gebhart/patrepeval huggingface dataset:
Specific Interaction of Eukaryotic Translation Initiation Factor 3 with the 5′ Nontranslated Regions of Hepatitis C Virus and Classical Swine Fever Virus RNAs (1998)

Translation of hepatitis C virus (HCV) and classical swine fever virus (CSFV) RNAs is initiated by cap-independent attachment (internal entry) of ribosomes to the approximately 350-nucleotide internal ribosomal entry segment (IRES) at the 5' end of both RNAs. Eukaryotic initiation factor 3 (eIF3) binds specifically to HCV and CSFV IRESs and plays an essential role in the initiation process on them. Here we report the results of chemical and enzymatic footprinting analyses of binary eIF3-IRES complexes, which have been used to identify the eIF3 binding sites on HCV and CSFV IRESs. eIF3 protected an internal bulge in the apical stem IIIb of domain III of the CSFV IRES from chemical modification and protected bonds in and adjacent to this bulge from cleavage by RNases ONE and V1. eIF3 protected an analagous region in domain III of the HCV IRES from cleavage by these enzymes. These results are consistent with the results of primer extension analyses and were supported by observations that deletion of stem-loop IIIb or of the adjacent hairpin IIIc from the HCV IRES abrogated the binding of eIF3 to this RNA. This is the first report that eIF3 is able to bind a eukaryotic mRNA in a sequence- or structure-specific manner. UV cross-linking of eIF3 to [32P]UTP-labelled HCV and CSFV IRES elements resulted in strong labelling of 4 (p170, p116, p66, and p47) of the 10 subunits of eIF3, 1 or more of which are likely to be determinants of these interactions. In the cytoplasm, eIF3 is stoichiometrically associated with free 40S ribosomal subunits. The results presented here are consistent with a model in which binding of these two translation components to separate, specific sites on both HCV and CSFV IRESs enhances the efficiency and accuracy of binding of these RNAs to 40S subunits in an orientation that promotes entry of the initiation codon into the ribosomal P site.
Reversible Biochemical Switching of Ionic Transport through Aligned Carbon Nanotube Membranes (2005)

Synthetic nanopore membranes can be used to mimic ion channels provided that molecular transport through membranes is precisely gated with selective and reversible chemical interactions. Aligned nanotubes of carbon or other inorganic materials can be assembled to construct higher-order supramolecular architectures using polymer films to force chemical flux through hollow cores. Open tips of carbon nanotubes (CNT) can be activated to have carboxylic groups, which can be easily derivatized with a molecule that binds to a bulky receptor that can open/close the pore entrance. In particular, the core entrances of an aligned CNT membrane were functionalized with a desthiobiotin derivative that binds reversibly to streptavidin, thereby enabling a reversible closing/opening of the core entrance. Ionic flux through the CNT membrane was monitored using optically absorbing charged marker molecules. The flux is reduced by a factor of 24 when the desthiobiotin on the CNT is coordinated with streptavidin; release of streptavidin increases the flux, demonstrating a reversible ion-channel flow. Analysis of solutions of released streptavidin shows approximately 16 bound streptavidin molecules per CNT tip.
Cardiac safety in cluster headache patients using the very high dose of verapamil (≥720 mg/day) (2011)

Use of high doses of verapamil in preventive treatment of cluster headache (CH) is limited by cardiac toxicity. We systematically assess the cardiac safety of the very high dose of verapamil (verapamil VHD) in CH patients. Our work was a study performed in two French headache centers (Marseilles-Nice) from 12/2005 to 12/2008. CH patients treated with verapamil VHD (≥720 mg) were considered with a systematic electrocardiogram (EKG) monitoring. Among 200 CH patients, 29 (14.8%) used verapamil VHD (877±227 mg/day). Incidence of EKG changes was 38% (11/29). Seven (24%) patients presented bradycardia considered as nonserious adverse event (NSAE) and four (14%) patients presented arrhythmia (heart block) considered as serious adverse event (SAE). Patients with EKG changes (1,003±295 mg/day) were taking higher doses than those without EKG changes (800±143 mg/day), but doses were similar in patients with SAE (990±316 mg/day) and those with NSAE (1,011±309 mg/day). Around three-quarters (8/11) of patients presented a delayed-onset cardiac adverse event (delay ≥2 years). Our work confirms the need for systematic EKG monitoring in CH patients treated with verapamil. Such cardiac safety assessment must be continued even for patients using VHD without any adverse event for a long time.
Discrimination between fibrin and fibrinogen by a monoclonal antibody against a synthetic peptide. (1985)

