gebhart/patrepeval huggingface dataset:
Occurrence of p53 Gene Abnormalities in Gastric Carcinoma Tumors and Cells Lines (1991)

We explored the state of the p53 gene in gastric cancer. Using one or more methods, we examined 15 specimens from primary carcinomas (14 tumors, one cell line), five cell lines derived from metastases, and seven paired samples of nonmalignant gastric mucosa. Sequence analyses of complementary DNA containing the entire p53 gene open reading frame demonstrated abnormalities in one of five samples from primary tumors and in all five samples from metastases. The single cell line derived from a primary carcinoma had no abnormality of the gene. The six abnormalities included four point mutations, one base-pair deletion resulting in a frame shift, and a 24 base-pair deletion caused by an intronic point mutation (as determined by sequence analysis of genomic DNA). Four of the six mutations mapped to regions highly conserved among species or involved in simian virus 40 T-antigen binding. Restriction fragment length polymorphism studies confirmed that chromosome 17p allelic deletions occur only in a minority of primary tumors, but that they may occur more frequently in metastases. Northern blotting and ribonuclease protection assays detected only a fraction of the p53 gene abnormalities detected by sequencing. Our findings indicate that mutations of the p53 gene are relatively rare in primary gastric tumors but appear to be relatively frequent in cell lines derived from metastatic lesions. Our results may help in understanding the molecular events associated with progression and metastasis in gastric carcinoma.
HrpW of Erwinia amylovora , a New Harpin That Contains a Domain Homologous to Pectate Lyases of a Distinct Class (1998)

Harpins, such as HrpN of Erwinia amylovora, are extracellular glycine-rich proteins that elicit the hypersensitive reaction (HR). We identified hrpW of E. amylovora, which encodes a protein similar to known harpins in that it is acidic, rich in glycine and serine, and lacks cysteine. A putative HrpL-dependent promoter was identified upstream of hrpW, and Western blot analysis of hrpL mutants indicated that the production of HrpW is regulated by hrpL. HrpW is secreted via the Hrp (type III) pathway based on analysis of wild-type strains and hrp secretion mutants. When infiltrated into plants, HrpW induced rapid tissue collapse, which required active plant metabolism. The HR-eliciting activity was heat stable and protease sensitive. Thus, we concluded that HrpW is a new harpin. HrpW of E. amylovora consists of two domains connected by a Pro and Ser-rich sequence. A fragment containing the N-terminal domain was sufficient to elicit the HR. Although no pectate lyase activity was detected, the C-terminal region of HrpW is homologous to pectate lyases of a unique class, suggesting that HrpW may be targeted to the plant cell wall. Southern analysis indicated that hrpW is conserved among several Erwinia species, and hrpW, provided in trans, enhanced the HR-inducing ability of a hrpN mutant. However, HrpW did not increase the virulence of a hrpN mutant in host tissue, and hrpW mutants retained the wild-type ability to elicit the HR in nonhosts and to cause disease in hosts.
Expression of DBC1 and Androgen Receptor Predict Poor Prognosis in Diffuse Large B Cell Lymphoma (2013)

We demonstrate that the expression of DBC1 and AR are significant prognostic indicators for DLBCL patients, especially for unfavorable non-GCB-type DLBCL.
A novel p-channel NAND-type flash memory with 2-bit/cell operation and high programming throughput (&lt;20 MB/sec) (2006)

A novel p-channel NAND-type non-volatile flash memory using nitride-trapping device is presented. The p-channel device is programmed by very efficient band-to-band tunneling hot electron (BBHE), and erased by self-converging channel hole tunneling. An ultra-thin bandgap engineered ONO tunneling dielectric as presented in H. T. Lue et al. (2005) is adopted to achieve efficient hole-tunneling erase at high electric field, but yet good data retention at low field. The operation of physically 2-bit/cell NAND-type architecture with depletion mode device (V/sub T/ > 0) is illustrated. Excellent P/E cycling endurance, data retention and read disturb immunity are demonstrated. This new non-volatile p-channel memory device is capable of very high-programming throughput (> 20 MB/sec) suitable for data Flash application.
Effects of nicotinamide and related compounds on the antileukemic activity of 2-amino-1,3,4-thiadiazole. (1960)

