gebhart/patrepeval huggingface dataset:
Biochemical characterization of the β-1,4-glucuronosyltransferase GelK in the gellan gum-producing strain Sphingomonas paucimobilis A.T.C.C. 31461 (2001)

Biosynthesis of bacterial polysaccharide-repeat units proceeds by sequential transfer of sugars, from the appropriate sugar donor to an activated lipid carrier, by committed glycosyltransferases (GTs). Few studies on the mechanism of action for this type of GT are available. Sphingomonas paucimobilis A.T.C.C. 31461 produces the industrially important polysaccharide gellan gum. We have cloned the gelK gene from S. paucimobilis A.T.C.C. 31461. GelK belongs to family 1 of the GT classification [Campbell, Davies, Bulone, Henrissat (1997) Biochem. J. 326, 929–939]. Sequence similarity studies suggest that GelK consists of two protein modules corresponding to the -NH2 and -CO2H halves, the latter possibly harbouring the GT activity. The gelK gene and the open reading frames coding for the -NH2 (GelKNH2) and -CO2H (GelKCOOH) halves were overexpressed in Escherichia coli. GelK and GelKNH2 were present in both the soluble and membrane fractions of E. coli, whereas GelKCOOH was only present in the soluble fraction. GelK catalysed the transfer of [14C]glucuronic acid from UDP-[14C]glucuronic acid into a glycolipid extracted from S. paucimobilis or E. coli, even in the presence of EDTA, and the radioactive sugar was released from the glycolipid by β-1,4-glucuronidase. GelK was not able to use synthetic glucosyl derivatives as acceptors, indicating that the PPi-lipid moiety is needed for enzymic activity. Recombinant GelKNH2 and GelKCOOH did not show detectable activity. Based on the biochemical characteristics of GelK and on sequence similarities with N-acetylglucosaminyltransferase, we propose that GT families 1 and 28 form a superfamily.
Type IV collagenase (M(r) 72,000) expression in human prostate: benign and malignant tissue. (1993)

The expression of type IV collagenase (M(r) 72,000) has been examined in tissues from patients with benign prostatic hyperplasia (6 patients) and varying Gleason grades of malignant prostate cancer (18 patients). Immunoperoxidase labeling indicated that expression of the type IV collagenase was weak or nonexistent in benign tissue but consistently strong in the glandular and ductal epithelial cells of prostate tumors diagnosed at Gleason grades 1-8. In moderate to advanced cancer (i.e., Gleason grades 2 to 8), invasive tumor foci in the stromal tissue produced relatively modest amounts of type IV collagenase. The normal stromal tissue (i.e., fibroblasts) uniformly failed to produce detectable levels of type IV collagenase in the 24 patients examined. Northern and quantitative slot blot hybridization assays demonstrated that collagenase type IV mRNA levels were low in benign tissue and high in malignant tumors. In contrast, the stromal cells did not express significant amounts of type IV collagenase mRNA. Enzyme-linked immunosorbent assays demonstrated that the amounts of type IV collagenase protein correlated directly with the mRNA levels in the tumor tissue. The studies suggest that type IV collagenase may be selectively overexpressed by malignant, preinvasive prostatic epithelial cells.
A RAP1-interacting protein involved in transcriptional silencing and telomere length regulation. (1992)

The yeast RAP1 protein is a sequence-specific DNA-binding protein that functions as both a repressor and an activator of transcription. RAP1 is also involved in the regulation of telomere structure, where its binding sites are found within the terminal poly(C1-3A) sequences. Previous studies have indicated that the regulatory function of RAP1 is determined by the context of its binding site and, presumably, its interactions with other factors. Using the two-hybrid system, a genetic screen for the identification of protein-protein interactions, we have isolated a gene encoding a RAP1-interacting factor (RIF1). Strains carrying gene disruptions of RIF1 grow normally but are defective in transcriptional silencing and telomere length regulation, two phenotypes strikingly similar to those of silencing-defective rap1s mutants. Furthermore, hybrid proteins containing rap1s missense mutations are defective in an interaction with RIF1 in the two-hybrid system. Taken together, these data support the idea that the rap1s phenotypes are attributable to a failure to recruit RIF1 to silencers and telomeres and suggest that RIF1 is a cofactor or mediator for RAP1 in the establishment of a repressed chromatin state at these loci. By use of the two-hybrid system, we have isolated a mutation in RIF1 that partially restores the interaction with rap1s mutant proteins.
Application access control at network level (1994)

