gebhart/patrepeval huggingface dataset:
Expression of the human fibroblast interferon gene in Escherichia coli. (1980)

We applied the method of Guarente et al. [Guarente, L., Lauer, G., Roberts, T.M. & Ptashne, M. (1980) Cell 20, 543-553] to construct plasmids that direct expression in Escherichia coli of the human fibroblast interferon (F-IF) gene. Two plasmids were recovered. One directs efficient synthesis of a protein whose primary sequence is that of pre-F-IF and the other, that of mature F-IF. Extracts of bacteria synthesizing mature F-IF display antiviral activity characteristic of human F-IF. This activity is lower than that expected from the differential rate of synthesis of the protein. We have detected no such activity in extracts of bacteria synthesizing pre-F-IF.
Isolation and culture of human alveolar type II epithelial cells. Characterization of their phospholipid secretion. (1984)

Alveolar type II epithelial cells have been isolated previously from rodents but not from humans. The aims of this study were to isolate and culture alveolar type II cells from human lungs, and to study their phospholipid secretion. Lung tissue was obtained from 13 patients after lobectomy or pneumonectomy. Type II cells were isolated by a modification of our method for isolating rat type II cells with porcine pancreatic elastase and discontinuous metrizamide density gradients. Cells were purified further by differential adherence and they were then cultured on an extracellular matrix prepared from bovine corneal endothelial cells. We obtained 1.3 to 4.8 X 10(6) cells per gram of tissue with cell viability on the day of isolation of 96 +/- 1% (mean +/- SE, n = 10). Type II cell purity, assessed by Papanicolaou stain on Day 1 in culture, was 84 +/- 4% (mean +/- SE) in 9 of the 13 experiments. In the remaining 4 experiments, the purity was less than 50%. Electron microscopy showed well-preserved ultrastructure. The cells, radiolabeled with 32Pi, secreted the phospholipids characteristic of pulmonary surfactant, primarily phosphatidylcholine (68%) and phosphatidylglycerol (12%). Phospholipid secretion was stimulated by tetradecanoyl phorbol acetate (4.5 times baseline) and by the beta adrenergic agonist terbutaline (2.0 times baseline), but not by the cholinergic agonist carbamylcholine chloride. In summary, human alveolar type II epithelial cells can be isolated from resected lung and maintained in culture, and they secrete the phospholipids characteristic of pulmonary surface active material.
Mosaicing new views: the crossed-slits projection (2003)

We introduce anew kind of mosaicing, where the position of the sampling strip varies as a function of the input camera location. The new images that are generated this way correspond to a new projection model defined by two slits, termed here the Crossed-Slits (X-Slits) projection. In this projection model, every 3D point is projected by a ray defined as the line that passes through that point and intersects the two slits. The intersection of the projection rays with the imaging surface defines the image. X-Slits mosaicing provides two benefits. First, the generated mosaics are closer to perspective images than traditional pushbroom mosaics. Second, by simple manipulations of the strip sampling function, we can change the location of one of the virtual slits, providing a virtual walkthrough of a X-Slits camera; all this can be done without recovering any 3D geometry and without calibration. A number of examples where we translate the virtual camera and change its orientation are given; the examples demonstrate realistic changes in parallax, reflections, and occlusions.
Chemoprevention of azoxymethane-induced colon cancer by ascorbylpalmitate, carbenoxolone, dimethylfumarate and p-methoxyphenol in male F344 rats. (1995)

