gebhart/patrepeval huggingface dataset:
Exonic Sequences Provide Better Targets for Antisense Oligonucleotides Than Splice Site Sequences in the Modulation of Duchenne Muscular Dystrophy Splicing (2010)

Antisense-mediated exon skipping is currently the most promising therapeutic approach for Duchenne muscular dystrophy (DMD). The rationale is to use antisense oligonucleotides (AONs) to hide exons from the splicing machinery, causing them to be skipped from the mature mRNA. Thus, the mutated, out-of-frame dystrophin transcripts as seen in DMD are reframed, allowing the generation of internally deleted, partly functional dystrophin proteins, rather than prematurely truncated, nonfunctional ones. This approach is mutation specific, so multiple AONs targeting all internal DMD exons have been designed and tested. Here, we have retrospectively compared our own set of 156 exon-internal AONs and 256 AONs as present in patents and publications from Dr. Wilton (Australia), which includes exon-internal as well as splice site-targeting AONs. Effective AONs are significantly more often exon-internal and, as anticipated, have better thermodynamic properties. Comparison of splice site and exon-internal AONs revealed that exon-internal AONs are more efficient and target more predicted exonic splicing enhancer and less predicted exon splicing silencer sites, but also have better thermodynamic properties. This suggests that exons may be better AON targets than introns per se, because of their higher GC content, which generally will result in improved AON binding.
Synthesis and characterization of magnetically responsive albumin microspheres containing cis‐hydroxyproline for scar inhibition (1991)

Magnetically responsive albumin microspheres containing the proline analog, cis-hydroxyproline, were synthesized and their in-vitro physical properties were characterized. These microspheres have an average size of 1.1 +/- 0.3 microns with 94% of the microspheres less than 2.0 microns. They are uniformly spherical and contain 67% albumin, 22% magnetite, and 8% cis-hydroxyproline. The cis-hydroxyproline is releasable during a 72-h period and demonstrates a slow, releasable pool that constitutes approximately 50% of the incorporated drug. cis-Hydroxyproline is neither chemically nor biologically altered during its incorporation into the microsphere. cis-Hydroxyproline release from microspheres results in the in vitro inhibition of collagen secretion, which is indistinguishable from unincorporated cis-hydroxyproline. In a rat-tail animal model these microspheres were selectively targeted using an external magnetic field applied to a 1.5-2.0-cm target site. Fifty to 80% of the infused microspheres were localized to this site, whereas without a magnetic field only 15-20% of the microspheres are localized to this site. cis-Hydroxyproline microspheres resulted in a 16% decrease in collagen content in a scar model when compared with untreated animals (p less than 0.05). With further refinement of this method of drug delivery, clinically useful inhibition of scar formation may result.
The Byte Guide to CD-ROM (1994)

The benefits of CD-ROM. Part 1 Nuts and bolts: what is a CD-ROM? anatomy of a CD-ROM how a CD-ROM drive works. Part 2 Standards: audio versus video standards multimedia extensions TV CDs. Part 3 How to: installing a CD-ROM drive (Mac, PC, Unix) CD-ROM on a network maintenance and troubleshooting. Part 4 CD-ROM publishing: why make your own CDs? how to do it. Part 5 Applications: the user/CD-ROM interface CD-ROM in the home CD-ROM in business CD-ROM as a means of software distribution. Part 6 What's coming: edutainment CD-ROM magazines.
Conjugation Methods toward Synthetic Vaccines (2008)

Introduction The observation at the beginning of the twentieth century that purified capsular polysaccharides (CPSs) of pneumococci are immunogenic in adults was followed by the discovery that the immune serum so formed can offer specific protection against infection by homologous bacteria.1 The protective effect of pneumococcal CPSs was firmly established in clinical trials reported in 1945.1 These findings were the basis for the development of polysaccharide (PS) based vaccines that include vaccines against Haemophilus influenzae type b, a 23-valent vaccine against pneumococci, a vaccine against Neisseria meningitides type A, C, Y, and W135, and the Vi vaccine against Salmonella typhi. The human immune response to PSs is developmentally regulated and, in contrast to proteins that can produce antibodies in infants, maturation of antibody production against PSs does not usually occur in young children before two years of age.2,3 The reason for this evolutionary difference remains unclear.4 Known exceptions to the
The PTPN22 C1858T functional polymorphism and autoimmune diseases--a meta-analysis (2006)