Circulating soluble fibrin, observed in the blood of patients with ongoing intravascular coagulation, is generated from the plasma protein fibrinogen by the limited proteolytic action of thrombin. We report the production of a monoclonal antibody that discriminates between fibrin and fibrinogen in blood. The synthetic hexapeptide Gly-Pro-Arg-Val-Val-Glu, representing the amino terminus of the alpha chain of human fibrin, was used as immunogen. This hexapeptide is located within the A alpha chain of fibrinogen but becomes the amino terminus of the fibrin alpha chain, after fibrinopeptide A is removed by the action of thrombin, and thus becomes accessible for antibody binding. The monoclonal antibody we have prepared can discriminate between fibrin and fibrinogen and thus can be used in assay systems to quantitate soluble fibrin or, potentially, to image fibrin-rich thrombi.
Connective tissue biomatrix: its isolation and utilization for long-term cultures of normal rat hepatocytes. (1980)

A new procedure is introduced for the isolation of connective tissue fibers, called biomatrix, containing a significant portion of the extracellular matrix (basement membrane components and components of the ground substance). Biomatrix isolated from normal rat liver contains >90% of the tissue's collagens and all of the known collagen types, including types I and III and basement membrane collagens. The purified collagenous fibers are associated with noncollagenous acidic proteins (including fibronectins and possibly small amounts of glycosaminoglycans). Procedures are also described for preparing tissue culture substrates with these fibers by either smearing tissue culture dishes with frozen sections or by shredding the biomatrix into small fibrils with a homogenizer. The biomatrix as a substrate has a remarkable ability to sustain normal rat hepatocytes long-term in culture. The hepatocytes, which on tissue culture plastic or on type I collagen gels do not survive more than a few weeks, have been maintained for more than 5 mo in vitro when cultured on biomatrix. These cells cultured on rat liver biomatrix show increased attachment and survival efficiencies, long-term survival (months) and retention of some hepatocyte-specific functions.
Structure of HP1 Chromodomain Bound to a Lysine 9-Methylated Histone H3 Tail (2002)

The chromodomain of the HP1 family of proteins recognizes histone tails with specifically methylated lysines. Here, we present structural, energetic, and mutational analyses of the complex between the Drosophila HP1 chromodomain and the histone H3 tail with a methyllysine at residue 9, a modification associated with epigenetic silencing. The histone tail inserts as a beta strand, completing the beta-sandwich architecture of the chromodomain. The methylammonium group is caged by three aromatic side chains, whereas adjacent residues form discerning contacts with one face of the chromodomain. Comparison of dimethyl- and trimethyllysine-containing complexes suggests a role for cation-pi and van der Waals interactions, with trimethylation slightly improving the binding affinity.
Normal values of serum IGF-1 in adults: results from a Brazilian population (2010)

This study established the reference range for IGF-1 determined with the Immulite 2000 assay for a large number of healthy Brazilian adults stratified according to age, and suggests that variations > 20% in IGF-1 levels within an interval of 12 weeks cannot be attributed to interassay variability.
Major histocompatibility complex class II-restricted presentation of an internally synthesized antigen displays cell-type variability and segregates from the exogenous class II and endogenous class I presentation pathways. (1993)

