gebhart/patrepeval huggingface dataset:
Neurotransmitter Methods (1997)

Neurotransmitter Methods is intended as a bench-side companion for researchers who seek to identify, locaHze, or measure neurotransmitters and/or to identify sites of neurotransmitter action. Each method is detailed in a user-friendly "recipe" format and the protocols are accompanied by extensive notes to high­ light and explain crucial steps. Approaches utilizing an incredibly diverse array of modem techniques are presented: methods including HPLC, histochemistry, immunocytochemistry, in situ hybridization, mass spectrometry, microdialysis, and electrochemistry all make at least one appearance. In addition, protocols for associated methodologies, including the production of brain slices, dissociated neurons, synaptosomes/synaptoneurosomes, and neuronal plasma membranes are presented. Methods applicable to most of the recognized chemical types of neu­ rotransmitter are to be found and, although you may find absent any mention of your favorite neurotransmitter, many of the protocols are sufficiently general to be adapted to alternative uses. So, how does this book contribute usefiilly to the horde of methods volumes stampeding across our bookshelves? 1 hope that the strength oiNeurotransmitter Methods lies in the variety of its content. The book provides in a single volume an array of techniques that could take a researcher from selection and preparation of a tissue source through to identification and measurement of neurotransmitter content and even onto characterization of neurotransmitter sites of action. Furthermore, the diversity of approaches presented reflects the need for today's bench neuroscientist to be a bit of a "jack (or a "jill"!) of all trades
Role of Endogenous Arginine Vasopressin in Potentiating Corticotropin-Releasing Hormone-Stimulated Corticotropin Secretion in Man* (1988)

Exogenously administered vasopressin (VP) augments ACTH secretion stimulated by CRH. This study was performed to elucidate the role of endogenous VP in potentiating CRH-induced ACTH secretion in man. Synthetic human CRH (100 micrograms) was injected iv into seven normal men after they had been water loaded (20 mL/kg; 60 and 30 min before CRH injection; WL-CRH test) and water deprived (water restriction for 18 h before CRH injection; WD-CRH test). Blood samples were obtained before and 5, 15, 30, 60, 90, and 120 min after CRH injection at 0900 h for determination of plasma ACTH, cortisol, arginine vasopressin (AVP), CRH, and catecholamine levels and osmolality. Urine was obtained immediately before and 120 min after CRH injection for determination of osmolality. The mean plasma AVP levels were significantly higher during the WD-CRH test [1.8 +/- 0.4 (+/- SE) to 1.9 +/- 0.4 pmol/L] than during the WL-CRH test (0.6 +/- 0.1 to 0.9 +/- 0.1 pmol/L). The mean plasma ACTH and cortisol levels rose significantly from basal (4.5 +/- 0.6 pmol/L and 320 +/- 20 nmol/L, respectively) to peak values of 14.0 +/- 2.1 pmol/L at 30 min and 700 +/- 50 nmol/L at 60 min, respectively, during the WD-CRH test. During the WL-CRH test, mean basal plasma ACTH and cortisol levels were 3.5 +/- 0.7 pmol/L and 420 +/- 50 nmol/L, respectively, and reached peak values of 7.7 +/- 1.1 pmol/L at 60 min and 550 +/- 40 nmol/L at 30 min, respectively. Both the mean peak levels and integrated ACTH and cortisol responses were significantly higher during the WD-CRH than during the WL-CRH test. There was no significant difference between the plasma CRH and catecholamine concentrations in both tests. These results suggest that endogenous AVP potentiates CRH-stimulated ACTH secretion and, thus, plays a physiologically significant role in regulating CRH-stimulated ACTH and cortisol secretion in man.
Intracellular Delivery of a Proapoptotic Peptide via Conjugation to a RAFT Synthesized Endosomolytic Polymer (2009)

