gebhart/patrepeval huggingface dataset:
Synapsis of Recombination Signal Sequences Located in cis and DNA Underwinding in V(D)J Recombination (2004)

V(D)J recombination requires binding and synapsis of a complementary (12/23) pair of recombination signal sequences (RSSs) by the RAG1 and RAG2 proteins, aided by a high-mobility group protein, HMG1 or HMG2. Double-strand DNA cleavage within this synaptic, or paired, complex is thought to involve DNA distortion or melting near the site of cleavage. Although V(D)J recombination normally occurs between RSSs located on the same DNA molecule (in cis), all previous studies that directly assessed RSS synapsis were performed with the two DNA substrates in trans. To overcome this limitation, we have developed a facilitated circularization assay using DNA substrates of reduced length to assess synapsis of RSSs in cis. We show that a 12/23 pair of RSSs is the preferred substrate for synapsis of cis RSSs and that the efficiency of pairing is dependent upon RAG1-RAG2 stoichiometry. Synapsis in cis occurs rapidly and is kinetically favored over synapsis of RSSs located in trans. This experimental system also allowed the generation of underwound DNA substrates containing pairs of RSSs in cis. Importantly, we found that the RAG proteins cleave such substrates substantially more efficiently than relaxed substrates and that underwinding may enhance RSS synapsis as well as RAG1/2-mediated catalysis. The energy stored in such underwound substrates may be used in the generation of DNA distortion and/or protein conformational changes needed for synapsis and cleavage. We propose that this unwinding is uniquely sensed during synapsis of an appropriate 12/23 pair of RSSs.
Comparative Analysis of Autoxidation of Haemoglobin (2001)

Autoxidation of oxyhaemoglobin (oxyHb) to methaemoglobin was measured at different temperatures in haemoglobin solutions from Atlantic hagfish, river lamprey, common carp, yellowfin tuna and pig. The aims were to evaluate the impact of the absent distal histidine in hagfish haemoglobin, the importance of oxyHb being either monomeric (hagfish and lamprey) or tetrameric (carp, tuna and pig) and to gain information on the temperature-sensitivity of autoxidation. The rate of autoxidation was lower in hagfish than in carp, yellowfin tuna and lamprey haemoglobins at any given temperature. Substitution of the distal histidine residue (His E7) with glutamine in hagfish haemoglobin was therefore not associated with an accelerated autoxidation, as might be expected on the basis of the normal protective role of His E7. Glutamine may have similar qualities to histidine and be involved in the low susceptibility to autoxidation. The low oxidation rate of hagfish haemoglobin, together with an oxidation rate of lamprey haemoglobin that did not differ from that of carp and yellowfin tuna haemoglobins, also revealed that autoxidation was not accelerated in the monomeric oxyhaemoglobins. Pig haemoglobin was oxidised more slowly than fish haemoglobins, demonstrating that fish haemoglobins are more sensitive to autoxidation than mammalian haemoglobins. The rate of autoxidation of hagfish haemoglobin was, however, only significantly greater than that of pig haemoglobin at high temperatures. Autoxidation was accelerated by rising temperature in all haemoglobins. Arrhenius plots of carp and yellowfin tuna haemoglobin revealed a break at 25 degrees C, reflecting a lower temperature-sensitivity between 5 and 25 degrees C than between 25 and 40 degrees C.
Collagen synthesis by cultured rabbit aortic smooth-muscle cells. Alteration with phenotype (1990)

