mallard/Alberta/76 virus offered no clear advantage as a donor virus, we will conduct our future evaluations on live influenza A virus reassortants derived from the more extensively characterized avian influenza A/Mallard/NY/78 virus.
Conjugation of fluorescein isothiocyanate to antibodies. I. Experiments on the conditions of conjugation. (1970)

In the present study experiments concerning the conjugation of fluorescein isothiocyanate (FITC) to antibodies, which were previously performed by Goldstein, Slizys and Chase (1961), McKinney, Spillane and Pearce (1964) and Wood, Thompson and Goldstein (1965) are compiled, reproduced, extended and discussed. The results of the experiments indicate that if a relatively pure IgG, obtained by DEAE Sephadex chromatography, is conjugated with FITC of high quality, a maximal molecular fluorescein/protein (F/P) ratio is reached in a short time if reaction temperature, pH and protein concentration are high. Maximal labelling was obtained in 30–60 minutes at room temperature, pH 9.5 and an initial protein concentration of 25 mg/ml. The separation of optimally labelled antibodies from under- and over-labelled proteins may be achieved by gradient DEAE Sephadex chromatography. Electrophoretically distinct IgG molecules proved to have about the same affinity for FITC. A correlation between the activity of antibodies in fluorescent and precipitation techniques was found.
Spinal Cord Stimulation (2002)

Some clinical or experimental support can be found in the literature for 10 specific mechanisms or proposed mechanisms of spinal cord stimulation.
Detection of Genomic Variation by Selection of a 9 Mb DNA Region and High Throughput Sequencing (2009)

Detection of the rare polymorphisms and causative mutations of genetic diseases in a targeted genomic area has become a major goal in order to understand genomic and phenotypic variability. We have interrogated repeat-masked regions of 8.9 Mb on human chromosomes 21 (7.8 Mb) and 7 (1.1 Mb) from an individual from the International HapMap Project (NA12872). We have optimized a method of genomic selection for high throughput sequencing. Microarray-based selection and sequencing resulted in 260-fold enrichment, with 41% of reads mapping to the target region. 83% of SNPs in the targeted region had at least 4-fold sequence coverage and 54% at least 15-fold. When assaying HapMap SNPs in NA12872, our sequence genotypes are 91.3% concordant in regions with coverage > or = 4-fold, and 97.9% concordant in regions with coverage > or = 15-fold. About 81% of the SNPs recovered with both thresholds are listed in dbSNP. We observed that regions with low sequence coverage occur in close proximity to low-complexity DNA. Validation experiments using Sanger sequencing were performed for 46 SNPs with 15-20 fold coverage, with a confirmation rate of 96%, suggesting that DNA selection provides an accurate and cost-effective method for identifying rare genomic variants.
Trust Assessment from Observed Behavior: Toward and Essential Service for Trusted Network Computing (2006)

Modern distributed information systems handle increasingly critical data and computation, but there is no systematic way to assess whether a given part of the system can be entrusted with such data and computation on a continuous basis. In a highly interconnected networked environment, components with varying levels of trustworthiness must interact with each other. Occurrence and spread of attack induced failure imply that hosts once trusted cannot remain equally trusted all the time. System components and human operators can benefit from a scheme that assesses the trustworthiness of hosts i.e., the confidence that individual hosts are not corrupt, on a continuous basis by adjusting and adapting their behavior when a host’s trustworthiness diminishes. In this work in progress report we present an accusation based trust assessment scheme.
The Kinase LKB1 Mediates Glucose Homeostasis in Liver and Therapeutic Effects of Metformin (2005)

