gebhart/patrepeval huggingface dataset:
Cancer after bone marrow transplantation. IBMTR and EBMT/EULEP Study Group on Late Effects. (1992)

Cancer may be serious late effect of marrow transplantation. Radiation, chemotherapy, immunosuppression and the original disease for which transplantation was performed may predispose to the development of cancer. 116 of 9732 patients reported to the IBMTR (International Bone Marrow Transplant Registry) have developed a new malignancy. Late effects were evaluated by the EBMT-EULEP (European Bone Marrow Transplant-European Late Effect Project) Late Effect Study Group in 147 patients surviving 6 years and 79 patients surviving more than 10 years. New malignancies developed in 11 of these patients. Lymphomas and leukemia comprised 73 cases reported to the IBMTR and one case reported to the EBMT-EULEP study. Tumors of the skin, oropharynx, vulva vagina and cervix prevailed in 41 patients with solid tumors. The distribution of malignancies is similar to that observed in organ transplant patients not given radiation or chemotherapy and suggests immunosuppression as a major contributory factor. In dogs the incidence of malignancies was studied after either chemotherapy or total body radiation in various regimens and marrow transplantation. Both chemotherapy and radiation shortened tumor-free survival in comparison to untreated dogs. Higher doses, larger fractions and shorter treatment schedules enhanced earlier tumor development. Soft tissue sarcomas and thyroid carcinoma were most frequent in treated, mammary carcinoma in untreated dogs. In treated dogs deaths from cancer were observed starting at the age of 5 years as compared to untreated dogs at the age of 9 years. The data from animal experiments indicate that the incidence of solid tumors in marrow transplant patients may still rise in the coming decades.
Enhancement of ribozyme catalytic activity by a contiguous oligodeoxynucleotide (facilitator) and by 2′-O-methylation (1992)

RNA catalysts (ribozymes) designed to cleave sequences unique to viral RNA's might be developed as therapeutics. For this purpose, they would require high catalytic efficiency and resistance to nucleases. Reported here are two approaches that can be used in combination to improve these properties. First, catalytic efficiency can be improved by oligonucleotides (facilitators) that bind to the substrate contiguously with the 3'-end of the ribozyme. Second, 2'-O-methylation of flanking sequences of the ribozyme increases catalytic activity as well as resistance to nucleases. In combination with a facilitator oligodeoxynucleotide, the cleavage rate was increased 20 fold over that of the unmodified ribozyme.
Structure of a human monoclonal antibody Fab fragment against gp41 of human immunodeficiency virus type 1. (1992)

The three-dimensional structure of a human monoclonal antibody (Fab), which binds specifically to a major epitope of the transmembrane protein gp41 of the human immunodeficiency virus type 1, has been determined by crystallographic methods to a resolution of 2.7 A. It has been previously determined that this antibody recognizes the epitope SGKLICTTAVPWNAS, belongs to the subclass IgG1 (kappa), and exhibits antibody-dependent cellular cytotoxicity. The quaternary structure of the Fab is in an extended conformation with an elbow bend angle between the constant and variable domains of 175 degrees. Structurally, four of the hypervariable loops can be classified according to previously recognized canonical structures. The third hypervariable loops of the heavy (H3) and light chain (L3) are structurally distinct. Hypervariable loop H3, residues 102H-109H, is unusually extended from the surface. The complementarity-determining region forms a hydrophobic binding pocket that is created primarily from hypervariable loops L3, H3, and H2.
An analysis of selected computer interchange color spaces (1992)

Important standards for device-independent color allow many different color encodings. This freedom obliges users of these standards to choose the color space in which to represent their data. A device-independent interchange color space must exhibit an exact mapping to a colorimetric color representation, ability to encode all visible colors, compact representation for given accuracy, and low computational cost for transforms to and from device-dependent spaces. The performance of CIE 1931 XYZ, CIELUV, CIELAB, YES, CCIR 601-2 YCbCr, and SMPTE-C RGB is measured against these requirements. With extensions, all of these spaces can meet the first two requirements. Quantizing error dominates the representational errors of the tested color spaces. Spaces that offer low quantization error also have low gain for image noise. All linear spaces are less compact than nonlinear alternatives. The choice of nonlinearity is not critical; a wide range of gammas yields acceptable results. The choice of primaries for RGB representations is not critical, except that high-chroma primaries should be avoided. Quantizing the components of the candidate spaces with varying precision yields only small improvements. Compatibility with common image data compression techniques leads to the requirement for low luminance contamination, a property that compromises several otherwise acceptable spaces. The conversion of a device-independent representation to popular device spaces by means of trilinear interpolation requires substantially fewer lookup table entries with CCIR 601-2 YCbCr and CIELAB.
Solvent removal during curing process of highly spheric and monodispersed-sized polystyrene capsules from density-matched emulsions composed of water and benzene/1,2-dichloroethane (2000)

