gebhart/patrepeval huggingface dataset:
Direct Isolation of Satellite Cells for Skeletal Muscle Regeneration (2005)

Muscle satellite cells contribute to muscle regeneration. We have used a Pax3(GFP/+) mouse line to directly isolate (Pax3)(green fluorescent protein)-expressing muscle satellite cells, by flow cytometry from adult skeletal muscles, as a homogeneous population of small, nongranular, Pax7+, CD34+, CD45-, Sca1- cells. The flow cytometry parameters thus established enabled us to isolate satellite cells from wild-type muscles. Such cells, grafted into muscles of mdx nu/nu mice, contributed both to fiber repair and to the muscle satellite cell compartment. Expansion of these cells in culture before engraftment reduced their regenerative capacity.
AHFS Drug Information (1994)

With extensive updated information on everything from treatment of hypertension to hepatitis C, AHFS (R) Drug Information (R) 2017 is a necessary addition to your pharmacy's resources. With content supported by more than 89,000 total references and reviewed by over 500 professionals, it helps you protect your patients and your practice. The only print compendium designated by the U.S. Congress, AHFS (R) Drug Information 2017 is also the only reference published by a professional and scientific society - ensuring it is the most authoritative and best-selling reference trusted by pharmacists for 59 years. AHFS (R) Drug Information 2017 contains the most trustworthy drug information available - all in one place. It is the most comprehensive evidence-based source of drug information complete with therapeutic guidelines and off-label uses.
Fast virtual functional assessment of intermediate coronary lesions using routine angiographic data and blood flow simulation in humans: comparison with pressure wire – fractional flow reserve (2014)

We developed a fast and simple CFD-powered virtual haemodynamic assessment model using only routine angiography and without requiring any invasive physiology measurements/hyperaemia induction. Virtual-FAI showed a high diagnostic performance and incremental value to QCA for predicting wire-FFR; this "less invasive" approach could have important implications for patient management and cost.
Tumor Necrosis Factor in Humans (1988)

When immune cells are stimulated in a variety of ways, they release soluble proteins called cytokines. Because of their far-reaching effects on many different types of cells and tissues, cytokines can be considered hormones. Among the cytokines, interferon and the interleukins are well established as important mediators of the inflammatory response. Only in the past decade has it been recognized that macrophages also make a cytokine that is responsible for most, if not all, of the major manifestations of endotoxin shock. The discovery of cachectin and of its identity with tumor necrosis factor engendered great excitement because it suggested new . . .
Management of Pediatric Congenital Atlantoaxial Dislocation: A Report of 23 Cases from Northern India (2002)

From July 1996 to August 2001, we operated on 23 children (age 4-12 years) with congenital atlantoaxial dislocation (AAD). Sixteen had reducible AAD and 6 had the fixed type, while a single patient had basilar invagination. Preoperatively, these children were divided into four functional grades depending on the level of neurological deficits and dependence on others for activities of daily living (Di Lorenzo grades I-IV). There were only 2 patients with no deficits (grade I), while 15 of the 23 children presented with severe neurological deficits and were completely dependent for all activities of daily living (grade IV). Stigmata suggestive of congenital AAD were documented in 6 children and radiological osseous anomalies in 18 children. Transoral decompression and posterior stabilization was performed in 7 children, while 16 patients underwent the posterior stabilization procedure only. All patients were immobilized with a hard cervical collar postoperatively. Six children developed one or other treatable complications, of whom reoperation was indicated in 3, but could only be undertaken in 2 children. Retightening of the wire was done in 1 and further decompression of the odontoid process was carried out in the other. There was no postoperative deterioration in patients with no preoperative deficits (grade I). Ten out of the 15 children who were completely dependent for all activities in the preoperative period (grade IV) improved, and 6 children achieved normalcy or near normalcy (grade I or II). Three children deteriorated in the postoperative period, of whom 2 subsequently improved at follow-up. There were 2 deaths in the series; both these patients belonged to the severely compromised group (grade IV) and in addition had respiratory compromise. Bony fusion at the posterior stabilization site could be seen in 14 out of 16 patients screened. The various problems faced by the authors in managing these very fragile and severely compromised children with cervicomedullary compression due to congenital atlantoaxial dislocation in a setting with limited resources are discussed.
Fertilization and Development of Mouse Oocytes Injected with Isolated Sperm Heads1 (1996)