This paper describes an access control mechanism that enforces at the network level an access control decision that is taken at the application level. The mechanism is based on the pre-computation of encrypted counters called tickets. An access enforcement device verifies the existence of a valid ticket in each packet that is subject to access control and kills unauthorized packets. Tickets are not computed as a function of the user data. Due to the timing constraints of shared media LANs the presence of a valid ticket in a packet proves that the operation implied by the user data has been authorized. The access control mechanism is elaborated for Internet protocols over Ethernet and we discuss its properties for internetworking and multicasting.
Carbon Nanotubes in Biomedicine and Biosensing (2011)

Carbon Nanotubes in Biomedicine and Biosensing 137 Noncovalent interactionThe noncovalent approach via electrostatic interaction, Van der Waals force, or π-π stacking is a feasible immobilization method for biomolecules.Particularly, it is promising for improving the dispersion proteins of CNTs without destructing of the nanotube structure.Generally, this route can be performed by physical adsorption or entrapment.(Arnold,
Prospective Study of Topical Testosterone Gel (AndroGel) Versus Intramuscular Testosterone in Testosterone-Deficient HIV-Infected Men (2007)

Daily testosterone gel produced stable testosterone concentrations and improved quality of life compared with intermittent intramuscular testosterone injections.
Proliferative potential of human fibroblasts: An inverse dependence on cell size (1987)

Human foreskin fibroblast-like cells were separated on the basis of DNA content and cell size by fluorescence-activated cell sorting. Subpopulations of "large" or "small" cells with the same (G1) DNA content were clonally expanded and found to contain predominantly nondividing or highly proliferative cells, respectively. From the rate of clonal growth, we deduce that small cells divide faster than large cells. Intermediate-sized cells were found to yield primarily smaller ("attenuated") clones. The clonal data can be incorporated into a previously reported kinetic model of clonal attenuation. This version of the model postulates that small "stem" cells yield larger daughters which have only a limited proliferative potential. We also postulate that a progressive increase in cell size can account for the decreasing concentration of DNA polymerase alpha, which has been reported in older cultures.
Improved Derivatives of Bactenecin, a Cyclic Dodecameric Antimicrobial Cationic Peptide (1999)

Both linear and cyclic derivatives of the cyclic 12-amino-acid antimicrobial peptide bactenecin were designed based on optimization of amphipathicity and charge location. In general, increasing the number of positive charges at the N and C termini and adding an extra tryptophan residue in the loop not only increased the activities against both gram-positive and gram-negative bacteria but also broadened the antimicrobial spectrum.
Thiol Chemistry in Peroxidase Catalysis and Redox Signaling (2008)

The oxidation chemistry of thiols and disulfides of biologic relevance is described. The review focuses on the interaction and kinetics of hydrogen peroxide with low-molecular-weight thiols and protein thiols and, in particular, on sulfenic acid groups, which are recognized as key intermediates in several thiol oxidation processes. In particular, sulfenic and selenenic acids are formed during the catalytic cycle of peroxiredoxins and glutathione peroxidases, respectively. In turn, these enzymes are in close redox communication with the thioredoxin and glutathione systems, which are the major controllers of the thiol redox state. Oxidants formed in the cell originate from several different sources, but the major producers are NADPH oxidases and mitochondria. However, a different role of the oxygen species produced by these sources is apparent as oxidants derived from NADPH oxidase are involved mainly in signaling processes, whereas those produced by mitochondria induce cell death in pathways including also the thioredoxin system, presently considered an important target for cancer chemotherapy.
Stereochemistry in Drug Action (2003)

The importance of stereochemistry in drug action is gaining greater attention in medical practice, and a basic knowledge of the subject will be necessary for clinicians to make informed decisions regarding the use of single-enantiomer drugs. Many of the drugs currently used in psychiatric practice are mixtures of enantiomers. For some therapeutics, single-enantiomer formulations can provide greater selectivities for their biological targets, improved therapeutic indices, and/or better pharmacokinetics than a mixture of enantiomers. This article reviews the nomenclature for describing stereochemistry and enantiomers, emphasizes the potential biological and pharmacologic differences between the 2 enantiomers of a drug, and highlights the clinical experience with single enantiomers of the selective serotonin reuptake inhibitors fluoxetine and citalopram. In some cases, both a mixture of enantiomers and a single-enantiomer formulation of a drug will be available simultaneously. In these cases, familiarity with stereochemistry and its pharmacologic implications will aid the practicing physician to provide optimal pharmacotherapy to his or her patients.
Efficient Enantiomeric Synthesis of Pyrrolidine and Piperidine Alkaloids from Tobacco (2001)

