gebhart/patrepeval huggingface dataset:
The amino acid sequence of rabbit skeletal muscle glycogenin (1989)

The amino acid sequence of glycogenin from rabbit skeletal muscle has been determined. The N-acetylated protein consists of 332 amino acids and has a molecular mass of 37278 Da. The novel tyrosyl-glucose linkage between glycogenin and glycogen [Smythe, C., Caudwell, F. B., Ferguson, M. & Cohen, P. (1988) EMBO J. 7, 2681-2686] is shown to occur at a single site, tyrosine-194. Although glycogenin is a UDP-Glc utilising glucosyltransferase that self-glucosylates [Pitcher, J., Smythe, C. & Cohen, P. (1988) Eur. J. Biochem. 176, 391-395], following addition by an unknown enzyme of the first glucose to tyrosine-194, it is not homologous to either human glycogen synthase or other UDP-Glc-requiring enzymes.
Aminopeptidases: towards a mechanism of action. (1993)

Aminopeptidases catalyse the removal of amino acids from peptide substrates. Although many functions have been ascribed to these enzymes, lack of knowledge of their complex structure has prevented detailed analysis. Several recent studies have now provided information on the structure and molecular biology of these enzymes, the kinetics of substrate hydrolysis and inhibitor binding. These new data allow prediction of a model mechanism of action for a large subgroup of aminopeptidases.
Identification of novel SNPs in the interleukin 6 receptor gene (IL6R) (2003)

The human interleukin-6 receptor (IL6R) is responsible for signal transduction of IL6 that might have associations with immune diseases and various infectious diseases. We have sequenced all 10 exons including the putative splicing site to identify single nucleotide polymorphisms in IL6R. Seven novel single nucleotide polymorphisms (SNPs) were identified; one SNP in the promoter region (-183G>A), one synonymous SNP in exon 2 (24013G>A: Ala31Ala), one non-synonymous SNP in exon 9 (48892A>C: Asp358Ala) and four in introns (29753A>C, 42700T>C, 48869T>A and 59818C>T). The frequencies of each SNP in the Korean population (n=300) were 0.48 (-183 G>A), 0.13 (24013 G>A), 0.41 (29753A>C), 0.41 (42700T>C), 0.1 (48869T>A), 0.42 (48892A>C), and 0.07 (59818C>T), respectively. Haplotypes and their frequencies were estimated by the EM algorithm. Linkage disequilibrium coefficients (/D'/) between each SNP pair were also calculated. The information on SNPs and haplotypes in IL6R would be useful for genetic studies of this gene.
Voltage gradients and ionic currents in injured and regenerating axons. (1988)

When an axon is damaged, a strong, persistent, injury current enters the damaged area, driven by the ionic pumps of the healthy portion of the cell. This current is associated with an electrical field, existing within the damaged axon and in the extracellular space around it. Such currents and fields are a common feature of neuronal damage and probably play a role in Ca2+-mediated degenerative events soon after transection, retrograde die-back, a structuring of the axonal terminus into zones, and perhaps organelle movement within damaged fibers. The long-term persistent currents may be a common feature of growing axons and might play a role in development and regeneration. Altogether, electrical effects of injury provide an alternative to conjecture concerning the physiological basis for immediate cellular responses to axonal injury. They also provide a possible basis for modulating the responses of neurons to injury by applied electric fields.
Hyperalgesia and allodynia induced by intrathecal (RS)-dihydroxyphenylglycine in rats (1998)

To investigate the role of Group I mGluRs in allodynia and hyperalgesia, we examined the behavioural responses of rats to noxious and non-noxious mechanical and thermal stimuli following intrathecal (i.t.) treatment (25 nmol) with the selective mGluR1/5 agonist, (RS)-dihydroxyphenylglycine ((RS)-DHPG). (RS)-DHPG administration produced a persistent decrease in response latency on a 48 degrees C hotplate, a reduction in the 50% response threshold to von Frey hairs, and an increase in responses to a tail pinch. These data suggest that activation of spinal mGluR1/5 receptors plays a role in the development of persistent allodynia and hyperalgesia associated with tissue or nerve injury.
Trafficking and Cellular Distribution of Voltage‐Gated Sodium Channels (2007)