The effect of nicotinamide and a variety of nicotinamide analogs and related compounds on the activity of 2-amino-1,3,4-thiadiazole against transplanted mouse leukemia B82 has been tested. 5-Fluoronicotinamide, 6-aminonicotinamide, N-hydroxy-bis-methylnicotinamide, N-N′-methylene-bis-nicotinamide, DPN, and 3-acetylpyridine were as potent as nicotinamide and nicotinic acid in reversing the thiadiazole effect. Other nicotinamide analogs, the analogs of nicotinic acid, precursors and catabolic products of nicotinamide have not shown such activity. The results of this study have been compared with results obtained by another author in a different system. It has been concluded that the term “niacin antagonist” represents several different metabolic activities, all reversible by niacin.
Expression of type IV collagenase and procollagen genes and its correlation with the tumorigenic, invasive, and metastatic abilities of oncogene-transformed human bronchial epithelial cells. (1989)

In a series of immortalized human bronchial epithelial cell lines continuing various oncogenes, the transcriptional levels of the type IV collagenase and the type IV procollagen genes were compared with the properties of invasiveness in vitro and tumorigenicity and metastatic ability in athymic nude mice. v-Ha-ras greatly enhanced invasion and metastasis, whereas v-Ki-ras, c-myc, and c-raf had lesser effects on these malignant phenotypes. In addition, cell lines derived from tumors obtained by injecting the original immortalized human bronchial epithelial cell lines into nude mice exhibited enhanced invasive and metastatic abilities and increased level of type IV collagenase mRNA when compared with the original immortalized human bronchial epithelial cell lines. Invasiveness and metastatic capacity correlated positively with expression of the type IV collagenase gene and negatively with the expression of the type IV procollagen gene, suggesting that these phenotypes are associated both with decreased production and increased dissolution of extracellular matrix.
An investigation of geographic mapping techniques for internet hosts (2001)

In this paper, we ask whether it is possible to build an IP address to geographic location mapping service for Internet hosts. Such a service would enable a large and interesting class of location-aware applications. This is a challenging problem because an IP address does not inherently contain an indication of location.We present and evaluate three distinct techniques, collectively referred to as IP2Geo , for determining the geographic location of Internet hosts. The first technique, Geo Track , infers location based on the DNS names of the target host or other nearby network nodes. The second technique, GeoPing , uses network delay measurements from geographically distributed locations to deduce the coordinates of the target host. The third technique, GeoCluster , combines partial (and possibly inaccurate) host-to-location mapping information and BGP prefix information to infer the location of the target host. Using extensive and varied data sets, we evaluate the performance of these techniques and identify fundamental challenges in deducing geographic location from the IP address of an Internet host.
Thermal conductivity measurement from 30 to 750 K: the 3ω method (1990)

An ac technique for measuring the thermal conductivity of dielectric solids between 30 and 750 K is described. This technique, the 3ω method, can be applied to bulk amorphous solids and crystals as well as amorphous films tens of microns thick. Errors from black-body radiation are calculated to be less than 2% even at 1000 K. Data for a-SiO2, Pyrex 7740, and Pyroceram 9606 are compared to results obtained by conventional techniques.
Glycine 119 of Bovine Growth Hormone is Critical for Growth-Promoting Activity (1991)

Bovine GH (bGH) analogs with single amino acid substitutions at positions 117 (bGH-E117L), 119 (bGH-G119R), and 122 (bGH-A122D) were generated. These analogs bind to mouse liver membrane preparations with affinities similar to native bGH. However, transgenic mice which express the analogs demonstrate different phenotypes ranging from dwarfism to gigantism. For example, expression of bGH or bGH-E117L result in large transgenic mice. In contrast, transgenic mice with a growth phenotype similar to nontransgenic animals result from expression of bGH-A122D. Surprisingly, transgenic mice with relatively high serum levels of bGH-G119R possessed a dwarf phenotype. Together these results suggest that Gly 119 and Ala 122 are involved in growth-promoting activity of GH.
Lanthanide Triflates Catalyzed Reactions of Imines with Indole in Protic Media (1999)

Lanthanide triflates Ln(OTf)3 were found to catalyze the electrophilic substitution reactions of indole with a variety of imines in protic media, affording predominately secondary indolyl amines as well as bisindolyl methanes as by-products.
Automatic 3D Roof Reconstruction using Digital Cadastral Map, Architectural Knowledge and an Aerial Image (2006)