An enantiomeric synthesis of six piperidine and pyrrolidine alkaloids, (S)-nornicotine 1, (S)-nicotine 2, (S)-anatabine 3, (S)-N-methylanatabine 4, (S)-anabasine 5, and (S)-N-methylanabasine 6, known as natural products in tobacco, was established from a common chiral homoallylic (S)-3-(1-azido-but-3-enyl)-pyridine 15. An intramolecular hydroboration-cycloalkylation of the homoallylic azide intermediate 15 served as the key step in the pyrrolidine ring formation. A ring closing metathesis reaction (RCM) of a diethylenic amine intermediate (S)-allyl-(1-pyridin-3-yl-but-3-enyl)-carbamic acid benzyl ester 20 served as the key step in the piperidine ring formation. From the commercially available 3-pyridinecarboxaldehyde 13, a short and convenient enantiomeric synthesis of tobacco alkaloids is described: (S)-nornicotine 1 (5 steps, with an overall yield of 70%), (S)-nicotine 2 (6 steps, 65%), (S)-anatabine 3 (8 steps, 30%), (S)-N-methylanatabine 4 (8 steps, 25%), (S)-anabasine 5 (8 steps, 35%), and (S)-N-methylanabasine 6 (8 steps, 25%).
Hepatotoxicity from anabolic androgenic steroids marketed as dietary supplements: contribution from ATP8B1/ABCB11 mutations? (2013)

AAS marketed as dietary supplements continue to cause hepatotoxicity in the UK; underlying mechanisms may include unmasking of genetic cholestatic syndromes.
Attenuation of Quorum Sensing in the Pathogen Acinetobacter baumannii Using Non-native N-Acyl Homoserine Lactones (2012)

Many bacterial pathogens use quorum sensing (QS) to control virulence. As a result, the development of methods to intercept QS has attracted significant interest as a potential anti-infective therapy. Acinetobacter baumannii has emerged as a pan-drug-resistant pathogen and displays a remarkable ability to persist in hospital settings despite desiccation and antimicrobial treatment. Recent studies have shown that A. baumannii QS mutants have limited motility and fail to form mature biofilms; these phenotypes are linked to its ability to persist on biotic and abiotic surfaces and increase its pathogenicity. A. baumannii uses N-(3-hydroxydodecanoyl)-l-homoserine lactone (OH-dDHL) and its putative cognate receptor, AbaR, for QS. We sought to identify non-native ligands capable of blocking or promoting AbaR activity in A. baumannii for use as chemical probes to modulate QS phenotypes in this pathogen. We screened a focused library of synthetic, non-native N-acyl homoserine lactones (AHLs) to identify such compounds, and several highly potent antagonists and agonists were uncovered, with IC(50) and EC(50) values in the low micromolar range, respectively. The strongest AbaR antagonists largely contained aromatic acyl groups, whereas the AbaR agonists closely resembled OH-dDHL. Notably, the 10 most potent AbaR antagonists also strongly inhibited A. baumannii motility, and five antagonists reduced biofilm formation in A. baumannii by up to 40%. The discovery of these compounds is significant, as they represent, to our knowledge, the first non-native modulators of QS in A. baumannii to be reported and could find utility as new tools to study the role and timing of QS phenotypes in A. baumannii infections.
Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails (2001)

Department of Biochemistry and Biophysics, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina 27599-7295, USA; Howard Hughes Medical Institute, Division of Nucleic Acids Enzymology, Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
The JAK-STAT Pathway: A Therapeutic Target in Hematological Malignancies (2006)

