gebhart/patrepeval huggingface dataset:
Properties and gene structure of the Thermotoga maritima alpha-amylase AmyA, a putative lipoprotein of a hyperthermophilic bacterium (1997)

Thermotoga maritima MSB8 has a chromosomal alpha-amylase gene, designated amyA, that is predicted to code for a 553-amino-acid preprotein with significant amino acid sequence similarity to the 4-alpha-glucanotransferase of the same strain and to alpha-amylase primary structures of other organisms. Upstream of the amylase gene, a divergently oriented open reading frame which can be translated into a polypeptide with similarity to the maltose-binding protein MalE of Escherichia coli was found. The T. maritima alpha-amylase appears to be the first known example of a lipoprotein alpha-amylase. This is in agreement with observations pointing to the membrane localization of this enzyme in T. maritima. Following the signal peptide, a 25-residue putative linker sequence rich in serine and threonine was found. The amylase gene was expressed in E. coli, and the recombinant enzyme was purified and characterized. The molecular mass of the recombinant enzyme was estimated at 61 kDa by denaturing gel electrophoresis (63 kDa by gel permeation chromatography). In a 10-min assay at the optimum pH of 7.0, the optimum temperature of amylase activity was 85 to 90 degrees C. Like the alpha-amylases of many other organisms, the activity of the T. maritima alpha-amylase was dependent on Ca2+. The final products of hydrolysis of soluble starch and amylose were mainly glucose and maltose. The extraordinarily high specific activity of the T. maritima alpha-amylase (about 5.6 x 10(3) U/mg of protein at 80 degrees C, pH 7, with amylose as the substrate) together with its extreme thermal stability makes this enzyme an interesting candidate for biotechnological applications in the starch processing industry.
Serial transplantation shows that early hematopoietic precursor cells are transduced by MDR-1 retroviral vector in a mouse gene therapy model. (1994)

The administration of high and repeated doses of chemotherapy has been hampered by the bone marrow toxicity imposed by these drugs. This obstacle can be circumvented by the introduction of chemotherapy resistance genes into the normal marrow cells, which are then transplanted back into the patient. To show that this approach can improve our ability to safely deliver high doses of chemotherapy, we used an animal model system to transplant bone marrow cells which have been transduced with a safety-modified retrovirus containing human multiple-drug resistance (MDR-1) cDNA into lethally irradiated mice. These studies produced mice whose bone marrow and peripheral blood displayed an increased level of MDR-1 expression and resistance to the myelotoxic side effects of Taxol. To determine whether sufficient numbers of early hematopoietic precursor cells were transduced with the MDR-1 retrovirus so that durable Taxol-resistant hematopoiesis would result, we serially transplanted the modified bone marrow cells into each of six successive cohorts of BALB/c mice. Taxol-resistant hematopoiesis with little or no myelosuppression was observed in all six of the cohorts. These data suggest that very early precursor cells were transduced by the vector. This animal model may be of use in the development of genetic therapy programs which use bone marrow to introduce therapeutic molecules into the systemic circulation, since it permits in vivo selection of genetically modified hematopoietic progenitor cells. Furthermore, the retroviral vector system we have used could have an immediate impact in the clinical setting, where it can protect patients from the myelosuppressive side effects of Taxol in advanced stages of human epithelial cancers.
The SWISS-PROT protein sequence data bank and its new supplement TREMBL (1996)

SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc), a minimal level of redundancy and a high level of integration with other databases. Recent developments of the database include: an increase in the number and scope of model organisms; cross-references to seven additional databases; a variety of new documentation files; the creation of TREMBL, and unannotated supplement to SWISS-PROT. This supplement consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except CDS already included in SWISS-PROT.
XBP1 Is Essential for Survival under Hypoxic Conditions and Is Required for Tumor Growth (2004)