The chemopreventive effect of 40 and 80% maximum tolerated dose (MTD) levels of ascorbylpalmitate (AP), carbenoxolone (CBX), dimethylfumarate (DMF) and p-methoxyphenol (p-MP) administrated in the diet before and during initiation and postinitiation phases of azoxymethane (AOM)-induced colon carcinogenesis was studied in male F344 rats. The MTD levels of AP, CBX, DMF and p-MP were determined in male F344 rats and found to be 5000 1500, 1000 and 1000 ppm, respectively, in modified AIN-76A diet. Based on these MTD values, 40 and 80% MTD levels of each agent was tested for their efficacy in color carcinogenesis. At 5 weeks of age, groups of animals were fed the control (modified AIN-76A diet or diets containing 40 and 80% MTD levels of each AP, CBX, DMF and p-MP. At 7 weeks of age, all animals, except those in the vehicle (normal saline)-treated groups, were given two weekly s.c. injections of AOM at a dose rate of 15 mg/kg body weight/week. All groups were continued on their respective dietary regimen until the termination of the experiment 52 weeks after the carcinogen treatment. Colonic tumors were evaluated histopathologically. The results indicate that dietary administration of 40% MTD of AP significantly inhibited multiplicities (tumor/animal) of noninvasive and total (invasive plus noninvasive) adenocarcinoma of the colon (P < 0.05) and 80% MTD of AP significantly inhibited the incidence (% animals with tumors) and the multiplicities of invasive and total adenocarcinomas of the colon (P < 0.01). Dietary CBX at 40 and 80% MTD levels suppressed the incidence and multiplicities of invasive and total adenocarcinomas (P < 0.05 to 0.001) whereas 40 and 80% MTD of DMF and p-MP had significantly inhibited invasive adenocarcinoma incidence and multiplicity (P < 0.05 to 0.001). However, DMF and p-MP had no significant effect on noninvasive and total adenocarcinoma incidence and multiplicity (P > 0.05). These results suggest that AP and CBX possess potential chemopreventive properties against colon cancer.
Identification of nucleolar protein No55 as a tumour-associated autoantigen in patients with prostate cancer (2000)

Four different genes were identified by immunoscreening of a cDNA expression library from the human prostate cancer cell line DU145 with allogeneic sera from four prostate cancer patients. A cDNA encoding the nucleolar protein No55 was further analysed and shown to be expressed at the mRNA level in several normal tissues, including ovaries, pancreas and prostate and in human prostate cancer cell lines PC-3, PC-3m and LNCaP. By reverse transcriptase/polymerase chain reaction, expression of No55 was several-fold higher in two out of nine prostate cancer primary tumours and two out of two metastatic lesions, compared to normal prostate tissue. Antibodies to No55 were detected in sera from seven out of 47 prostate cancer patients but not in sera from 20 healthy male controls. Sequence analysis of the No55 open reading frame from normal and tumour tissues revealed no tumour-specific mutations. The No55 gene was located to chromosome 17q21, a region reported to be partially deleted in prostate cancer. Considering the immunogenicity of the No55 protein in the tumour host, the expression profile and chromosomal localization of the corresponding gene, studies evaluating No55 as a potential antigen for immunological studies in prostate cancer may be warranted.
Extensive Immunoglobulin Production Sensitizes Myeloma Cells for Proteasome Inhibition (2007)

Multiple myeloma is an incurable plasma cell neoplasia characterized by the production of large amounts of monoclonal immunoglobulins. The proteasome inhibitor bortezomib (PS-341, Velcade) induces apoptosis in various malignant cells and has been approved for treatment of refractory multiple myeloma. Inhibition of the antiapoptotic transcription factor nuclear factor-kappaB (NF-kappaB) apparently contributes to the antitumor effects of bortezomib; however, this mechanism cannot fully explain the exceptional sensitivity of myeloma cells. Extensive protein synthesis as in myeloma cells is inherently accompanied by unfolded proteins, including defective ribosomal products (DRiPs), which need to be degraded by the ubiquitin-proteasome system. Therefore, we hypothesized that the proapoptotic effect of bortezomib in multiple myeloma is mainly due to the accumulation of unfolded proteins in cells with high protein biosynthesis. Using the IgG-secreting human myeloma cell line JK-6L and murine muH-chain-transfected Ag8.H myeloma cells, apoptosis induction upon proteasome inhibition was clearly correlated with the amount of immunoglobulin production. Preferentially in immunoglobulin-high myeloma cells, bortezomib triggered activation of caspases and induction of proapoptotic CHOP, a component of the terminal unfolded protein response induced by endoplasmic reticulum (ER) stress. In immunoglobulin-high cells, bortezomib increased the levels of proapoptotic Bax while reducing antiapoptotic Bcl-2. Finally, IgG-DRiPs were detected in proteasome inhibitor-treated cells. Hence, proteasome inhibitors induce apoptosis preferentially in cells with high synthesis rate of immunoglobulin associated with accumulation of unfolded proteins/DRiPs inducing ER stress. These findings further elucidate the antitumor activities of proteasome inhibitors and have important implications for optimizing clinical applications.
Spin-Stabilized Membrane Antenna Structures (2015)