To determine whether spermatozoa must be structurally intact before microsurgical injection into oocytes for normal fertilization, intact spermatozoa, as well as sperm heads separated from tails by sonication, were individually injected into oocytes. When whole spermatozoa were injected immediately after their immobilization, the majority of the oocytes were fertilized and developed normally. Sonication in the presence or absence of Triton X-100 decapitated more than 95% of spermatozoa. Although all decapitated spermatozoa were diagnosed as "dead" by live/dead sperm staining, separated sperm heads (nuclei) could participate in normal embryo development when injected into the oocytes. The ability of isolated sperm heads (nuclei) to participate in normal embryo development was maintained under cryopreservation conditions that were not suitable for the survival of plasma membrane-intact spermatozoa. These results indicate that 1) spermatozoa do not need to be structurally intact for intracytoplasmic injection, 2) the plasma and acrosomal membranes and all tail components are not essential for normal embryo development, at least in the mouse, and 3) the cryopreservation conditions required for maintenance of the genetic integrity of sperm nuclei are less stringent than those necessary for keeping plasma membrane-intact spermatozoa alive.
Static optimization of conjunctive queries with sliding windows over infinite streams (2004)

We define a framework for static optimization of sliding window conjunctive queries over infinite streams. When computational resources are sufficient, we propose that the goal of optimization should be to find an execution plan that minimizes resource usage within the available resource constraints. When resources are insufficient, on the other hand, we propose that the goal should be to find an execution plan that sheds some of the input load (by randomly dropping tuples) to keep resource usage within bounds while maximizing the output rate. An intuitive approach to load shedding suggests starting with the plan that would be optimal if resources were sufficient and adding "drop boxes" to this plan. We find this to be often times suboptimal - in many instances the optimal partial answer plan results from adding drop boxes to plans that are not optimal in the unlimited resource case. In view of this, we use our framework to investigate an approach to optimization that unifies the placement of drop boxes and the choice of the query plan from which to drop tuples. The effectiveness of our optimizer is experimentally validated and the results show the promise of this approach.
Discontinuous IgE‐binding epitopes contain multiple continuous epitope regions: results of an epitope mapping on recombinant Hol l 5, a major allergen from velvet grass pollen (2001)

The knowledge of IgE-binding epitopes on allergen molecules is important for better understanding allergen-antibody interactions and, thus, for developing new strategies for immunotherapy. Our purpose was to more precisely define the number and structure of IgE-binding epitopes of a paradigmatic major grass pollen allergen. We performed an IgE-binding epitope mapping of rHol l 5, a group V pollen allergen of velvet grass (Holcus lanatus), with overlapping fragments (length between 15 and 186 amino acids), which were expressed in E. coli as MBP fusion proteins. Using sera of 65 grass pollen allergic patients, the fragments were analysed by immunoblotting for IgE reactivity. Specificity of antibody binding was confirmed by competitive blot inhibition assays. At least four different continuous IgE-binding epitopes were identified on small fragments (about 30 amino acids), and at least five different discontinuous IgE-binding epitopes on larger fragments, which were destroyed by further fragmentation. The fragments were differentially recognized by individual patients' sera. By investigating IgE-binding to one of the small fragments in more detail, we found further epitope regions on this fragment. It was noteworthy that IgE reactivity to small fragments was weak compared to large fragments or to the complete molecule. Competitive blot inhibition experiments showed that binding of IgE antibodies to the small fragments was specific but with lower avidity than to the complete rHol l 5. rHol l 5 harbours multiple discontinuous as well as continuous IgE-binding epitopes spread over the whole molecule, which were individually recognized by IgE antibodies from different patients. Low avidity of IgE antibodies to small fragments suggests that the continuous epitope regions do not represent the complete epitope and are most probably parts of discontinuous epitopes.
Subcellular Localization of Aft1 Transcription Factor Responds to Iron Status in Saccharomyces cerevisiae (2002)