This meta-analysis demonstrates that the PTPN22 1858T allele confers susceptibility to RA, SLE, GD, T1D and JIA, supporting evidence of association of the PTPN22 gene with subgroup of autoimmune diseases.
Sickle Cell Disease (2017)

Sickle cell disease is caused by an alteration in a single DNA base, but its clinical manifestations are influenced by other genes and behavioral and environmental factors. Recent findings may indicate an acceleration in the discovery of interventions that alter the disease course.
Image registration and mosaicing using a self-calibrating camera (2002)

We introduce a new approach for the solution of three interrelated problems: image registration, mosaicing and camera calibration. First we use well known similarity measures with particular interest in enhancing the performance for image registration. After initial registration we use a camera model to refine the alignment updating estimated camera parameters. A relaxation method applied on this model automatically estimates the lens parameters and uses them to eliminate the perspective and lens distortion observed in the overlap area of two images. Image mosaics are constructed by combining corrected images blending the border that contains pixels with optimally low total absolute difference in different spatial frequencies resulting in seamless mosaic images.
Novel Hinge Binder Improves Activity and Pharmacokinetic Properties of BRAF Inhibitors (2010)

Mutated BRAF serine/threonine kinase is implicated in several types of cancer, with particularly high frequency in melanoma and colorectal carcinoma. We recently reported on the development of BRAF inhibitors based on a tripartite A-B-C system featuring an imidazo[4,5]pyridin-2-one group hinge binder. Here we present the design, synthesis, and optimization of a new series of inhibitors with a different A-B-C system that has been modified by the introduction of a range of novel hinge binders (A ring). The optimization of the hinge binding moiety has enabled the development of compounds with low nanomolar potencies in both BRAF inhibition and cellular assays. These compounds display optimal pharmacokinetic properties that warrant further in vivo investigations.
Vanillins--a novel family of DNA-PK inhibitors (2003)

Non-homologous DNA end-joining (NHEJ) is a major pathway of double strand break (DSB) repair in human cells. Here we show that vanillin (3-methoxy-4-hydroxybenzaldehyde)--a naturally occurring food component and an acknowledged antimutagen, anticlastogen and anticarcinogen--is an inhibitor of NHEJ. Vanillin blocked DNA end-joining by human cell extracts by directly inhibiting the activity of DNA-PK, a crucial NHEJ component. Inhibition was selective and vanillin had no detectable effect on other steps of the NHEJ process, on an unrelated protein kinase or on DNA mismatch repair by cell extracts. Subtoxic concentrations of vanillin did not affect the ATM/ATR-dependent phosphorylation of Chk2 or the S-phase checkpoint response after ionising radiation. They significantly potentiated the cytotoxicity of cisplatin, but did not affect sensitivity to UVC. A limited screen of structurally related compounds identified two substituted vanillin derivatives that were 100- and 50-fold more potent than vanillin as DNA-PK inhibitors. These compounds also sensitised cells to cisplatin. The inhibition of NHEJ is consistent with the antimutagenic and other biological properties of vanillin, possibly altering the balance between DSB repair by NHEJ and homologous recombination.
Immunochemical Analysis of Cod Fish Allergen M: Locations of the Immunoglobulin Binding Sites as Demonstrated by the Native and Synthetic Peptides (1983)

