gebhart/patrepeval huggingface dataset:
Phospholipid:diacylglycerol acyltransferase: An enzyme that catalyzes the acyl-CoA-independent formation of triacylglycerol in yeast and plants (2000)

Triacylglycerol (TAG) is known to be synthesized in a reaction that uses acyl-CoA as acyl donor and diacylglycerol (DAG) as acceptor, and which is catalyzed by the enzyme acyl-CoA:diacylglycerol acyltransferase. We have found that some plants and yeast also have an acyl-CoA-independent mechanism for TAG synthesis, which uses phospholipids as acyl donors and DAG as acceptor. This reaction is catalyzed by an enzyme that we call phospholipid:diacylglycerol acyltransferase, or PDAT. PDAT was characterized in microsomal preparations from three different oil seeds: sunflower, castor bean, and Crepis palaestina. We found that the specificity of the enzyme for the acyl group in the phospholipid varies between these species. Thus, C. palaestina PDAT preferentially incorporates vernoloyl groups into TAG, whereas PDAT from castor bean incorporates both ricinoleoyl and vernoloyl groups. We further found that PDAT activity also is present in yeast microsomes. The substrate specificity of this PDAT depends on the head group of the acyl donor, the acyl group transferred, and the acyl chains of the acceptor DAG. The gene encoding the enzyme was identified. The encoded PDAT protein is related to lecithin:cholesterol acyltransferase, which catalyzes the acyl-CoA-independent synthesis of cholesterol esters. However, budding yeast PDAT and its relatives in fission yeast and Arabidopsis form a distinct branch within this protein superfamily, indicating that a separate PDAT enzyme arose at an early point in evolution.
A gene expression-based method to diagnose clinically distinct subgroups of diffuse large B cell lymphoma (2003)

To classify cancer specimens by their gene expression profiles, we created a statistical method based on Bayes' rule that estimates the probability of membership in one of two cancer subgroups. We used this method to classify diffuse large B cell lymphoma (DLBCL) biopsy samples into two gene expression subgroups based on data obtained from spotted cDNA microarrays. The germinal center B cell-like (GCB) DLBCL subgroup expressed genes characteristic of normal germinal center B cells whereas the activated B cell-like (ABC) DLBCL subgroup expressed a subset of the genes that are characteristic of plasma cells, particularly those encoding endoplasmic reticulum and golgi proteins involved in secretion. We next used this predictor to discover these subgroups within a second set of DLBCL biopsies that had been profiled by using oligonucleotide microarrays [Shipp, M. A., et al. (2002) Nat. Med. 8, 68-74]. The GCB and ABC DLBCL subgroups identified in this data set had significantly different 5-yr survival rates after multiagent chemotherapy (62% vs. 26%; P < or = 0.0051), in accord with analyses of other DLBCL cohorts. These results demonstrate the ability of this gene expression-based predictor to classify DLBCLs into biologically and clinically distinct subgroups irrespective of the method used to measure gene expression.
“Lego” Chemistry for the Straightforward Synthesis of Dendrimers (2003)

A new straightforward method of synthesis of dendrimers, using two branched monomers (CA(2) and DB(2)), is described. Each generation is obtained in a single quantitative step, with only N(2) or H(2)O as byproducts; generation 4 is obtained in only four steps. The end groups are alternatively phosphines and hydrazines; their versatile reactivity is illustrated by the reaction of generation 4 with a branched CD(5) monomer, which increases the number of end groups in a single step from 48 to 250.
The Long Form of the Leptin Receptor (OB-Rb) Is Widely Expressed in the Human Brain (2000)

