gebhart/patrepeval huggingface dataset:
Nanoengineered Bioplatforms Based on DNA Origami [Point of View] (2014)

DNA is generally associated with the storage of genetic information. However, in many ways, it is also an ideal building material. The shape of a DNA structure is determined by the sequences of the DNA strands within the structure. DNA origami [1] has recently evolved as a method for producing programmable structures at the nanoscale. In a DNA origami, a long single-stranded DNA molecule is folded and held in place with shorter DNA strands. This process can be visualized by taking a very long tube or hose and folding it into a desired shape. Smaller strands of the same material can then be used to tie the large tube into a space-filling structure. In the case of DNA origami the shorter strands are called staples. The staples crosslink and stabilize the entire structure, enabling the formation of complex and programmable 2-D and 3-D shapes. Structures with considerable complexity can be designed and produced.
Do you want an articulation plan? This is how the Colorado Model was developed. (1991)

Directors and faculty members of all the Colorado LPN, ADN, and BSN programs have joined together to formulate a model for statewide nursing program articulation. All schools will activate the model by January, 1992. The process by which this was accomplished is discussed in this article.
Characteristics of HIV-Tat protein transduction domain. (2004)

The human immunodeficiency virus type 1 (HIV-1) Tat protein transduction domain (PTD), which contains rich arginine and lysine residues, is responsible for the highly efficient transduction of protein through the plasma membrane. In addition, it can be secreted from infected cells and has the ability to enter neighboring cells. When the PTD of Tat is fused to proteins and exogenously added to cells, the fusion protein can cross plasma membranes. Recent reports indicate that the endogenously expressed Tat fusion protein can demonstrate biodistribution of several proteins. However, intercellular transport and protein transduction have not been observed in some studies. Therefore, this study examined the intercellular transport and protein transduction of the Tat protein. The results showed no evidence of intercellular transport (biodistribution) in a cell culture. Instead, the Tat fusion peptides were found to have a significant effect on the transduction and intercellular localization properties. This suggests that the HIV-1 PTD passes through the plasma membrane in one direction.
Complex Systems: From Biology to Computation (1993)

Part 1 Life - natural and artificial: as large as life and twice as natural - bioinformatics and the artificial life, Paulien Hogeweg the emergence of connectivity and fractal time in the evolution of random diagraphs, Doug Seeley and Simon Ronald emergent behaviour in biological systems, David G. Green the wave-cluster model of water-protein interactions, John Watterson computer viruses - the inevitability of evolution?, Paul-Michael Agapow pattern formation in physical and biological growth, Tony Roberts and Mark A. Knackstedt recovery of model coral communities - complex behaviours from interaction of parameters operating at different spatial scales, Ann L. Preece and Craig R. Johnson methodological issues within a framework to support a class of artificial-life worlds in cellular automata, Pedro Paulo Balbi de Oliveira computation in inhomogeneous cellular automata, Zoran Aleksic. Part 2 Fractals, chaos and nonlinear dynamics: nonlinear dynamics and chaos in musical instruments, Neville H. Fletcher interactive evolution of L-system grammars for computer graphics modelling, Jon McCormack the effect of permeability heterogeneity on viscous fingers in porous media, Mark Knackstedt and Muhammad Sahimi recognition and generation of fractal patterns by using syntactic techniques, Jacques Blanc-Talon from beta-expansions to chaos and fractals, Dominique Luzeaux the uniform emergence of points on a circle, Keith Tognetti and Graham Winley complexity and emergence - the seduction and reduction of nonlinear models in the social sciences, Margot L. Lyon steps to an ecology of form, Jean Pierre Paillet fractal computer image analysis of particle morphology, Thomas B. Kirk and Gwidon W. Stachowiak. Part 3 Information and control systems: taming large complex information systems, C.N.G. (Kit) Dampney et al complexity in C31 systems, Clive Cooper soft systems methodology - an alternative approach to knowledge elicitation in complex and poorly defined systems, Andrew Finegan a self-organizing load balancing system, George M. Bryan and Wane E. Moore central fusion of sensor information using reasoned feedback, Tim Payne reduction of modelling error of complex biosystems by an AI approach, Patrick C. Fu and John P. Barford. Part 4 Parallel and emergent computation: parallel computers and complex systems, Geoffrey C. Fox parallel algorithms for distance embedding problem, Hong Xie convergence of symmetric shunting in competitive neural networks, Abdesselam Bouzerdoum the evolution of learning algorithms for artificial neural networks, Jonathan Baxter self-annealing when learning a Markov random field image model, David Howard and William Moran external inputs to attractor neural networks, Anthony N. Burkitt a computer simulation of plasticity in the primary motor cortex, David Cake neural dynamics in biological visual information processing, Terry Bossomaier et al.
Association of IgA-Fc receptors (Fc alpha R) with Fc epsilon RI gamma 2 subunits in U937 cells. Aggregation induces the tyrosine phosphorylation of gamma 2. (1994)