In this paper we present a low cost approach to automated reconstruction of 3D roof models which can be used for generation of a realistic 3D environment of an urban area in a virtual reality application. The key aspect of the method which differs from the other studies is that only one aerial view is used and architectural knowledge is introduced to form 3D roof models of buildings. First buildings in the aerial image are located using footprints of buildings in the digital cadastre map and roof image of each building is retrieved from the original image. The corresponding roof lines of the buildings are obtained by processing each roof image separately. Finally by merging 2D roof model and architectural knowledge about the building such as the building type and possible roof slope angles, 3D roof models are created.
The oxazolidinone eperezolid binds to the 50S ribosomal subunit and competes with binding of chloramphenicol and lincomycin (1997)

The oxazolidinones are a novel class of antibiotics that act by inhibiting protein synthesis. It as been reported that the drug exerts its primary activity on the initiation phase of translation. In order to study the possibility of direct interaction between the drug and the ribosome, we have developed a binding assay using 14C-labelled eperezolid (PNU-100592; formerly U-100592). Eperezolid binds specifically to the 50S ribosomal subunit of Escherichia coli. The specific binding of eperezolid is dose dependent and is proportional to the ribosome concentrations. Scatchard analysis of the binding data reveals that the dissociation constant (Kd) is about 20 microM. The binding of eperezolid to the ribosome is competitively inhibited by chloramphenicol and lincomycin. However, unlike chloramphenicol and lincomycin, eperezolid does not inhibit the puromycin reaction, indicating that the oxazolidinones have no effect on peptidyl transferase. In addition, whereas lincomycin and, to some extent, chloramphenicol inhibit translation termination, eperezolid has no effect. Therefore, we conclude that the oxazolidinones inhibit protein synthesis by binding to the 50S ribosomal subunit at a site close to the site(s) to which chloramphenicol and lincomycin bind but that the oxazolidinones are mechanistically distinct from these two antibiotics.
Vaccination Against Experimental Allergic Encephalomyelitis with T Cell Receptor Peptides (1989)

Experimental allergic encephalomyelitis (EAE) is an autoimmune disease of the central nervous system mediated by CD4+ T cells reactive with myelin basic protein (MBP). Rats were rendered resistant to the induction of EAE by vaccination with synthetic peptides corresponding to idiotypic determinants of the beta chain VDJ region and J alpha regions of the T cell receptor (TCR) that are conserved among encephalitogenic T cells. These findings demonstrate the utility of TCR peptide vaccination for modulating the activity of autoreactive T cells and represent a general therapeutic approach for T cell-mediated pathogenesis.
Clinical Actionability of Comprehensive Genomic Profiling for Management of Rare or Refractory Cancers (2016)

Identification of key factors that facilitate use of genomic tumor testing results and implementation of genomically guided therapy may lead to enhanced benefit for patients with rare or difficult to treat cancers. Clinical use of a targeted next-generation sequencing assay in the setting of an institutional molecular tumor board led to implementable clinical action in over one third of patients with rare and poor prognosis cancers. The major barriers to implementation of genomically guided therapy were clinical status of the patient and drug access both on trial and off label. Approaches to increase actionability include early and serial sequencing in the clinical course and expanded access to genomically guided early phase clinical trials and targeted agents.
Influence of in vivo growth on human glioma cell line gene expression: Convergent profiles under orthotopic conditions (2005)

Defining the molecules that regulate tumor cell survival is an essential prerequisite for the development of targeted approaches to cancer treatment. Whereas many studies aimed at identifying such targets use human tumor cells grown in vitro or as s.c. xenografts, it is unclear whether such experimental models replicate the phenotype of the in situ tumor cell. To begin addressing this issue, we have used microarray analysis to define the gene expression profile of two human glioma cell lines (U251 and U87) when grown in vitro and in vivo as s.c. or as intracerebral (i.c.) xenografts. For each cell line, the gene expression profile generated from tissue culture was significantly different from that generated from the s.c. tumor, which was significantly different from those grown i.c. The disparity between the i.c gene expression profiles and those generated from s.c. xenografts suggests that whereas an in vivo growth environment modulates gene expression, orthotopic growth conditions induce a different set of modifications. In this study the U251 and U87 gene expression profiles generated under the three growth conditions were also compared. As expected, the profiles of the two glioma cell lines were significantly different when grown as monolayer cultures. However, the glioma cell lines had similar gene expression profiles when grown i.c. These results suggest that tumor cell gene expression, and thus phenotype, as defined in vitro is affected not only by in vivo growth but also by orthotopic growth, which may have implications regarding the identification of relevant targets for cancer therapy.
A CONVENIENT, LARGE-SCALE SYNTHESIS OF ABIRATERONE ACETATE [3β-ACETOXY-17-(3-PYRIDYL)ANDROSTA-5,16-DIENE], A POTENTIAL NEW DRUG FOR THE TREATMENT OF PROSTATE CANCER (1997)