Leptin exerts important effects on the regulation of food intake and energy expenditure by acting in the brain. Leptin action is mediated by the interaction with a receptor that is alternatively spliced, resulting in at least five different isoforms. The long form (OB-Rb) has a long intracellular domain that is essential for intracellular signal transduction. The specific aim of this study was to further investigate the role that the brain may play in the pathogenesis of obesity in humans. We studied the expression of OB-R mRNA (both short or common and long isoforms) in the brains of obese, lean and diabetic subjects, by in situ hybridization, semiquantitative RT-PCR and Northern blots analysis. We used two alternative probes: one that recognizes all known splice variants (OB-Ra) and a second that recognizes only the long form, OB-Rb. Several brain regions, including hypothalamus, cerebellum, neocortex, entorrhinal cortex, amygdala, and rostral medulla, were evaluated. In situ hybridization studies revealed that both OB-Ra and OB-Rb mRNAs are widely distributed in the human brain. The specific hybridization signal with both probes was detected exclusively in the cytoplasm of the cell body, dendrites and proximal axons of neurons. Hypothalamic nuclei, Purkinje cells and dentate nuclei of the cerebellum, inferior olivary and cranial nerves nuclei in the medulla, amygdala and neurons from both neocortex and entorrhinal cortex demonstrated positive signals. The hybridization signal obtained in ependyma was lower than that in neurons and no specific hybridization was detected in glial cells. No significant differences were identified among the regions or among the three groups studied. These results match those previously obtained by us [Couce et al.: Neuroendocrinology 1997;66:145] in which the distribution of the OB-R protein in the human brain was first described. RT-PCR indicated that the OB-Rb was highly expressed in the hypothalamus and cerebellum. No significant differences of OB-Ra or OB-Rb mRNA expression were identified in lean or obese individuals in these two cerebral regions. The levels of OB-Rb were significantly higher in cerebellum compared to hypothalamus in lean and obese individuals. The original hypothesis that OB-Rb is present only in the hypothalamus needs to be reconsidered. This OB-Rb isoform seems to be widely expressed in the human brain with highest levels in the cerebellum. Obesity and hyperleptinemia appears not to be associated with down-regulation of the OB-Rb in the human brain.
High-affinity autoantibodies specifically eliminate granulocyte-macrophage colony-stimulating factor activity in the lungs of patients with idiopathic pulmonary alveolar proteinosis (2003)

Deficiency of granulocyte-macrophage colony-stimulating factor (GM-CSF) in mice results in pulmonary alveolar proteinosis (PAP) from impaired surfactant catabolism by alveolar macrophages (AMs). Recently, we have shown that neutralizing anti-GM-CSF autoantibodies develop specifically in patients with idiopathic pulmonary alveolar proteinosis (iPAP). Analogous to murine PAP models, it is plausible that the autoantibodies reduce GM-CSF activity, resulting in AM dysfunction and surfactant accumulation. To examine this hypothesis, we estimated the neutralizing activity of the autoantibodies in the lungs of patients and characterized their biologic properties. GM-CSF bioactivity was completely abrogated in the bronchoalveolar lavage fluid (BALF) of patients with iPAP but not in healthy subjects. Autoantibodies were present in the alveoli in high concentrations and colocalized with GM-CSF. They recognized human GM-CSF with high avidity (K(AV) = 20.0 +/- 7.5 pM) and high specificity, reacting with its superstructure and neutralizing GM-CSF activity to a level 4000 to 58 000 times the levels of GM-CSF normally present in the lung. Although target epitopes varied among patients, GM-CSF amino acids 78 to 94 were consistently recognized. Thus, autoantibodies bind GM-CSF with high specificity and high affinity, exist abundantly in the lung, and effectively block GM-CSF binding to its receptor, inhibiting AM differentiation and function. Our data strengthen the evidence associating anti-GM-CSF autoantibodies with the pathogenesis of this disease.
Ultra-low-loss high-aspect-ratio Si_3N_4 waveguides (2011)

We characterize an approach to make ultra-low-loss waveguides using stable and reproducible stoichiometric Si3N4 deposited with low-pressure chemical vapor deposition. Using a high-aspect-ratio core geometry, record low losses of 8-9 dB/m for a 0.5 mm bend radius down to 3 dB/m for a 2 mm bend radius are measured with ring resonator and optical frequency domain reflectometry techniques. From a waveguide loss model that agrees well with experimental results, we project that 0.1 dB/m total propagation loss is achievable at a 7 mm bend radius with this approach.
The safety and efficacy of combination N-butyl-deoxynojirimycin (SC-48334) and zidovudine in patients with HIV-1 infection and 200-500 CD4 cells/mm3. (1994)