Enzymically isolated rabbit aortic smooth-muscle cells (SMC) in the first few days of primary culture express a 'contractile phenotype', but with time these cells modulate to a 'synthetic phenotype'. Synthetic-state SMC are able to proliferate, and, provided that they undergo fewer than 5 cumulative population doublings, return to the contractile phenotype after reaching confluency [Campbell, Kocher, Skalli, Gabbiani & Campbell (1989) Arteriosclerosis 9, 633-643]. The present study has determined the synthesis of collagen, at the protein and mRNA levels, by cultured SMC as they undergo a change in phenotypic state. The results show that, upon modulating to the synthetic phenotype, SMC synthesized 25-30 times more collagen than did contractile cells. At the same time, non-collagen-protein synthesis increased only 5-6-fold, indicating a specific stimulation of collagen synthesis. Steady-state mRNA levels are also elevated, with alpha 2(I) and alpha 1(III) mRNA levels 30 times and 20 times higher respectively, probably reflecting increased transcriptional activity. Phenotypic modulation was also associated with an alteration in the relative proportions of type I and III collagens synthesized, contractile SMC synthesizing 78.1 +/- 3.6% (mean +/- S.D.) type I collagen and 17.5 +/- 4.7% type III collagen, and synthetic cells synthesizing 90.3 +/- 2.0% type I collagen and 5.8% +/- 1.8% type III collagen. Enrichment of type I collagen was similarly noted at the mRNA level. On return to the contractile state, at confluency, collagen production and the percentage of type I collagen decreased. This further illustrates the close association between the phenotypic state of SMC and their collagen-biosynthetic phenotype.
Visualization of a primary anti-tumor immune response by positron emission tomography (2005)

Current methodologies that monitor immune responses rely on invasive techniques that sample tissues at a given point in time. New technologies are needed to elucidate the temporal patterns of immune responses and the spatial distribution of immune cells on a whole-body scale. We describe a noninvasive, quantitative, and tomographic approach to visualize a primary anti-tumor immune response by using positron emission tomography (PET). Bone marrow chimeric mice were generated by engraftment of hematopoietic stem and progenitor cells transduced with a trifusion reporter gene encoding synthetic Renilla luciferase (hRluc), EGFP, and Herpes virus thymidine kinase (sr39TK). Mice were challenged with the Moloney murine sarcoma and leukemia virus complex (M-MSV/M-MuLV), and the induced immune response was monitored by using PET. Hematopoietic cells were visualized by using 9-[4-[(18)F]fluoro-3-(hydroxymethyl)butyl]guanine ([(18)F]FHBG), a radioactive substrate specific for the sr39TK PET reporter protein. Immune cell localization and expansion were seen at the tumor and draining lymph nodes (DLNs). 2-[(18)F]fluoro-2-deoxy-D-glucose ([(18)F]FDG), which is sequestered in metabolically active cells, was used to follow tumor growth and regression. Elevated glucose metabolism was also seen in activated lymphocytes in the DLNs by using the [(18)F]FDG probe. When M-MSV/M-MuLV-challenged mice were treated with the immunosuppressive drug dexamethasone, activation and expansion of immune cell populations in the DLNs could no longer be detected with PET imaging. The method we describe can be used to kinetically measure the induction and therapeutic modulations of cell-mediated immune responses.
Tregs and rheumatoid arthritis. (2008)

Regulatory T cells (Tregs) are a subset of T cells which are involved in peripheral immune tolerance. Their role in autoimmune disease which occurs through a breakdown of tolerance is of particular interest in trying to ascertain the mechanism(s) of disease progression. It is hoped that by understanding the role of Tregs in autoimmunity a reliable therapy may be developed to aid in both the treatment and potentially cure of disease. This review will focus on the naturally-occurring CD4+ CD25+ regulatory T cell subset and their possible involvement in rheumatoid arthritis.
The working set model for program behavior (1968)

Probably the most basic reason behind the absence of a general treatment of resource allocation in modern computer systems is an adequate model for program behavior. In this paper a new model, the "working set model," is developed. The working set of pages associated with a process, defined to be the collection of its most recently used pages, provides knowledge vital to the dynamic management of paged memories. "Process" and "working set" are shown to be manifestations of the same ongoing computational activity; then "processor demand" and "memory demand" are defined; and resource allocation is formulated as the problem of balancing demands against available equipment.
Selection of a human T helper type 1-like T cell subset by mycobacteria. (1991)