This paper explores the possibility of using spin-stabilized membrane structures for large phased array microwave antennas (typically L-Band or S-Band from 1 GHz to 4 GHz). The biggest challenge is to be able to sufficiently stabilize the system in order to limit its sensitivity to space disturbances (maneuvering, reaction wheels, and other imposed forces) and manufacturing imperfections. First, a flatness requirement for microwave antennas is derived. Then a frequency analysis of orthotropic flat structures spinning at different angular velocities and with different bending stiffnesses is carried out. These analyses, together with finite element simulations, are used to derive scaling laws to study the behavior of structures spinning in space. A test case, based on a spinning structure perturbed at the hub, is considered. An analytical solution of the free vibration of this test case is compared to the results of finite-element method simulations with Abaqus/Standard. Finally a test setup to study the dynamics of scaled spinning membranes in the laboratory is presented. Gravity effects in such an experiment are expected to be small.
A triad of costimulatory molecules synergize to amplify T-cell activation. (1999)

The activation of a T cell has been shown to require two signals via molecules present on professional antigen-presenting cells: signal 1, via a peptide/MHC complex; and signal 2, via a costimulatory molecule. Here, the role of three costimulatory molecules in the activation of T cells was examined. Poxvirus (vaccinia and avipox) vectors were used because of their ability to efficiently express multiple genes. Murine cells provided with signal 1 and infected with either recombinant vaccinia or avipox vectors containing a TRIad of COstimulatory Molecules (B7-1/ICAM-1/LFA-3, designated TRICOM) induced the activation of T cells to a far greater extent than cells infected with any one or two costimulatory molecules. Despite this T-cell "hyperstimulation" using TRICOM vectors, no evidence of apoptosis above that seen using the B7-1 vector was observed. Results using the TRICOM vectors were most dramatic under conditions of either low levels of first signal or low stimulator cell:T-cell ratios. Experiments using a four-gene construct also showed that TRICOM recombinants can enhance antigen-specific T-cell responses in vivo. These studies thus demonstrate for the first time the ability of vectors to introduce three costimulatory molecules into cells, thereby activating both CD4+ and CD8+ T-cell populations to levels greater than those achieved with the use of only one or two costimulatory molecules. This new threshold of T-cell activation has broad implications in vaccine design and development.
Gene Expression in Peripheral Blood Differs after Cardioembolic Compared with Large-Vessel Atherosclerotic Stroke: Biomarkers for the Etiology of Ischemic Stroke (2008)

There are no biomarkers that differentiate cardioembolic from large-vessel atherosclerotic stroke, although the treatments differ for each and approximately 30% of strokes and transient ischemic attacks have undetermined etiologies using current clinical criteria. We aimed to define gene expression profiles in blood that differentiate cardioembolic from large-vessel atherosclerotic stroke. Peripheral blood samples were obtained from healthy controls and acute ischemic stroke patients (<3, 5, and 24 h). RNA was purified, labeled, and applied to Affymetrix Human U133 Plus 2.0 Arrays. Expression profiles in the blood of cardioembolic stroke patients are distinctive from those of large-vessel atherosclerotic stroke patients. Seventy-seven genes differ at least 1.5-fold between them, and a minimum number of 23 genes differentiate the two types of stroke with at least 95.2% specificity and 95.2% sensitivity for each. Genes regulated in large-vessel atherosclerotic stroke are expressed in platelets and monocytes and modulate hemostasis. Genes regulated in cardioembolic stroke are expressed in neutrophils and modulate immune responses to infectious stimuli. This new method can be used to predict whether a stroke of unknown etiology was because of cardioembolism or large-vessel atherosclerosis that would lead to different therapy. These results have wide ranging implications for similar disorders.
Shape correspondence between a spatial curve and a manipulator with hyper degrees of freedom (2002)

