gebhart/patrepeval huggingface dataset:
Preparation of regular sized Ca-alginate microspheres using membrane emulsification method (2001)

Monodisperse Ca-alginate microspheres were prepared using the membrane emulsification method. Three ionic types of drugs (anionic, cationic and non-ionic) were incorporated into the microspheres, and the effects of sodium alginate concentration and the pressure applied during the dispersing process on the properties of the microspheres were examined. Monodisperse microspheres were obtained when the concentration of alginate solution was 2 wt% and the pressure applied was 0.4 x 10(5) Pa. The mean size of microspheres was approximately 4 microm. Lidocaine x HCl (cationic), sodium salicylate (anionic) and 4-acetamidophenol (non-ionic) were selected as ionic model drugs and included in the alginate microspheres. Lidocaine x HCl (cationic drug) release was more retarded than that of the anionic drug, because of the electrostatic attraction between the negative charge of the ionized carboxyl group in the alginate chain and the positive charge of the cationic drug. In acidic release medium, a slow release was observed due to the low swelling characteristic and the increased viscosity of alginate, regardless of ionic type of drug.
A low‐selenium diet increases thyroxine and decreases 3,5,3′triiodothyronine in the plasma of kittens (2002)

The effect of a low-selenium diet on thyroid hormone metabolism was investigated in growing kittens. Twelve specific-pathogen-free kittens with ages ranging from 16 to 18 weeks were divided into two groups of equal number with equal sex distribution in each group. One group was fed a yeast-based low-selenium diet (0.02 mg Se/kg diet) while the other group was fed the same diet supplemented with Na2SeO3 at 0.4 mg Se/kg diet for 8 weeks. Food intake, body weight and body weight gain were not affected by the low-Se diet during the study period. However, kittens given the low-Se diet had significantly reduced plasma selenium concentration and glutathione peroxidase activity. Plasma total thyroxine (T4) increased and total 3,5,3'triiodothyronine (T3) decreased significantly in kittens fed the low-Se diet at the end of the study. These results suggest that type I deiodinase in cats is a selenoprotein- or a selenium-dependent enzyme.
Mass spectrometry-based proteomics: principles, perspectives, and challenges. (2008)

Mass spectrometry-based proteomics is a modern and rapidly developing methodology for qualitative and quantitative characterization of proteins and their posttranslational modification, subcellular localization, and interaction partners. It enables characterization of entire proteomes with unprecedented sensitivity and precision, providing platforms for identification of biomarkers and drug targets.
Pulse Jet Orchard Heater System Development: Part I. Design, Construction, and Optimization (2009)

The objective of this six-year project was to develop a more efficient and effective supplemental orchard field heater technology. In addition to being low-cost and mobile, these devices should be useable with or without wind machines, reduce labor requirements, and greatly reduce air pollutants compared to conventional orchard heating systems. The new generation orchard heaters that were developed in this process are portable, auto-regulating, horizontal pulse jet engines (combustors) with no moving parts. These devices utilize air ejector technology to reduce the temperature of the high-velocity combustion stream by thoroughly mixing it with the surrounding ambient (cold) air, producing a net effective temperature increase of only 2C to 5C above ambient. Buoyant forces of warm air are therefore small, and fewer heaters would be needed. The design achieved pressure oscillations that were free of combustion instabilities, and amplitudes were maximized for high exhaust jet velocities for deep hot jet penetration and mixing into the surrounding cold air. The overall size and weight of the heater system were minimized while maintaining optimum operation. Finally, anti-phase operation of paired heaters for noise level reduction from 130 dB to near 75 dB was achieved by implementing optimized silencing plenums at the inlet and exhaust of the paired heaters.
A Convergent Synthetic Route to (+)-Dynemicin A and Analogs of Wide Structural Variability (1997)

