gebhart/patrepeval huggingface dataset:
Malignant transformation of NIH‐3T3 cells after subcutaneous co‐injection with a reconstituted basement membrane (matrigel) (1992)

NIH-3T3 cells are non-tumorigenic when injected into athymic mice. If these cells are mixed with an extract of basement-membrane proteins (matrigel) and injected s.c., they form locally invasive and highly vascularized tumors. Cells cultured from the NIH-3T3-matrigel-induced tumors showed a transformed phenotype and lacked contact inhibition. When cultured in a gel of matrigel, they proliferated and formed branched and invasive colonies. In contrast, the parental NIH-3T3 cells cultured on matrigel remained as cell aggregates and were not invasive. I.V. injections of the tumor-derived NIH-3T3 cells produced many colonies on the surface of the lungs, whereas the parental NIH-3T3 cells were not metastatic. Zymographic analysis of the conditioned media obtained from both the tumor-derived and parental NIH-3T3 cells demonstrated higher amounts of the 72-kDa gelatinase (type-IV collagenase) enzyme in the tumor-derived cells. Also, tumor-derived NIH-3T3 cells, but not parental NIH-3T3 cells, secreted the 92-kDa type-IV collagenase. These studies suggest that the interaction of pre-malignant NIH-3T3 cells with extracellular matrix components may contribute to the process of tumor progression.
X-ray and Neutron Diffraction Studies on “Li4.4Sn” (2003)

A chemical analysis and detailed structural characterization, using X-ray single crystal and neutron powder diffraction, of the binary lithium-tin compound "Li(4.4)Sn" is presented. Phase analyses and subsequent structural refinements result in the reformulation of "Li(4.4)Sn" as Li(17)Sn(4). The lithium-rich binary phase crystallizes with a complex cubic structure in the space group Ffourmacr;3m, with a = 19.6907(11) A, Z = 20. The improved crystal structure determination indicates well-defined lithium atom positions, some of which differ from those previously reported. The nearly Zintl phase Li(17)Sn(4) exhibits poor metallic behavior similar to that of heavily doped semiconductors. Comparisons of the refined crystal structure with previously reported X-ray crystal structures associated with "Li(4.4)Sn" are discussed.
Effect of calcium carbonate particle size on calcium retention in adolescent girls (2008)

In an era where adolescents fail to achieve the recommended calcium (Ca) intake, effort is needed to increase the absorption of the Ca consumed. Previously we reported that substituting small (13μm) for large (18.5μm - commercial standard) Ca carbonate (CaCO3) particles in diets of growing female rats resulted in higher Ca retention. Here we assessed the effect of large versus small CaCO3 particle size and small CaCO3 versus placebo on Ca retention in adolescent girls. Twenty-eight adolescent girls participated in two 3-wk controlled feeding trials separated by a 1-wk washout period. During both sessions, the subjects consumed a diet containing 804mg Ca/d. Using a cross-over design, one group (n=18) received an additional 650mg/d Ca via supplementation delivered twice a day in a 325mg Ca dose as either the large or small particle supplement. A second group (n=10) received the small particle CaCO3 or placebo. All 24-h urine and feces were collected and analyzed for Ca content. The overall balance results (Ca intake – urine Ca – fecal Ca) indicated that the small particle CaCO 3 resulted in greater Ca retention compared to placebo (p<0.05). However, there was no significant difference (p>0.05) in Ca retention due to particle size of the CaCO3. Thus, the rat model did not predict the effect of particle size on Ca retention in humans. Unlike the rat study which started the treatment diet during weanling and continued throughout adolescence, the human subjects received the treatment during peak skeletal acquisition. Perhaps the overwhelming effects of growth during puberty overpowered the more subtle effect of CaCO3 particle size treatment.
From Bench to Bedside: Lessons Learned in Translating Preclinical Studies in Cancer Drug Development (2013)

The development of targeted agents in oncology has rapidly expanded over the past 2 decades and has led to clinically significant improvements in the treatment of numerous cancers. Unfortunately, not all success at the bench in preclinical experiments has translated to success at the bedside. As preclinical studies shift toward defining proof of mechanism, patient selection, and rational drug combinations, it is critical to understand the lessons learned from prior translational studies to gain an understanding of prior drug development successes and failures. By learning from prior drug development, future translational studies will provide more clinically relevant data, and the underlying hope is that the clinical success rate will improve and the treatment of patients with ineffective targeted therapy will be limited.
[Experiences with adjuvant prostaglandin therapy in vascular surgery interventions]. (1991)