In this paper, we give a definition of a shape correspondence between a manipulator with hyper degrees of freedom and a spatial curve. The shape correspondence is defined by using the solution of a nonlinear optimization problem, termed the shape inverse problem. We also provide results on the existence and a well-posed region of the solution.
Dynamic Analysis of Software Systems using Execution Pattern Mining (2006)

Software system analysis for extracting system functionality remains as a major problem in the reverse engineering literature and the early approaches mainly rely on static properties of software. In this paper, we propose a novel technique for dynamic analysis of software systems to identify the implementation of the software features that are specified through a number of feature-specific task scenarios. The execution of task scenarios and application of data mining algorithm sequential pattern discovery on the generated traces allow us to extract common functionality associated with the corresponding feature-specific task scenarios. The extracted patterns are used to identify the groups of core functions that implement software features. The proposed approach can be used for program comprehension and feature to source code assignment. A case study on the Unix Xfig drawing tool has been provided
Immunotherapy of renal cell cancer (1991)

Immunotherapy of metastatic renal adenocarcinoma (RCC) is currently an alternative to cytotoxic chemotherapy. Bacillus Calmette-Guérin has been associated with a 22% response rate in small series, but no large-scale clinical trials have been completed. Transfer factor, in combination with other immunotherapeutic and chemotherapeutic compounds, has a reported 13% incidence of response. Tumor vaccines have caused clinical response in only 5% of patients while monoclonal antibodies have produced partial remission in one of nine patients. Immune RNA has been associated with a 14% overall incidence of response. Tumor necrosis factor has not as yet been studied in any large-scale clinical investigations but preliminary studies are not promising. Leukocyte-derived and recombinant interferons alone have produced responses in 10-20% of patients with tolerable toxicity. Combinations of interferons or with cytotoxic chemotherapy have produced slightly improved responses with short duration and substantial toxicity. Adoptive immunotherapy using Interleukin-2 alone, or with IL-2 plus lymphocyte-activated killer cells, or tumor infiltrating lymphocytes or interferons have produced clinical responses in 10-30% of patients treated. Combinations of specific forms of immune therapy may hold promise for better rates of clinical response in the future.
Expression of herpes simplex virus type 1 glycoprotein I in baculovirus: preliminary biochemical characterization and protection studies (1992)

We have constructed a recombinant baculovirus expressing the herpes simplex virus type 1 (HSV-1) glycoprotein I (gI). Sf9 cells infected with this recombinant virus synthesized gI-related polypeptides with apparent molecular sizes of 52 and 56 kDa. The recombinant gI appeared to be glycosylated, since it was susceptible to both tunicamycin and endoglycosidase H, and the expressed gI was transported to the surface of infected cells as judged by indirect immunofluorescence. Antibodies to the recombinant gI raised in mice neutralized HSV-1 infectivity. Finally, we show here for the first time that vaccination with gI can protect mice against HSV-1 challenge.
Considerations for ISDN planning and implementation (1984)

THE INFORMATION AGE has created such a diversity between the Communications needs of the business user and the residential Community that one common-denominator public telephone network can no longer serve everyone. The time when evolutionary network enhancements can be justified and implemented will come too late to be acceptable to a large body of business users, because of this diversity of needs. The emerging proliferation of technological bypass of local telephone facilities in the United States is symptomatic of the need for one or more shared wideband/ broadband overlay networks to serve the business community. This environment requires accelerated introduction of digital technologies in the telephone network for provision of high-speed end-to-end digital services including data, facsimile, and video. This necessitates the use of Overlay facilities and networks to meet present business customer demands until the loop plant in the common-denominator network can evolve to optimally meet the varied demands of the whole community. This paper describes past progress and current plans for the introduction of digital technologies for switching, interexchange trunking, and the local loop for an end-to-end digital network. The paper also discusses the implementation of common-channel signaling, based on CCITT's SSN07 in the circuit-switched network, as well as the use of an overlay packet-switched network for provision of data commumcations and videotex services.
The effects of recombinant human erythropoietin on mean corpuscular volume in patients with the anemia of chronic renal failure. (1995)