The development and function of hematopoietic cells depends on complex signaling pathways that are mediated by numerous cytokines and their receptors. The Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathway is prominent both in normal hematopoiesis and in hematological malignancies. STATs are phosphorylated on tyrosine residues via JAK kinases and on serine residues by a variety of serine/threonine kinases. STATs then dimerize, translocate to the nucleus and bind DNA, initiating the transcription of target genes. STAT proteins mediate cell growth, differentiation, apoptosis, transformation, and other fundamental cell functions. Recently, mutations in the JAK2 gene driving the proliferation of the neoplastic clone have been identified in myeloproliferative disorders. In addition constitutive activation of the JAK-STAT pathway has been reported in various types of leukemias such as acute myelogenous leukemia, T-LGL leukemia, and multiple myeloma. This review describes the pathophysiological role of this pathway in hematological malignancies and the potential benefits of JAK-STAT inhibition.
faBrickation (2014)

We present a new approach to rapid prototyping of functional objects, such as the body of a head-mounted display. The key idea is to save 3D printing time by automatically substituting sub-volumes with standard building blocks'in our case Lego bricks. When making the body for a head-mounted display, for example, getting the optical path right is paramount. Users thus mark the lens mounts as "high-resolution" to indicate that these should later be 3D printed. faBrickator then 3D prints these parts. It also generates instructions that show users how to create everything else from Lego bricks. If users iterate on the design later, faBrickator offers even greater benefit as it allows re-printing only the elements that changed. We validated our system at the example of three 3D models of functional objects. On average, our system fabricates objects 2.44 times faster than traditional 3D printing while requiring only 14 minutes of manual assembly.
Potential Selection System for Mutants with Increased Lysine, Threonine, and Methionine in Cereal Crops1 (1974)

Simultaneous addition of lysine and threonine inhibits growth in maize ( Zea mays L.) callus cultures and embryo cultures from several cereals. Methionine or homoserine reverses lysine‐threonine inhibition. Isolation of feedback inhibition resistance mutants is proposed for several cereals by selecting callus or seedlings which grow in the presence of lysine‐threonine. Resulting mutants may be overproducers of lysine, threonine, or methionine.
Identification of alternative exons, including a novel exon, in the tyrosine kinase receptor gene Etk2/tyro3 that explain differences in 5' cDNA sequences. (1995)

Protein tyrosine kinase transmembrane receptors trigger signal transduction cascades upon ligand binding, resulting in cellular proliferation, differentiation, differentiation inhibition or apoptosis depending upon the cell target. The ETK2/TYRO3 receptor is a tyrosine kinase expressed in embryonic stem cells, brain and testis that has recently been cloned by several groups. Analysis of cDNA clones isolated from several tissues shows 2 isoforms of the Etk2/tyro3 gene product that result from usage of alternative exons near the 5' end of the gene. In addition, our data suggest that a third alternative exon is positioned between these two alternative exons. This novel exon encodes yet another isoform that predicts a unique amino-terminal protein sequence. The alternative exons (exons 2A, 2B and 2C), predict three isoforms with different initiation codons, signal sequences and lengths. The existence of these multiple isoforms may be important for protein processing, translocation, or function.
Defective removal of cellular cholesterol and phospholipids by apolipoprotein A-I in Tangier Disease. (1995)

Tangier disease is a rare genetic disorder characterized by extremely low plasma levels of HDL and apo A-I, deposition of cholesteryl esters in tissues, and a high prevalence of cardiovascular disease. We examined the possibility that HDL apolipoprotein-mediated removal of cellular lipids may be defective in Tangier disease. With fibroblasts from normal subjects, purified apo A-I cleared cells of cholesteryl esters, depleted cellular free cholesterol pools available for esterification, and stimulated efflux of radiolabeled cholesterol, phosphatidylcholine, and sphingomyelin. With fibroblasts from two unrelated Tangier patients, however, apo A-I had little or no effect on any of these lipid transport processes. Intact HDL also was unable to clear cholesteryl esters from Tangier cells even though it promoted radiolabeled cholesterol efflux to levels 50-70% normal. Passive desorption of radiolabeled cholesterol or phospholipids into medium containing albumin or trypsinized HDL was normal for Tangier cells. Binding studies showed that the interaction of apo A-I with high-affinity binding sites on Tangier fibroblasts was abnormal. These results indicate that apo A-I has an impaired ability to remove cholesterol and phospholipid from Tangier fibroblasts, possibly because of a defective interaction of apo A-I with cell-surface binding sites. Failure of apo A-I to acquire cellular lipids may account for the rapid catabolism of nascent HDL particles and the low plasma HDL levels in Tangier disease.
The osteopontin – CD44 pathway is superfluous for the development of autoimmune myocarditis (2006)

