gebhart/patrepeval huggingface dataset:
Specific inhibition of hepatitis C virus expression by antisense oligodeoxynucleotides. In vitro model for selection of target sequence. (1994)

The effect of sense and antisense oligodeoxynucleotides (ODNs) on hepatitis C virus (HCV) gene expression was studied to determine the role of the highly conserved 5'-untranslated region in the life cycle of the virus. It was found that antisense ODNs complementary to nucleotides (nt) 38-65, 134-175, and 312-339 in the 5' noncoding region and 341-377 in the core open reading frame efficiently blocked HCV RNA translation. Overlapping ODNs that differed by only several nucleotides showed substantially different inhibition of HCV RNA translation. Fine sequence specificity testing at nt positions 351-377 revealed that ODNs as small as a 12-mer (nt 351-363) retained a high degree (80%) of inhibitory activity compared to ODNs of longer sequences. These results suggest that there are three highly specific domains in the 5' noncoding region and a sequence immediately downstream of the HCV core initiation codon that may be critical for translation of HCV RNA. This study also provides an experimental approach for the selection of target HCV RNA sequences susceptible to antisense effects, as well as for definition of functional regions of the genome necessary for viral replication.
Estimated Glomerular Filtration Rate (2007)

Letters2 January 2007Estimated Glomerular Filtration RateAndrew S. Levey, MD, Josef Coresh, MD, PhD, and Frederick Van Lente, PhDAndrew S. Levey, MDFrom Tufts-New England Medical Center, Boston, Massachusetts.Search for more papers by this author, Josef Coresh, MD, PhDFrom Tufts-New England Medical Center, Boston, Massachusetts.Search for more papers by this author, and Frederick Van Lente, PhDFrom Tufts-New England Medical Center, Boston, Massachusetts.Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-146-1-200701020-00021 SectionsAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail IN RESPONSE: Dr. Delanaye and colleagues question whether the precision of the creatinine assay within the reference range is sufficient for accurate GFR estimation. The Beckman Synchron CX3 assay used during the MDRD Study had analytic CVs of 4.3% and 1.5% at creatinine values of 88.4 µmol/L (1.0 mg/dL) and 477.3 µmol/L (5.4 mg/dL), respectively (1). The enzymatic assay used to calibrate the MDRD Study laboratory to standardized creatinine had analytic CVs of 2.0% and 1.8% at creatinine values of 78.7 µmol/L (0.89 mg/dL) and 518.0 µmol/L (5.86 mg/dL), respectively, in 2004 (n = 194) and 1.6% and 1.1% at creatinine ...References1. Coresh J, Astor BC, McQuillan G, Kusek J, Greene T, Van Lente F, et al. Calibration and random variation of the serum creatinine assay as critical elements of using equations to estimate glomerular filtration rate. Am J Kidney Dis. 2002;39:920-9. [PMID: 11979335] CrossrefMedlineGoogle Scholar2. Stevens LA, Coresh J, Greene T, Levey AS. Assessing kidney function—measured and estimated glomerular filtration rate. N Engl J Med. 2006;354:2473-83. [PMID: 16760447] CrossrefMedlineGoogle Scholar Author, Article, and Disclosure InformationAuthors: Andrew S. Levey, MD; Josef Coresh, MD, PhD; Frederick Van Lente, PhDAffiliations: From Tufts-New England Medical Center, Boston, Massachusetts.Disclosures: None disclosed. PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetailsSee AlsoUsing Standardized Serum Creatinine Values in the Modification of Diet in Renal Disease Study Equation for Estimating Glomerular Filtration Rate Andrew S. Levey , Josef Coresh , Tom Greene , Lesley A. Stevens , Yaping (Lucy) Zhang , Stephen Hendriksen , John W. Kusek , and Frederick Van Lente , for the Chronic Kidney Disease Epidemiology Collaboration*Estimated Glomerular Filtration Rate Pierre Delanaye , Etienne Cavalier , and Jean-Marie Krzesinski Metrics 2 January 2007Volume 146, Issue 1 Page: 74-75 Keywords Conflicts of interest Creatinine Enzyme assays Estimated glomerular filtration rate Kidneys Research laboratories ePublished: 2 January 2007 Issue Published: 2 January 2007 Copyright & PermissionsCopyright © 2007 by American College of Physicians. All Rights Reserved.PDF downloadLoading ...
Oncolytic Viruses as Anticancer Vaccines (2014)