An enantioselective synthetic route to (+)-dynemicin A (1) is described that involves as the key and final step the Diels−Alder cycloaddition of the quinone imine 6 with the isobenzofuran 107 followed by an oxidative workup to provide (+)-1 in 40% yield. The synthetic route begins with the condensation of (−)-menthyl acetoacetate and trans-ethyl crotonate to form the crystalline cyclohexanedione 14, which is then transformed to the enantiomerically pure quinone imine 6 in 23 steps with an average yield of 85% and an overall yield of 2−3%. Key features of this sequence include the coupling of the enol triflate 11 and the arylboronic acid 10 (90%), the thermal deprotection/internal amidation of the coupling product 18 (84%), the use of 2-chloropyridine as an economical alternative to 2,6-di-tert-butylpyridine to promote the reaction of the quinolone 9 and triflic anhydride (85%), the highly stereoselective addition of the (Z)-enediyne 31 to the quinoline 61 (89%), intramolecular acetylide addition within the acetylenic ketone 66 (94%), and oxidation of the phenol 76 with iodosobenzene to afford the quinone imine precursor 77 in 89% yield. Both the quinone imine and isobenzofuran components of the final coupling reaction can be varied, thus providing an ideal route for the preparation of a wide variety of dynemicin analogs.
The bovine fatty acid binding protein 4 gene is significantly associated with marbling and subcutaneous fat depth in Wagyu x Limousin F2 crosses (2006)

Fatty acid binding protein 4 (FABP4), which is expressed in adipose tissue, interacts with peroxisome proliferator-activated receptors and binds to hormone-sensitive lipase and therefore, plays an important role in lipid metabolism and homeostasis in adipocytes. The objective of this study was to investigate associations of the bovine FABP4 gene with fat deposition. Both cDNA and genomic DNA sequences of the bovine gene were retrieved from the public databases and aligned to determine its genomic organization. Primers targeting two regions of the FABP4 gene were designed: from nucleotides 5433-6106 and from nucleotides 7417-7868 (AAFC01136716). Direct sequencing of polymerase chain reaction (PCR) products on two DNA pools from high- and low-marbling animals revealed two single nucleotide polymorphisms (SNPs): AAFC01136716.1:g.7516G>C and g.7713G>C. The former SNP, detected by PCR-restriction fragment length polymorphism using restriction enzyme MspA1I, was genotyped on 246 F2 animals in a Waygu x Limousin F2 reference population. Statistical analysis showed that the FABP4 genotype significantly affected marbling score (P = 0.0398) and subcutaneous fat depth (P = 0.0246). The FABP4 gene falls into a suggestive/significant quantitative trait loci interval for beef marbling that was previously reported on bovine chromosome 14 in three other populations.
Recombinant tumor necrosis factor causes activation of human granulocytes (1987)

We have tested the hypothesis that tumor necrosis factor (TNF), by binding to and activating granulocytes, may contribute to the pathogenesis of gram-negative sepsis and the adult respiratory distress syndrome (ARDS). Buffy coat granulocytes incubated with as little as 0.5 ng/mL of recombinant TNF (rTNF) showed a dose-related increase in nitroblue tetrazolium dye reduction, in granulocyte polarization, in superoxide anion release, and in visually apparent aggregation. Purified lipopolysaccharide (1 microgram/mL) caused polymorphonuclear (PMN) aggregation and activation that was neutralized by polymyxin B. The release of superoxide was augmented by preincubation of the PMNs with gamma-interferon. The effect of TNF was neutralized by TNF- specific murine monoclonal antibodies but not by polymyxin B. Scatchard analysis of 125I-rTNF binding to granulocytes revealed about 1,200 receptors per cell with a Kd of 4.9 X 10(-10) mol/L. These results suggest that the release of TNF by mononuclear phagocytes contributes to granulocyte activation and aggregation during inflammation.
iTRAQ Underestimation in Simple and Complex Mixtures: “The Good, the Bad and the Ugly” (2009)

The increasing popularity of iTRAQ for quantitative proteomics applications makes it necessary to evaluate its relevance, accuracy, and precision for biological interpretation. Here, we have assessed (a) the accuracy and precision of iTRAQ quantification in a controlled experimental setup, using low- and high-complexity protein mixtures; and (b) the potential pitfalls that hamper the applicability and attainable dynamic range of iTRAQ: isotopic contamination, background interference, and signal-to-noise ratio. Our data suggest greater dynamic crosstalk between interfering factors affecting underestimations, and that these interferences were largely scenario-specific, dependent on sample complexity. The good is the potential for iTRAQ to provide accurate quantification spanning 2 orders of magnitude. This potential is however limited by two factors. (1) The bad: the existence of isotopic impurities that can be corrected for; provided accurate isotopic factors are at one's disposal. (2) The ugly: we demonstrate here the interference of mixed MS/MS contribution occurring during precursor selection, an issue that is currently very difficult to minimize. In light of our results, we propose a list of advice for iTRAQ data analysis that could routinely ameliorate quantitative interpretation of proteomic data sets.
Structural changes in the 530 loop ofEscherichia coli16S rRNA in mutants with impaired translational fidelity (1995)