The major allergen of codfish (Allergen M) is a muscle protein belonging to the family of calcium binding parvalbumins. The primary structure of the molecule was established and the molecular weight was estimated from the sequence data to be 12,328. Allergen M consists of 113 amino acid residues and one residue of glucose. A molecular arrangement of three domains (AB, CD and EF--the latter two bind one Ca2+ ion each) was described for Allergen M, analogous to carp parvalbumin pI 4.25. The suggested structure was based on the extensive intramolecular amino acid homologies and the immunochemical cross-reactivities of the intact molecule and the two major isolated fragments. The immunological structure of Allergen M was studied by: 1. Modification of certain amino acids residues and study of the reactivity of the modified derivatives. 2. Examination of the immunochemical reactivity of a large number of overlapping peptides obtained by limited and selective tryptic hydrolyses. 3. Solid phase peptide synthesis (SPPS) of segments selected in regard to the reactivity of pre-examined native peptides. The immunological reactivity of the derivatives of Allergen M was assigned by: 1. Rocket line immunoelectrophoresis and quantitative precipitation using rabbit anti-Allergen M in precipitating antibody-mediated reactions and, 2. RAST/RAST-inhibition and PK test/PK-test inhibition using sera from individuals allergic to codfish in IgE-mediated reactions. The modification of Tyr-30 and Arg-75 in isolated and purified peptides indicated that the former was part of a reactive site whereas the latter did not contribute to the activity. Masking of Arg-residue or unchelating the two calcium ions from the native Allergen M, with the resulting perturbation of the tertiary structure, decreased the allergenicity by approximately 25%. Two major fragments of Allergen M were produced and purified: TM1 (residues 1-75) comprising domains AB and CD, and TM2 (residues 76-113) covering domain EF. Both were immunologically reactive; TM1 showing intermediate reactivity between Allergen M and TM2. A high degree of immunological cross reactivity was evident between TM1 and TM2. The finding was in concert with the high intramolecular amino acid homologies of Allergen M, and suggested that the reactive sites were repetitively distributed along the polypeptide chain. The immunological reactivity of several long-sequence overlapping peptides obtained by limited and selective trypsin hydrolysis of Allergen M was studied. The immunologically reactive sites were accordingly assigned to the following regions of the chain: 1. Residues 33-44 on the junction between the AB and CD domains.(ABSTRACT TRUNCATED AT 400 WORDS)
Development of a Diphtheria Toxin Based Antiporcine CD3 Recombinant Immunotoxin (2011)

Anti-CD3 immunotoxins, which induce profound but transient T-cell depletion in vivo by inhibiting eukaryotic protein synthesis in CD3+ cells, are effective reagents in large animal models of transplantation tolerance and autoimmune disease therapy. A diphtheria toxin based antiporcine CD3 recombinant immunotoxin was constructed by fusing the truncated diphtheria toxin DT390 with two identical tandem single chain variable fragments (scFv) derived from the antiporcine CD3 monoclonal antibody 898H2-6-15. The recombinant immunotoxin was expressed in a diphtheria-toxin resistant yeast Pichia pastoris strain under the control of the alcohol oxidase promoter. The secreted recombinant immunotoxin was purified sequentially with hydrophobic interaction chromatography (Butyl 650 M) followed by strong anion exchange (Poros 50 HQ). The purified antiporcine CD3 immunotoxin was tested in vivo in four animals; peripheral blood CD3+ T-cell numbers were reduced by 80% and lymph node T-cells decreased from 74% CD3+ cells pretreatment to 24% CD3+ cells remaining in the lymph node following 4 days of immunotoxin treatment. No clinical toxicity was observed in any of the experimental swine. We anticipate that this conjugate will provide an important tool for in vivo depletion of T-cells in swine transplantation models.
Passage of Chemicals into Human and Animal Semen: Mechanisms and Significance (1982)

This review will begin with a brief account of the secretory mechanisms operating in the male reproductive tract. The entry of the different chemicals will be dealt with; with separate reference to testicular fluids, epididymal plasma, prostatic and vesicular secretions, and whole semen. Examples will be given of a number of chemical substances capable of passing into the secretions of the male reproductive tract and semen, in man and in animals--antispermatogenic and antiandrogenic agents, industrial chemicals, chemotherapeutic drugs, food additives, etc. The review will end with a critical appraisal of the methods involved and the results obtained from analyses of various chemicals in semen.
The long‐term effects of capsaicin aqueous spray on the nasal mucosa (1998)

Capsaicin aqueous nasal spray has previously been shown to reduce nasal complaints without affecting cellular homeostasis or overall neurogenic staining up to 9 months after treatment. Immunocompetent cells are not involved in non-allergic non-infectious perennial rhinitis.
Global epidemiology of tuberculosis. Morbidity and mortality of a worldwide epidemic. (1995)