Oncolytic virotherapy has shown impressive results in preclinical studies and first promising therapeutic outcomes in clinical trials as well. Since viruses are known for a long time as excellent vaccination agents, oncolytic viruses are now designed as novel anticancer agents combining the aspect of lysis-dependent cytoreductive activity with concomitant induction of antitumoral immune responses. Antitumoral immune activation by oncolytic virus infection of tumor tissue comprises both, immediate effects of innate immunity and also adaptive responses for long lasting antitumoral activity, which is regarded as the most prominent challenge in clinical oncology. To date, the complex effects of a viral tumor infection on the tumor microenvironment and the consequences for the tumor-infiltrating immune cell compartment are poorly understood. However, there is more and more evidence that a tumor infection by an oncolytic virus opens up a number of options for further immunomodulating interventions such as systemic chemotherapy, generic immunostimulating strategies, dendritic cell-based vaccines, and antigenic libraries to further support clinical efficacy of oncolytic virotherapy.
Structural Factors Contributing to DM Susceptibility of MHC Class II/Peptide Complexes (2002)

Peptide loading of MHC class II (MHCII) molecules is assisted by HLA-DM, which releases invariant chain peptides from newly synthesized MHCII and edits the peptide repertoire. Determinants of susceptibility of peptide/MHCII complexes to DM remain controversial, however. Here we have measured peptide dissociation in the presence and the absence of DM for 36 different complexes of varying intrinsic stability. We found large variations in DM susceptibility for different complexes using either soluble or full-length HLA-DM. The DM effect was significantly less for unstable complexes than for stable ones, although this correlation was modest. Peptide sequence- and allele-dependent interactions along the entire length of the Ag binding groove influenced DM susceptibility. We also observed differences in DM susceptibility during peptide association. Thus, the peptide repertoire displayed to CD4(+) T cells is the result of a mechanistically complicated editing process and cannot be simply predicted from the intrinsic stability of the complexes in the absence of DM.
Proinflammatory and Immunoregulatory Functions of Interleukin-12 (1998)

Interleukin-12 (IL-12) is a cytokine composed of two chains, a heavy chain or p40, and a light chain or p35, forming a disulfite-linked heterodimer, or p70. IL-12 was originally discovered as a product of human B lymphoblastoid cell lines; however, the most important physiological producers of IL-12 in vitro are phagocytic cells and antigen-presenting cells rather than B cells. The major target cells of IL-12 action are natural killer and T cells, on which IL-12 induce: (1) production of cytokine, particularly interferon-gamma (IFN-gamma); (2) proliferation, in synergy with other mitogenic or costimulatory signals; (3) enhancement of cytotoxic activity. In addition, IL-12 has been described to have stimulatory effects on hematopoietic precursor cells and on B lymphocytes. In vivo, IL-12 is produced very early during infections or immune response, and exerts important proinflammatory functions and enhancement of innate resistance by activating natural killer cells and, through IFN-gamma induction, phagocytic cells. The IL-12 produced during this inflammatory phase, both by direct action and, indirectly, by determining the composition of the cytokine milieu at the site of the murine response, induces differentiation of T helper type 1 (Th1) cells while inhibiting the generation of Th2 cells. Thus, because of its double function of a proinflammatory cytokine and an immunoregulatory factor, IL-12 plays a key role in the resistance to infections, particularly those mediated by bacteria or intracellular parasites, against which phagocytic cell activation and Th1-mediated responses are particularly effective. However, because of the same activities, IL-12 also plays a role in pathological situations, such as septic shock, tissue damage during inflammation and organ-specific autoimmune diseases.
Influence of Lignin Type on the Mechanical Properties of Lignin Based Compounds (2001)