The Peutz-Jegher syndrome tumor-suppressor gene encodes a protein-threonine kinase, LKB1, which phosphorylates and activates AMPK [adenosine monophosphate (AMP)-activated protein kinase]. The deletion of LKB1 in the liver of adult mice resulted in a nearly complete loss of AMPK activity. Loss of LKB1 function resulted in hyperglycemia with increased gluconeogenic and lipogenic gene expression. In LKB1-deficient livers, TORC2, a transcriptional coactivator of CREB (cAMP response element-binding protein), was dephosphorylated and entered the nucleus, driving the expression of peroxisome proliferator-activated receptor-gamma coactivator 1alpha (PGC-1alpha), which in turn drives gluconeogenesis. Adenoviral small hairpin RNA (shRNA) for TORC2 reduced PGC-1alpha expression and normalized blood glucose levels in mice with deleted liver LKB1, indicating that TORC2 is a critical target of LKB1/AMPK signals in the regulation of gluconeogenesis. Finally, we show that metformin, one of the most widely prescribed type 2 diabetes therapeutics, requires LKB1 in the liver to lower blood glucose levels.
Structure and boosting activity of a starch-degrading lytic polysaccharide monooxygenase (2015)

Lytic polysaccharide monooxygenases (LPMOs) are recently discovered enzymes that oxidatively deconstruct polysaccharides. LPMOs are fundamental in the effective utilization of these substrates by bacteria and fungi; moreover, the enzymes have significant industrial importance. We report here the activity, spectroscopy and three-dimensional structure of a starch-active LPMO, a representative of the new CAZy AA13 family. We demonstrate that these enzymes generate aldonic acid-terminated malto-oligosaccharides from retrograded starch and boost significantly the conversion of this recalcitrant substrate to maltose by β-amylase. The detailed structure of the enzyme's active site yields insights into the mechanism of action of this important class of enzymes.
A practical approach to wavelength selectable DWDM sources (2002)

A wavelength selectable source within a transmitter for high-speed, dense wavelength division multiplexed systems must tune across a substantial number of channels while meeting rigorous system specifications in each channel. It must offer the same level of stability, reliability and ease of use as single wavelength counterparts. We examine a tunable source designed to meet the needs of high bit-rate DWDM systems for long-haul and metro applications.
Emergence and decay of the human Mx homolog in cancer patients during and after interferon-alpha therapy. (1990)

The human Mx, an interferon (IFN)-alpha- and IFN-beta-induced 76-kd protein, is a homolog (Mx-homolog) to the murine Mx protein, which is necessary and sufficient to provide adequate resistance against influenza virus in murine cells and in mice. Leukocytes from 36 patients with tumors (chronic myelogenic leukemia, hairy cell leukemia, and malignant melanoma) were monitored for their Mx-homolog content before, during, and after rIFN-alpha-2b therapy. Before therapy, only one patient was slightly positive for Mx-homolog. All 36 patients showed a significant increase of Mx-homolog in their mononuclear cells within the first day of IFN therapy. During therapy, the Mx-homolog levels remained elevated. After cessation of treatment, the Mx-homolog content in the mononuclear cells decreased slowly; within 2 weeks, it was about 20-30% of its value during therapy. However, even after 3 weeks, the Mx-homolog was still detectable. The maximally induced Mx-homolog concentration showed a significant correlation to the IFN dose given in vivo. These data indicate that the Mx-homolog is an excellent marker for monitoring the activity of IFN during IFN therapy. In addition, the in vivo endogenous activation of the IFN system might be detectable by the determination of the Mx-homolog despite the lack of circulating IFN.
Properties of Extracts from Defatted Rice Bran by Its Subcritical Water Treatment (2007)

Defatted rice bran was extracted with water and subcritical water at 50-250 degrees C for 5 min. The highest extract yield was achieved at 200 degrees C, at which the maximum amounts of protein and carbohydrate were also obtained. The total phenolic and furfural contents, radical scavenging activity, and antioxidative activity for the autoxidation of linoleic acid increased with increasing treatment temperature. The bran extracts exhibited emulsifying activity except for the extract prepared at 250 degrees C, which was concomitant with the disappearance of its high-molecular-mass substances. The extract prepared at 200 degrees C also had the highest emulsion-stabilizing activity.
A Nonionic Surfactant and Blood Viscosity (1973)