We conducted a double-blind, randomized phase II study to evaluate the safety and activity of combination therapy with N-butyl-deoxynojirimycin (SC-48334) (an alpha-glucosidase I inhibitor) and zidovudine versus zidovudine alone. Patients with 200 to 500 CD4 cells/mm3 who tolerated < or = 12 weeks of prior zidovudine therapy received SC-48334 (1000 mg every 8 h) and zidovudine (100 mg every 8 h) or zidovudine and placebo. Sixty patients received combination therapy and 58, zidovudine and placebo. Twenty-three patients (38%) and 15 (26%), in the combination and zidovudine groups, respectively, discontinued therapy (p = 0.15). The mean SC-48334 steady-state trough level (4.04 +/- 0.99 micrograms/ml) was below the in vitro inhibitory concentration for human immunodeficiency virus (HIV). The mean increase in CD4 cells at week 4 was 73.8 cells/mm3 and 52.4 cells/mm3 for the combination and zidovudine groups, respectively (p > 0.36). For patients with prior zidovudine therapy, the mean change in CD4 cells in the combination and zidovudine groups was 63.7 cells/mm3 and 4.9 cells/mm3 at week 8 and 6.8 cells/mm3 and -45.1 cells/mm3 at week 16, respectively. The number of patients with suppression of HIV p24 antigenemia in the combination and zidovudine groups was six (40%) and two (11%) at week 4 (p = 0.10) and five (45%) and two (14%) at week 24 (p = 0.08), respectively. Diarrhea, flatulence, abdominal pain, and weight loss were common for combination recipients.(ABSTRACT TRUNCATED AT 250 WORDS)
Alzheimer's Disease--Genotypes, Phenotype, and Treatments (1997)

What causes Alzheimer's disease? Selkoe's Perspective reviews recent research identifying four different genetic causes of Alzheimer's disease and suggests that all four point toward the deposition of amyloid beta in the brain as the initial trigger for the disease.
Virus diseases. (2001)

<title>Abstract</title> A description of a virus and a discussion on viral disease symptoms are presented. The different viruses of fungi are mentioned, and the transmission and spread of viruses are discussed. A summary of the characteristics of some plant virus genera is given. Different procedures for screening or indexing plant material for viruses are provided. A list of some indicator species commonly used as test plants and the crops to which they relate is also given. Different control measures of virus diseases, which include the use of genetically resistant cultivars and isolation and timely removal of any crops retained for seed production, are mentioned.
Generation of chemiluminescence upon reaction of aliphatic amines with tris(2,2'-bipyridine)ruthenium(III) (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGeneration of chemiluminescence upon reaction of aliphatic amines with tris(2,2'-bipyridine)ruthenium(III)James B. Noffsinger and Neil D. DanielsonCite this: Anal. Chem. 1987, 59, 6, 865–868Publication Date (Print):March 15, 1987Publication History Published online1 May 2002Published inissue 15 March 1987https://pubs.acs.org/doi/10.1021/ac00133a017https://doi.org/10.1021/ac00133a017research-articleACS PublicationsRequest reuse permissionsArticle Views1807Altmetric-Citations380LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Divergent N-terminal Sequences of a Deubiquitinating Enzyme Modulate Substrate Specificity (2001)

Ubiquitin-specific processing proteases (UBPs) are characterized by a conserved core domain with surrounding divergent sequences, particularly at the N-terminal end. We previously cloned two isoforms of a testis UBP, UBP-t1 and UBP-t2, which contain identical core regions but distinct N termini that target the two isoforms to different subcellular locations (Lin, H., Keriel, A., Morales, C. R., Bedard, N., Zhao, Q., Hingamp, P., Lefrancois, S., Combaret, L., and Wing, S. S. (2000) Mol. Cell. Biol. 20, 6568-6578). To determine whether the N termini also influence the biochemical functions of the UBP, we expressed UBP-t1, UBP-t2, and the common core domain, UBP core, in Escherichia coli. The three isoforms cleaved branched triubiquitin at >20-fold faster rates than linear diubiquitin, suggesting that UBP-testis functions as an isopeptidase. Both N-terminal extensions inhibited the ability of UBP-core to generate free ubiquitin when linked in a peptide bond with itself, another peptide, or to small adducts. The N-terminal extension of UBP-t2 increased the ability of UBP-core to cleave branched triubiquitin. UBP-core removed ubiquitin from testis ubiquitinated proteins more rapidly than UBP-t2 and UBP-t1. Thus, UBP enzymes appear to contain a catalytic core domain, the activities and specificities of which can be modulated by N-terminal extensions. These divergent N termini can alter localization and confer multiple functions to the various members of the large UBP family.
Production of Glutaconic Acid in a RecombinantEscherichia coliStrain (2010)