Although reported examples of endogenous antigen (Ag) presentation by major histocompatibility complex (MHC) class II molecules have increased, the mechanisms governing this process remain poorly defined. In this communication, we describe an experimental system designed to examine the mechanisms governing class II presentation of internal Ag. Our target peptide is processed from a transmembrane protein constitutively expressed by a variety of nucleated cells (MHC class I, H-2Ld), is naturally displayed by MHC class II molecules in vivo, and is recognized by a class II-restricted, CD4+ T cell hybridoma. Our results indicate that presentation of the Ld target Ag is independent of its plasma membrane expression, may not involve endosomal proteolysis, and thus may be distinct from the classically defined class II presentation pathway. In addition, the observations that Ld presentation does not require a functional TAP-1 complex, is not blocked by invariant chain, and cannot utilize cytoplasmic forms of H-2Ld, suggest that a classical class I pathway is not involved in this presentation event. Finally, our data suggest that different cofactors participate in MHC class II presentation of exogenous and endogenous Ag, and that disparate Ag presenting cells, such as B, T, and pancreatic islet cells, may differentially express these two class II pathways of Ag presentation.
Control of intracellular trafficking of ICAM-1-targeted nanocarriers by endothelial Na+/H+exchanger proteins (2005)

Targeting nanocarriers (NC) loaded by antioxidant enzymes (e.g., catalase) to endothelial cell adhesion molecules (CAM) alleviates oxidative stress in the pulmonary vasculature. However, antioxidant protection is transient, since CAM-targeted catalase is internalized, delivered to lysosomes, and degraded. To design means to modulate the metabolism and longevity of endothelial cell (EC)-targeted drugs, we identified and manipulated cellular elements controlling the uptake and intracellular trafficking of NC targeted to ICAM-1 (anti-ICAM/NC). BAPTA, thapsigargin, amiloride, and EIPA inhibited anti-ICAM/NC uptake by EC and actin rearrangements induced by anti-ICAM/NC (required for uptake), suggesting that member(s) of Na(+)/H(+) exchanger family proteins (NHE) regulate these processes. Consistent with this hypothesis, an siRNA specific for the plasmalemma NHE1, but not the endosome-associated NHE6, inhibited actin remodeling induced by anti-ICAM/NC and internalization. Anti-ICAM/NC binding to EC stimulated formation of a transient ICAM-1/NHE1 complex. One hour after uptake, ICAM-1 dissociated from NHE1, and anti-ICAM/NC were transported to NHE6-positive vesicles en route to lysosomes. Inhibition of PKC (an activator of intracellular NHE) accelerated nanocarrier lysosomal trafficking. In contrast, monensin, which enhances the endosomal sodium influx and proton efflux maintained by NHE6, inhibited delivery of anti-ICAM/NC to lysosomes by switching their trafficking to a plasma membrane recycling pathway. This markedly prolonged the protective effect of catalase-coated anti-ICAM/NC. Therefore, 1) NHE1 and NHE6 regulate distinct phases of anti-ICAM/NC uptake and trafficking; 2) pharmacological agents affecting these regulatory elements alter the itinerary of anti-ICAM/NC intracellular trafficking; and 3) these agents modulate duration of the therapeutic effects of targeted drugs.
On Finding All Suboptimal Foldings of an RNA Molecule (1989)

An algorithm and a computer program have been prepared for determining RNA secondary structures within any prescribed increment of the computed global minimum free energy. The mathematical problem of determining how well defined a minimum energy folding is can now be solved. All predicted base pairs that can participate in suboptimal structures may be displayed and analyzed graphically. Representative suboptimal foldings are generated by selecting these base pairs one at a time and computing the best foldings that contain them. A distance criterion that ensures that no two structures are "too close" is used to avoid multiple generation of similar structures. Thermodynamic parameters, including free-energy increments for single-base stacking at the ends of helices and for terminal mismatched pairs in interior and hairpin loops, are incorporated into the underlying folding model of the above algorithm.
Purification of a fibroblast growth factor from bovine pituitary. (1975)

The purification from bovine pituitary gland of a growth factor responsible for the control of animal cell division in tissue culture is reported. This growth factor is a polypeptide of 13,300 molecular weight and is homogeneous when analyzed by polyacrylamide gel electrophoresis, carboxymethyl-Sephadex gradient elution chromatography, and Sephadex G-50 chromatography. The yield of growth factor is 5 mg per kg of pituitary. It is active in stimulating DNA synthesis in 3T3 cells at concentrations as low as 2 times 10-13 M with saturation at 1 times 10-10 M.
Genetics and Innate and Adaptive Immunity in IBD (2014)