Two prospective randomized trials were referred. In the first study 50 patients with femorotibial greater saphenous vein in situ bypasses were treated intraarterially with 0.2 ng PGE 1/kg body weight/min and 15,000 i.U. of heparine continuously. The control group of 50 patients also got 15,000 i.U. of heparine and 3 x 0.5 g of Aspirin. We observed 2 (4%) immediate occlusions in the PGE 1 group and 7 (14%) immediate occlusions in the control group. This difference proved to be statistically significant. In the second study 83 patients with three level occlusions (ilio-femoro-tibial) in stage III and IV were treated with a profundaplasty. 42 patients received 60 micrograms PGE 1 in 250 ml saline twice daily. The control group of 41 patients only got twice 250 ml saline over a period of three weeks. In the PGE 1 group 26 patients (61%) showed disappearance of rest pain and healing of necrotic lesions, whereas in the control group this could only be achieved in 15 patients (35%). The difference proved to be statistically significant.
Automatic retinal image registration scheme using global optimization techniques (1999)

Retinal image registration is commonly required in order to combine the complementary information in different retinal modalities. In this paper, a new automatic scheme to register retinal images is presented and is currently tested in a clinical environment. The scheme considers the suitability and efficiency of different image transformation models and function optimization techniques, following an initial preprocessing stage. Three different transformation models--affine, bilinear and projective--as well as three optimization techniques--downhill simplex method, simulated annealing and genetic algorithms--are investigated and compared in terms of accuracy and efficiency. The registration of 26 pairs of Fluoroscein Angiography and Indocyanine Green Chorioangiography images with the corresponding Red-Free retinal images, showed the superiority of combining genetic algorithms with the affine and bilinear transformation models. A comparative study of the proposed automatic registration scheme against the manual method, commonly used in the clinical practice, is finally presented showing the advantage of the proposed automatic scheme in terms of accuracy and consistency.
Allocating power ground vias in 3D ICs for simultaneous power and thermal integrity (2009)

The existing work on via allocation in 3D ICs ignores power/ground vias' ability to simultaneously reduce voltage bounce and remove heat. This article develops the first in-depth study on the allocation of power/ground vias in 3D ICs with simultaneous consideration of power and thermal integrity. By identifying principal ports and parameters, effective electrical and thermal macromodels are employed to provide dynamic power and thermal integrity as well as sensitivity with respect to via density. With the use of sensitivity, an efficient via allocation simultaneously driven by power and thermal integrity is developed. Experiments show that, compared to sequential power and thermal optimization using static integrity, sequential optimization using the dynamic integrity reduces nonsignal vias by up to 18%, and simultaneous optimization using dynamic integrity further reduces nonsignal vias by up to 45.5%.
Antiviral and Antiluteolytic Activity of Recombinant Bovine IFN-ω1 Obtained from Pichia pastoris (2000)

The gene coding for bovine interferon-omega1 (BoIFN-omega1) was recently cloned and expressed at high levels in the yeast Pichia pastoris. The recombinant BoIFN-omega1 protein shows antiviral activity in different cell lines and has an antiluteolytic effect in cyclic ewes. In this article, we describe a method for purification of BoIFN-omega1 expressed in the methylotrophic yeast P. pastoris and characterization of its activity in vivo. The recombinant protein secreted to the culture medium had low activity because of self-aggregation. BoIFN-omega1 was solubilized using urea and desalting and finally purified by ion exchange chromatography on Q-Sepharose Fast Flow. The yield of purified product was approximately 300 mg/L of fermentation culture, with a specific antiviral activity of 10(8) IU/mg. Its purity was at least 80%. The biologic characterization of purified BoIFN-omega1 was determined by induction of an antiviral state on ewes challenged with 100 lethal doses (LD) of Aujeszky virus and by the extension of the corpus luteum life span and interestrous interval in cyclic cows. Ewes treated with 2 x 106 IU/kg BoIFN-omega1 were protected from Aujeszky virus infection. In cows receiving an intrauterine infusion of 1 mg BoIFN-omega1, equally distributed between the two uterine horns, twice daily from day 14 to day 22 of the experimental estrous cycle, the lifespan of the corpus luteum (25 vs. 19 days) and the interestrous intervals (26 vs. 21 days) were extended when compared with a control group (p < 0.05). We show that recombinant BoIFN-omega1 purified from P. pastoris has high antiviral activity and is an effective antiluteolytic agent in cattle.
Blood’s 70th anniversary: CARs on theBloodhighway (2016)