ABSTRACT The assembly of six genes that encode enzymes from glutamate-fermenting bacteria converted Escherichia coli into a glutaconate producer when grown anaerobically on a complex medium. The new anaerobic pathway starts with 2-oxoglutarate from general metabolism and proceeds via ( R )-2-hydroxyglutarate, ( R )-2-hydroxyglutaryl-coenzyme A (CoA), and ( E )-glutaconyl-CoA to yield 2.7 ± 0.2 mM ( E )-glutaconate in the medium.
Analysis of Pre-existing IgG and IgM Antibodies against Polyethylene Glycol (PEG) in the General Population (2016)

Circulating antibodies (Ab) that specifically bind polyethylene glycol (PEG), a biocompatible polymer routinely used in protein and nanoparticle therapeutics, have been associated with reduced efficacy of and/or adverse reactions to therapeutics modified with or containing PEG. Unlike most antidrug antibodies that are induced following initial drug dosing, anti-PEG Ab can be found in treatment-naïve individuals (i.e., individuals who have never undergone treatment with PEGylated drugs but most likely have been exposed to PEG through other means). Unfortunately, the true prevalence, quantitative levels, and Ab isotype of pre-existing anti-PEG Ab remain poorly understood. Here, using rigorously validated competitive ELISAs with engineered chimeric anti-PEG monoclonal Ab standards, we quantified the levels of anti-PEG IgM and different subclasses of anti-PEG IgG (IgG1-4) in both contemporary and historical human samples. We unexpectedly found, with 90% confidence, detectable levels of anti-PEG Ab in ∼72% of the contemporary specimens (18% IgG, 25% IgM, 30% both IgG and IgM). The vast majority of these samples contained low levels of anti-PEG Ab, with only ∼7% and ∼1% of all specimens possessing anti-PEG IgG and IgM in excess of 500 ng/mL, respectively. IgG2 was the predominant anti-PEG IgG subclass. Anti-PEG Ab's were also observed in ∼56% of serum samples collected during 1970-1999 (20% IgG, 19% IgM, and 16% both IgG and IgM), suggesting that the presence of PEG-specific antibodies may be a longstanding phenomenon. Anti-PEG IgG levels demonstrated correlation with patient age, but not with gender or race. The widespread prevalence of pre-existing anti-PEG Ab, coupled with high Ab levels in a subset of the population, underscores the potential importance of screening patients for anti-PEG Ab levels prior to administration of therapeutics containing PEG.
Anti‐(Raf‐1) RNA aptamers that inhibit Ras‐induced Raf‐1 activation (2002)

RNA aptamers with affinity for the Ras-binding domain (RBD) of Raf-1 were isolated from a degenerate pool by in vitro selection. These aptamers efficiently inhibited the Ras interaction with the Raf-1 RBD, and also inhibited Ras-induced Raf-1 activation in a cell-free system. The RNA aptamer with the most potent inhibitory effect specifically inhibited the Ras-Raf-1 interaction and had no affinity for the RBD of the RGL protein, a homolog of the Ral GDP dissociation stimulator. Although the aptamer was capable of binding to the B-Raf RBD, the RNA did not inhibit the interaction between Ras and the B-Raf RBD. Enzymatic and chemical probing experiments indicated that the aptamer was folded into a pseudoknot structure, and some loop regions of the pseudoknot were located at the binding interface for the Raf-1 RBD.
Structure of the gene for the transition state regulator, abrB: regulator synthesis is controlled by the spo0A sporulation gene in Bacillus subtilis (1988)