Mycobacteria elicit a cellular immune response in their hosts. This response usually leads to protective immunity, but may sometimes be accompanied by immunopathology due to delayed type hypersensitivity (DTH). A striking example in man is tuberculoid leprosy, which is characterized by high cellular immunity to Mycobacterium leprae and immunopathology due to DTH. Skin lesions of patients suffering from this disease have the characteristics of DTH reactions in which macrophages and CD4+ T lymphocytes predominate. In animal models, it has been shown that DTH responses are associated with the presence of a particular subset of CD4+ T cells (T helper type 1 [Th1]) that secrete only certain cytokines, such as interleukin 2 (IL-2), interferon gamma (IFN-gamma), and lymphotoxin, but no IL-4 or IL-5. We studied the cytokine release of activated M. leprae-reactive CD4+ T cell clones derived from tuberculoid leprosy patients. These T cell clones, which were reactive with mycobacterial heat shock proteins, exhibited a Th1-like cytokine secretion pattern with very high levels of IFN-gamma. Half of these clones secreted low levels of IL-4 and IL-5, but the ratio of IFN-gamma to IL-4 and IL-5 was much higher than that of T cell clones reactive with nonmycobacterial antigens. A Th1-like cytokine secretion pattern was also observed for T cell clones and polyclonal T cell lines from control individuals that recognized both heat shock and other mycobacterial antigens. The levels of IFN-gamma secreted by these clones were, however, significantly less than those of patient-derived T cell clones. This Th1-like pattern was not found with T cell clones from the same patients and healthy individuals generated in the same manner, but reactive with nonmycobacterial antigens. Our data thus indicate that mycobacteria selectively induce human T cells with a Th1-like cytokine secretion profile.
Dynamics of gene silencing by RNA interference (2004)

The large number of candidate genes identified by modern high-throughput technologies require efficient methods for generating knockout phenotypes or gene silencing in order to study gene function. RNA interference (RNAi) is an efficient method that can be used for this purpose. Effective gene silencing by RNAi depends on a number of important parameters, including the dynamics of gene expression and the RNA dose. Using mouse hepatoma cells, we detail some of the principal characteristics of RNAi as a tool for gene silencing, such as the RNA dose level, RNA complex exposure time, and the time of transfection relative to gene induction, in the context of silencing a green fluorescent protein reporter gene. Our experiments demonstrate that different levels of silencing can be attained by modulating the dose level of RNA and the time of transfection and illustrate the importance of a dynamic analysis in designing robust silencing protocols. By quantifying the kinetics of RNAi-based gene silencing, we present a model that may be used to help determine key parameters in more complex silencing experiments and explore alternative gene silencing protocols.
Formulation, Characterization, and Sensing Applications of Transparent Poly(vinyl alcohol)−Polyelectrolyte Blends (1998)

Several new optically clear polymer blends have been formulated for selectively incorporating solution-phase anions and cations. In all of the blends poly(vinyl alcohol) was the host matrix and it was cross-linked with glutaraldehyde to entrap polyelectrolytes including poly(acrylic acid), Nafion, poly(diallyldimethylammonium chloride), poly(vinylbenzyltrimethylammonium chloride), and poly(styrenesulfonic acid). [Ru(BiPy)3]2+ and Fe(CN)63- were used as prototypical analytes to study the ion-exchange properties of the new blends. The thicknesses of spin-coated thin films of the blends were variable over a wide range (0.70 μm being typical), as determined by an optical interference method. Thin film coatings of three of the blends were optimized for single-step covalent coating on activated oxide surfaces. Two silane coupling agents, 3-glycidoxypropyltrimethoxysilane and 3-aminopropyltriethoxysilane, were used to covalently attach these three blends to glass and ITO-coated glass surfaces. The potential use of these materials for chemical sensing has been demonstrated by applying them to multiple internal reflection and spectroelectrochemical devices as thin films.
Rational prescribing of drugs. (1977)

A rational prescription is defined as one which proposes the best pharmacological approach to obtain the therapeutic objective. To achieve this goal requires a careful consideration of factors related to: patient, disease, medication, and doctor. Concepts of risk/benefit and cost/benefit are of relevance for the therapeutic decision. The doctor also has to make an effort to assure the compliance of his patients. This requires a good understanding of the personality and of the socio-cultural background of the patient. Social pharmacology helps to appreciate and understand the role of these factors and to use them for improvement of therapeutic results.
4D Printing of Shape Memory‐Based Personalized Endoluminal Medical Devices (2016)