This paper describes in terms of the mass of the solvents in the oil, water, and distillate phases the curing process of highly spheric monodispersed 4-mm-in-diameter polystyrene capsules of a uniform thickness. It was determined that the water solubility of the solvents is crucial in the solvent selection in order to prepare the capsules by this method. The curing process started from the water/oil/water emulsions, where the boiling temperature and the densities of the oil were well matched by mixing benzene and 1,2-dichloroethane. The masses of the solvents were measured for the oil phases and the distillate and then calculated for the water phase. The analysis of the solvents in the water phase indicated that the process was governed by the kinetics of their dissolving from the oil phase to the outer water phase rather than by the vapor pressure of the solvents in the early stage before the oil phase lost its fluidity. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 3412–3418, 2000
High-speed switchable lens enables the development of a volumetric stereoscopic display (2009)

Stereoscopic displays present different images to the two eyes and thereby create a compelling three-dimensional (3D) sensation. They are being developed for numerous applications including cinema, television, virtual prototyping, and medical imaging. However, stereoscopic displays cause perceptual distortions, performance decrements, and visual fatigue. These problems occur because some of the presented depth cues (i.e., perspective and binocular disparity) specify the intended 3D scene while focus cues (blur and accommodation) specify the fixed distance of the display itself. We have developed a stereoscopic display that circumvents these problems. It consists of a fast switchable lens synchronized to the display such that focus cues are nearly correct. The system has great potential for both basic vision research and display applications.
N-myc can cooperate with ras to transform normal cells in culture. (1985)

N-myc, a cellular gene bearing homology to the c-myc protooncogene, is frequently amplified and overexpressed in a highly restricted set of related tumors, most notably neuroblastomas and retinoblastomas. We have examined the possibility that N-myc may play a causal role in the genesis of these tumors by defining its ability to transform primary cells in tissue culture. Using an N-myc expression construct capable of producing constitutively deregulated levels of full-length murine N-myc mRNA, we demonstrate that a deregulated N-myc gene can cooperate with the activated Ha-ras oncogene to cause tumorigenic conversion of normal embryonic fibroblasts in a manner indistinguishable from the deregulated c-myc oncogene. Cell lines established from N-myc/ras-transformed foci express high levels of the N-myc gene, and such lines are similar to c-myc/ras transformants in their ability to grow in soft agar and cause tumors in syngeneic rats. These results illustrate that N-myc does encode a c-myc-like transforming activity and that this transforming activity is not specific for the very restricted set of tumors in which N-myc is normally amplified or overexpressed.
The Lymphocyte Function-Associated Lfa-1, Cd2, And Lfa-3 Molecules: Cell Adhesion Receptors Of The Immune System (1987)

Exhausted CD8 T (Tex) cells are a distinct cell lineage that arise during chronic infections and cancers in animal models and humans. Tex cells are characterized by progressive loss of effector functions, high and sustained inhibitory receptor expression, ...Read More
Antigen-inducible, H-2-restricted, interleukin-2-producing T cell hybridomas. Lack of independent antigen and H-2 recognition (1981)