Hypoxia within solid tumors is a major determinant of outcome after anticancer therapy. Analysis of gene expression changes during hypoxia indicated that unfolded protein response genes were one of the most robustly induced groups of genes. In this study, we investigated the hypoxic regulation of X-box binding protein (XBP1), a major transcriptional regulator of the unfolded protein response. Hypoxia induced XBP1 at the transcriptional level and activated splicing of its mRNA, resulting in increased levels of activated XBP1 protein. After exposure to hypoxia, apoptosis increased and clonogenic survival decreased in XBP1-deficient cells. Loss of XBP1 severely inhibited tumor growth due to a reduced capacity for these transplanted tumor cells to survive in a hypoxic microenvironment. Taken together, these studies directly implicate XBP1 as an essential survival factor for hypoxic stress and tumor growth.
Perfidious Albion? Britain, Plan G and European integration, 1955–1956 (1996)

In 1956, the British government proposed to complement the embryonic EEC with a wider European Free Trade Area, known in London as Plan G. At that time, British policy was accused by some of attempting to sabotage the development of the Six Messina Powers. Those contemporary charges of ‘Perfidious Albion’ have been sustained by the majority of historiographical opinion. The following article argues that the need to either acquit or condemn Britain of perfidy has obscured the intricacies of the policy beneath the Free Trade Area proposal. Concentrating on the Whitehall decision‐making process from 1955–56, it suggests that Plan G evolved from consideration of a counter‐initiative to the Common Market in Autumn 1955 but that it eventually became an attempt to come to terms with the Six, mainly to defend British interests. Furthermore, Plan G is only fully understood when placed in the framework of wider foreign and economic policies.
Induction of indoleamine 2,3-dioxygenase in mouse lung during virus infection. (1979)

Indoleamine 2,3-dioxygenase [indoleamine: oxygen 2,3-oxidoreductase (decyclizing)] activity in the supernatant fraction (30,000 X g, 30 min) of mouse lung homogenate increased approximately 120-fold after infection with PR8 influenza virus. Both specific and total enzyme activities started to increase linearly from the 5th day after infection, reached the highest level around the 11th day, and then gradually decreased to normal values in about 3 weeks. Other enzymes in the lung, such as certain lysosomal enzymes and monoamine oxidase, did not change significantly throughout the experiments. The time course of the increase in the enzyme activity was quite different from that of virus replication in the lung (a peak by the 3rd day and persistence until the 9th day) or that of serum antibody content (started to rise on the 9th day). Rather, it appeared to be closely related to the infiltrations of mononuclear and lymphocytic cells. When mice were exposed to a higher dose of virus and did not recuperate, the time course of the increase of the enzyme activity was essentially identical to that seen with a low concentration of virus. A maximum stimulation of the enzyme activity in the lung occurred on the 9th day after infection; the increase was approximately 100-fold. However, serum antibody content was slight and virus titer in the lung remained high.
Methods for Treating HIV by Gene Therapy Using Ribozymes (2003)

Ribozymes are small catalytic RNAs with the ability to reversibly cleave covalent bonds in RNA in the complete absence of protein (). With the exception of the RNA component of bacterial RNase P, presently characterized ribozymes catalyze a one-time intramolecular self-cleavage in their natural settings (, , , , , , , , ). However, they can be engineered to act in trans in a truly catalytic manner to cleave multiple copies of a specific RNA target molecule. The first ribozyme to be identified was the self-splicing ribosomal RNA precursor of the protozoan Tetrahymena (,). Several other classes of RNA-cleaving RNAs have since been discovered (. Investigations of ribozymes have begun to yield diverse outcomes that range from novel hypotheses about pre-biotic evolution () to potential human gene therapies (,)
The C‐terminal binding domain of hirullin P18 (1990)