Osteopontin (OPN) and CD44 have been implicated in the development of autoimmune diseases, including arthritis and multiple sclerosis, as well as chronic inflammatory diseases, such as atherosclerosis and colitis. To investigate their roles in autoimmune myocarditis induced by immunization with heart alpha-myosin (MyHC-alpha), a mouse model of human cardiomyopathy, we analyzed mice lacking OPN or CD44v6/v7, a CD44 isoform that binds OPN. Both, OPN(-/-) and CD44v6/v7(-/-) mice developed myocarditis with the same prevalence and severity as BALB/c wild-type controls. Furthermore, treatment of BALB/c mice with a pan-neutralizing anti-CD44 antibody did not affect the disease outcome. Consistently, expansion of MyHC-alpha-specific autoimmune CD4(+) T cells and MyHC-alpha autoantibody responses from either CD44v6/v7(-/-) mice or OPN(-/-) mice was indistinguishable from their wild-type controls. Thus, OPN and CD44v6/v7 are merely spectators rather than protagonists in autoimmune myocarditis.
Multi-Task Bayesian Optimization (2013)

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Targeting Human γδ T Cells with Zoledronate and Interleukin-2 for Immunotherapy of Hormone-Refractory Prostate Cancer (2007)

The increasing evidence that gammadelta T cells have potent antitumor activity suggests their value in immunotherapy, particularly in areas of unmet need such as metastatic carcinoma. To this end, we initiated a phase I clinical trial in metastatic hormone-refractory prostate cancer to examine the feasibility and consequences of using the gammadelta T-cell agonist zoledronate, either alone or in combination with low-dose interleukin 2 (IL-2), to activate peripheral blood gammadelta cells. Nine patients were enlisted to each arm. Neither treatment showed appreciable toxicity. Most patients were treated with zoledronate + IL-2, but conversely only two treated with zoledronate displayed a significant long-term shift of peripheral gammadelta cells toward an activated effector-memory-like state (T(EM)), producing IFN-gamma and perforin. These patients also maintained serum levels of tumor necrosis factor-related apoptosis inducing ligand (TRAIL), consistent with a parallel microarray analysis showing that TRAIL is produced by gammadelta cells activated via the T-cell receptor and IL-2. Moreover, the numbers of T(EM) gammadelta cells showed a statistically significant correlation with declining prostate-specific antigen levels and objective clinical outcomes that comprised three instances of partial remission and five of stable disease. By contrast, most patients treated only with zoledronate failed to sustain either gammadelta cell numbers or serum TRAIL, and showed progressive clinical deterioration. Thus, zoledronate + IL-2 represents a novel, safe, and feasible approach to induce immunologic and clinical responses in patients with metastatic carcinomas, potentially providing a substantially increased window for specific approaches to be administered. Moreover, gammadelta cell phenotypes and possibly serum TRAIL may constitute novel biomarkers of prognosis upon therapy with zoledronate + IL-2 in metastatic carcinoma.
Occurrence of Soybean Sudden Death Syndrome in East-Central Illinois and Associated Yield Losses (1995)

Sudden death syndrome (SDS) of soybeans, causal organism Fusarium solani, occurred for the first time in epidemic proportions in east-central Illinois in 1993. SDS occurred in 46% of the soybean fields, based on air and ground surveys. Within fields containing plants with SDS, the percent area affected ranged from 1 to 70% with an average of 7.3 and 13.9% for ground and aerial surveys, respectively. Soil samples taken in 25 fields in areas where all plants showed SDS symptoms and in adjacent areas where plants appeared healthy did not differ in cyst populations of soybean cyst nematode (Heterodera glycines). Disease severity and yield components were compared from replicated plots at an experimental farm and in a commercial field and in a nonreplicated commercial field. Diseased plants from infested areas had fewer pods and seeds and less 300-seed weights. Plant yields were 46, 41, and 20% less for plantsin plots with a high incidence of SDS than were the yields for those with a low incidence of SDS in a nonreplicated commercial field, replicated plots at an experimental farm, and a commercial field, respectively. Seed germination was less and the frequency of Phomopsis spp. was greater on seeds harvested from plants in plots with a high occurrence of SDS compared to plots with a low occurrence of SDS