Poloxamer 188, (Pluronic F68), a nonionic surface active agent, was investigated for its effect on blood viscosity. Ten dogs were given poloxamer 188 prior to, during, and after one hour of total cardiopulmonary bypass. Viscosity measurements were compared in control and treated animals perfused for 6 and 12 hours. Six dogs received repeated intravenous injections of poloxamer 188; and in vitro studies were also performed. In all groups, administration of this agent was found to lower blood viscosity, without affecting hemodilution. However, the combination of hemodilution coupled with repeated hourly doses of poloxamer 188 caused the greatest and statistically most significant reduction of viscosity. The addition of poloxamer 188 to perfusion systems is advocated, and further investigation into its antisludging properties, mechanisms of action, and its future use in diseases characterized by high blood viscosity is encouraged.
Immunization with a peptide epitope (p369-377) from HER-2/neu leads to peptide-specific cytotoxic T lymphocytes that fail to recognize HER-2/neu+ tumors. (1998)

The oncogene HER-2/neu is genetically amplified and overexpressed in a large number of human adenocarcinomas and has been implicated in the tumorigenic phenotype. Although it is a nonmutated self-protein, it is barely detectable in adult tissues, and immune responses toward it have been described in a number of patients. It is, thus, an attractive candidate antigen for the immunotherapy of cancer patients. HLA-A2+ patients with metastatic breast, ovarian, or colorectal adenocarcinomas that overexpressed HER-2/neu were immunized with the HLA-A2-binding epitope p369-377 (p369). Patients were treated by repeated immunization with 1 mg of p369 in Freund's incomplete adjuvant every 3 weeks. Peripheral blood mononuclear cells were collected prior to immunization and following two and four immunizations and were stimulated in vitro with peptide and assayed for peptide and tumor recognition. In three of four patients, peptide-specific CTLs were detected in post- but not preimmunization blood. These CTLs recognized peptide-pulsed target cells at peptide concentrations of > or =1 ng/ml yet failed to react with a panel of HLA-A2+ HER-2/neu+ tumor lines. In addition, infecting HLA-A2+ cells with recombinant vaccinia virus encoding HER-2/neu or up-regulating HLA-A2 with IFN-gamma in HER-2/neu+ cells also failed to confer reactivity by p369-reactive T-cells. A T-cell response to the HLA-A2 binding epitope p369 can be easily generated by immunizing patients with peptide in Freund's incomplete adjuvant. However, the CTLs failed to react with HER-2/neu+ tumor cells. Further studies are needed to determine whether and how HER-2 might serve as an antigen for tumor immunotherapy.
Hepatocyte Transplantation: Development of New Systems for Liver Repopulation and Gene Therapy (1992)

Following recent advances in molecular and cell biology, development of hepatocyte transplantation has been considerably invigorated. To study the fate of hepatocytes transplanted into the liver, new strategies have included the use of endogenously marked transgenic hepatocytes. Release of peripherally quantifiable marker proteins by transgenic hepatocytes has provided noninvasive ways to determine hepatocyte engraftment and prolonged survival. Further characterization of intrasplenic hepatocyte transplantation has established this to be the most suitable method for targeting hepatocytes to the liver. Advances in gene cloning, retrovirology, and gene transfer technology have provided further tools for accomplishing gene therapy. Practical strategies for ex vivo gene therapy involving hepatocytes have been developed by exploiting these new technologies. The potential value of hepatocyte transplantation in acute hepatic failure has begun to be reexamined. Therefore, hepatocyte transplantation can be predicted to provide new ammunition for continuing our assault on untreatable disorders. Resolution of outstanding issues should accelerate this process.
Initial clinical evaluation of an immunoradiometric assay for CA 19‐9 using the nci serum bank (1984)