Hirullin P18 is a 61-amino acid hirudin-related protein having potent antithrombin activity. Similar to hirudin, it contains a highly acidic C-terminus, but has a significantly different sequence from any other known hirudin variant. The present study demonstrates that the C-terminal fragment acetyl-hirullin P18(41-62) [corrected] possesses an antithrombin potency similar to that of acetyl-desulfatohirudin(45-65). Additionally, like the hirudin fragment analog, it inhibits fibrin-clot formation by binding to a non-catalytic site on thrombin. Sequential shortening of the hirullin P18 C-terminal fragment demonstrates the critical nature of Phe51, which corresponds to the important Phe56 residue of hirudin. Although the sequences of hirullin P18(54-61) and hirudin(59-65) have substantial differences, the C-terminal functional domain represented by hirullin P18(50-61) appears to be comparable to hirudin(55-65) in terms of its functional role in antithrombin activity.
Clinical and Laboratory Diagnosis of Respiratory Syncytial Virus Infection (1981)

Infection with RSV is one of the most common respiratory viral infections in childhood, particularly in infants under 1 year of age. The disease is characterized by epidemic proportions of infection which occur regularly in all parts of the world in the winter months. The spectrum of the clinical disease is quite variable, and the infection may present as bronchiolitis, pneumonia, croup, or exacerbation of pre-existing reactive airway disease. Recent evidence has suggested that RSV infection may be frequently associated with apnea in infancy and possibly sudden-infant-death syndrome. Although the laboratory diagnosis of this infection can be successfully accomplished by any well-known and conventional procedures, such as tissue culture infectivity and determination of serologic response, recently it has become possible to diagnose the infection very rapidly by application of such techiques as immunofluorescent staining and enzyme-linked immunonoabsorbent assay (ELISA).
Widespread Peroxynitrite-Mediated Damage in Alzheimer’s Disease (1997)

Increasing evidence suggests that oxidative damage to proteins and other macromolecules is a salient feature of the pathology of Alzheimer's disease. Establishing the source of oxidants is key to understanding what role they play in the pathogenesis of Alzheimer's disease, and one way to examine this issue is to determine which oxidants are involved in damage. In this study, we examine whether peroxynitrite, a powerful oxidant produced from the reaction of superoxide with nitric oxide, is involved in Alzheimer's disease. Peroxynitrite is a source of hydroxyl radical-like reactivity, and it directly oxidizes proteins and other macromolecules with resultant carbonyl formation from side-chain and peptide-bond cleavage. Although carbonyl formation is a major oxidative modification induced by peroxynitrite, nitration of tyrosine residues is an indicator of peroxynitrite involvement. In brain tissue from cases of Alzheimer's disease, we found increased protein nitration in neurons, including but certainly not restricted to those containing neurofibrillary tangles (NFTs). Conversely, nitrotyrosine was undetectable in the cerebral cortex of age-matched control brains. This distribution is essentially identical to that of free carbonyls. These findings provide strong evidence that peroxynitrite is involved in oxidative damage of Alzheimer's disease. Moreover, the widespread occurrence of nitrotyrosine in neurons suggests that oxidative damage is not restricted to long-lived polymers such as NFTs, but instead reflects a generalized oxidative stress that is important in disease pathogenesis.
Molecular Epidemiology of Pseudomonas aeruginosa Colonization in a Burn Unit: Persistence of a Multidrug-Resistant Clone and a Silver Sulfadiazine-Resistant Clone (2003)