Electrical excitability in cells such as neurons and myocytes depends not only upon the expression of voltage-gated sodium channels but also on their correct targeting within the plasma membrane. Placing sodium channels within a broader cell biological context is beginning to shed new light on a variety of important questions such as the integration of neuronal signaling. Mutations that affect sodium channel trafficking have been shown to underlie several life-threatening conditions including cardiac arrhythmias, revealing an important clinical context to these studies.
Isolation and Epitope Characterization of Human Monoclonal Antibodies to Hepatitis C Virus Core Antigen (1994)

In this study we describe the establishment of two hybridoma cell lines secreting human monoclonal antibodies to the 22-kD nucleocapsid protein (core, p22) of the hepatitis C virus (HCV). For this purpose we isolated B lymphocytes from an anti-HCV positive blood donor and infected them with Epstein-Barr (EBV). We obtained several lymphoblastoid cell clones secreting antibodies to the recombinant HCV core protein. The B-cell cultures were oligoclonally expanded and two of them were fused with the (mouse:human) heteromyeloma cell line K6H6/B5. The resulting stable hybridomas produce antibodies of the IgG1/kappa (U1/F10) and the IgM/kappa (Ul/F11) isotype reacting specifically with the recombinant core protein p22. To identify the epitopes recognized by these antibodies we synthesized overlapping peptides (13-mer and 6-mer) from the amino terminus of the core amino acid sequence. Antibody reactivity to these peptides was analyzed in an immunoblot assay. Finally, we were able to define a linear epitope recognized by the Ul/F10 antibody on the nucleocapsid protein. The antibody shows specificity to the sequence N-VYLLPR-C, which corresponds to the amino acids 34-39 of the core sequence.
Factors affecting the accuracy of urine-based biomarkers of BSE (2011)

Despite the presence of confounding factors, the disease specific changes in abundance exhibited by a panel of urine proteins permitted the creation of classifiers able to discriminate between control and infected cattle with a high degree of accuracy.
Prophylactic Gene Therapy With Human Tissue Kallikrein Ameliorates Limb Ischemia Recovery in Type 1 Diabetic Mice (2004)

Diabetes macro- and microvascular disease causes tissue hypoperfusion. This deficit, together with a failure to mount an adequate angiogenic response, might explain why vascular occlusion evolves more severely among diabetic patients. The present study investigated whether prophylactic gene therapy with human tissue kallikrein (hTK) may protect diabetic limbs from the consequences of supervening ischemia. Vehicle (saline) or an adenovirus carrying the gene for either hTK (Ad.hTK) or luciferase (Ad.Luc) was injected into left adductor muscles of streptozotocin-induced type 1 diabetic mice 2 weeks before operative occlusion of the ipsilateral femoral artery. Saline-injected nondiabetic mice served as controls. Hindlimb blood flow recovery was analyzed sequentially over the 2 weeks after ischemia induction. At necroscopy, microvessel density and endothelial cell proliferation and apoptosis were quantified in skeletal muscles. We found that limb perfusion recovery of saline-injected type 1 diabetic mice is delayed because of insufficient reparative neovascularization and excessive activation of endothelial cell apoptosis. By contrast, prophylactic Ad.hTK renewed the ability to mount an appropriate neovascularization response to ischemia, suppressed apoptosis, and upregulated endothelial nitric oxide synthase expression. Ultimately, correction of diabetic endotheliopathy by Ad.hTK allowed proper perfusion recovery as seen in nondiabetic mice. These discoveries disclose new therapeutic options for the treatment of diabetic complications.
A fractional programming approach to efficient DNA melting temperature calculation (2005)

The software is available for academic purposes from the authors. A web interface is provided at http://www.zaik.uni-koeln.de/bioinformatik/fptm.html
Efficient Phrase-Table Representation for Machine Translation with Applications to Online MT and Speech Translation (2007)

In phrase-based statistical machine translation, the phrase-table requires a large amount of memory. We will present an efficient representation with two key properties: on-demand loading and a prefix tree structure for the source phrases. We will show that this representation scales well to large data tasks and that we are able to store hundreds of millions of phrase pairs in the phrase-table. For the large Chinese– English NIST task, the memory requirements of the phrase-table are reduced to less than 20 MB using the new representation with no loss in translation quality and speed. Additionally, the new representation is not limited to a specific test set, which is important for online or real-time machine translation. One problem in speech translation is the matching of phrases in the input word graph and the phrase-table. We will describe a novel algorithm that effectively solves this combinatorial problem exploiting the prefix tree data structure of the phrase-table. This algorithm enables the use of significantly larger input word graphs in a more efficient way resulting in improved translation quality. 1
The phenotype of “pure” autosomal dominant spastic paraplegia (1994)