The higher order structure of the functionally important 530 loop in Escherichia coli 16S rRNA was studied in mutants with single base changes at position 517, which significantly impair translational fidelity. The 530 loop has been proposed to interact with the EF-Tu-GTP-aatRNA ternary complex during decoding. The reactivity at G530, U531 and A532 to the chemical probes kethoxal, CMCT and DMS respectively was increased in the mutant 16S rRNA compared with the wild-type, suggesting a more open 530 loop structure in the mutant ribosomes. This was supported by oligonucleotide binding experiments in which probes complementary to positions 520-526 and 527-533, but not control probes, showed increased binding to the 517C mutant 70S ribosomes compared with the non-mutant control. Furthermore, enzymatic digestion of 70S ribosomes with RNase T1, specific for single-stranded RNA, substantially cleaved both wild-type and mutant rRNAs between G524 and C525, two of the nucleotides involved in the 530 loop pseudoknot. This site was also cleaved in the 517C mutant, but not wild-type rRNA, by RNase V1. Such a result is still consistent with a more open 530 loop structure in the mutant ribosomes, since RNase V1 can cut at appropriately stacked single-stranded regions of RNA. Together these data indicate that the 517C mutant rRNA has a rather extensively unfolded 530 loop structure. Less extensive structural changes were found in mutants 517A and 517U, which caused less misreading. A correlation between the structural changes in the 530 loop and impaired translational accuracy is proposed.
Activated microglia mediate neuronal cell injury via a nitric oxide mechanism (1992)

Activated microglial have been proposed to play a pathogenetic role in immune-mediated neurodegenerative diseases. To test this hypothesis, purified murine neonatal microglial were cocultured with neuronal cells derived from fetal brain. Activation with IFN-gamma and LPS of these cocultures brought about a sharp decrease in uptake of gamma-amino butyric acid and a marked reduction in neuronal cell survival. These effects varied with the density of microglia, the concentrations of the activation signals (IFN-gamma and LPS), and the duration of coculture. Inasmuch as addition of NG-monomethyl-L-arginine blocked these effects, a L-arginine-dependent neurocytotoxic mechanism was implicated. Abundant nitrite, a metabolite of the free radical nitric oxide (NO) derived from L-arginine, was detected in activated microglial/neuronal cell cocultures and in purified microglial cell cultures but not in purified astrocyte or neuronal cell cultures, suggesting that microglial were the principal source of the NO. These findings support the hypothesis that microglia are the source of a neurocytotoxic-free radical, and shed light on an additional mechanism of immune-mediated brain injury.
Design aspects of network assisted device-to-device communications (2012)

Device-to-device (D2D) communications underlaying a cellular infrastructure has been proposed as a means of taking advantage of the physical proximity of communicating devices, increasing resource utilization, and improving cellular coverage. Relative to the traditional cellular methods, there is a need to design new peer discovery methods, physical layer procedures, and radio resource management algorithms that help realize the potential advantages of D2D communications. In this article we use the 3GPP Long Term Evolution system as a baseline for D2D design, review some of the key design challenges, and propose solution approaches that allow cellular devices and D2D pairs to share spectrum resources and thereby increase the spectrum and energy efficiency of traditional cellular networks. Simulation results illustrate the viability of the proposed design.
Rapid spread of a unique strain of Pasteurella haemolytica serotype 1 among transported calves (1998)

Pasteurella haemolytica serotype 1 was horizontally transmitted among calves within days of commingling, which continued after calves were transported to a feedlot.
Prodrugs in cancer chemotherapy (1986)

Conference Article| April 01 1986 Prodrugs in cancer chemotherapy DERRY E. V. WILMAN DERRY E. V. WILMAN 1Drug Development Section, Institute of Cancer Research, Cancer Research Campaign Laboratory, Clifton Avenue, Sutton, Surrey, SM2 5PX, U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1986) 14 (2): 375–382. https://doi.org/10.1042/bst0140375 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation DERRY E. V. WILMAN; Prodrugs in cancer chemotherapy. Biochem Soc Trans 1 April 1986; 14 (2): 375–382. doi: https://doi.org/10.1042/bst0140375 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search © 1986 Biochemical Society1986 Article PDF first page preview Close Modal You do not currently have access to this content.
Nanoarrays of tethered lipid bilayer rafts on poly(vinyl alcohol) hydrogels (2008)

