gebhart/patrepeval huggingface dataset:
Direct Identification of Nonreducing GlcNAc Residues on N-Glycans of Glycoproteins Using a Novel Chemoenzymatic Method (2007)

The mutant beta1,4-galactosyltransferase (beta4Gal-T1), beta4Gal-T1-Y289L, in contrast to wild-type beta4Gal-T1, can transfer GalNAc from the sugar donor UDP-GalNAc to the acceptor, GlcNAc, with efficiency as good as that of galactose from UDP-Gal. Furthermore, the mutant can also transfer a modified sugar, C2 keto galactose, from its UDP derivative to O-GlcNAc modification on proteins that provided a functional handle for developing a highly sensitive chemoenzymatic method for detecting O-GlcNAc post-translational modification on proteins. We report herein that the modified sugar, C2 keto galactose, can be transferred to free GlcNAc residues on N-linked glycoproteins, such as ovalbumin or asialo-agalacto IgG1. The transfer is strictly dependent on the presence of both the mutant enzyme and the ketone derivative of the galactose. Moreover, the PNGase F treatment of the glycoproteins, which cleaves the N-linked oligosaccharide chain, shows that the modified sugar has been transferred to the N-glycan chains of the glycoproteins and not to the protein portion. The application of the mutant galactosyltransferase, beta4Gal-T1-Y289L, to produce glycoconjugates carrying sugar moieties with reactive groups, is demonstrated. We envision a broad potential for this technology such as the possibilities to link cargo molecules to glycoproteins, such as monoclonal antibodies, via glycan chains, thereby assisting in the glycotargeting of drugs to the site of action or used as biological probes.
Localization of components involved in protein transport and processing through the yeast Golgi apparatus. (1991)

Saccharomyces cerevisiae sec7 mutants exhibit pleiotropic deficiencies in the transit of proteins through the Golgi apparatus, and elaborate an array of Golgi apparatus-like cisternae at a restrictive growth temperature (37 degrees C). The SEC7 gene encodes an essential high-molecular weight protein (227 kD) that is phosphorylated in vivo. In cell lysates, Sec7 protein (Sec7p) is recovered in both sedimentable and soluble fractions. A punctate immunofluorescent pattern of Sec7p-associated structures seen in SEC cells coalesces in sec14 mutant yeast that accumulate exaggerated Golgi cisternae at 37 degrees C. Sec7p may function as a peripheral membrane protein that cycles between a soluble, cytosolic pool and a sedimentable, membrane-associated complex for its essential role in vesicular traffic through the Golgi apparatus. The transmembrane Kex2 protease, which processes precursors of secreted peptides within the yeast secretory pathway, is also localized by indirect immunofluorescence to multiple structures in the yeast cell (Redding, K., and R. Fuller, manuscript submitted for publication). In double-immunofluorescence labeling experiments, significant colocalization of Sec7 and Kex2 proteins was found. Colocalization of the two antigens, one implicated in protein transport through the Golgi apparatus and the other in processing within a late Golgi compartment, supports the conclusion that we have visualized the yeast Golgi apparatus.
Multiple Sclerosis: Distribution of T Cell Subsets Within Active Chronic Lesions (1983)

The distribution of T cells and T cell subsets was examined within the human central nervous system in active lesions from seven patients with chronic multiple sclerosis. The monoclonal antibodies anti-T11, anti-T4, and anti-T8 were used to detect total (whole) T cells, helper T cells, and suppressor-cytotoxic T cells, respectively, and a monoclonal antibody against human Ia was used for macrophages and B cells. Lesion progression was associated with large numbers of T4+ cells at the lesion margin and these extended great distances into the adjacent normal-appearing white matter. T8+ cells were most commonly concentrated around the lesion margin and displayed a preferential perivascular distribution. Within the lesion center, only a few T cells were found. Ia+ macrophages were most numerous within the centers of active lesions and were always present in the adjacent normal white matter. The monoclonal antibodies to T cells did not cross-react with glial cells including oligodendrocytes. These results indicate that T4+ cells are actively involved in lesion extension and Ia+ cells, in demyelination.
Anti-allergic properties of a new histamine antagonist, 4-(p-chlorobenzyl)-2- [N-methyl-perhydroazepinyl-(4)]-1-(2H)-phthalazinone hydrochloride (azelastine). (1979)