We investigated the possibility that IgA-binding chains of Fc alpha R on monocytic cells are physically associated with gamma 2 subunits of Fc epsilon RI (Fc epsilon RI gamma 2 or gamma 2). Fc alpha R was precipitated from lysates of IFN gamma-treated U937 cells, subclone 10.6, and probed by immunoblotting with Ab against human gamma 2. Fc alpha R was precipitated through anti-Fc alpha R mAbs A59 or A62, through A62 from lysates that had been exhaustively precleared of high affinity IgG-Fc receptors (Fc gamma RI) and of low affinity Fc gamma RII, and through anti-Fc alpha R mAb A77 from Fc gamma RI-precleared lysates of untreated 10.6 cells. precipitation was also performed through F(ab')2 A77 and through the native ligand of the receptor, hlgA. In all cases, Fc alpha R precipitates contained co-isolated 22-kDa gamma 2 (unreduced). The Fc alpha R alpha-chain/gamma 2 complex did not readily dissociate in 1% Nonidet P-40 as did Fc gamma RI alpha-chain/gamma 2, suggesting a novel aspect to the Fc alpha R subunit interaction. Specific Fc alpha R aggregation on cells triggered a robust respiratory burst and the tyrosine phosphorylation of several proteins. Among them was phospho-gamma 2, which migrated as a 24- to 28-kDa gamma 2 phosphoprotein on gels and was detected as a 28-kDa phosphoprotein by anti-phosphotyrosine immunoblot. Aggregated Fc alpha Rs that were precipitated from Fc alpha R-triggered cells also contained a phosphoprotein of the same mobility and immunoreactivity, as did aggregated Fc gamma RI from which the 28-kDa phosphoprotein could be more readily eluted and identified (as phospho-gamma 2). We concluded that myelocytic Fc alpha Rs are multichain complexes containing gamma 2 subunits that are tyrosine phosphorylated upon Fc alpha R aggregation. As IgA is the predominant Ig on mucosal surfaces, gamma-subunits may play an important role in mucosal immunity involving leukocytic Fc alpha R.
Synthetic Nitroimidazoles: Biological Activities and Mutagenicity Relationships (2009)

Parasitic and bacterial infections affecting the gastrointestinal tract represent a significant cause of morbidity and mortality worldwide. Nitroheterocyclic drugs have been available since the early 1960s for the treatment of anaerobic protozoa. The application of these drugs has widened and they are presently used to treat anaerobic pathogenic bacteria and protozoa. 5-nitroimidazoles are a well-established group of antiprotozoal and antibacterial agents that inhibit the growth of both anaerobic bacteria and certain anaerobic protozoa, such as Trichomonas vaginalis, Entamoeba histolytica and Giardia lamblia. The important antibacterial and antiprotozoal activities of nitroimidazoles are associated with reductive metabolism that has led to considerable interest in nitroimidazole reduction chemistry and the synthesis of new, highly effective drugs. The present review provides a brief account of various biological activities exhibited by synthetic nitroimidazole derivatives as well as their structure–mutagenicity relationships.
The development of an experimental model of subretinal neovascularization in disciform macular degeneration. (1979)