The Aft1 transcription factor regulates the iron regulon in response to iron availability in Saccharomyces cerevisiae. Aft1 activates a battery of genes required for iron uptake under iron-starved conditions, whereas Aft1 function is inactivated under iron-replete conditions. Previously, we have shown that iron-regulated DNA binding by Aft1 is responsible for the controlled expression of target genes. Here we show that this iron-regulated DNA binding by Aft1 is not due to the change in the total expression level of Aft1 or alteration of DNA binding activity. Rather, nuclear localization of Aft1 responds to iron status, leading to iron-regulated expression of the target genes. We identified the nuclear export signal (NES)-like sequence in the AFT1 open reading frame. Mutation of the NES-like sequence causes nuclear retention of Aft1 and the constitutive activation of Aft1 function independent of the iron status of the cells. These results suggest that the nuclear export of Aft1 is critical for ensuring iron-responsive transcriptional activation of the Aft1 regulon and that the nuclear import/export systems are involved in iron sensing by Aft1 in S. cerevisiae.
Plasma levels of coagulation inhibitors, fibrinolytic markers and platelet-derived growth factor-AB in patients with failed hip prosthesis (2003)

We studied the plasma levels of coagulation inhibitors, of fibrinolysis and PDGF-AB, in patients with aseptic loosening of the hip replacement. 23 patients having loose hip prostheses were compared to patients having 15 stable hip prostheses, and 26 undergoing primary hip replacement. The levels of the coagulation inhibitors antithrombin III and protein C were determined by chromogenic assays. Fibrinolysis was evaluated by the changes in fibrin degradation products (D-dimer), determined by enzyme immunoassay, and in the plasminogen activator inhibitor-1 (PAl-1), by enzymatic assay. PDGF-AB was determined by enzyme immunoassay. In patients with failed prostheses, we found fibrinolysis activation, as shown by a statistically significant increase in D-dimer and a significant decrease of PAI-1. No significant differences were obseved in antithrombin III, protein C, and PDGF-AB. PAI-1 and D-dimer assays in failed prostheses may be useful for the pathogenetic evaluation, because the continuous inflammatory stimulus associated with fibrin deposition may also affect the systemic levels.
Cytotoxic T-Lymphocyte Epitopes for HLA-B53 and Other HLA Types in the Malaria Vaccine Candidate Liver-Stage Antigen 3 (2000)

The development of an effective preerythrocytic vaccine against Plasmodium falciparum malaria is likely to require inclusion of components from several preerythrocytic antigens. The association of HLA-B53 with resistance to severe malaria in West Africa provided evidence that HLA class I-restricted CD8(+) T-cell responses play a role in protective immunity in African children, supporting data from rodent models of malaria. Previously, a single epitope from liver-stage-specific antigen 1 (LSA-1) has been shown to be recognized by HLA-B53-specific cytotoxic T lymphocytes (CTL), but HLA-B53 epitopes were not found in four other antigens. In this study we measured CTL responses to peptides from the recently sequenced antigen liver-stage antigen 3 (LSA-3) and identified in it a new epitope restricted by HLA-B53. Several CTL epitopes restricted by other class I types were also identified within LSA-3 in studies in The Gambia and Tanzania. CTL were also identified to an additional P. falciparum antigen, exported protein 1 (Exp-1), the homologue of which is a protective antigen in a rodent model of malaria. These findings emphasize the diversity of P. falciparum antigens recognized by CD8(+) T cells in humans and support the inclusion of components from several antigens in new CTL-inducing vaccines against malaria.
Synthetic Approaches to Regioregular Unsymmetrical Dialkoxy-Substituted Poly(1,4-phenylene ethynylene)s (2008)