Inflammatory bowel disease (IBD) is an abnormal inflammatory response within the gut to a trigger that has yet to be identified. The family history in many patients, especially those with Crohn's disease, suggests a genetic predisposition. It has been hypothesized that the abnormal inflammatory response is due in part to genetic alterations in the normal homeostatic processes that regulate host interactions with the normal gut microbes. Genetic studies have identified increasing numbers of genetic risk factors that involve a diverse series of pathways such as receptors of innate immune response, defects in epithelial barrier function, immune- and cytokine-related genes and genes involved in autophagy. Studies further suggest that abnormal immune responses in IBD patients are directed against the intestinal microbiota, with activation of both innate and adaptive immune responses. Indeed, studies have shown bacterial-derived antigen as drivers of T cell immune responses. More recently, Th17, regulatory T cells and unconventional innate-like T cells have been implicated in the induction and regulation of intestinal inflammation. The seminal discoveries of pathogen recognition receptors including Toll-like receptors and nucleotide-binding oligomerization domain receptors have changed our understanding of how immune cells respond to microbes and the role this may play in IBD pathogenesis. Understanding these mechanism will lead to new strategies in the treatment and prevention of IBD.
SCHOLARLY OPINION: Unintended Consequences: The United States Supreme Court's Mission to Restrict Remedies for State Prisoners Backfires (1994)

the Director of the Illinois Capital Resource Center, an agency which recruits, trains and gives litigation support to a panel of attorneys representing indigent death row inmates on collateral review in state and federal courts, as well as
Robust embedded egomotion estimation (2011)

This work presents a method for estimating the egomotion of an aerial vehicle in challenging industrial environments. It combines binocular visual and inertial cues in a tightly-coupled fashion and operates in real time on an embedded platform. An extended Kalman filter fuses measurements and makes motion estimation rely more on inertial data if visual feature constellation is degenerate. Errors in roll and pitch are bounded implicitly by the gravity vector. Inertial sensors are used for efficient outlier detection and enable operation in poorly and repetitively textured environments. We demonstrate robustness and accuracy in an industrial scenario as well as in general indoor environments. The former is accompanied by a detailed performance evaluation supported with ground truth measurements from an external tracking system.
The Central Role of CD4+ T Cells in the Antitumor Immune Response (1998)

The induction of optimal systemic antitumor immunity involves the priming of both CD4(+) and CD8(+) T cells specific for tumor-associated antigens. The role of CD4(+) T helper cells (Th) in this response has been largely attributed to providing regulatory signals required for the priming of major histocompatibility complex class I restricted CD8(+) cytolytic T lymphocytes, which are thought to serve as the dominant effector cell mediating tumor killing. However, analysis of the effector phase of tumor rejection induced by vaccination with irradiated tumor cells transduced to secrete granulocyte/macrophage colony-stimulating factor indicates a far broader role for CD4(+) T cells in orchestrating the host response to tumor. This form of immunization leads to the simultaneous induction of Th1 and Th2 responses, both of which are required for maximal systemic antitumor immunity. Cytokines produced by these CD4(+) T cells activate eosinophils as well as macrophages that produce both superoxide and nitric oxide. Both of these cell types then collaborate within the site of tumor challenge to cause its destruction.
IFATS Collection: Adipose Stromal Cell Differentiation Is Reduced by Endothelial Cell Contact and Paracrine Communication: Role of Canonical Wnt Signaling (2008)