As part of a year-long celebration in honor of Blood's 70th anniversary, we are publishing a series of editorials written by past Editors-in-Chief of the journal. The authors reflect on their experience at Blood in light of the journal's publication history. Each of these special pieces will
Can, a putative oncogene associated with myeloid leukemogenesis, may be activated by fusion of its 3' half to different genes: characterization of the set gene. (1992)

The translocation (6;9)(p23;q34) in acute nonlymphocytic leukemia results in the formation of a highly consistent dek-can fusion gene. Translocation breakpoints invariably occur in single introns of dek and can, which were named icb-6 and icb-9, respectively. In a case of acute undifferentiated leukemia, a breakpoint was detected in icb-9 of can, whereas no breakpoint could be detected in dek. Genomic and cDNA cloning showed that instead of dek, a different gene was fused to can, which was named set. set encodes transcripts of 2.0 and 2.7 kb that result from the use of alternative polyadenylation sites. Both transcripts contain the open reading frame for a putative SET protein with a predicted molecular mass of 32 kDa. The set-can fusion gene is transcribed into a 5-kb transcript that contains a single open reading frame predicting a 155-kDa chimeric SET-CAN protein. The SET sequence shows homology with the yeast nucleosome assembly protein NAP-I. The only common sequence motif of SET and DEK proteins is an acidic region. SET has a long acidic tail, of which a large part is present in the predicted SET-CAN fusion protein. The set gene is located on chromosome 9q34, centromeric of c-abl. Since a dek-can fusion gene is present in t(6;9) acute myeloid leukemia and a set-can fusion gene was found in a case of acute undifferentiated leukemia, we assume that can may function as an oncogene activated by fusion of its 3' part to dek, set, or perhaps other genes.
Generator-produced 99m TcO4-: carrier free. (1975)

A solution of 99m-TCO4-minus, as eluted from a 99Mo-99mTc radionuclide generator contains a greater chemical quantity of technetium than that attributable to the metastable isomer alone. The isomeric transition of the radionuclide of interest, 99mTc, gives rise to a determinable and chemically significant quantity of technetium carrier, 99Tc. A method is presented for calculating the total chemical quantity of technetium in a generator eluate.
Alterations of the Hsp70/Hsp90 chaperone and the HOP/CHIP co-chaperone system in cancer (2012)

Activation of the Hsp90 chaperone system is a characteristic of cancer cells. The regulation of chaperone activities involves their interaction with cochaperones; therefore we investigated the expression of Hsp70 and Hsp90 and their specific co-chaperones HOP and CHIP in cancer cell lines and primary cancers. Inhibition of Hsp90 by 17AAG increased the levels of Hsp70, Hsp90 and HOP but not CHIP mRNA in cancer cells. These changes are linked to activation of the HSF1 transcription factor and we show that the HOP promoter contains HSF1 binding sites, and that HSF1 binding to the HOP promoter is increased following 17AAG. The lack of alteration in the co-chaperone CHIP is explained by a lack of HSF response elements in the CHIP promoter. Non-proliferating cells expressed higher levels of CHIP and lower HOP, Hsp70 and Hsp90 levels compared to proliferating cells. Decreased expression of CHIP in proliferating cancer cells is in keeping with its proposed tumor suppressor properties, while over-expression of HOP in proliferating cells may contribute to excessive Hsp90 activity and stabilization of client proteins in tumors. In a panel of colorectal cancer samples, increased expression of Hsp70 and an increased ratio of HOP to CHIP were found, and were associated with decreased median survival. These data indicate that multiple changes occur in the chaperone/co-chaperone system in cancer that impact patient survival. It is likely that the ability to identify individual alterations to this system will be beneficial for treatment strategy decisions, particularly those that employ chaperone inhibitors.
NF-kappa B and I kappa B alpha: an inducible regulatory system in endothelial activation. (1994)