We studied 23 families with "pure" autosomal dominant spastic paraplegia. Examination of 142 at-risk individuals allowed identification of 70 patients, including 12 who were clinically affected but unaware of symptoms. The frequency of lower limb muscle weakness, decreased vibration sense, hyperreflexia in the upper limbs, and sphincter disturbances increased with the disease duration. The distribution of age at onset was unimodal, with a mean onset of 29 years (range, 1 to 68). The clinical manifestations of "early-onset" (< 29 years) and "late-onset" (> 29 years) patients were not significantly different. Age at onset varied as much within families as among families; anticipation and imprinting did not occur. No clinical criteria allowed differentiation among the families studied. Only linkage studies can provide accurate classification of this disease.
A continuous modulated single sideband bandwidth extension (2010)

Bandwidth extension (BWE) is an important parametric technique applied by modern audio coders in order to achieve efficient data rate compression at low bitrates. The perceptual quality of BWE enhanced signals is, however, often hampered by artifacts caused by inharmonicity. We propose hence a bandwidth extension method that avoids inharmonicity, and, at the same time, avoids the costly transmission of additional control parameters for frequency shifts. Harmonicity of the decoded signal is ensured by calculation of the autocorrelation function of the magnitude spectrum. The proposed bandwidth extension method is implemented by single sideband modulation (SSM). Fitting nicely in the general scheme of well established spectral band replication (SBR), the new method has some potential to replace the SBR patching algorithm. Potentially, the SSM can additionally govern the subsequent spectral shaping. Listening test results demonstrate an advantage of the novel scheme compared to SBR as used in high efficiency advanced audio coding (HE-AAC).
Lck Phosphorylates the Activation Loop Tyrosine of the Itk Kinase Domain and Activates Itk Kinase Activity (1997)

The Tec family tyrosine kinase Itk has been implicated in T cell receptor (TCR) signaling, yet its precise role and mechanism of activation remain undefined. To investigate these issues, we examined the biochemical response of Itk to TCR stimulation. We found that Itk is tyrosine-phosphorylated after TCR cross-linking and that this phosphorylation depends on the presence of functional Lck. To determine if this Lck dependence results from direct phosphorylation of Itk by Lck, we generated recombinant Itk and Lck using a baculovirus expression system and used these proteins in subsequent biochemical analyses. We found that Lck phosphorylates Itk upon co-expression in insect cells and, further, that this phosphorylation of Itk results in increased Itk in vitro kinase activity. The major site of Lck phosphorylation on Itk was mapped to the conserved tyrosine (Tyr511) in the activation loop of the Itk kinase domain. Substitution of this tyrosine with phenylalanine abolishes Itk kinase activity in insect cells, indicating that phosphorylation at this site plays a critical role in regulating Itk function.
MicroRNA Expression, Survival, and Response to Interferon in Liver Cancer (2009)

The expression patterns of microRNAs in liver tissue differ between men and women with hepatocellular carcinoma. The miR-26 expression status of such patients is associated with survival and response to adjuvant therapy with interferon alfa.
The Control of Angiogenesis and Tumor Invasion by Platelet Factor-4 and Platelet Factor-4-Derived Molecules (2004)

Platelet factor-4 (PF-4) is an ELR-negative chemokine that exhibits antiangiogenesis properties. PF-4 inhibits endothelial cell proliferation and migration, angiogenesis in vitro and in vivo, and tumor growth. However, tumor cells are not directly inhibited by PF-4. To date, a cell surface receptor that would explain the biological effects mediated by PF-4 has not been identified. PF-4 is able to interact directly with angiogenesis growth factors such as fibroblast growth factors (FGFs) and vascular endothelial growth factors and inhibits their interaction with cell surface receptors. Furthermore, dimerization of fibroblast growth factors is abrogated by PF-4. Whether PF-4 plays a role as an endogenous angiogenesis regulator is at present not clear. Several PF-4 fragments and modified molecules have been made that exhibit antiangiogenesis properties. Among these is a C-terminal fragment that has a defined structure, retains all the antiangiogenesis properties of the parent molecule, inhibits growth factor receptor binding, associates with FGFs, and destabilizes their three-dimensional structure. The relevance of these observations for the treatment of malignant disease is discussed.
Low Threshold PbSnSeTe-PbSeTe Lattice-Matched Double-Heterostructure Lasers (1981)