We developed a method for production of antigen-specific, H-2-restricted T cell hybrids. The tumor cell partner in the fusions was itself a T cell hybrid, FS6-14.13.AG2 (or its derivatives), which could be induced to produce the growth factor, interleukin-2 (IL-2), in response to a challenge with concanavalin A, but had no known antigen specificity. The normal T cell partner in the fusions was a population of lymph node T cell blasts that had been highly enriched in antigen-specific, H-2-restricted T cells by in vivo immunization, followed by in vitro challenge with antigen and clonal expansion in IL-2-containing medium. These fusions produced hybrids that grew constitutively in culture. A sizable proportion of the hybrids demonstrated the ability to produce IL-2 in response to a challenge with specific antigen presented by irradiated spleen cells of the appropriate H-2 type. Four cloned antigen/H-2-specific hybrid lines were produced. AO-40.10 responded to chicken ovalbumin (OVA) when presented by I-A(k)-bearing cells. DC1.18.3 responded to the apo form of beef cytochrome c when presented with I-A(d). AODK-10.4 responded to keyhole limpet hemocyanin (KLH) presented with I-A (d). AODK-1.16 also responded to KLH presented by a product of the I region of H-2(d), but the data were consistent with either a product of the I-J-I-E(d) region or a combinatorial molecule with elements from both I-A(d) and I-E(d)/I-C(d). Coincidentally, AO-40.10 was shown to have an unexpected alloreactivity with a product of H-2(b) mapping to the K-I-A region. These hybrids should prove invaluable as sources of monoclonal material for the study of the receptor(s) on T cells with H-2-restricted antigen specificities. We also generated T cell hybrids with two antigen/H-2 specificities by fusing an azaguanine-resistant clone of AO-40.10 to normal T cells with a different antigen/H-2 specificity. Many of the hybrids retained reactivity to OVA plus H-2(a) and to the second antigen/H-2 combination. None reacted to either OVA plus the second H-2 type or to the second antigen plus H-2(a). One of these hybrids was successfully cloned to produce the line AOFK- 11.11.1. It retained the ability to recognize OVA plus I-A(k) inherited from one parent, and KLH plus IA(f) inherited from the other. It did not recognize OVA plus IA(f) or KLH plus I-A(k). These results have some bearing on models describing the nature of T cell receptors for antigen recognized in association with H-2 products. They do not support models in which antigen and H-2 are recognized separately by two independent T cell receptors.
Salt Taste Transduction Occurs Through an Amiloride-Sensitive Sodium Transport Pathway (1984)

An important early event in mammalian gustatory transduction with respect to sodium chloride has been found to be the passage of sodium ions through specific transport pathways in the apical region of the taste bud. The inward current caused by sodium chloride placed on the mucosal surface of an in vitro preparation of rat dorsal lingual epithelium can be substantially reduced by the blocker of sodium ion transport, amiloride. The data show (i) that amiloride is a specific blocker of the chorda tympani response to sodium chloride, but not to potassium chloride, (ii) that the sodium and potassium gustatory systems are largely independent at the peripheral level, and (iii) that the classical ion taste "receptor" is actually a specific transport pathway permitting the cation to enter the taste-bud cell and thereby to spread depolarizing current.
Cross-Reactivity of Antibodies against PorA after Vaccination with a Meningococcal B Outer Membrane Vesicle Vaccine (2003)

The cross-reactivity of PorA-specific antibodies induced by a monovalent P1.7-2,4 (MonoMen) and/or a hexavalent (HexaMen) meningococcal B outer membrane vesicle vaccine (OMV) in toddlers and school children was studied by serum bactericidal assays (SBA). First, isogenic vaccine strains and PorA-identical patient isolates were compared as a target in SBA, to ensure that the vaccine strains are representative for patient isolates. Geometric mean titers (GMTs) in SBA against patient isolates with subtypes P1.5-2,10 and P1.5-1,2-2 after vaccination with HexaMen were generally lower than those against vaccine strains with the same subtype, although the percentage of vaccine responders (> or =4-fold increase in SBA after vaccination) was not affected. Using various P1.7-2,4 patient isolates, GMTs as well as the number of vaccine responders were higher than for the P1.7-2,4 vaccine strain, indicating that the use of the P1.7-2,4 vaccine strain may have underestimated the immunogenicity of this subtype in HexaMen. Secondly, the cross-reactivity of antibodies induced by MonoMen and HexaMen was studied using several patient isolates that differed from the vaccine subtypes by having minor antigenic variants of one variable region (VR), by having a completely different VR or by having a different combination of VRs. MonoMen induced P1.4-specific antibodies that were cross-reactive with P1.4 variants P1.4-1 and P1.4-3. HexaMen induced a broader cross-reactive antibody response against various patient isolates with one VR identical to a vaccine subtype or a combination of VRs included in HexaMen. Cross-reactivity, measured by a fourfold increase in SBA after vaccination, against these strains ranged from 23 to 92% depending on the subtype of the tested strain and was directed against both VR1 and VR2. The extended cross-reactivity of vaccinee sera induced by HexaMen against antigenic variants has important favorable implications for meningococcal B OMV vaccine coverage.
Race, Breast Cancer Subtypes, and Survival in the Carolina Breast Cancer Study (2006)