The convergence of additive manufacturing and shape-morphing materials is promising for the advancement of personalized medical devices. The capability to transform 3D objects from one shape to another, right off the print bed, is known as 4D printing. Shape memory thermosets can be tailored to have a range of thermomechanical properties favorable to medical devices, but processing them is a challenge because they are insoluble and do not flow at any temperature. This study presents here a strategy to capitalize on a series of medical imaging modalities to construct a printable shape memory endoluminal device, exemplified by a tracheal stent. A methacrylated polycaprolactone precursor with a molecular weight of 10 000 g mol<sup>-1</sup> is printed with a UV-LED stereolithography printer based on anatomical data. This approach converges with the zeitgeist of personalized medicine and it is anticipated that it will broadly expand the application of shape memory-exhibiting biomedical devices to myriad clinical indications.
Is botulinum toxin type A effective in the treatment of spastic shoulder pain in patients after stroke? A double-blind randomized clinical trial (2007)

Patients with spastic shoulder pain treated with a botulinum toxin type A infiltration in the pectoralis major muscle of the paretic side have a higher likelihood of pain relief (between 2.43- and 3.11-fold).
Regularized reconstruction to reduce blocking artifacts of block discrete cosine transform compressed images (1993)

The reconstruction of images from incomplete block discrete cosine transform (BDCT) data is examined. The problem is formulated as one of regularized image recovery. According to this formulation, the image in the decoder is reconstructed by using not only the transmitted data but also prior knowledge about the smoothness of the original image, which complements the transmitted data. Two methods are proposed for solving this regularized recovery problem. The first is based on the theory of projections onto convex sets (POCS) while the second is based on the constrained least squares (CLS) approach. For the POCS-based method, a new constraint set is defined that conveys smoothness information not captured by the transmitted BDCT coefficients, and the projection onto it is computed. For the CLS method an objective function is proposed that captures the smoothness properties of the original image. Iterative algorithms are introduced for its minimization. Experimental results are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
2,2-Difluoro-1,3-dimethylimidazolidine (DFI). A new fluorinating agentElectronic supplementary information (ESI) available: experimental data. See http://www.rsc.org/suppdata/cc/b2/b204471d/ (2002)

2,2-Difluoro-1,3-dimethylimidazolidine (DFI) is a new deoxo-fluorinating agent that is useful for the conversion of alcohols to monofluorides, and aldehydes/ketones to gemdifluorides under mild conditions.
HIV-1 receptors and cell tropism (2001)

HIV virus particles interact with several receptors on cell surfaces. Two receptors, CD4 and a co-receptor act sequentially to trigger fusion of viral and cellular membranes and confer virus entry into cells. For HIV-1, the chemokine receptor CCR5 is the predominant co-receptor exploited for transmission and replication in vivo. Variants that switch to use CXCR4 and perhaps other co-receptors evolve in some infected individuals and have altered tropism and pathogenic properties. Other cell surface receptors including mannose binding protein on macrophages and DC-SIGN on dendritic cells also interact with gp120 on virus particles but do not actively promote fusion and virus entry. These receptors may tether virus particles to cells enabling interactions with suboptimal concentrations of CD4 and/or co-receptors. Alternatively such receptors may transport cell surface trapped virions into lymph nodes before transmitting them to susceptible cells. Therapeutic strategies that prevent HIV from interacting with receptors are currently being developed. This review describes how the interaction and use of different cellular receptors influences HIV tropism and pathogenesis in vivo.
Potentiation of Anticancer-Drug Cytotoxicity by Multidrug-Resistance Chemosensitizers Involves Alterationsin Membrane Fluidity Leading to Increased Membrane Permeability (1995)