Very low threshold current density lasers with an 11 µm emission wavelength at 4.2 K have been fabricated from the lattice-matched Pb 0.85 Sn 0.15 Se 0.02 Te 0.98 -PbSe 0.08 Te 0.92 DH wafers grown by liquid phase epitaxy on a Pb 0.8 Sn 0.2 Te substrate. The active layer thickness, which minimizes the threshold current density, has been determined to be about 1 µm from the calculated optical confinement factors assuming a linear gain-current relationship. Lasers with a 1 µm active layer thickness and a 500 µm cavity length exhibited threshold current densities as low as 65 A/cm 2 at 4.2 K and 350 A/cm 2 at 77 K. The measured internal optical loss was as low as 2.8 cm -1 at 4.2 K.
Direct Detection of Oxygen Intermediates in the Non-Heme Fe Enzyme Taurine/α-Ketoglutarate Dioxygenase (2004)

The reaction of substrate-bound taurine/alpha-ketoglutarate dioxygenase with O2 has been studied using cryogenic continuous-flow spectroscopy. Transient absorption spectra acquired at -38 degrees C show an exponential decay of a 318-nm chromophore with an apparent rate of 1.3 s-1. The observed optical changes and their kinetics are consistent with the profile of an Fe(IV) species detected recently by Mössbauer spectroscopy (Price et al., Biochemistry 2003, 42, 7497-7508). Resonance Raman measurement upon excitation at 363.7 nm reveal at least two oxygen isotope-sensitive vibrations at 821/787 cm-1 and 583/555 cm-1 for 16O and 18O derivatives, respectively. An additional mode is likely to be obscured by an ethylene glycol vibration at 865 cm-1 and/or 1089 cm-1. The 821 cm-1 vibration is assigned to the stretching mode of Fe(IV)=O species on the basis of its frequency and isotopic shift amplitude. The 583 cm-1 band is likely to originate from an Fe-O2 precursor of the Fe(IV)=O species, although its structural details are unclear at present.
Reviews Preclinical Safety and Immune-Modulating Effects of Therapeutic Monoclonal Antibodies to Interleukin-6 and Tumor Necrosis Factor-α in Cynomolgus Macaques (2005)

Inhibitors of tumor necrosis factor-alpha (TNF-alpha) and interleukin-6 (IL-6) have been shown to be efficacious in a number of autoimmune diseases. In this study, the safety of long-term administration of anti-TNF-alpha and anti-IL-6 monoclonal antibodies (mAbs) was evaluated in cynomolgus macaques. Effects on the immune system were evaluated by analysis of lymphocyte subsets and histopathology of lymphoid tissues. To evaluate the functioning of the immune system, the ability of mAb-treated monkeys to mount a humoral immune response (IgG and IgM) to keyhole limpet hemocyanin (KLH) was evaluated. Treatment with the anti-TNF-alpha mAb produced no histopathological changes in any of the lymphoid tissues examined. There was a small (< 2-fold) elevation in circulating T-and B-lymphocytes during anti-TNF-alpha mAb treatment that was not considered to be toxicologically significant. The antibody response to KLH was unaffected by anti-TNF-alpha mAb treatment. Treatment with anti-IL-6 mAb resulted in a decrease in the size of germinal centers in the spleens of a minority of the animals and a modest but significant decrease in the IgG antibody response to KLH. Weekly intravenous treatment with the anti-IL-6 mAb and twice-weekly subcutaneous treatment with the anti-TNF-alpha mAb for up to 6 months was not associated with any signs of toxicity, and no animal developed an infection throughout the study period. This study demonstrates that the anti-IL-6 and anti-TNF-alpha mAbs produce specific modulating effects on the immune system without rendering the animals immune compromised.
Nearly Azeotropic Mixtures To Replace Refrigerant 12 (1992)