A reproducible model of subretinal neovascularization has been developed, an important first step in the study of disciform macular degeneration. The methodology and clinical description of subretinal neovascularization in the primate have been provided and histopathologic and electron microscopic correlations included. This model provides a most promising and useful mechanism for the evaluation of the many different factors and hypotheses that have been proposed for the genesis of the disciform response. In humans, it probably has more relevance to the traumatically induced disciform process, particularly that after laser therapy, than to the senile degenerative process. The purpose of this investigation is to develop the animal model by which many different theories regarding the pathogenesis of the disciform response can be tested. These initial studies relate to ischemia, hemorrhage, the inflammatory response, and position in relation to the center of the vascular-free zone as factors important in the development and evolution of subretinal neovascularization.
Epithelial membrane protein 2, a 4-transmembrane protein that suppresses B-cell lymphoma tumorigenicity (2001)

A murine homologue of the epithelial membrane protein 2 (EMP2) gene was identified in a search for genes associated with B-cell lymphoma tumorigenicity by using suppression subtractive hybridization. Expression of EMP2 messenger RNA in primary mouse tissues was limited to certain epithelial cell types and the peritoneal lymphoid compartment. EMP2 was expressed in the poorly tumorigenic DAC B-lymphoma cell line but was significantly down-regulated in a subline selected for in vivo tumor formation in Balb/c mice. Recombinant restoration of EMP2 expression in the subline suppressed its tumorigenicity, suggesting that loss of EMP2 was a causal factor in the malignant phenotype. Recombinant overexpression of EMP2 was studied in B lymphoma and NIH3T3 cells. EMP2 in both cell types induced cell death on serum deprivation. EMP2-induced cell death correlated with the expression level of EMP2 protein and was prevented by caspase inhibitors Z-VAD and Z-DEVD. These findings for the first time describe an apoptotic effect of a GAS3 family gene in lymphocytes. They also suggest that EMP2 may influence B-lymphoma tumorigenicity through a functional tumor suppressor phenotype. (Blood. 2001;97:3890-3895)
Nucleotide Pyrophosphatases/Phosphodiesterases on the Move (2000)

Nucleotide pyrophosphatases/phosphodiesterases (NPPs) release nucleoside 5′-monophosphates from nucleotides and their derivatives. They exist both as membrane proteins, with an extracellular active site, and as soluble proteins in body fluids. The only well-characterized NPPs are the mammalian ecto-enzymes NPP1 (PC-1), NPP2 (autotaxin) and NPP3 (B10; gp130RB13-6). These are modular proteins consisting of a short N-terminal intracellular domain, a single transmembrane domain, two somatomedin-B-like domains, a catalytic domain, and a C-terminal nuclease-like domain. The catalytic domain of NPPs is conserved from prokaryotes to mammals and shows remarkable structural and catalytic similarities with the catalytic domain of other phospho-/sulfo-coordinating enzymes such as alkaline phosphatases. Hydrolysis of pyrophosphate/phosphodiester bonds by NPPs occurs via a nucleotidylated threonine. NPPs are also known to auto(de)phosphorylate this active-site threonine, a process accounted for by an intrinsic phosphatase activity, with the phosphorylated enzyme representing the catalytic intermediate of the phosphatase reaction. NPP1-3 have been implicated in various processes, including bone mineralization, signaling by insulin and by nucleotides, and the differentiation and motility of cells. While it has been established that most of these biological effects of NPPs require a functional catalytic site, their physiological substrates remain to be identified.
Mortality in systemic sclerosis (2014)

Studies have consistently shown a substantially increased mortality in SSc, predominantly due to cardio-pulmonary complications. A better understanding of risk factors for mortality holds the promise of improving outcomes in this devastating multiorgan autoimmune disease.
Screening of protein kinase inhibitors identifies PKC inhibitors as inhibitors of osteoclastic acid secretion and bone resorption (2010)

In conclusion, a group of inhibitors all indicated to inhibit PKC reduced acidification in human osteoclasts, and thereby bone resorption, indicating that acid secretion by osteoclasts may be specifically regulated by PKC in osteoclasts.
Ligation-mediated PCR amplification of specific fragments from a Class-II restriction endonuclease total digest (1997)