Basal-like breast tumors occurred at a higher prevalence among premenopausal African American patients compared with postmenopausal African American and non-African American patients in this population-based study. A higher prevalence of basal-like breast tumors and a lower prevalence of luminal A tumors could contribute to the poor prognosis of young African American women with breast cancer.
Cloning and Characterization of Three Fatty Alcohol Oxidase Genes from Candida tropicalis Strain ATCC 20336 (2004)

Candida tropicalis (ATCC 20336) converts fatty acids to long-chain dicarboxylic acids via a pathway that includes among other reactions the oxidation of omega-hydroxy fatty acids to omega-aldehydes by a fatty alcohol oxidase (FAO). Three FAO genes (one gene designated FAO1 and two putative allelic genes designated FAO2a and FAO2b), have been cloned and sequenced from this strain. A comparison of the DNA sequence homology and derived amino acid sequence homology between these three genes and previously published Candida FAO genes indicates that FAO1 and FAO2 are distinct genes. Both genes were individually cloned and expressed in Escherichia coli. The substrate specificity and K(m) values for the recombinant FAO1 and FAO2 were significantly different. Particularly striking is the fact that FAO1 oxidizes omega-hydroxy fatty acids but not 2-alkanols, whereas FAO2 oxidizes 2-alkanols but not omega-hydroxy fatty acids. Analysis of extracts of strain H5343 during growth on fatty acids indicated that only FAO1 was highly induced under these conditions. FAO2 contains one CTG codon, which codes for serine (amino acid 177) in C. tropicalis but codes for leucine in E. coli. An FAO2a construct, with a TCG codon (codes for serine in E. coli) substituted for the CTG codon, was prepared and expressed in E. coli. Neither the substrate specificity nor the K(m) values for the FAO2a variant with a serine at position 177 were radically different from those of the variant with a leucine at that position.
A cytomegalovirus-encoded inhibitor of apoptosis that suppresses caspase-8 activation (2001)

We have identified a human cytomegalovirus cell-death suppressor, denoted vICA, encoded by the viral UL36 gene. vICA inhibits Fas-mediated apoptosis by binding to the pro-domain of caspase-8 and preventing its activation. vICA does not share significant sequence homology with FLIPs or other known suppressors of apoptosis, suggesting that this protein represents a new class of cell-death suppressors. Notably, resistance to Fas-mediated apoptosis is delayed in fibroblasts infected with viruses that encode mutant vICA, suggesting that vICA suppresses death-receptor-induced cell death in the context of viral infection. Although vICA is dispensable for viral replication in vitro, the common targeting of caspase-8 activation by diverse herpesviruses argues for an important role for this antiapoptotic mechanism in the pathogenesis of viral infection in the host, most likely in avoiding immune clearance by cytotoxic lymphocytes and natural killer cells.
Mechanistic Studies on Thiaminase I (1996)

Thiaminase I (EC 2.5.1.2) catalyzes the replacement of the thiazole moiety of thiamin with a wide variety of nucleophiles. Here we report the sequencing of a thiaminase I clone from Bacillus thiaminolyticus, the overexpression of the cloned gene in Escherichia coli, and the purification and characterization of the enzyme. Recombinant thiaminase I functions as a monomer with a Km for thiamin of 3.7 +/- 0.6 microM and a kcat of 34 s-1. Electrospray ionization Fourier-transform mass spectrometry identified a single sequencing error and demonstrated heterogeneity, finding molecular weights of 42,127, 42,198, and 42,255 due to added Ala and Gly-Ala at the amino terminus. Similar analysis of the 4-amino-2-methyl-6-chloropyrimidine inactivated enzyme indicated that the active site nucleophile involved in catalysis of the substitution reaction is located between Pro79 and Thr177. Subsequent cysteine-specific labeling and site-directed mutagenesis identified Cys113 as the active site nucleophile.
A Detailed Genetic Portrait of the Deadliest Human Cancers (2008)