More than 1,600 coded sera obtained from blood donors and the NCI/Mayo Clinic Serum Bank were analyzed with an improved immunoradiometric assay for the carbohydrate antigenic determinant, CA 19-9. Results indicated that CA 19-9 is elevated in a large fraction of sera (67%) from patients with advanced adenocarcinomas of the upper gastrointestinal (GI) tract, including those with pancreatic, hepatobiliary and gastric carcinomas. Several of these sera had CA 19-9 exceeding 300,000 U/ml. A smaller fraction (18%) of patients with carcinomas of the large bowel had elevated serum CA 19-9 levels, the majority among patients with metastatic disease. In contrast, none of the healthy donors from the serum bank and only 4 of 1,023 of the blood donor specimens (0.4%) had CA 19-9 levels greater than or equal to 40 U/ml. Three of 235 sera (1.3%) from benign disease patients had levels of CA 19-9 in excess of 40 U/ml. These data suggest that the improved CA 19-9 immunoradiometric assay may have clinical utility as a diagnostic adjunct for adenocarcinoma of the upper GI tract and that the assay also may have some value in monitoring patients with advancing colorectal carcinoma, particularly in combination with CEA determinations. Rigorous prospective clinical trials will be necessary to verify these hypotheses.
Shifting the frequency response of switched-capacitor filters by nonuniform sampling (1991)

A clock with nonuniformly spaced sampling times can be used to shift the frequency response of switched-capacitor filters. By using such a clock, which deviates only slightly from a uniform sampling clock, small shifts in the frequency response of a switched-capacitor filter can be realized. The nonuniform sampling generates undesired modulation sidebands which are small if the deviation from uniform sampling is small. Computer simulations and measured data are presented to support equations that predict the frequency response shift and the amplitude of the undesired sidebands. This technique can be used to correct frequency response errors in monolithic switched-capacitor filters caused by capacitor ratio inaccuracies. It may also be useful in applications such as spectrum analyzers and tone generators.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cyclic AMP is both a pro‐apoptotic and anti‐apoptotic second messenger (2011)

The second messenger cyclic AMP (cAMP) can either stimulate or inhibit programmed cell death (apoptosis). Here, we review examples of cell types that show pro-apoptotic or anti-apoptotic responses to increases in cAMP. We also show that cells can have both such responses, although predominantly having one or the other. Protein kinase A (PKA)-promoted changes in phosphorylation and gene expression can mediate pro-apoptotic responses, such as in murine S49 lymphoma cells, based on evidence that mutants lacking PKA fail to undergo cAMP-promoted, mitochondria-dependent apoptosis. Mechanisms for the anti-apoptotic response to cAMP likely involve Epac (Exchange protein activated by cAMP), a cAMP-regulated effector that is a guanine nucleotide exchange factor (GEF) for the low molecular weight G-protein, Rap1. Therapeutic approaches that activate PKA-mediated pro-apoptosis or block Epac-mediated anti-apoptotisis may provide a means to enhance cell killing, such as in certain cancers. In contrast, efforts to block PKA or stimulate Epac have the potential to be useful in diseases settings (such as heart failure) associated with cAMP-promoted apoptosis.
Stability of ketoprofen-dextran ester prodrugs in homogenates of various segments of the pig GI tract. (1991)

Initial velocities of ketoprofen formation from ketoprofen-dextran ester prodrugs incubated in homogenates of various segments of the pig GI-tract were determined. Enzyme-mediated drug release was found in caecum and colon homogenates with their contents, whereas release rates in the stomach, duodenum, jejunum and ileum homogenates were comparable to those determined in pure buffer solutions of identical pH. In colon homogenates adjusted to various pH values between 6.0 and 7.9, little variation in release rates was observed. However, the contribution of enzyme-catalyzed drug regeneration to the overall initial velocity of ketoprofen formation increased significantly as a function of decreasing pH. The presence of several antibiotics and betamethasone in colon homogenates did not affect the drug activation process, whereas the addition of various enzyme inhibitors slowed down the ketoprofen release rates. During incubation in colon homogenates the average molecular weight of the dextran esters decreased. The drug release may therefore involve an initial fragmentation of the drug-liganded dextran chains carried out by dextranases secreted from the microflora which reside in the pig's large bowel.