This article describes the global epidemiology of tuberculosis and reviews recent estimates of tuberculosis incidence and mortality in the world. The highest prevalence of tuberculosis infection and estimated annual risk of tuberculosis infection are in sub-Saharan Africa and Southeast Asia. Overall, almost 3.8 million cases of tuberculosis were reported in the world in 1990, of which 49% were in Southeast Asia. From the period 1984 through 1986 to the period 1989 through 1991, notification rates increased in all World Health Organization regions, except the American and the European regions. In 1990, there were an estimated 7.5 million cases of tuberculosis and 2.5 million deaths worldwide. The human immunodeficiency virus epidemic is causing increases in the number of tuberculosis cases, particularly in Africa, although increases are also expected in Southeast Asia. In many industrialized countries, tuberculosis has recently failed to decline, and in eastern Europe and the former Soviet Union, cases and deaths are increasing. Drug resistance is a serious problem, especially in the United States. If worldwide control of tuberculosis does not improve, 90 million new cases and 30 million deaths are expected in the decade 1990 through 1999.
A homologous in vitro system to analyze transcription of a mouse immunoglobulin μ heavy‐chain gene (1988)

In order to investigate the molecular mechanisms of the regulation of immunoglobulin (Ig) gene transcription, a cell-free system was developed in which a cloned mouse Ig mu heavy-chain gene was transcribed using nuclear extracts prepared from a mouse B cell hybridoma line. To monitor transcription, an RNA.RNA hybridization assay was developed in which a 32P-labeled, SP6-synthesized RNA probe complementary to Ig mu RNA was hybridized to unlabeled RNA transcribed in the nuclear extract. Accurate initiation of transcription, which resulted in the protection of the RNA probe from digestion with nuclease S1, was detected by the separation of the products on denaturing polyacrylamide gels, followed by autoradiography. Using this assay, an in-vitro-synthesized RNA was detected. The 5' end of the in-vitro-transcribed Ig mu RNA maps exactly to the same position as the 5' end of the corresponding in vivo mRNA and its formation was sensitive to the addition of low levels of alpha-amanitin (1 microgram/ml), indicating transcription by RNA polymerase II. It was shown by competition experiments with oligonucleotides containing the 'decamer recognition site' that this sequence interacts with (a) decamer-binding factor(s) and plays a positive role in transcription. The competition effects of the decamer-containing oligonucleotide appeared to be restricted to the decamer motif present in the promoter region. No effects of the enhancer region were detectable in vitro. Little or no transcriptional activity was found in transcription experiments using the Ig mu promoter and nuclear extracts prepared from HeLa cells. This suggests that tissue-specific factors involved in Ig mu heavy-chain gene transcription are present in the mouse B cell extracts.
The posttranslational modification of phosphoglucomutase is regulated by galactose induction and glucose repression in Saccharomyces cerevisiae (1995)

The enzyme phosphoglucomutase functions at a key point in carbohydrate metabolism. In this paper, we show that the synthesis of the major isoform of yeast phosphoglucomutase, encoded by the GAL5 (PGM2) gene, is regulated in a manner that is distinct from that previously described for other enzymes involved in galactose metabolism in the yeast Saccharomyces cerevisiae. Accumulation of this isoform increased four- to sixfold when the culture experienced either glucose depletion or heat shock. However, heat shock induction did not occur unless the cells were under glucose repression. This nonadditive increase in expression suggests that the regulatory mechanisms controlling the heat shock induction and glucose repression of the GAL5 gene are functionally related. We previously demonstrated that phosphoglucomutase is modified by a posttranslational Glc-phosphorylation reaction. We now show that this posttranslational modification, like phosphoglucomutase expression itself, is also regulated by galactose induction and glucose repression. Finally, no evidence was found to indicate that the Glc-phosphorylation of phosphoglucomutase alters its enzymatic activity under the conditions examined.
Distribution, levels and phosphorylation of Raf‐1 in Alzheimer's disease (2006)