Sporulation begins coincidentally with the expression of several stationary-phase-associated gene products during the transition state of a culture from exponential to stationary phase. Mutations in the stage 0 sporulation genes prevent the expression of these gene products in addition to blocking sporulation. Suppressor mutations in the abrB gene, in a spo0 background, restore stationary-phase-associated gene expression but not sporulation. The nature of the abrB gene product was investigated by isolating and sequencing the abrB gene. The abrB gene coded for a 96-amino-acid protein (molecular weight 10773) and contained a helix-turn-helix structure common to DNA binding proteins. Analysis of expression of the abrB gene using lacZ transcription fusions and direct measurement of mRNA content by hybridization showed that the spo0A gene repressed transcription of the abrB gene. Primer extension analysis of abrB gene mRNA revealed two initiation sites. The downstream site was dramatically repressed in spo0A+ strains, while the upstream site appeared not to be regulated by spo0A. Five abrB mutant alleles were cloned and sequenced. One mutation, abrB4, resided within the structural gene and continued to overexpress abrB messenger RNA from both promoters. A promoter mutation, abrB15, reduced transcription from the downstream promoter but not the upstream promoter. Thus, the phenotype of abrB mutations results from inactivation of the abrB gene product or by prevention of its overexpression. The results suggest that the abrB gene codes for a regulator which controls several genes whose products are normally produced during the transition phase between active growth and sporulation. The level of this regulator is, in turn, controlled by the spo0A gene. The pleiotropic phenotypes of spo0A mutants result from uncontrolled overexpression of the abrB regulator.
Virtual artificial sensor technique for functional electrical stimulation (1998)

In the control of Functional Electrical Stimulation (FES) gait systems artificial sensors are used to provide the controller with feedback information. The sensors used range in complexity from simple heel or hand switches to tri-axial accelerometers. There are three basic problems connected with the selection of sensors: the type(s) of sensor(s) to be used, the number of sensors required and the optimum location of the sensor set. In general the choice of the sensor sets has been based on the availability of actual sensors and the experts understanding of where these sensors should be located. Using motion analysis data it is possible to construct an almost unlimited number of virtual sensors on any location of the body surface. Our aim was to develop this technique for construction of virtual sensors and compare these virtual sensors with their physical counterparts. Virtual goniometers, inclinometers, accelerometers and foot switches were constructed and compared with their physical counterparts. In addition visualisation tools were developed to aid in the choice of sensor location. There was a very good correlation between all the virtual and physical sensors. This technique gives flexibility to place virtual sensors almost anywhere on the body surface and also allows the construction of novel sensors.
Enhancement of hydrogen peroxide formation by protophores and ionophores in antimycin-supplemented mitochondria (1980)

Rat and pigeon heart mitochondria supplemented with antimycin produce 0.3-1.0nmol of H(2)O(2)/min per mg of protein. These rates are stimulated up to 13-fold by addition of protophores (carbonyl cyanide p-trifluoromethoxyphenylhydrazone, carbonyl cyanide m-chloromethoxyphenylhydrazone and pentachlorophenol). Ionophores, such as valinomycin and gramicidin, and Ca(2+) also markedly stimulated H(2)O(2) production by rat heart mitochondria. The enhancement of H(2)O(2) generation in antimycin-supplemented mitochondria and the increased O(2) uptake of the State 4-to-State 3 transition showed similar protophore, ionophore and Ca(2+) concentration dependencies. Thenoyltrifluoroacetone and N-bromosuccinimide, which inhibit succinate-ubiquinone reductase activity, also decreased mitochondrial H(2)O(2) production. Addition of cyanide to antimycin-supplemented beef heart submitochondrial particles inhibited the generation of O(2) (-), the precursor of mitochondrial H(2)O(2). This effect was parallel to the increase in cytochrome c reduction and it is interpreted as indicating the necessity of cytochrome c(1) (3+) to oxidize ubiquinol to ubisemiquinone, whose autoxidation yields O(2) (-). The effect of protophores, ionophores and Ca(2+) is analysed in relation to the propositions of a cyclic mechanism for the interaction of ubiquinone with succinate dehydrogenase and cytochromes b and c(1) [Wikstrom & Berden (1972) Biochim. Biophys. Acta283, 403-420; Mitchell (1976) J. Theor. Biol.62, 337-367]. A collapse in membrane potential, increasing the rate of ubisemiquinone formation and O(2) (-) production, is proposed as the molecular mechanism for the enhancement of H(2)O(2) formation rates observed on addition of protophores, ionophores and Ca(2+).
Immunization With Mutantp53- andK-ras–Derived Peptides in Cancer Patients: Immune Response and Clinical Outcome (2005)

Custom-made peptide vaccination is feasible without any toxicity. CTL and cytokine responses specific to a given mutation can be induced or enhanced with peptide vaccines. Cellular immunity to mutant p53 and K-ras oncopeptides is associated with longer survival.