(1997). A CONVENIENT, LARGE-SCALE SYNTHESIS OF ABIRATERONE ACETATE [3β-ACETOXY-17-(3-PYRIDYL)ANDROSTA-5,16-DIENE], A POTENTIAL NEW DRUG FOR THE TREATMENT OF PROSTATE CANCER. Organic Preparations and Procedures International: Vol. 29, No. 1, pp. 123-128.
Analytical partitioning of poly(ethyleneglycol)-modified proteins (1997)

Covalently grafting proteins with varying numbers (n) of poly(ethylene glycol) molecules (PEGs) often enhances their biomedical and industrial usefulness. Partition between the phases in aqueous po ...
DNA strand annealing is promoted by the yeast Rad52 protein. (1996)

The Saccharomyces cerevisiae RAD52 gene plays a pivotal role in genetic recombination. Here we demonstrate that yeast Rad52 is a DNA binding protein. To show that the interaction between Rad52 and DNA is direct and not mediated by other yeast proteins and to facilitate protein purification, a recombinant expression system was developed. The recombinant protein can bind both single- and double-stranded DNA and the addition of either Mg2+ or ATP does not enhance the binding of single-stranded DNA. Furthermore, a DNA binding domain was found in the evolutionary conserved N terminus of the protein. More importantly, we show that the protein stimulates DNA annealing even in the presence of a large excess of nonhomologous DNA. Rad52-promoted annealing follows second-order kinetics and the rate is 3500-fold faster than that of the spontaneous reaction. How this annealing activity relates to the genetic phenotype associated with rad52 mutant cells is discussed.
Dominant suppressors of yeast actin mutations that are reciprocally suppressed. (1989)

A gene whose product is likely to interact with yeast actin was identified by the isolation of pseudorevertants carrying dominant suppressors of the temperature-sensitive (Ts) act1-1 mutation. Of 30 independent revertants analyzed, 29 were found to carry extragenic suppressor mutations and of these, 24/24 tested were found to be linked to each other. This linkage group identifies a new gene SAC6, whose product, by several genetic criteria, is likely to interact intimately with actin. First, although act1-1 sac6 strains are temperature-independent (Ts+), 4/17 sac6 mutant alleles tested are Ts in an ACT1+ background. Moreover, four Ts+ pseudorevertants of these ACT1+ sac6 mutants carry suppressor mutations in ACT1; significantly, three of these are again Ts in a SAC6+ background, and are most likely new act1 mutant alleles. Thus, mutations in ACT1 and SAC6 can suppress each other's defects. Second, sac6 mutations can suppress the Ts defects of the act1-1 and act1-2, but not act1-4, mutations. This allele specificity indicates the sac6 mutations do not suppress by simply bypassing the function of actin at high temperature. Third, act1-4 sac6 strains have a growth defect greater than that due to either of the single mutations alone, again suggesting an interaction between the two proteins. The mutant sac6 gene was cloned on the basis of dominant suppression from an act1-1 sac6 mutant library, and was then mapped to chromosome IV, less than 2 cM from ARO1.
Biotechnological Applications of Proteases in Food Technology (2018)

This review presents some of the hottest topics in biotechnological applications: proteases in biocatalysis. Obviously, one of the most relevant areas of application is in the hydrolysis of proteins in food technology, and that has led to a massive use on proteomics. The aim is to identify via peptide maps the different proteins obtained after a specific protease hydrolysis. However, concepts like degradomics are also taking on a more relevant importance in the use and study of proteases and will also be discussed. Other protease applications, as seem in cleaning (detergent development), the pharmaceutical industry, and in fine chemistry, will be analyzed. This review progresses from basic areas such as protease classification to a discussion of the preparation of protease-immobilized biocatalysts, considering the different problems raised by the use of immobilized proteases due to the peculiar features of the substrates, usually large macromolecules. Production of bioactive peptides via limited hydrolysis of proteins will occupy an important place in this review.
Interaction of thrombospondin with resting and stimulated human platelets. (1986)