Number of nearly azeotropic fluid mixtures have saturation pressures similar to Refrigerant 12 while being about 2 percent as damaging to ozone layer. Five mixtures of R134a, R152a, R124, and R142b have low boiling-point spreads, low toxicity, and low ozone-damaging capability, are nonflammable, and more compatible with conventional oils than R134a. Pressure of combinations nearly equal to R12, and mixtures may be good drop-in substitutes. Overall composition not altered by leakage. Usable in commercial, automotive, and household refrigerators and air conditioners.
The 1996 Albert Lasker Medical Research Awards. Prevention of systemic infections, especially meningitis, caused by Haemophilus influenzae type b. Impact on public health and implications for other polysaccharide-based vaccines (1996)

The development of Haemophilus influenzae type b (Hib) conjugate vaccines has led to the virtual elimination of systemic infections caused by that pathogen, has provided insights into the pathogenesis of and immunity to other capsulated bacteria, and has contributed to the development of new vaccines. Meningitis, a common and serious infection of children, and other infections caused by Hib have been virtually eliminated in countries that have achieved widespread vaccination with Hib conjugates, including the United States, Canada, the United Kingdom, Iceland, Scandinavia, France, and Germany. Hib conjugates have also been shown to be highly effective in developing countries. The principles derived from the use of these vaccines, along with studies of other capsulated pathogens, should allow the rapid inclusion of new polysaccharide-based conjugates into routine vaccination schedules of infants, and should help to realize further reductions in serious systemic infectious diseases.
Tolerization of Tumor-Specific T Cells Despite Efficient Initial Priming in a Primary Murine Model of Prostate Cancer (2007)

In this report, we studied T cell responses to a prostate cancer Ag by adoptively transferring tumor Ag-specific T cells into prostate tumor-bearing mice. Our findings demonstrate that CD8(+) T cells initially encountered tumor Ag in the lymph node and underwent an abortive proliferative response. Upon isolation from the tumor, the residual tumor-specific T cells were functionally tolerant of tumor Ag as measured by their inability to degranulate and secrete IFN-gamma and granzyme B. We next sought to determine whether providing an ex vivo-matured, peptide-pulsed dendritic cell (DC) vaccine could overcome the tolerizing mechanisms of tumor-bearing transgenic adenocarcinoma of the mouse prostate model mice. We demonstrate that tumor Ag-specific T cells were protected from tolerance following provision of the DC vaccine. Concurrently, there was a reduction in prostate tumor size. However, even when activated DCs initially present tumor Ag, T cells persisting within the tolerogenic tumor environment gradually lost Ag reactivity. These results suggest that even though a productive antitumor response can be initiated by a DC vaccine, the tolerizing environment created by the tumor still exerts suppressive effects on the T cells. Furthermore, our results demonstrate that when trying to elicit an effective antitumor immune response, two obstacles must be considered: to maintain tumor Ag responsiveness, T cells must be efficiently primed to overcome tumor Ag presented in a tolerizing manner and protected from the suppressive mechanisms of the tumor microenvironment.
Heparosan, a promising ‘naturally good’ polymeric conjugating vehicle for delivery of injectable therapeutics (2014)

Many therapeutics have issues with delivery due to nonoptimal pharmacokinetics and/or detrimental side effects due to their nonhuman nature. Injectable biologic drugs are one class that often needs assistance. The pharma industry has employed a variety of delivery strategies and this Editorial focuses on drug-polymer conjugates, in particular those utilizing a newly introduced system using a natural carbohydrate called heparosan. This molecule, the biosynthetic precursor to the well-known drug heparin, appears tolerated due to its 'self' nature as well as exhibits intrinsically favorable behavior in the bloodstream and tissues. The polysaccharide is stable in the extracellular spaces of mammals, but degraded by lysosomal enzymes following entry into the cell. Heparosan manufacture utilizes a novel synchronized, stoichiometrically controlled reaction employing a sugar-polymerizing enzyme in an aqueous buffer system that results in a quasi-monodisperse product. Heparosan is predicted to serve as a conjugating vehicle to extend the plasma half-life of biologics without liabilities of polydispersity, immunogenicity and/or unwanted accumulation in the body that are observed for other types of polymer such as PEG, hydroxyethyl starch, or poly(sialic acid).