Anti-allergic properties of 4-(p-chlorobenzyl)-2 [N-methyl-perhydroazepinyl-(4)]-1-(2H)-phthalazinone hydrochloride (azelastine, A-5610) were investigated focusing the most attention on its decongestive effect. Intravenous injection of azelastine into anesthetized dogs with doses more than 0.1 mg/kg prevented the changes in nasal impedance provoked by histamine sprayed into the nasal cavity. When azelastine was given orally, the minimum effective dose to abolish the impedance reduction due to histamine was 2 mg/kg, in the case of cleamastine the same dose was required. Histamine release from the rat mesentery pieces by the condensation product of N-methyl-homoanisylamine formaldehyde (compound 48/80) (0.005%) was inhibited almost completely by pretreatment with azelastine at the concentrations of 10(-4) to 10(-3) g/ml, and in those concentrations azelastine alone released histamine scarcely. When 5 mg/kg of azelastine was given i.v. to rabbits, the characteristic changes in EEG -- a high-voltage low-frequency pattern -- persisted more than 1 h, but not the least inhibition in arousal response was noted. With the dose of 0.5 mg/kg, diphenhydramine impaired arousal response and slow waves with high amplitude dominantly appeared in EEG.
Erythritol Production by a Yeastlike Fungus (1964)

A yeastlike fungus, probably belonging to the genus Torula, was isolated from fresh pollen and was shown to produce erythritol in yields of 35 to 40% of the sugar utilized. The ability to produce erythritol is an inherent characteristic of the isolate, but unfavorable fermentation conditions can lead to the production of glycerol at the expense of erythritol. By the use of a synthetic medium, it was shown that the concentrations of both nitrogen and phosphorous in the medium must be closely controlled to obtain satisfactory erythritol yields.
Galectin-3, Cardiac Structure and Function, and Long-Term Mortality in Patients with Acutely Decompensated Heart Failure (2010)

Among dyspnoeic patients with and without ADHF, galectin-3 concentrations are associated with echocardiographic markers of ventricular function. In patients with ADHF, a single admission galectin-3 level predicts mortality to 4 years, independent of echocardiographic markers of disease severity.
Multicenter Evaluation of the COBAS AMPLICOR HCV Assay, an Integrated PCR System for Rapid Detection of Hepatitis C Virus RNA in the Diagnostic Laboratory (1998)

The benefits shown by the recent introduction of PCR for the in vitro diagnosis of hepatitis C virus (HCV) infection has prompted the development of standardized, ready-to-use assays that can be implemented in routine clinical laboratories. We have evaluated the clinical performance of COBAS AMPLICOR HCV (COBAS), the first instrument system that allows the automation of HCV RNA amplification and detection, to determine its performance in the routine laboratory setting. More than 2,000 specimens collected at five centers were analyzed in parallel by the COBAS and the manual AMPLICOR HCV (AMPLICOR) tests, and the results were compared with the results for biochemical and serological markers of HCV. In this study the two PCR systems showed the same accuracy, with a concordance rate of 99.8%. As expected, the correlation between serology and PCR was not absolute because the presence of anti-HCV antibodies may be associated with a latent or past infection. On the other hand, if the presence of confirmed anti-HCV antibodies and elevated alanine aminotransferase levels are taken as the "gold standard," indicating an active, ongoing infection, the COBAS and AMPLICOR tests show high and comparable sensitivities (100%) and specificities (98%), with positive and negative predictive values of 100 and 97%, respectively. During the study no false-positive reactions were detected. The use of an internal control allowed the identification of inhibitory substances that prevented amplification for 0.3 and 0.4% of samples tested by the COBAS and AMPLICOR tests, respectively. Compared to the manual system, the COBAS system allowed a significant reduction of hands-on time and could improve the overall laboratory work flow. In conclusion, these results support the use of the COBAS and AMPLICOR tests for the molecular diagnosis of active HCV infections.
Exploring How Industrial Designers Can Contribute to Scientific Research (2011)