Structural analysis of the promoters of several endothelial genes induced at sites of inflammatory or immune responses reveals binding sites for the transcription factor nuclear factor kappa B (NF-kappa B). Endothelial cells express transcripts encoding the p50/p105 and p65 components of NF-kappa B and the rel-related proto-oncogene c-rel; steady state levels of these transcripts are transiently increased by tumor necrosis factor alpha (TNF-alpha). Western blotting revealed that stimulation of endothelial cells with TNF-alpha resulted in nuclear accumulation of the p50 and p65 components of NF-kappa B. Ultraviolet crosslinking and immunoprecipitation demonstrated binding of the p50 and p65 components of NF-kappa B to the E-selectin kappa B site. Endothelial cells express an inhibitor of NF-kappa B activation, I kappa B-alpha (MAD-3). Protein levels of this inhibitor fall rapidly after TNF-alpha stimulation. In parallel, p50 and p65 accumulate in the nucleus and RNA transcript levels for I kappa B-alpha are dramatically upregulated. Recombinant p65 stimulates expression of E-selectin promoter-reporter constructs. I kappa B-alpha inhibits p65 or TNF-alpha-stimulated E-selectin promoter-reporter gene expression in transfected endothelial cells. The NF-kappa B and I kappa B-alpha system may be an inducible regulatory mechanism in endothelial activation.
Chemically bonded stationary phases that use synthetic hosts containing aromatic binding clefts: HPLC analysis of nitro-substituted polycyclic aromatic hydrocarbons. (1993)

The synthesis of hosts with improved binding affinities for nitroaromatic guests is described. Association constants for several host-guest complexes were measured in chloroform solution and ranged over three orders of magnitude. Two hosts were covalently linked to silica gel to produce chemically bonded stationary phases for HPLC. The use of these phases for HPLC analysis of nitro-substituted polycyclic aromatic hydrocarbons is discussed.
A comparison study: applying segmentation to array CGH data for downstream analyses (2005)

http://www.bioconductor.org
Monte Carlo low pressure deposition profile simulations (1991)

The models and algorithms used for simulation of chemical vapor deposition (CVD) profiles in Stanford profile emulator for etching and deposition in integrated circuit engineering are described. In the CVD simulation direct deposition, re-emission, and surface diffusion are considered as the mechanisms for near surface mass transport. The re-emission process is characterized by a single surface reaction coefficient (or sticking coefficient) which condenses the complex physico-chemical mechanisms (physisorption, chemisorption, desorption) in a single probability that defines the final attachment of a reactive to a surface. For desorption process, different desorption models can be selected (cosine re-emission, specular reflection). Surface diffusion is modeled with a gaussian distribution function characterized by the diffusion length. A Monte Carlo approach is used to determine the deposition rates in arbitrary topologies and a string algorithm is used for the evolution of the surface. Iteration between them allows taking into account self-shadowing effects. Comparisons of experimental versus simulation results for SiO2 trench filling, that can be characterized by direct deposition and re-emission with a pure cosine desorption law and no surface diffusion are included.
Cell-Type-Specific Gene Transfer into Human Cells with Retroviral Vectors That Display Single-Chain Antibodies (1998)

The successful application of human gene therapy protocols on a broad clinical basis will depend on the availability of in vivo cell-type-specific gene delivery systems. We have developed retroviral vector particles, derived from spleen necrosis virus (SNV), that display the antigen binding site of an antibody on the viral surface. Using retroviral vectors derived from SNV that displayed single-chain antibodies (scAs) directed against a carcinoembryonic antigen-cross-reacting cell surface protein, we have shown that an efficient, cell-type-specific gene delivery can be obtained. In this study, we tested whether other scAs displayed on SNV vector particles can also lead to cell-type-specific gene delivery. We displayed the following scAs on the retroviral surface: one directed against the human cell surface antigen Her2neu, which belongs to the epidermal growth factor receptor family; one directed against the stem cell-specific antigen CD34; and one directed against the transferrin receptor, which is expressed on liver cells and various other tissues. We show that retroviral vectors displaying these scAs are competent for infection in human cells which express the antigen recognized by the scA. Infectivity was cell type specific, and titers above 10(5) CFU per ml of tissue culture supernatant medium were obtained. The density of the antigen on the target cell surface does not influence virus titers in vitro. Our data indicate that the SNV vector system is well suited for the development of a large variety of cell-type-specific targeting vectors.
Expression of cartilage-specific molecules is retained on long-term culture of human articular chondrocytes (1995)