To study the epidemiology of Pseudomonas aeruginosa colonization in a 32-bed burn wound center (BWC), 321 clinical and 45 environmental P. aeruginosa isolates were collected by prospective surveillance culture over a 1-year period and analyzed by serotyping, drug susceptibility testing, and amplified fragment length polymorphism (AFLP) analysis. Among 441 patients treated at the center, 70 (16%) were colonized with P. aeruginosa, including 12 (17%) patients who were colonized on admission and 58 (83%) patients who acquired the organism during their stay. Of the 48 distinct AFLP genotypes found, 21 were found exclusively in the environment, 15 were isolated from individual patients only, and 12 were responsible for the colonization of 57 patients, of which 2 were also isolated from the environment, but secondary to patient carriage. Polyclonal P. aeruginosa colonization with strains of two to four genotypes, often with different antibiotic susceptibility patterns, was observed in 19 patients (27%). Two predominant genotypes were responsible for recurrent outbreaks and the colonization of 42 patients (60% of all colonized patients). The strain with one of those genotypes appeared to be endemic to the BWC and developed multidrug resistance (MDR) at the end of the study period, whereas the strain with the other genotype was antibiotic susceptible but resistant to silver sulfadiazine (SSD(r)). The MDR strain was found at a higher frequency in sputum samples than the SSD(r) strain, which showed a higher prevalence in burn wound samples, suggesting that anatomic habitat selection was associated with adaptive resistance to antimicrobial drugs. Repeated and thorough surveys of the hospital environment failed to detect a primary reservoir for any of those genotypes. Cross-acquisition, resulting from insufficient compliance with infection control measures, was the major route of colonization in our BWC. In addition to the AFLP pattern and serotype, analysis of the nucleotide sequences of three (lipo)protein genes (oprI, oprL, and oprD) and the pyoverdine type revealed that all predominant strains except the SSD(r) strain belonged to recently identified clonal complexes. These successful clones are widespread in nature and therefore predominate in the patient population, in whom variants accumulate drug resistance mechanisms that allow their transmission and persistence in the BWC.
Quantitation of SR 27417 in human plasma using electrospray liquid chromatography-tandem mass spectrometry: A study of ion suppression (1996)

The effect of coeluting matrix compounds on the quantitation of SR 27417 in human plasma using electrospray liquid chromatography-tandem mass spectrometry has been examined. During the method development stage of this assay, plasma samples spiked with the analyte at 100 pg/mL were extracted using three different procedures: a hexane liquid-liquid extraction, an ethyl acetate back-extraction, and a solid phase extraction. Ion intensity of the analyte was found to be related inversely to the percent ionization of coeluting matrix components as evidenced by full scan spectra. The ethyl acetate back-extraction, which contained the fewest coeluting components, resulted in the highest ion intensity for the analyte. An assay comparison was done by using the liquid-liquid hexane and the ethyl acetate back-extractions for sample preparation. Replicate 1-mL samples (n=5) at 11 concentrations from 5 to 2000 pg/mL were extracted and analyzed. The results for the ethyl acetate back-extracted samples were acceptable from 2000 to 5 pg/mL with accuracy ranging from -11.6 to 2.61% of the nominal concentrations. In contrast, the hexane liquid-liquid method had poor accuracy and precision below 20 pg/mL. The difference is explained by suppression of analyte ion intensity. These results are consistent with the current theory of electrospray ionization.
InGaAsP-lnGaAsP-InAsP MQW polarization-independent modulator with high optical power saturation (2002)

In summary, we proposed the use of shallow, all-tensile-strained InGaAsP-InGaAsP MQW polarisation independent electro-optical modulators with InAsP relief layers. Very low polarization dependence (<0.5 dB) is observed and efficient modulation observed (-1 V drive voltage). The measurements suggest the optical power saturation >20 dBm (100 mW), as confirmed by the very low carrier escape time (20 ps). With such high optical power handling capacity, this type of QW should contribute to faster, more practical soliton systems.
MPEx: A tool for exploring membrane proteins (2009)

Hydropathy plot methods form a cornerstone of membrane protein research, especially in the early stages of biochemical and structural characterization. Membrane Protein Explorer (MPEx), described in this article, is a refined and versatile hydropathy-plot software tool for analyzing membrane protein sequences. MPEx is highly interactive and facilitates the characterization and identification of favorable protein transmembrane regions using experiment-based physical and biological hydrophobicity scales. Besides allowing the consequences of sequence mutations to be examined, it provides tools for aiding the design of membrane-active peptides. MPEx is freely available as a Java Web Start application from our web site at http://blanco.biomol.uci.edu/mpex.
Fiber draw synthesis (2011)