This paper describes the initial findings of an empirical study exploring how industrial designers might be able to support scientists in their research activities.The paper compares and contrasts the findings of a literature review, a series of interviews with scientists and three case studies in which designers collaborated with scientific teams at a University.It reflects on the designers' contribution to research and highlights potential barriers and enablers to collaboration.In addition to the expected contribution of designers to supporting commercialisation of technology, the research demonstrated the potential for industrial design to have an impact on research itself.When involved earlier in the scientific research process, designers can challenge the research direction and support scientists in demonstrating, communicating and exploring potential future applications.
Scintigraphic imaging using technetium-99m-labeled ceftizoxime in an experimental model of acute osteomyelitis in rats (2008)

The 99mTc-CFT presented a high tropism and retention for an infected region in this model of osteomyelitis, thereby constituting an interesting strategy to distinguish aseptic from septic sites.
A survey on wind power ramp forecasting. (2011)

The increasing use of wind power as a source of electricity poses new challenges with regard to both power production and load balance in the electricity grid. This new source of energy is volatile and highly variable. The only way to integrate such power into the grid is to develop reliable and accurate wind power forecasting systems. Electricity generated from wind power can be highly variable at several different timescales: sub-hourly, hourly, daily, and seasonally. Wind energy, like other electricity sources, must be scheduled. Although wind power forecasting methods are used, the ability to predict wind plant output remains relatively low for short-term operation. Because instantaneous electrical generation and consumption must remain in balance to maintain grid stability, wind power's variability can present substantial challenges when large amounts of wind power are incorporated into a grid system. A critical issue is ramp events, which are sudden and large changes (increases or decreases) in wind power. This report presents an overview of current ramp definitions and state-of-the-art approaches in ramp event forecasting.
Biophysical interaction between phospholamban and protein phosphatase 1 regulatory subunit GM (1998)

Regulation of the sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA 2a) depends on the phosphorylation state of phospholamban (PLB). When PLB is phosphorylated, its inhibitory effect towards SERCA 2a is relieved, leading to an enhanced myocardial performance. This process is reversed by a sarcoplasmic reticulum (SR)-associated type 1 protein phosphatase (PP1) composed of a catalytic subunit PP1C and a regulatory subunit GM. Human GM and PLB have been produced in an in vitro transcription/translation system and used for co-immunoprecipitation and biosensor experiments. The detected interaction between the two partners suggests that cardiac PPI is targeted to PLB via GM and we believe that this process occurs with the identified transmembrane domains of the two proteins. Thus, the interaction between PLB and GM may represent a specific way to modulate the SR function in human cardiac muscle.
Hybrid solar cells: basic principles and the role of ligands (2011)

For the last decade, researchers have attempted to construct photovoltaic (PV) devices using a mixture of inorganic nanoparticles and conjugated polymers. The goal is to construct layers that use the best properties of each material e.g., flexibility from the polymer and high charge mobility from the nanoparticles or blue absorbance from the polymer complementing red absorbance from the nanoparticles. This critical review discusses the main obstacles to efficient hybrid organic/inorganic PV device design in terms of contributions to the external and internal quantum efficiencies. We discuss in particular the role that ligands on the nanoparticles play for mutual solubility and electronic processes at the nanoscale. After a decade of work to control the separation distance between unlike domains and the connectivity between like domains at the nanoscale, hybrid PV device layers are gaining in efficiency, but the goal of using the best properties of two mixed materials is still elusive.
Protein Hydration in Aqueous Solution (1991)

High-resolution proton nuclear magnetic resonance studies of protein hydration in aqueous solution show that there are two qualitatively different types of hydration sites. A well-defined, small number of water molecules in the interior of the protein are in identical locations in the crystal structure and in solution, and their residence times are in the range from about 10(-2) to 10(-8) second. Hydration of the protein surface in solution is by water molecules with residence times in the subnanosecond range, even when they are located in hydration sites that contain well-ordered water in the x-ray structures of protein single crystals.
Multiresolution blind source separation method using sparsity for harmonic retrieval (2009)

The goal of this paper is to give a multiresolution blind source separation(BSS) algorithm using sparsity for harmonic retrieval. After the perspective of BSS is briefly presented, the general and detailed definition of the multiresolution BSS model is given. The multiresolution BSS algorithm for harmonic retrieval by sparsity property using multiscale independent component analysis(ICA) method is constructed in detail. Some simulations of the proposed algorithm are also exhibited. The paper concludes by discussing the impact of multiresolution BSS research and outlining potential future research directions and applications.
RNA Processing and Translation (2008)