A method is described which permits the ligation- mediated PCR amplification of specific fragments from a Class-II restriction endonuclease total digest. Feasibility was tested using Bcl I and phage lambda DNA as a model enzyme and amplicon system, respectively. Bcl I is one of many widely used restriction enzymes which cleave at palindromic recognition sequences and leave 5'-protruding ends of defined sequence. Using a single pair of universal primers, a given fragment can be specifically amplified after joining the fragments to adaptors consisting of a duplex primer region and a 9-nucleotide protruding single-stranded 5'-end containing the sequence complementary to the cleaved restriction site and a 4-nucleotide 'indexing sequence.' The protruding strand anneals to a restriction fragment by displacing its corresponding strand in the same fragment-specific indexing sequence located juxtaposed to the restriction site. The adaptor is covalently linked to the restriction fragment by T4 DNA ligase, and amplification is carried out under conditions for long-distance PCR using the M13 forward and reverse primers. The technique discriminated robustly between mismatches and perfect matches for the 16 indexing sequences tested to allow individual lambda Bcl I fragments to be amplified from their respective adaptor pairs. A strategy is proposed enabling a non-cloning approach to the accession, physical mapping and sequencing of genomic DNA. The method could also have application in high-throughput genetic mapping and fingerprinting and should expand the enzyme base for ligation- mediated indexing technology which has previously been limited to the Class-IIS and IP restriction endonucleases.
Pseudomonas exotoxin A mutants. Replacement of surface exposed residues in domain II with cysteine residues that can be modified with polyethylene glycol in a site-specific manner. (1994)

Pseudomonas exotoxin A (PE) is a three-domain protein in which domain Ia is involved in recognition of receptors on eukaryotic target cells, domain I1 promotes translocation of PE into the cytosol, and domain 1 1 1 enzymatically ADP-ribosylates elongation factor 2. Modification of proteins with polyethylene glycol (PEG) has been shown to prolong circulating plasma lifetime and may reduce or eliminate immunogenicity.However, in the case of toxins, PEG may interfere with or block toxin activity.To investigate the effect of polyethylene glycolation on specific residues located on the surface of PE domain 11, we substituted cysteine, for each of the five most exposed surface amino acids (H276, E282, N306, R313, and E327) in domain 11.These cysteines can serve as unique sites for PEG modification.The PE-Cys proteins retained most of their cytotoxicity even when the free sulfhydryl group was blocked by 5,5'-dithiobis(nitrobenzoic acid) or glutathione.When the PE-Cys proteins were conjugated with ovalbumin using a cleavable disulfide linkage, cytotoxicity was retained, but it was lost with a non-cleavable thioether linkage.In contrast, cytotoxicity was maintained when PE-Cys mutants were coupled to 5-or 20-kDa mPEG, using either a disulfide or a thioether linkage.Unexpectedly in some cases, the thioether conjugate was more active than the disulfide linkage.Pharmacokinetic studies on one of the polyethylene-glycolated molecules (R313C) showed that the mean residence time (t,) was prolonged to 72 min, compared to 20 min for unpolyethylene glycolated PE-Cys(R313C).These studies show it is possible to derivatize PE at specific residues in domain 11, maintain significant cytotoxic activity, and alter pharmacokinetics.These studies also suggest that large mPEG molecules can be translocated to the cytosol while still attached to domain I1 of PE.Pseudomonas exotoxin A (PE)l is a 66-kDa single-chain bacterial protein that kills eukaryotic cells by ADP-ribosylating elongation factor 2 (Allured et al., 1986;Gray et al., 1984;Iglewski and Kabat, 1975).PE consists of three major functional domains.Domain Ia is involved in recognition of eukary-* The costs of publication of this article were defrayed in part by the payment of page charges.
Computer Simulation Study of Human Locomotion with a Three-Dimensional Entire-Body Neuro-Musculo-Skeletal Model. I. Acquisition of Normal Walking. (2002)

A model having a three-dimensional entire-body structure and consisting of both the neuronal system and the musculo-skeletal system was proposed to precisely simulate human walking motion. The dynamics of the human body was represented by a 14-rigid-link system and 60 muscular models. The neuronal system was represented by three sub-systems: the rhythm generator system consisting of 32 neural oscillators, the sensory feedback system, and the peripheral system expressed by static optimization. Unknown neuronal parameters were adjusted by a numerical search method using the evaluative criterion for locomotion that was defined by a hybrid between the locomotive energy efficiency and the smoothness of the muscular tensions. The model could successfully generate continuous and three-dimensional walking patterns and stabilized walking against mechanical perturbation. The walking pattern was more stable than that of the model based on dynamic optimization, and more precise than that of the previous model based on a similar neuronal system.
Distinct characteristics of lymphokine-activated killer (LAK) cells derived from patients with B-cell chronic lymphocytic leukemia (B-CLL). A factor in B-CLL serum promotes natural killer cell-like LAK cell growth (1990)