The interaction of isolated and radioiodinated thrombospondin with washed human platelets has been characterized. The ligand bound to nonstimulated and thrombin-stimulated platelets in a time-dependent manner, and apparent steady state was reached within 25 min. Binding was not due to iodination of the ligand and was inhibited by nonlabeled thrombospondin but not by unrelated proteins, and bound ligand was identical with thrombospondin in terms of subunit structure. Nonlinear curve-fitting analyses of binding to resting platelets suggested the presence of a single class of sites which bound 3,100 +/- 1,000 molecules/platelet with an apparent Kd of 50 +/- 20 nM. This interaction was not attributable to contaminating cells or inadvertant platelet activation. Binding to thrombin-stimulated platelets had a lower apparent affinity (Kd = 250 +/- 100 nM) and higher apparent capacity (35,600 +/- 9,600 molecules/platelet). Thrombin-enhanced binding was dependent upon agonist dose and platelet stimulation. Fibrinogen, a monoclonal antibody to GPIIb-IIIa, temperature, and divalent ions had differential effects upon thrombospondin binding to resting and stimulated platelets, suggesting the presence of two distinct mechanisms of thrombospondin binding to platelets. While thrombospondin binding to thrombin-stimulated platelets occurs with characteristics similar to those observed for fibrinogen, fibronectin, and von Willebrand Factor, its high affinity interaction with resting platelets is unique to this adhesive glycoprotein.
Role of the Insulin-Like Growth Factor Family in Cancer Development and Progression (2000)

The insulin-like growth factors (IGFs) are mitogens that play a pivotal role in regulating cell proliferation, differentiation, and apoptosis. The effects of IGFs are mediated through the IGF-I receptor, which is also involved in cell transformation induced by tumor virus proteins and oncogene products. Six IGF-binding proteins (IGFBPs) can inhibit or enhance the actions of IGFs. These opposing effects are determined by the structures of the binding proteins. The effects of IGFBPs on IGFs are regulated in part by IGFBP proteases. Laboratory studies have shown that IGFs exert strong mitogenic and antiapoptotic actions on various cancer cells. IGFs also act synergistically with other mitogenic growth factors and steroids and antagonize the effect of antiproliferative molecules on cancer growth. The role of IGFs in cancer is supported by epidemiologic studies, which have found that high levels of circulating IGF-I and low levels of IGFBP-3 are associated with increased risk of several common cancers, including those of the prostate, breast, colorectum, and lung. Evidence further suggests that certain lifestyles, such as one involving a high-energy diet, may increase IGF-I levels, a finding that is supported by animal experiments indicating that IGFs may abolish the inhibitory effect of energy restriction on cancer growth. Further investigation of the role of IGFs in linking high energy intake, increased cell proliferation, suppression of apoptosis, and increased cancer risk may provide new insights into the etiology of cancer and lead to new strategies for cancer prevention.
Purification and characteristics of a gamma-glutamyl kinase involved in Escherichia coli proline biosynthesis (1984)

gamma-Glutamyl kinase, the first enzyme of the proline biosynthetic pathway, was purified to homogeneity from an Escherichia coli strain resistant to the proline analog 3,4-dehydroproline. The enzyme had a native molecular weight of 236,000 and was apparently comprised of six identical 40,000-dalton subunits. Enzymatic activity of the protein was detectable only in assays containing highly purified gamma-glutamyl phosphate reductase, the second enzyme of the proline pathway. Plots of gamma-glutamyl kinase activity as a function of glutamate concentration were sigmoidal, with a half-saturation value for glutamate of 33 mM, whereas plots of enzyme activity as a function of ATP concentration displayed typical Michaelis-Menten kinetics with a Km for ATP of 4 X 10(-4) M. Enzyme activity was insensitive to the glutamate analog L-methionine-DL-sulfoximine, but ADP was a potent competitive inhibitor. Characteristics of the enzyme were compared with those of a gamma-glutamyl kinase partially purified from a 3,4-dehydroproline-sensitive E. coli. These results indicated that the only major difference was that the enzyme from the 3,4-dehydroproline-resistant strain was 100-fold less sensitive to feedback inhibition by proline.