Several types of sulfur-free lignins were melt compounded in a Werner & Pfleiderer twin screw extruder (ZSK 25) together with polyamide 11 (PA11), a biodegradable polyester (Ecoflex®) and a biodegradable polyesteramide (BAK®). Sulfur-free lignins, precipitated from black liquors of alkaline pulping of annual plants, like sisal and abaca, were compared to a sulfur-free lignin (Alcell™) obtained by organosolv wood pulping. Lignin content and lignin type were varied systematically in order to examine stress/strain characteristics and impact behavior. Compounds with lignins from annual plants showed similar or better mechanical properties in comparison to compounds with Alcell™ lignin. A polyamid 11 compound containing 30 wt.-% abaca lignin gave a Young's modulus of 1 890 MPa, compared to 1 420 MPa for PA11 and a 28% increase of yield stress. The morphology of the lignin compounds was investigated by means of environmental scanning electron microscopy (ESEM) and transmission electron microscopy (TEM).
Dip-pen nanolithography (2015)

AccessScience is an authoritative and dynamic online resource that contains incisively written, high-quality educational material covering all major scientific disciplines. An acclaimed gateway to scientific knowledge, AccessScience is continually expanding the ways it can demonstrate and explain core, trustworthy scientific information that inspires and guides users to deeper knowledge.
In Situ Combustion (1971)

The in situ combustion process attained world wide interest in the early 1950's. The process offered the possibility of recovery of a large fraction of oil from known deposits of heavy oils. By the end of the decade, most of the important features of the process had been investigated and described in the literature. During the early 1960's several large-scale commercial applications were started, and are still in operation. But there are probably fewer than 10 large-scale operations in the world today. The small number of commerical developments is a result of several factors. These include: realization of serious operational problems, high investment and operating costs, discovery of the cyclic steam injection process and realignment of investment priorities caused by offshore and arctic exploration efforts. But improvements in the process continue, and it is likely that in situ combustion will be an important process in world-wide operations in the future. (34 refs.)
Unique Spatiotemporal Neuromodulation of the Lumbosacral Circuitry Shapes Locomotor Success after Spinal Cord Injury (2016)

Spinal cord epidural stimulation has resulted in the initiation of voluntary leg movements and improvement in postural, bladder, and sexual function. However, one of the limitations in reaching the full potential of epidural stimulation for therapeutic purposes in humans has been the identification of optimal stimulation configurations that can neuromodulate the spinal cord for stepping. In the present work, we investigated the mechanisms underlying the specificity of interaction between the rostral and caudal spinal cord circuitries in enabling locomotion in spinal rats (n = 10) by epidural spinal cord stimulation. By using unique spatiotemporal epidural stimulation parameters of the lumbar and sacral spinal cords, a robust stepping pattern in spinal rats was observed with only six training sessions and as early as 3 weeks post-injury. Electrophysiological evidence reveals that in addition to frequency of stimulation pulses at the stimulation sites, the relative timing between stimulation pulses applied at the lumbar (L2) and sacral (S1) segments of the spinal cord heavily impacted stepping performance. Best stepping was established at a higher stimulation frequency (40 Hz vs. 5, 10, 15, and 20Hz) and at specific relative time-intervals between the stimulation pulses (L2 pulse applied at 18-25 msec after the onset of the S1 pulse; S1 pulse applied 0-7 msec after the L2 pulse). Our data suggest that controlling pulse-to-pulse timing at multiple stimulation sources provides a novel strategy to optimize spinal stepping by fine-tuning the physiological state of the locomotor networks. These findings hold direct relevance to the clinician who will incorporate electrical stimulation strategies for optimizing control of locomotion after complete paralysis.
Synthesis of a PNA-Peptide Conjugate by Chemical Ligation (2001)

A convergent synthetic route to the construction of a PNA-N-to-C-peptide conjugate (PKKKRKVGC-ttgcatt) by regioselective condensation of a thioester peptide and a cysteine-PNA adduct under denaturating conditions is described.
Selective C-H Fluorination of Pyridines and Diazines Inspired by a Classic Amination Reaction (2013)

Fluorinated heterocycles are prevalent in pharmaceuticals, agrochemicals, and materials. However, reactions that incorporate fluorine into heteroarenes are limited in scope and can be hazardous. We present a broadly applicable and safe method for the site-selective fluorination of a single carbon-hydrogen bond in pyridines and diazines using commercially available silver(II) fluoride. The reactions occur at ambient temperature within 1 hour with exclusive selectivity for fluorination adjacent to nitrogen. The mild conditions allow access to fluorinated derivatives of medicinally important compounds, as well as a range of 2-substituted pyridines prepared by subsequent nucleophilic displacement of fluoride. Mechanistic studies demonstrate that the pathway of a classic pyridine amination can be adapted for selective fluorination of a broad range of nitrogen heterocycles.
Culture of Mammary Epithelial Cells from Bovine Milk (1990)