Three studies published this week have given researchers their most detailed look so far at the genetic mutations that underlie the deadliest of human cancers: pancreatic cancer and the brain tumor glioblastoma. They have firmed up the role of key genes and also found that scores of aberrant genes are involved in relatively few cell signaling pathways. One study also unearthed a gene never before linked to cancer that is mutated in a substantial fraction of glioblastoma tumors. “It shows we can still be surprised” by the biology of cancer, says Michael Stratton, who oversees a cancer gene sequencing project at the Sanger Institute in Hinxton, U.K.
HIV protein Nef causes dyslipidemia and formation of foam cells in mouse models of atherosclerosis (2014)

Patients with HIV are at an increased risk of cardiovascular disease. In this study we investigated the effect of Nef, a secreted HIV protein responsible for the impairment of cholesterol efflux, on the development of atherosclerosis in two animal models. ApoE(-/-) mice fed a high-fat diet and C57BL/6 mice fed a high-fat, high-cholesterol diet were injected with recombinant Nef (40 ng/injection) or vehicle, and the effects of Nef on development of atherosclerosis, inflammation, and dyslipidemia were assessed. In apoE(-/-) mice, Nef significantly increased the size of atherosclerotic lesions and caused vessel remodeling. Nef caused elevation of total cholesterol and triglyceride levels in the plasma while reducing high-density lipoprotein cholesterol levels. These changes were accompanied by a reduction of ABCA1 abundance in the liver, but not in the vessels. In C57BL/6 mice, Nef caused a significant number of lipid-laden macrophages presented in adventitia of the vessels; these cells were absent from the vessels of control mice. Nef caused sharp elevations of plasma triglyceride levels and body weight. Taken together, our findings suggest that Nef causes dyslipidemia and accumulation of cholesterol in macrophages within the vessel wall, supporting the role of Nef in pathogenesis of atherosclerosis in HIV-infected patients.-Cui, H. L., Ditiatkovski, M., Kesani, R., Bobryshev, Y. V., Liu, Y., Geyer, M., Mukhamedova, N., Bukrinsky, M., Sviridov, D. HIV protein Nef causes dyslipidemia and formation of foam cells in mouse models of atherosclerosis.
Quantitative Polymerase Chain Reaction for the Detection of Micrometastases in Patients With Breast Cancer (1999)

Quantitative RT-PCR for CK-19 detects a percentage of patients with breast cancer and may enable the progression or regression of the disease to be monitored.
Massive scale cyber traffic analysis (2013)

We consider cyber traffic analysis (TA) as a challenge problem for research in graph database systems. TA involves observing and analyzing connections between clients, servers, hosts, and actors within IP networks, over time, to detect suspicious patterns. Towards that end, NetFlow (or more generically, IPFLOW) data are available from routers and servers which summarize coherent groups of IP packets flowing through the network. The ability to cast IPFLOW data as a massive graph and query it interactively is potentially transformative for cybersecurity, but issues of scale and data complexity pose challenges for current technology. In this paper, we outline requirements and opportunities for graph-structured IPFLOW analytics based on our experience with real IPFLOW databases. We describe real use cases from the security domain, cast them as graph patterns, show how to express them in two graph-oriented query languages (SPARQL and Datalog), and use these examples to motivate a new class of "hybrid" graph-relational systems.
Imaging blood flow in human port-wine stain in situ and in real time using optical Doppler tomography. (2001)

We have demonstrated that ODT may be used for noninvasive imaging of blood vessels in PWS skin. Moreover, ODT will potentially allow laser therapy to be optimized on an individual patient basis by providing a fast, semiquantitative evaluation of the efficacy of PWS laser therapy in situ and in real time.
Simultaneous detection of TDT-mediated dUTP-biotin nick end-labeling (TUNEL)-positive cells and multiple immunohistochemical markers in single tissue sections. (1995)

We have modified the terminal deoxynucleotidyl transferase (TDT)-mediated dUTP-biotin nick end-labeling (TUNEL) method to permit the immunogold-silver intensification detection of apoptotic cells in tissue sections. Such sections can subsequently be processed for multi-labeling fluorescence microscopy, thus permitting the simultaneous detection of silver-positive apoptotic cells and three additional fluorescent signals. In this report, we combined TUNEL labeling with the fluorescent detection of bromodeoxyuridine-positive proliferating cells, growth-associated protein-43 (GAP-43) immunoreactive neurons and bisbenzimide-positive pyknotic cells in the embryonic mouse nervous system. This combination of stains allowed the simultaneous detection of proliferative, differentiated and apoptotic cells in the developing nervous system.