Abstract We show that lymphokine-activated killer (LAK) cell precursors derived from patients with B-cell chronic lymphocytic leukemia (B-CLL) and cultured in the presence of recombinant interleukin-2 and normal human serum (NHS), develop into primarily NK cell-like (CD 57+) LAK cells, whereas identically prepared LAK cell precursors from normal subjects develop into mainly T cell-like (CD 3+, CD 8+) LAK cells. B-CLL LAK cells exhibited greater proliferative capacity than did normal LAK cells. When normal LAK cells were grown in B-CLL serum instead of NHS, their proliferation increased; NK cell levels also increased to those found in B-CLL LAK cells, suggesting that B-CLL serum contains a factor that promotes NK cell-like growth, LAK cells derived from normal or B- CLL patients demonstrated similar lytic activity toward K562 and Raji cells. Growth in B-CLL serum did not reduce their lytic potential. Thus, the altered phenotype and growth exhibited by B-CLL LAK cells and normal LAK cells grown in B-CLL serum does not lead to abnormalities in their cytolytic functions. We propose instead that the predominance of NK-like cells in B-CLL LAK cell populations and the presence of an NK cell-like growth factor in B-CLL serum reflect abnormalities related to NK cell-mediated B-cell regulation; ie, either inhibition of normal B- cell growth and/or growth stimulation of the leukemic clone in B-CLL.
THE EFFECTS OF CATALYST, FREE FATTY ACIDS, AND WATER ON TRANSESTERIFICATION OF BEEF TALLOW (1998)

Transesterification of beef tallow and methanol is affected by many factors. Catalyst, free fatty acids, andwater in beef tallow, and reaction time were investigated. Sodium hydroxide (NaOH) was a more effective catalyst thansodium methoxide (NaMeO). NaOH and NaMeO reached their maximum activities at 0.3% and 0.5%, w/w of beef tallow,respectively. The presence of water had more negative effect on transesterification than did the presence of free fatty acids(FFA). For best results, the water content of beef tallow should be kept not beyond 0.06%, w/w. FFA content of beef tallowshould be kept below 0.5%, w/w. The transesterification of beef tallow was very slow in the first minute. The production ofbeef tallow methyl esters (BTME) was complete after about 15 min. There were still some mono- and diglycerides in theBTME phase after the reaction was finished.
RHEUMATOID ARTHRITIS: TREATMENT WHICH CONTROLS THE C-REACTIVE PROTEIN AND ERYTHROCYTE SEDIMENTATION RATE REDUCES RADIOLOGICAL PROGRESSION (1986)

One hundred and fifty consecutive patients with active, rheumatoid arthritis were assessed and treated with gold, D-penicillamine, chloroquine or dapsone. Four groups were selected from these patients. Group I consisted of 60 patients who did not complete 12 months' therapy. Group II consisted of patients in whom ESR and C-reactive protein (CRP) fell to less than 30 mm/h and less than 20 mg/l, respectively, and remained at these levels between 6 and 12 months. In group IV the ESR and CRP fell but remained greater than 30 and greater than 20, respectively, during the same period. Group III patients had variable ESRs and CRPs between 6 and 12 months. In groups II, III and IV there was a significant deterioration (p less than 0.01) in the hand and foot radiographs from 0 to 6 months. Between 6 and 12 months the radiographs in groups III and IV continued to show significant radiological progression (p less than 0.01), but those of group II did not alter. These results suggest radiological deterioration continues during the first 6 months regardless of clinical response but thereafter, further deterioration is less likely to occur when the ESR and CRP are consistently controlled.
Durable Complete Responses in Heavily Pretreated Patients with Metastatic Melanoma Using T-Cell Transfer Immunotherapy (2011)

Cell transfer therapy with autologous TILs can mediate durable complete responses in patients with metastatic melanoma and has similar efficacy irrespective of prior treatment. Clin Cancer Res; 17(13); 4550-7. ©2011 AACR.