Mammary epithelial cells are exfoliated into cows' milk and comprise a component of the somatic cells enumerated for milk quality control. This paper described the finding that these epithelial cells can be recovered from milk and grown in culture. The cultured cells were characterized for growth rate and growth potential, morphology by light and electron microscopy, presence of esterases and cytokeratins, and sensitivity to storage at 4 degrees C. Cultured mammary epithelial cells from milk may be useful to dairy scientists and mammary gland biologists.
TSG-6 Modulates the Interaction between Hyaluronan and Cell Surface CD44 (2004)

Interactions between CD44 and hyaluronan are implicated in the primary adhesion of lymphocytes to endothelium at inflammatory locations. Here we show that preincubation of hyaluronan with full-length recombinant TSG-6 or its Link module domain (Link_TSG6) enhances or induces the binding of hyaluronan to cell surface CD44 on constitutive and inducible cell backgrounds, respectively. These effects are blocked by CD44-specific antibodies and are absent in CD44-negative cells. Enhancement of CD44-mediated interactions of lymphoid cells with hyaluronan by TSG-6 proteins was seen under conditions of flow at shear forces that occur in post-capillary venules. Increases in the number of rolling cells were observed on substrates comprising TSG-6-hyaluronan complexes as compared with a substrate containing hyaluronan alone. In ligand competition experiments, cell surface-bound TSG-6-hyaluronan complexes were more potent than hyaluronan alone in inhibiting cell adhesion to immobilized hyaluronan. Link_TSG6 mutants with impaired hyaluronan binding function had a reduced ability to modulate ligand binding by cell surface CD44. However, some mutants that exhibited close to wild-type hyaluronan binding were found to have either reduced or increased activity, suggesting that some amino acid residues outside of the hyaluronan binding site might be involved in protein self-association, potentially leading to the formation of cross-linked hyaluronan fibers. In turn, cross-linked hyaluronan could increase the binding avidity of CD44 by inducing receptor clustering. The ability of TSG-6 to modulate the interaction of hyaluronan with CD44 has important implications for CD44-mediated cell activity at sites of inflammation, where TSG-6 is expressed.
Heart Rate and Cardiac Rhythm Relationships With Bisoprolol Benefit in Chronic Heart Failure in CIBIS II Trial (2001)

BHR and HRC are significantly related to prognosis in heart failure. beta-Blockade with bisoprolol further improves survival at any level of BHR and HRC and to a similar extent. The benefit of bisoprolol is questionable, however, in patients with atrial fibrillation.
Excited state (excitation) interactions in polyene aggregates. Resonance Raman and absorption spectroscopic evidence (1977)

Abstract The carotenoids astaxanthin, lutein and zeaxanthin form high molecular weight aggregates in aqueous solvent systems. The absorption spectra of the aggregates, compared to those of the monomer molecules, show significant bandwidth narrowing and blue shifts of 600–800 Å. The resonance Raman spectra of these aggregated polyenes are anomalous in that ν CC occurs near 1518 cm −1 whereas a well‐established ν CC vs 1/λ max correlation predicts that ν CC should be near 1560 cm −1 . The Raman and absorption data together demonstrate that strong excited state interactions are taking place and these results illustrate the utility of the resonance Raman technique for recognizing excited state perturbations. Raman excitation profiles (the variation of Raman intensity with wavelength) on aggregated astaxanthin and low temperature (−100 °C) absorption spectra on aggregates of astaxanthin and lutein establish that a pronounced change in vibronic structure occurs upon aggregation. In contrast to astaxanthin or lutein monomers whose electronic absorption spectra are made up of 0–0, 0–1, 0–2,… transitions, only the 0–0 transition is seen in the aggregates. The results are explained in terms of the molecular exciton model.
Transgenic animals in medicine: integration and expression of foreign genes, theoretical and applied aspects. (2004)