Normal human adult articular chondrocytes were used to determine how the chondrocyte phenotype is modulated by culture conditions following long-term culture. We report here for the first time that human articular chondrocytes have a lifespan in the range of 34-37 population doublings. While chondrocytes cultured as monolayers displayed a fibroblastoid morphology and grew faster, those cultured as suspensions over agarose adopted a round morphology and formed clusters of cells reminiscent of chondrocyte differentiation in intact cartilage, with little or no DNA synthesis. These morphologies were independent of the age of the culture. Despite, these morphological differences, however, chondrocytes expressed markers at mRNA and protein levels characteristic of cartilage: namely, types II and IX collagens and the large aggregating proteoglycans, aggrecan, versican and link protein, but not syndecan, under both culture conditions. However, they also expressed type I collagen alpha 1(I) and alpha 2(I) chains. It has been suggested that expression of collagen alpha 1(I) by chondrocytes cultured as monolayers is a marker of the loss of the chondrocyte phenotype. However, we show here, using reverse transcriptase/polymerase chain reaction, that normal fresh intact human articular cartilage expresses collagen alpha 1(I). The data show that following long-term culture human articular chondrocytes retain their differentiated characteristics and that cell shape does not correlate with the expression of the chondrocyte phenotype. It is proposed that loss of the chondrocyte phenotype is marked by the loss of one or more cartilage-specific molecules rather than by the appearance of non-cartilage-specific molecules.
Effect of carbon sources differing in oxidation state and transport route on succinate production in metabolically engineered Escherichia coli (2005)

In mixed-acid fermentation, succinate synthesis requires one mole of phosphoenolpyruvate (PEP), one mole of CO2, and two moles of NADH for every mole of succinate to be formed. Different carbon sources with different properties were used to address these requirements. Sorbitol generates one more mole of NADH than glucose. Fermentation of sorbitol was shown in this study (and by others) to produce significantly more succinate than fermentation of glucose, due to increased NADH availability. Xylose fermentation conserves the intracellular PEP pool, since its transport does not require the phosphotransferase system normally used for glucose transport. The extra PEP can then be assimilated in the succinate pathway to improve production. In this study, fermentation of xylose did yield higher succinate production than glucose fermentation. Subsequent inactivation of the acetate and lactate pathways was performed to study metabolite redistribution and the effect on succinate production. With the acetate pathway inactivated, significant carbon flux shifted toward lactate rather than succinate. When both acetate and lactate pathways were inactivated, succinate yield ultimately increased with a concomitant increase in ethanol yield.
Automatic number plate reading for transport applications (1993)

Accident rates remain high for some roads. In many of the instances excess speed was a contributing factor and, consistent with established theories, evidence suggests that the excessive speed increased the level of injury. The role that technology can play in the development and trial of a speed detection and deterrent system which automatically reads vehicle registration plates and displays those exceeding the speed threshold, together with the recorded speed, on a variable message sign. The system has become known as SVDD. (Speed Violation Detection Deterrent). >
Recent Developments in Chemistry of 3(5)-Aminopyrazoles (1983)

potentiality of 3(5)-aminopyrazoles are reported.
An Access Control Architecture for Distributing Trust in Pervasive Computing Environments (2010)

Pervasive computing infrastructure is highly distributed and it is essential to develop security mechanisms that enhance the security of the system by distributing trust among the various infrastructure components. We present a novel access control architecture explicitly designed to distribute trust that combines threshold cryptography, multi-layer encryption, and mediated access to contextual data to support dynamically changing access control permissions. We present several models of our access control infrastructure and evaluate how well each design distributes trust and limits the behavior of misbehaving components. We also simulate the behavior of our threshold based access control scheme and evaluate the overhead of each infrastructure model.