Lipid rafts are cholesterol- and sphingolipid-rich domains that function as platforms for signal transduction and other cellular processes. Tethered lipid bilayers have been proposed as a promising model to describe the structure and function of cell membranes. We report a nano(submicro) array of tethered lipid bilayer raft membranes (tLBRMs) comprising a biosensing platform. Poly(vinyl alcohol) (PVA) hydrogel was directly patterned onto a solid substrate, using ultraviolet-nanoimprint lithography (UV-NIL), as an inert barrier to prevent biofouling. The robust structures of the nanopatterned PVA hydrogel were stable for up to three weeks in phosphate-buffered saline solution despite significant swelling (100% in height) by hydration. The PVA hydrogel strongly restricted the adhesion of vesicles, resulting in an array of highly selective hydrogel nanowells. tLBRMs were not formed by direct vesicle fusion, although raft vesicles containing poly(ethylene glycol) lipopolymer were selectively immobilized on gold substrates patterned with PVA hydrogel. The deposition of tLBRM nano(submicro) arrays was accomplished by a mixed, self-assembled monolayer-assisted vesicle fusion method. The monolayer was composed of a mixture of 2-mercaptoethanol and poly(ethylene glycol) lipopolymer, which promoted vesicle rupture. These results suggest that the fabrication of inert nanostructures and the site-selective modification of solid surfaces to induce vesicle rupture may be essential in the construction of tLBRM nano(submicro) arrays using stepwise self-assembly.
Cloning and characterization of an endothelin-3 specific receptor (ETC receptor) from Xenopus laevis dermal melanophores. (1993)

We report here the presence of a receptor specific for endothelin-3 (termed ETc receptor or ETcR) on Xenopus laevis dermal melanophores. Activation of ETcR causes the dispersion of the pigment granules within the melanophores. The EC50 for ET-3 to induce the pigment dispersion is 24 +/- 7 nM, compared to greater than 10 microM for both ET-1 and -2. This effect desensitizes in a manner that is dependent on both time and the concentration of ET-3 used to stimulate the cells. A cDNA encoding for ETcR was isolated by a polymerase chain reaction-mediated DNA amplification strategy using degenerate oligonucleotides prepared based on conserved regions of other known G-protein-coupled receptor sequences and by the subsequent screening of a frog melanophore cDNA library. The cloned cDNA consists of 2,240 nucleotides, with an open reading frame coding for 444 amino acids containing an initial 20-amino acid signal sequence. The predicted mature peptide consists of 424 amino acids with a heptahelical structure common to the G-protein-coupled receptor surperfamily. Its deduced amino acid sequence is 47 and 52% identical to ETA and ETB receptors, respectively, while ETA and ETB are 48% identical to each other. Expression of cDNA in HeLa cells, which do not contain endothelin receptors, enables the cells to specifically bind [125I]ET-3. Competition binding experiments performed on HeLa cells transiently expressing pETc show that the apparent Ki values for ET-3 and ET-1 to displace [125I]ET-3 are 45.5 +/- 16 and 114 +/- 22 nM, respectively.
Mechanism of Gram-positive Shock: Identification of Peptidoglycan and Lipoteichoic Acid Moieties Essential in the Induction of Nitric Oxide Synthase, Shock, and Multiple Organ Failure (1998)

The incidence of septic shock caused by gram-positive bacteria has risen markedly in the last few years. It is largely unclear how gram-positive bacteria (which do not contain endotoxin) cause shock and multiple organ failure. We have discovered recently that two cell wall fragments of the pathogenic gram-positive bacterium Staphylococcus aureus, lipoteichoic acid (LTA) and peptidoglycan (PepG), synergize to cause the induction of nitric oxide (NO) formation, shock, and organ injury in the rat. We report here that a specific fragment of PepG, N-acetylglucosamine-beta-[1--> 4]-N-acetylmuramyl-L-alanine-D-isoglutamine, is the moiety within the PepG polymer responsible for the synergism with LTA (or the cytokine interferon gamma) to induce NO formation in the murine macrophage cell line J774.2. However, this moiety is also present in the PepG of the nonpathogenic bacterium Bacillus subtilis. We have discovered subsequently that S. aureus LTA synergizes with PepG from either bacterium to cause enhanced NO formation, shock, and organ injury in the rat, whereas the LTA from B. subtilis does not synergize with PepG of either bacterium. Thus, we propose that the structure of LTA determines the ability of a particular bacterium to cause shock and multiple organ failure (pathogenicity), while PepG acts to amplify any response induced by LTA.
Location of cAMP-Dependent Protein Kinase Type I with the TCR-CD3 Complex (1994)