Adipose stromal cells (ASC) are multipotential mesenchymal progenitor cells that are readily induced to undergo adipogenic differentiation, and we have recently demonstrated them to have functional and phenotypic overlap with pericytes lining microvessels in adipose tissues. In this study we addressed the hypothesis that modulation of ASC fate within this perivascular niche can occur via interaction with endothelial cells (EC), which serve to modulate the adipogenic potential of ASC. To this end, we investigated contact as well as paracrine effects of EC on ASC adipogenesis, in two-dimensional coculture and via conditioned medium and analyzed mutual gene expression changes by real-time reverse transcription polymerase chain reaction (PCR). A significant decrease in adipogenic differentiation was observed in ASC when they were cocultured with EC but not control fibroblasts. This endothelial cell-specific effect was accompanied by increased expression of factors involved in Wnt signaling, most prominently Wnt1, Wnt4, and Wnt10a, which are well-known inhibitors of adipogenesis. Suppression of Wnt1 but not Wnt 10a or scrambled control short interfering RNA in cocultures partially reversed the endothelial cell effect, thus increasing adipogenic differentiation, suggesting a plausible role of Wnt1 ligand in modulation of adipogenesis by the vasculature. Furthermore, addition of recombinant Wnt ligand or the Wnt signaling agonist inhibited adipogenic differentiation of ASC in the absence of EC. In conclusion, these data define the relationship in adipose tissue between ASC and EC in the perivascular niche, in which the latter act to repress adipogenesis, thereby stabilizing vasculature. It is tempting to speculate that abnormal endothelial function may be associated with pathologic derepression of adipogenesis. Disclosure of potential conflicts of interest is found at the end of this article.
Apolipoprotein CIISt. Michael. Familial apolipoprotein CII deficiency associated with premature vascular disease. (1987)

A 60-yr-old woman and her brother, products of a consanquinous mating, were chylomicronemic. The chylomicronemia in both subjects was found to be due to the absence of functional apoCII. A mutant form, designated apoCIISt. Michael (apoCIIs), was identified by two-dimensional electrophoresis and Western blot using anti-apoCII antiserum. The isoelectric point of apoCIIs was similar to that of normal apoCII, but its apparent molecular weight was 3,000 greater. Tryptic peptides of apoCIIs were identified that had retention times in reverse-phase high pressure liquid chromatography and amino acid compositions indistinguishable from that of residues 1 to 48 and 51 to 55 of normal apoCII. The complete sequence of apoCIIs was deduced from a combination of the sequence analysis of tryptic peptides corresponding to residues 56 through 96 and the known sequence of the apoCII gene. ApoCIIs differed from apoCII at residue 70 where Gln70 was replaced by Pro70 and the sequence terminated with Pro96. This is consistent with a base insertion in the codon for Asp69 or Gln70 in the apoCII gene and a subsequent translation reading frame shift. Both patients were homozygous for apoE-4. This and the absence of normal apoCII is consistent with homozygozity at the apoE-CII gene locus on chromosome 19. Both siblings and several relatives had premature ischemic vascular disease, in contrast with its apparent absence in other apoCII-deficient families.
Isolation of disaturated phosphatidylcholine with osmium tetroxide (1976)

A simple, rapid, inexpensive method for isolating disaturated phosphatidylcholine from adult rat lung has been devised. Total lipids are reacted with osmium tetroxide dissolved in carbon tetrachloride, and the disaturated phosphatidylcholine is isolated on a column of neutral alumina. More than 99% of the fatty acids in the phosphatidylcholine fraction are saturated and 94% of this material migrates as phosphatidylcholine on subsequent thin-layer chromatography.
Distinct roles for CREB-binding protein and p300 in hematopoietic stem cell self-renewal (2002)

Hematopoietic stem cells (HSC) are tightly regulated through, as yet, undefined mechanisms that balance self-renewal and differentiation. We have identified a role for the transcriptional coactivators CREB-binding protein (CBP) and p300 in such HSC fate decisions. A full dose of CBP, but not p300, is crucial for HSC self-renewal. Conversely, p300, but not CBP, is essential for proper hematopoietic differentiation. Furthermore, in chimeric mice, hematologic malignancies emerged from both CBP(-/-) and p300(-/-) cell populations. Thus, CBP and p300 play essential but distinct roles in maintaining normal hematopoiesis, and, in mice, both are required for preventing hematologic tumorigenesis.
The ISL statistical translation system for spoken language translation. (2004)

In this paper we describe the components of our statistical machine translation system used for the spoken language translation evaluation campaign. This system is based on phrase-to-phrase translations extracted from a bilingual corpus. A new phrase alignment approaches will be introduced, which finds the target phrase by optimizing the overall word-to-word alignment for the sentence pair under the constraint that words within the source phrase are only aligned to words within the target phrase. The system will be used for Chinese-to-English translations under the small, additional and unlimited data conditions, and for the small Japanese-to-English translation track.