In historical studies erythropoietin stimulated bone marrow was shown to produce less stable, macrocytic, "stress erythrocytes". Recent work from our lab suggests that erythropoietin serves as both a growth factor and as a survival factor. To investigate the effects of recombinant human erythropoietin (rHuEPO) on development of red blood cell size of these longer lived erythrocytes, rHuEPO in 50-150 U/kg/dose was administered to patients with the anemia of chronic renal failure (CRF). Mean corpuscular volume (MCV) was determined at control, short term (n = 117, avg. 53 d), intermediate term (n = 73, avg. 136 d) and at long term (n = 66, avg. 221d) for effects of rHuEPO. Statistical evaluation at these time points was made comparing all patients to themselves as their own controls and using contingency tables for distribution of RBC size change. MCV at both short term (p = .02) and intermediate-term (p < .01) was decreased; there was no change (p = .71) at the long term. Analysis of distribution showed a significant (p < .01) trend toward microcytosis at short- and intermediate terms. This decrease of MCV and trend toward microcytosis is consistent with iron deficiency secondary to the early, rapid increase in bone marrow iron utilization and early increased reticulocytosis. Previous reports from our laboratory coupled with data presented in this report refute earlier findings that rHuEPO creates a "stress" mechanism producing less stable macrocytes.
Identification of the p53 protein domain involved in formation of the simian virus 40 large T-antigen-p53 protein complex (1986)

An expression vector utilizing the enhancer and promoter region of the simian virus 40 (SV40) DNA regulating a murine p53 cDNA clone was constructed. The vector produced murine p53 protein in monkey cells identified by five different monoclonal antibodies, three of which were specific for the murine form of p53. The murine p53 produced in monkey cells formed an oligomeric protein complex with the SV40 large tumor antigen. A large number of deletion mutations, in-frame linker insertion mutations, and linker insertion mutations resulting in a frameshift mutation were constructed in the cDNA coding portion of the p53 protein expression vector. The wild-type and mutant p53 cDNA vectors were expressed in monkey cells producing the SV40 large T antigen. The conformation and levels of p53 protein and its ability to form protein complexes with the SV40 T antigen were determined by using five different monoclonal antibodies with quite distinct epitope recognition sites. Insertion mutations between amino acid residues 123 and 215 (of a total of 390 amino acids) eliminated the ability of murine p53 to bind to the SV40 large T antigen. Deletion (at amino acids 11 through 33) and insertion mutations (amino acids 222 through 344) located on either side of this T-antigen-binding protein domain produced a murine p53 protein that bound to the SV40 large T antigen. The same five insertion mutations that failed to bind with the SV40 large T antigen also failed to react with a specific monoclonal antibody, PAb246. In contrast, six additional deletion and insertion mutations that produced p53 protein that did bind with T antigen were each recognized by PAb246. The proposed epitope for PAb246 has been mapped adjacent (amino acids 88 through 109) to the T-antigen-binding domain (amino acids 123 through 215) localized by the mutations mapped in this study. Finally, some insertion mutations that produced a protein that failed to bind to the SV40 T antigen appeared to have an enhanced ability to complex with a 68-kilodalton cellular protein in monkey cells.
Regulated expression of Sindbis and vesicular stomatitis virus glycoproteins in Saccharomyces cerevisiae. (1986)

cDNAs encoding either the structural proteins (capsid and glycoproteins E1 and E2) of Sindbis virus or the glycoprotein of vesicular stomatitis virus (VSV) were fused to the Saccharomyces cerevisiae galactokinase gene (GAL1) promoter and inserted into a yeast shuttle vector. After addition of galactose to yeast transformed with this vector, 2.5-3% of total yeast protein synthesis was detected as virus proteins by specific anti-virus protein antibodies. In cells containing the Sindbis virus structural genes, the virus capsid protein was effectively released from the nascent polypeptide and two endoglycosidase H-sensitive glycoproteins were produced. One of these was identical in its gel mobility to E1 and the other appeared to be p62, a precursor to E2. A low level of E1 protein was detected on the cell's surface membranes. A single molecular weight species of glycosylated VSV glycoprotein was produced and half of the total protein could be detected at the surface membranes of yeast. Addition of long mannose chains and acylation of the virus proteins with fatty acids were not observed. Formation of virus proteins was also examined in yeast secretory mutants; one of these (sec53) failed to glycosylate the virus proteins.