The synthesis of a high-melting temperature semiconductor in a low-temperature fiber drawing process is demonstrated, substantially expanding the set of materials that can be incorporated into fibers. Reagents in the solid state are arranged in proximate domains within a fiber preform. The preform is fluidized at elevated temperatures and drawn into fiber, reducing the lateral dimensions and bringing the domains into intimate contact to enable chemical reaction. A polymer preform containing a thin layer of selenium contacted by tin–zinc wires is drawn to yield electrically contacted crystalline ZnSe domains of sub-100-nm scales. The in situ synthesized compound semiconductor becomes the basis for an electronic heterostructure diode of arbitrary length in the fiber. The ability to synthesize materials within fibers while precisely controlling their geometry and electrical connectivity at submicron scales presents new opportunities for increasing the complexity and functionality of fiber structures.
The Cholesterol Derivative of a Triantennary Galactoside with High Affinity for the Hepatic Asialoglycoprotein Receptor: a Potent Cholesterol Lowering Agent (1995)

Cholesterol-derivatized galactosides have been devised in order to induce liver uptake of lipoproteins via the galactose-recognizing asialoglycoprotein receptor in the liver. In this study we describe the derivatization of a newly developed triantennary cluster galactoside having high affinity for the asialoglycoprotein receptor, N-[[tris-O-(3,6,9-trioxaundecanyl-beta-D-galactopyranosyl)metho xym ethyl] -N alpha-[1-(6-methyladipyl)]glycinamide (TG(20A)) with cholesterol. Hereto, TG(20A) was coupled to glycine-(5-cholesten-3 beta-yl ester) in the presence of (benzotriazol-1-yloxy)tris(dimethylamino)phosphonium hexafluorophosphate, affording N-[[tris-O-(3,6,9-trioxaundecanyl-beta-D- galactopyranosyl)methoxymethyl]methyl]-N alpha-[1-(6-(5-cholesten-3 beta-yloxy)glycyl)adipyl]glycinamide (TG(20A)C) in 46% yield. This compound is an amphiphilic, water-soluble compound. In aqueous solution it readily formed small micelles (4.9 +/- 1.2 nm) consisting of approximately 20 molecules. Upon incubation with human serum, TG(20A)C spontaneously incorporated into the most prominent serum lipoproteins, i.e., low-density lipoprotein (LDL) and high-density lipoprotein (HDL), thereby inducing an increase in buoyant density of these lipoproteins. The integrity of HDL and LDL, as judged from particle size analysis of both lipoproteins, was not altered by incubation with up to 0.33% of TG(20A)C (w/v). Following intravenous bolus injection into rats, TG(20A)C induced a dose-dependent decrease in the serum cholesterol content of maximally 44%, at a dose of 1.9 mg kg-1. This makes TG(20A)C at least 30-fold more effective than the previously developed N-[[tris-O-(beta-D-galactopyranosyl)methyl]methyl]-N alpha-[4-(5- cholesten-3 beta-yloxy)succinyl]glycinamide (TG(4A)C), provided with a cluster galactoside that displayed a 2000-fold lower affinity for the asialoglycoprotein receptor than TG(20A). In conclusion, the hypocholesterolemic activity of a cholesterylated galactoside can be strongly enhanced by using a cluster galactoside with higher affinity for the asialoglycoprotein receptor.
Electrophysiological Studies of Cervical Vagus Nerve Stimulation in Humans: I. EEG Effects (1992)

Evidence from studies of experimental animals indicates that electrical stimulation of the vagus nerve alters EEGs under certain stimulus parameters. We report EEG effects of electrical stimulation of the vagus nerve in 9 patients with medically intractable seizures as part of a clinical trial of chronic vagal stimulation for control of epilepsy. The mechanism of action of the vagal antiepileptic effect is unknown, and we believed that analysis of electrophysiologic effects of vagal nerve stimulation would help elucidate the brain areas affected. The left vagus nerve in the neck was stimulated with a programmable implanted stimulator. Stimulation at various stimulus frequencies and amplitudes had no noticeable effect on EEG activity whether the patient was under general anesthesia, awake, or asleep, but vagus nerve stimulation may interrupt ongoing ictal EEG activity.