The production of different pharmaceutically important human proteins in the mammary gland of transgenic animals constitutes an important field of modern biotechnology. In addition, transgenic animals are used to develop suitable models of various human diseases and the possibility of using transgenic technologies to adapt pigs for xenotransplantation of their organs to humans is widely discussed. All these practical applications depend on the availability of reliable techniques to obtain transgenic animals with the necessary spectrum of transgene(s) expression. In the present review we discuss different aspects of producing transgenic animals by microinjection procedure, including both technical aspects and theoretical issues. As far as the technical aspects are concerned, special emphasis is placed on DNA preparation, microinjection timing, vectors permitting delivery of large genomic fragments, and approaches used to increase integration frequency. The molecular basis of the advantage of transgene microinjection into a male pronucleus is discussed. Finally, different strategies used to obtain polytransgenic animals are critically reviewed. In the section devoted to theoretical issues, the mechanisms of integration and molecular systems regulating transgene expression are extensively discussed. In particular, the importance of the domain-level regulatory systems is outlined and experimental approaches permitting the use of the domain-level regulatory systems of the genes encoding milk proteins are described and discussed.
Paroxysmal dyskinesias: Clinical features and classification (1995)

We studied 46 patients with paroxysmal dyskinesia and classified them according to phenomenology, duration of attacks, and etiology. There were 13 patients, 7 females, who had paroxysmal kinesigenic dyskinesia (PKD), 10 with attacks lasting 5 minutes or less (short lasting) and 3 with attacks lasting longer than 5 minutes (long lasting). Twenty-six patients, 18 females, had paroxysmal nonkinesigenic dyskinesia (PNKD), 9 with short-lasting and 17 with long-lasting PNKD. Five patients, 3 females, had paroxysmal exertion-induced dyskinesia (PED), 3 with short-lasting PED and the other 2 with long-lasting PED. In addition, there was 1 patient with paroxysmal hypnogenic dyskinesia (PHD) and 1 with paroxysmal superior oblique myokymia. Only 2 patients, 1 with PKD and 1 with PHD, had family history of paroxysmal dyskinesias. No specific cause could be identified in 21 patients; in the other 23 patients the etiologies included the following: psychogenic (9 patients), cerebrovascular diseases (4), multiple sclerosis (2), encephalitis (2), cerebral trauma (2), peripheral trauma (2), migraine (1), and kernicterus (1). Nine of 10 (90%) patients with PKD improved with medications, mostly anticonvulsants, compared with only 7 of 19 (37%) with PNKD. This new classification, based chiefly on precipitating events, allowed appropriate categorization of the attacks in all our patients with paroxysmal dyskinesias.
<title>Digital image watermarking using visual models</title> (1997)

The huge success of the Internet permits the transmission and wide distribution and access of electronic data in an effortless manner. Content providers are faced with the challenge of how to protect their electronic data. This problem has generated a flurry of recent research activity in the area of digital watermarking of electronic content for copyright protection. Unlike the traditional visible watermark found on paper, the challenge here is to introduce a digital watermark that does not alter the perceived quality of the electronic content while being extremely robust to attack. For instance, in the case of image data, editing the picture or illegal tampering should not destroy or alter the watermark. Equally important, the watermark should not alter the perceived visual quality of the image. From a signal processing viewpoint, the two basic requirements for an effective watermarking scheme, robustness and transparency, conflict with each other. We propose a watermarking technique for digital images that is based on utilizing visual models which have been developed in the context of image compression. Specifically, we propose a watermarking scheme where visual models are used to determine image dependent modulation masks for watermark insertion. In other words, for each image we can determine the maximum amount of watermark signal that each portion of the image can tolerate without affecting the visual quality of the image. This allow us to provide the maximum strength watermark which in turn, is extremely robust to common image processing and editing such as JPEG compression, rescaling, and cropping. We have watermarking results in a DCT framework as well as a wavelet framework. The DCT framework allows the direct insertion of watermarks to JPEG -- compressed data whereas the wavelet based scheme provides a framework where we can take advantage of both a local and global approach. Our scheme is shown to provide dramatic improvement over the current state-of-the-art both in terms of transparency and robustness.