Poly(2,5-disubstituted-1,4-phenylene ethynylene)s, PPEs, are generally synthesized by Pd-catalyzed coupling polymerizations of appropriately substituted 1,4-diiodobenzenes and 1,4-diethynylbenzenes (i.e., condensation polymerization of A−A and B−B type monomers). If the monomers are not symmetrically substituted, this results in an irregular substitution pattern of the side chains along the polymer backbone. As with other classes of conjugated polymers, the relative placement of side chains along the backbone should influence the properties of the materials. We report a new synthetic approach to prepare regioregular unsymmetrically substituted PPEs by polymerization of 4-iodophenylacetylenes (i.e., a condensation polymerization of a single A−B type monomer). We have synthesized both the regiorandom and regioregular PPEs from unsymmetrically substituted monomers. We provide a detailed discussion of various approaches to the synthesis of PPEs with different regioregularities and provide a preliminary description of the differences between regioregular and regiorandom analogues.
CTL Response and Protection Against P815 Tumor Challenge in Mice Immunized with DNA Expressing the Tumor-Specific Antigen P815A (1997)

A DNA immunization approach was used to induce an immune response against the tumor-specific antigen P815A in DBA/2 mice. The P1A gene, which encodes the P815A antigen, was modified by the addition of a short sequence coding for a tag epitope recognized by the monoclonal antibody AU1, and cloned into the eukaryotic expression vector pBKCMV, resulting in plasmid pBKCMV-P1A. L1210 cells stably transfected with pBKCMV-P1A expressed P1A mRNA and were lysed by the syngeneic P815A-specific cytotoxic clone CTL-P1:5, thus confirming that the tag-modified P1A protein underwent correct processing and presentation. A single intramuscular injection of 100 microg of pBKCMV-P1A induced the expression of P1A mRNA for at least 4 months. Eighty percent of DBA/2 mice injected three times with 100 microg of pBKCMV-P1A generated cytotoxic T lymphocytes (CTL) that lysed P815 tumor cells, whereas mock-inoculated animals failed to show any cytotoxicity. Moreover, experiments designed to evaluate the protection of pBKCMV-P1A-immunized mice against a lethal challenge with P815 tumor cells showed that 6 of 10 immunized mice rejected the tumor, and 2 mice showed prolonged survival compared to control animals.
High-resolution mapping of mammalian genes by in situ hybridization to free chromatin. (1992)

Fluorescence in situ hybridization to metaphase chromosomes or chromatin fibers in interphase nuclei is a powerful technique in mapping genes and DNA segments to specific chromosome region. We have been able to release the chromatin fibers from cells arrested at G1 and G2 phases using different drugs and a simple alkaline lysis procedure. We have also demonstrated specific hybridization of fluorescence-labeled probes to single-copy genomic DNA sequences on the free chromatins. Fluorescence in situ hybridization signals have been detected for sequences separated as close as 21 kilobase pairs and as far as 350 kilobase pairs, with excellent correspondence between the observed and expected distances. The resolution of this technique should approach 10 kilobase pairs and its coverage should span millions of base pairs. Therefore, free chromatin mapping can be generally used to study the structure and organization of mammalian genomes.
Oligonucleotide Conjugates as Potential Antisense Drugs with Improved Uptake, Biodistribution, Targeted Delivery, and Mechanism of Action (2002)

This review summarizes the effect of conjugating small molecules and large biomacromolecules to antisense oligonucleotides to improve their therapeutic potential. In many cases, favorable changes in pharmacokinetic and pharmacodynamic properties were observed. Opportunities exist to change the terminating mechanism of antisense action or to enhance the RNase H mode of action via conjugate formation.
Computational Insights into the Interactions between DNA and siRNA with “Rigid” and “Flexible” Triazine Dendrimers (2010)

In this study, simulation challenges intuitive models of "flexible" and "rigid" generation two triazine dendrimers as it pertains to solution conformation and conformation on binding DNA or siRNA sequences. These results derive from structural and energetic analyses of the binding events. Simulations of the rigid structure reinforce the role of the constrained piperazine linker in positioning the peripheral groups at significant distance from each other and the core of the dendrimer. In contrast, the flexible dendrimer, characterized by triethyleneglycol-like linkers, collapses in solution. On binding DNA and siRNA, these conformations are largely retained. The rigid dendrimer undergoes reorganization of peripheral groups to generate a large number of contacts to the nucleic acid. In contrast, the flexible dendrimer, originally conceived to create multivalent interactions with nucleic acids, generates only a few contacts and collapses further. This paper provides unique insight in the role played by molecular flexibility in the binding phenomenon.
The Complete Nucleotide Sequence of the Genome of a Hepatitis B Virus Isolated from a Naturally Infected Chimpanzee (1988)