The information that codes for all proteins in a cell is found on specific segments within the DNA. When a cell requires the function of a particular protein, it must initiate the steps involved in the synthesis of this protein. The overall process is termed gene expression. Transcription is the process whereby the cell makes a copy of the genetic information required to build that particular protein. Transcription yields the copy of a particular gene termed the primary transcript, which undergoes several processing events to generate the mature messenger RNA (mRNA). The mRNA molecule is then transported to the cytoplasm where it associates with the ribosome. Here, the information within the transcript is decoded into a polypeptide chain of amino acids to give rise to a particular protein with a specific function. The details of RNA processing and translation are discussed in this chapter.
Five-year administration of fenretinide: pharmacokinetics and effects on plasma retinol concentrations. (1993)

4HPR, at 200 mg/d for 5 years, resulted in constant drug plasma levels and constant retinol level reduction. After treatment interruption, 4HPR plasma concentrations decreased at the limit of detectability at 6 months and baseline retinol plasma concentrations were recovered after 1 month.
Up-regulation of METCAM/MUC18 promotes motility, invasion, and tumorigenesis of human breast cancer cells (2011)

These findings support the notion that human METCAM/MUC18 expression promotes the progression of human breast cancer cells by increasing their motility, invasiveness and tumorigenesis.
Incidence of Bloodstream Infections Due to Candida Species and In Vitro Susceptibilities of Isolates Collected from 1998 to 2000 in a Population-Based Active Surveillance Program (2004)

To determine the incidence of Candida bloodstream infections (BSI) and antifungal drug resistance, population-based active laboratory surveillance was conducted from October 1998 through September 2000 in two areas of the United States (Baltimore, Md., and the state of Connecticut; combined population, 4.7 million). A total of 1,143 cases were detected, for an average adjusted annual incidence of 10 per 100,000 population or 1.5 per 10,000 hospital days. In 28% of patients, Candida BSI developed prior to or on the day of admission; only 36% of patients were in an intensive care unit at the time of diagnosis. No fewer than 78% of patients had a central catheter in place at the time of diagnosis, and 50% had undergone surgery within the previous 3 months. Candida albicans comprised 45% of the isolates, followed by C. glabrata (24%), C. parapsilosis (13%), and C. tropicalis (12%). Only 1.2% of C. albicans isolates were resistant to fluconazole (MIC, > or = 64 microg/ml), compared to 7% of C. glabrata isolates and 6% of C. tropicalis isolates. Only 0.9% of C. albicans isolates were resistant to itraconazole (MIC, > or = 1 micro g/ml), compared to 19.5% of C. glabrata isolates and 6% of C. tropicalis isolates. Only 4.3% of C. albicans isolates were resistant to flucytosine (MIC, > or = 32 microg/ml), compared to < 1% of C. parapsilosis and C. tropicalis isolates and no C. glabrata isolates. As determined by E-test, the MICs of amphotericin B were > or = 0.38 microg/ml for 10% of Candida isolates, > or =1 microg/ml for 1.7% of isolates, and > or = 2 microg/ml for 0.4% of isolates. Our findings highlight changes in the epidemiology of Candida BSI in the 1990s and provide a basis upon which to conduct further studies of selected high-risk subpopulations.
Immunotherapy for non-Hodgkinʼs lymphoma (1996)

Humanized monoclonal anti-CD20 has impressive activity and radioimmunoconjugates. Targeting the same molecule has led to prolonged remissions in both moderate and myeloablative doses. Idiotype-based vaccination has produced an apparent prolongation in disease-free and overall survival in selected patients with follicular lymphoma. Adoptive cellular therapy is active in the setting of Epstein-Barr virus-induced lymphoma after allogenic bone marrow transplantation. Improvements in each of these developments are readily in sight.
Completion of the gene coding assignments of SA11 rotavirus: gene products of segments 7, 8, and 9 (1983)