Extracellular signal-regulated kinase (ERK), a member of the mitogen-activated protein kinase pathway, has been increasingly implicated in the pathogenesis of Alzheimer's disease due to its critical role in brain function. While we previously demonstrated that ERK is activated in Alzheimer's disease, the upstream cascade leading to its activation had not been fully examined. In this study, we focused on Raf-1, one of the physiological activators of the ERK pathway. Raf-1 is activated by phosphorylation at Ser338 and Tyr340/341 and inhibited by phosphorylation at Ser259. Interestingly, phosphorylation at all three sites on Raf-1 was increased as evidenced by both immunocytochemistry and immunoblot analysis in Alzheimer's disease brains compared to age-matched controls. Both phospho-Raf-1 (Ser259) and phospho-Raf-1 (Ser338) were localized to intracytoplasmic granular structures, whereas phospho-Raf-1 (Tyr340/341) was localized to neurofibrillary tangles and granules in pyramidal neurons in Alzheimer's disease hippocampus. There is extensive overlap between phospho-Raf-1 (Ser338) and phospho-Mek1/2, the downstream effector of Raf-1, suggestive of a mechanistic link. Additionally, increased levels of Raf-1 are associated with Ras and MEK1 in Alzheimer's disease as evidenced by its coimmunoprecipitation with Ras and Mek1, respectively. Based on these findings, we speculate that Raf-1 is activated to effectively mediate Ras-dependent signals in Alzheimer's disease.
Evaluation and Management of Chronic Mitral Regurgitation (2001)

This Journal feature begins with a case vignette highlighting a common clinical problem. Evidence supporting various strategies is then presented, followed by a review of formal guidelines, when they exist. The article ends with the author's clinical recommendations.A 56-year-old man with no history of cardiac disease and no cardiac symptoms has a holosystolic murmur at the apex that radiates to the axilla. Echocardiography shows moderate mitral regurgitation with mild left ventricular dilatation. How should this patient's care be managed?There are about 500,000 discharge diagnoses of mitral-valve disease annually in the United States.1 However, estimates of the prevalence of mitral regurgitation are confounded by the presence of benign flow murmurs in many adults and by the small amount of physiologic regurgitation detected on echocardiography in 80 percent of adults. Only about 18,000 patients undergo mitral-valve surgery . . .
Interaction of the regulatory subunit (RII) of cAMP-dependent protein kinase with RII-anchoring proteins occurs through an amphipathic helix binding motif (1991)

The type II cAMP-dependent protein kinase is localized to specific subcellular environments through the binding of the regulatory subunit (RII) dimer to RII-anchoring proteins. Computer-aided analysis of secondary structure, performed on four RII-anchoring protein sequences (the microtubule-associated protein 2, P150, and two thyroid proteins Ht 21 and Ht 31), has identified common regions of approximately 14 residues which display high probabilities of forming amphipathic helices. The potential amphipathic helix region of Ht 31 (Leu-Ile-Glu-Glu-Ala-Ala-Ser-Arg-Ile-Val-Asp-Ala-Val-Ile) lies between residues 494 and 507. A bacterially expressed 318-amino acid fragment, Ht 31 (418-736), containing the amphipathic helix region, was able to bind RII alpha. Site-directed mutagenesis designed to disrupt the secondary structure in the putative binding helix reduced binding dramatically. Specifically, substitution of proline for Ala-498 significantly diminished RII alpha binding, and similar mutation of Ile-502 or Ile-507 abolished interaction. Mutation of Ala-522 to proline, which is located outside the predicted amphipathic helix region, had no effect on RII alpha binding. These data suggest that anchoring proteins interact with RII alpha via an amphipathic helix binding motif.
Targeting interleukin-17 in patients with active rheumatoid arthritis: rationale and clinical potential (2013)

Clinical and experimental evidence suggest that interleukin-17A (IL-17A; also known as IL-17) is an attractive therapeutic target in rheumatoid arthritis (RA). Rheumatoid synovial tissue produces IL-17A, which causes cartilage and bone degradation in synovial and bone explants. Overexpression of IL-17A induces synovial inflammation and joint destruction in animal RA models. These effects are attenuated in IL-17A-deficient animals and by agents that block IL-17A. Serum IL-17A levels and, to a greater extent, synovial fluid IL-17A levels are elevated in many patients with RA. In some RA cohorts, higher IL-17A levels have been associated with a more severe clinical course. Several IL-17A blockers, including the anti-IL-17A monoclonal antibodies secukinumab and ixekizumab, and the anti-IL-17 receptor subunit A monoclonal antibody brodalumab have been evaluated in phase II clinical trials. Of these, secukinumab is the most advanced with respect to clinical evaluation in RA, with phase III trials ongoing in patients on background methotrexate who had inadequate responses to previous tumor necrosis factor blocker therapy.