We are studying the mechanism underlying chemosensitization of anticancer-drug cytotoxicity in wild-type and multidrug-resistant (MDR) mammalian cells. We show here that the chemosensitizers, reserpine and verapamil, display a dramatic potentiation of taxol, anthracycline and Vinca alkaloids cytotoxicity in P-glycoprotein-(P-gp)-deficient hamster and human nasopharyngeal carcinoma cells. We have therefore utilized this phenomenon to probe for the putative P-gp-independent component of cytotoxicity chemosensitization. These chemosensitizers yielded a marked increase in the accumulation of taxol in parental hamster and human carcinoma cells that are devoid of P-gp. These chemosensitizers and non-ionic detergents brought about a pronounced increase in the accumulation of structurally and mechanistically diverse lipophilic chromophores in parental and MDR hamster cells. Furthermore, non-toxic concentrations of these non-ionic detergents yielded a marked potentiation of taxol cytotoxicity in parental cells. These findings were consistent with a chemosensitizer-mediated, P-gp-independent increase in membrane permeability. Thus, several aspects of chemosensitizers' interaction with lipid bilayers and biomembranes were studied. In this respect, like various mild detergents, chemosensitizers induced a dose-dependent leakage of carboxyfluorescein encapsulated in liposomes. Like specialized membrane fluidizers, various chemosensitizers induced a dose-dependent membrane fluidization (and sometimes rigidification) in both liposomes and various wild-type and MDR animal and human cells, as revealed by diphenylhexatriene fluorescence polarization. Furthermore, a favorable correlation was observed between the ability of chemosensitizers to permeabilize lipid bilayers and their capacity to potentiate anticancer-drug cytotoxicity. Thus, we propose that chemosensitizer-mediated changes in the physical properties of biomembranes, including altered fluidity and increased permeability, may be important factors in achieving potentiation of anticancer-drug cytotoxicity in wild-type and MDR mammalian cells. This study offers a basis for the chemosensitizer-mediated potentiation of drug toxicity to healthy tissues, thus emphasizing the importance of a prior evaluation of the potential untoward toxicity when simultaneously using MDR chemosensitizers and cytotoxic agents in the clinic.
Cell-type-specific synthesis of murine immunoglobulin mu RNA from an adenovirus vector. (1986)

The mouse immunoglobulin heavy-chain mu constant region gene was cloned into the early region 1B of an adenovirus type 5 vector to allow reproducible kinetics of expression of the mu gene in the presence of continuous host protein synthesis after infection by the recombinant. The immunoglobulin-adenovirus recombinant is helper independent in infecting human fibroblastic and B- and T-cell lines and expresses mu in a cell-type-specific manner. By Northern blot analysis, correctly polyadenylated and spliced E1B-mu S and E1B-mu m mRNAs are found to be equally abundant at steady state in fibroblasts. In contrast, and appropriately, only E1B-mu S mRNAs accumulate in a lambda light-chain-secreting myeloma cell line. Analysis of nascent transcripts pulse labeled in isolated nuclei demonstrates equimolar polymerase loading throughout the mu region in all cell types infected by mu-Ad. Thus, correct polyadenylation and splicing of E1B-mu S and E1B-mu m in fibroblasts does not require transcription termination in the region separating the mu S and mu m polyadenylation sites. Furthermore, differential expression of mu transcripts in the background of myeloma cells is regulated at the level of RNA processing and does not require the presence of the immunoglobulin heavy-chain enhancer or promoter element.
Regulation of Transforming Growth Factor-β Signaling and PDK1 Kinase Activity by Physical Interaction between PDK1 and Serine-Threonine Kinase Receptor-associated Protein (2005)

To gain more insights about the biological roles of PDK1, we have used the yeast two-hybrid system and in vivo binding assay to identify interacting molecules that associate with PDK1. As a result, serine-threonine kinase receptor-associated protein (STRAP), a transforming growth factor-beta (TGF-beta) receptor-interacting protein, was identified as an interacting partner of PDK1. STRAP was found to form in vivo complexes with PDK1 in intact cells. Mapping analysis revealed that this binding was only mediated by the catalytic domain of PDK1 and not by the pleckstrin homology domain. Insulin enhanced a physical association between PDK1 and STRAP in intact cells, but this insulin-induced association was prevented by wortmannin, a phosphatidylinositol 3-kinase inhibitor. In addition, the association between PDK1 and STRAP was decreased by TGF-beta treatment. Analysis of the activities of the interacting proteins showed that PDK1 kinase activity was significantly increased by coexpression of STRAP, probably through the inhibition of the binding of 14-3-3, a negative regulator, to PDK1. Consistently, knockdown of the endogenous STRAP by the transfection of the small interfering RNA resulted in the decrease of PDK1 kinase activity. PDK1 also exhibited an inhibition of TGF-beta signaling with STRAP by contributing to the stable association between TGF-beta receptor and Smad7. Moreover, confocal microscopic study and immunostaining results demonstrated that PDK1 prevented the nuclear translocation of Smad3 in response to TGF-beta. Knockdown of endogenous PDK1 with small interfering RNA has an opposite effect. Taken together, these results suggested that STRAP acts as an intermediate signaling molecule linking between the phosphatidylinositol 3-kinase/PDK1 and the TGF-beta signaling pathways.