Improved fractionation of double-stranded RNA segments 7, 8, and 9 of simian rotavirus SA11 has permitted their isolation and individual translation in vitro. Segment 7 codes for p31 (NS2), segment 8 codes for p33 (NS1), and the segment 9 gene product resembles the gp34 precursor observed in SA11 virus-infected cells. In vitro glycosylation of translation products of segments 5 and 10 was also observed.
O-Antigen Modulates Infection-Induced Pain States (2012)

The molecular initiators of infection-associated pain are not understood. We recently found that uropathogenic E. coli (UPEC) elicited acute pelvic pain in murine urinary tract infection (UTI). UTI pain was due to E. coli lipopolysaccharide (LPS) and its receptor, TLR4, but pain was not correlated with inflammation. LPS is known to drive inflammation by interactions between the acylated lipid A component and TLR4, but the function of the O-antigen polysaccharide in host responses is unknown. Here, we examined the role of O-antigen in pain using cutaneous hypersensitivity (allodynia) to quantify pelvic pain behavior and using sacral spinal cord excitability to quantify central nervous system manifestations in murine UTI. A UPEC mutant defective for O-antigen biosynthesis induced chronic allodynia that persisted long after clearance of transient infections, but wild type UPEC evoked only acute pain. E. coli strains lacking O-antigen gene clusters had a chronic pain phenotype, and expressing cloned O-antigen gene clusters altered the pain phenotype in a predictable manner. Chronic allodynia was abrogated in TLR4-deficient mice, but inflammatory responses in wild type mice were similar among E. coli strains spanning a wide range of pain phenotypes, suggesting that O-antigen modulates pain independent of inflammation. Spinal cords of mice with chronic allodynia exhibited increased spontaneous firing and compromised short-term depression, consistent with centralized pain. Taken together, these findings suggest that O-antigen functions as a rheostat to modulate LPS-associated pain. These observations have implications for an infectious etiology of chronic pain and evolutionary modification of pathogens to alter host behaviors.
Congestion control in IP/TCP internetworks (1984)

Congestion control is a recognized problem in complex networks. We have discovered that the Department of Defense's Internet Protocol (IP), a pure datagram protocol, and Transmission Control Protocol (TCP), a transport layer protocol, when used together, are subject to unusual congestion problems caused by interactions between the transport and datagram layers. In particular, IP gateways are vulnerable to a phenomenon we call congestion collapse, especially when such gateways connect networks of widely different bandwidth. We have developed solutions that prevent congestion collapse.
TNF-alpha and TNF-alpha receptor-1 in the retina of normal and glaucomatous eyes. (2001)

Upregulation of TNF-alpha and its receptor-1 in glaucomatous retina suggest that TNF-alpha-mediated cell death is involved in the neurodegeneration process of glaucoma.
Efficient and Reproducible Myogenic Differentiation from Human iPS Cells: Prospects for Modeling Miyoshi Myopathy In Vitro (2013)

The establishment of human induced pluripotent stem cells (hiPSCs) has enabled the production of in vitro, patient-specific cell models of human disease. In vitro recreation of disease pathology from patient-derived hiPSCs depends on efficient differentiation protocols producing relevant adult cell types. However, myogenic differentiation of hiPSCs has faced obstacles, namely, low efficiency and/or poor reproducibility. Here, we report the rapid, efficient, and reproducible differentiation of hiPSCs into mature myocytes. We demonstrated that inducible expression of myogenic differentiation1 (MYOD1) in immature hiPSCs for at least 5 days drives cells along the myogenic lineage, with efficiencies reaching 70-90%. Myogenic differentiation driven by MYOD1 occurred even in immature, almost completely undifferentiated hiPSCs, without mesodermal transition. Myocytes induced in this manner reach maturity within 2 weeks of differentiation as assessed by marker gene expression and functional properties, including in vitro and in vivo cell fusion and twitching in response to electrical stimulation. Miyoshi Myopathy (MM) is a congenital distal myopathy caused by defective muscle membrane repair due to mutations in DYSFERLIN. Using our induced differentiation technique, we successfully recreated the pathological condition of MM in vitro, demonstrating defective membrane repair in hiPSC-derived myotubes from an MM patient and phenotypic rescue by expression of full-length DYSFERLIN (DYSF). These findings not only facilitate the pathological investigation of MM, but could potentially be applied in modeling of other human muscular diseases by using patient-derived hiPSCs.