The complete nucleotide sequence of a strain of hepatitis B virus, originally isolated from a naturally infected chimpanzee, has been determined. Interesting features of the sequence include the presence of an in-phase stop codon in the 'pre-core' region of the core antigen open reading frame. The sequence shows approximately 10% nucleotide divergence from all of the other hepatitis B virus sequences previously published and the possibility that this divergence is the result of passage through chimpanzees is discussed.
Specific Interaction between Gangliotriaosylceramide (Gg3) and Sialosyllactosylceramide (GM3) as a Basis for Specific Cellular Recognition between Lymphoma and Melanoma Cells (1989)

In view of the possible role of glycosphingolipids in defining the specificity of cell-cell interactions, the key molecules for recognition of cell surface glycosphingolipids have been studied. In addition to previously suggested recognition mechanisms involving endogenous lectins and glycosyltransferases, an alternative possibility, based on carbohydrate-carbohydrate (Lex-Lex) interaction, has been raised (Eggens, I., Fenderson, B., Toyokuni, T., Dean, B., Stroud, M., and Hakomori, S. (1989) J. Biol. Chem. 264, 9476-9484). We now report a highly specific interaction between gangliotriaosylceramide (Gg3, GalNAc beta 1----4Gal beta 1----4Glc beta 1----Cer) and sialosyllactosylceramide (GM3, NeuAc alpha 2----3Gal beta 1----4Glc beta 1----Cer). The interaction requires a bivalent cation (Ca2+ or Mg2+) and can be inhibited by sialosyl 2----3 lactose, anti-GM3 antibody (DH2), anti-Gg3 antibody (2D4), or EDTA. The strength of interaction between GM3 liposome and the Gg3-coated plastic surface was highly density-dependent. The mouse lymphoma L5178 AA12 cell line (high expressor of Gg3) interacted specifically with the mouse B16 melanoma cell line (high expressor of GM3). The interaction was inhibited by 5 mM sialosyllactose, anti-GM3 antibody, anti-Gg3 antibody, and EDTA in analogy to GM3-Gg3 interaction. L5178 AV27, a genetically related variant clone which does not express Gg3, showed no interaction with B16 cells. Untreated AA12 cells, but not 2D4-treated AA12 cells or AV27 cells, interacted with GM3 coated on the plastic surface. These findings suggest a specific interaction between AA12 cells and B16 cells based on Gg3-GM3 interaction.
The complete amino acid sequence of the human transglutaminase K enzyme deduced from the nucleic acid sequences of cDNA clones. (1991)

In order to study the expression and role of transglutaminases in the formation of the cross-linked cell envelope of human epidermis, we have used a synthetic oligonucleotide encoding the consensual active site sequence of known transglutaminase sequences. By Northern blot analysis, newborn foreskin epidermis expresses three different mRNA species of about 3.7, 3.3, and 2.9 kilobases while normal cultured epidermal keratinocytes express only the 3.7- and 2.9-kilobase species. The largest species corresponds to a known ubiquitous tissue type II or transglutaminase C activity, the smallest corresponds to a known type I or transglutaminase K activity, and the mid-sized component apparently encodes a transglutaminase E activity that has recently been shown to be expressed in terminally differentiating epidermis (Kim, H. C., Lewis, M. S., Gorman, J. L., Park, S. C., Girard, J. E., Folk, J. E. & Chung, S. I. (1990) J. Biol. Chem., in press). Using the active site oligonucleotide as a probe, we have isolated and sequenced cDNA clones encoding the transglutaminase K enzyme. The deduced complete protein sequence has 813-amino acid residues of 89.3 kDa, has a pl of 5.7, and is likely to be an essentially globular protein, which are properties expected from the partially purified enzyme. It shares 49-53% sequence homology with the other transglutaminases of known sequence, especially in regions carboxyl-terminal to the active site, and possesses sequences likely to confer its Ca2+ dependence. Interestingly, its larger size is due to extended sequences on its amino and carboxyl termini, absent on the other transglutaminases, that may define its unique properties.