Selective activation of cyclic adenosine 3',5'-monophosphate (cAMP)-dependent protein kinase type I (cAKI), but not type II, is sufficient to mediate inhibition of T cell replication induced through the antigen-specific T cell receptor-CD3 (TCR-CD3) complex. Immunocytochemistry and immunoprecipitation studies of the molecular mechanism by which cAKI inhibits TCR-CD3-dependent T cell replication demonstrated that regulatory subunit I alpha, along with its associated kinase activity, translocated to and interacted with the TCR-CD3 complex during T cell activation and capping. Regulatory subunit II alpha did not. When stimulated by cAMP, the cAKI localized to the TCR-CD3 complex may release kinase activity that, through phosphorylation, might uncouple the TCR-CD3 complex from intracellular signaling systems.
The Roles of Interleukin-6 in the Pathogenesis of Rheumatoid Arthritis (2011)

Several clinical studies have demonstrated that the humanized anti-interleukin-6 (IL-6) receptor antibody tocilizumab (TCZ) improves clinical symptoms and prevents progression of joint destruction in rheumatoid arthritis (RA). However, the precise mechanism by which IL-6 blockade leads to the improvement of RA is not well understood. IL-6 promotes synovitis by inducing neovascularization, infiltration of inflammatory cells, and synovial hyperplasia. IL-6 causes bone resorption by inducing osteoclast formation via the induction of RANKL in synovial cells, and cartilage degeneration by producing matrix metalloproteinases (MMPs) in synovial cells and chondrocytes. Moreover, IL-6 is involved in autoimmunity by altering the balance between T(h)17 cells and T(reg). IL-6 also acts on changing lipid concentrations in blood and on inducing the production of hepcidin which causes iron-deficient anemia. In conclusion, IL-6 is a major player in the pathogenesis of RA, and current evidence indicates that the blockade of IL-6 is a beneficial therapy for RA patients.
Cloning of a cDNA Encoding a Novel Putative G-Protein–Coupled Receptor Expressed in Specific Rat Brain Regions (1991)

A cDNA clone encoding a novel putative G-protein-coupled receptor was isolated from a rat brain cDNA library using a PCR-amplified cDNA fragment as a hybridization probe. The 3,615-bp-long nucleotide sequence predicts a single open reading frame of 1,173 bp coding for 391 amino acids, giving a calculated molecular weight of 42.75 kD. The amino acid sequence shares features common to many other receptors, including the seven membrane-spanning hydrophobic regions and putative asparagine-linked glycosylation and phosphorylation sites. Northern blot analysis reveals that a corresponding approximately 3.7-kb mRNA is expressed in specific brain regions such as hypothalamus, cortex, hippocampus, and thalamus but not in other organs analyzed. Although the ligand for this receptor has not yet been identified, it shares some similarities with the vascular type-1 angiotensin II receptor, the vasoactive intestinal peptide (VIP) receptor, and the chemotactic receptors for human C5a anaphylatoxin and the formyl peptide fMet-Leu-Phe.
Dynamics of Polymer Translocation through Nanopores: Theory Meets Experiment (2006)

The dynamics of translocation of polymer molecules through nanopores is investigated via molecular dynamics. We find that an off-lattice minimalist model of the system is sufficient to reproduce quantitatively all the experimentally observed trends and scaling behavior. Specifically, simulations show (i) two translocation regimes depending on the ratio of pore and polymer length, (ii) two different regimes for the probability of translocation depending on applied voltage, (iii) an exponential dependence of translocation velocity upon applied voltage, and (iv) an exponential decrease of the translocation time with temperature. We also propose a simple theoretical explanation of each of the observed trends within a free energy landscape framework.