Peptides derived from the third B-cell lymphoma 2 (Bcl-2) homology domain (BH3) can heterodimerize with antiapoptotic Bcl-2 family members to block their activity and trigger apoptosis. Use of these peptides presents a viable anticancer approach, but delivery barriers limit the broad application of intracellular-acting peptides as clinical therapeutics. Here, a novel diblock copolymer carrier is described that confers desirable pharmaceutical properties to intracellular-acting therapeutic peptides through site-specific molecular conjugation. This polymer was prepared using reversible addition-fragmentation chain transfer (RAFT) to form a pyridyl disulfide end-functionalized, modular diblock copolymer with precisely controlled molecular weight (M(n)) and low polydispersity (PDI). The diblock polymer (M(n) 19,000 g/mol, PDI 1.27) was composed of an N-(2-hydroxypropyl) methacrylamide (HPMA) first block (M(n) 13,800 g/mol, PDI 1.13) intended to enhance water solubility and circulation time. The second polymer block was a pH-responsive composition designed to enhance endosomal escape and consisted of equimolar quantities of dimethylaminoethyl methacrylate (DMAEMA), propylacrylic acid (PAA), and butyl methacrylate (BMA). A hemolysis assay indicated that the diblock polymer undergoes a physiologically relevant pH-dependent switch from a membrane inert (1% hemolysis, pH 7.4) to a membrane disruptive (61% hemolysis, pH 5.8) conformation. Thiol-disulfide exchange reactions were found to efficiently produce reversible polymer conjugates (75 mol % peptide reactivity with polymer) with a cell-internalized proapoptotic peptide. Microscopy studies showed that peptide delivered via polymer conjugates effectively escaped endosomes and achieved diffusion into the cytosol. Peptide-polymer conjugates also produced significantly increased apoptotic activity over peptide alone in HeLa cervical carcinoma cells as found using flow cytometric measurements of mitochondrial membrane depolarization (2.5-fold increase) and cell viability tests that showed 50% cytotoxicity after 6 h of treatment with 10 muM peptide conjugate. These results indicate that this multifunctional carrier shows significant promise for proapoptotic peptide cancer therapeutics and also as a general platform for delivery of peptide drugs with intracellular targets.
Template Secondary Structure Promotes Polymerase Jumping During PCR Amplification (1999)

Pairs of primers flanking known miniTn10 transposon insertion sites were used to confirm the presence of the transposon in DNA isolated from Legionella pneumophila mutants. It was expected that the polymerase chain reaction products derived from the mutant template would be larger than those from the wild-type (WT) template due to the presence of the 1.8-kb transposon. Instead, it was observed that the mutant template yielded a product of almost the same size as that yielded by WT template. We present evidence to indicate that the aberrant product from the mutant template is a direct result of secondary structure of the template resulting from an inverted repeat sequence present in the miniTn10 transposon.
Scanning polyhedra with DO loops (1991)

Article Scanning polyhedra with DO loops Share on Authors: Corinne Ancourt View Profile , François Irigoin View Profile Authors Info & Claims PPOPP '91: Proceedings of the third ACM SIGPLAN symposium on Principles and practice of parallel programmingApril 1991 Pages 39–50https://doi.org/10.1145/109625.109631Online:01 April 1991Publication History 253citation825DownloadsMetricsTotal Citations253Total Downloads825Last 12 Months27Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Transcriptional control and the role of silencers in transcriptional regulation in eukaryotes (1998)

Mechanisms controlling transcription and its regulation are fundamental to our understanding of molecular biology and, ultimately, cellular biology. Our knowledge of transcription initiation and integral factors such as RNA polymerase is considerable, and more recently our understanding of the involvement of enhancers and complexes such as holoenzyme and mediator has increased dramatically. However, an understanding of transcriptional repression is also essential for a complete understanding of promoter structure and the regulation of gene expression. Transcriptional repression in eukaryotes is achieved through 'silencers', of which there are two types, namely 'silencer elements' and 'negative regulatory elements' (NREs). Silencer elements are classical, position-independent elements that direct an active repression mechanism, and NREs are position-dependent elements that direct a passive repression mechanism. In addition, 'repressors' are DNA-binding trasncription factors that interact directly with silencers. A review of the recent literature reveals that it is the silencer itself and its context within a given promoter, rather than the interacting repressor, that determines the mechanism of repression. Silencers form an intrinsic part of many eukaryotic promoters and, consequently, knowledge of their interactive role with enchancers and other transcriptional elements is essential for our understanding of gene regulation in eukaryotes.
The Role of RIB Infarcts in the Acute Chest Syndrome of Sickle Cell Diseases (2001)

The acute chest syndrome is a generic term for pulmonary complications of sickle cell diseases with heterogeneous etiologies that include pneumonia, vaso-occlusion of pulmonary arterioles, rib infarction, and fat embolism syndrome. My review summarizes these etiologies, the evidence, and pathophysiology supporting the hypothesis that infarction of segments of ribs by the same vaso-occlusive process responsible for the acute episodes of pain (characteristic of the sickle cell diseases) is often involved in the acute chest structure. Inflammation associated with the infarct then causes splinting, hypoventilation, and hypoxia and further vaso-occlusion. The relationship with adult respiratory distress syndrome and fat embolism is also discussed. Use of the incentive spirometer combined with effective analgesia when chest pain is present is advocated for prevention of the pulmonary infiltrates. Newer understanding of the role of nitric oxide in regulating oxygen transport and its relationship to blood transfusions used in therapy of the acute chest syndrome are discussed.
Paclitaxel And Docetaxel Resistance: Molecular Mechanisms and Development of New Generation Taxanes (2007)

Taxanes represent one of the most promising classes of anticancer agents. Unfortunately, their clinical success has been limited by the insurgence of cellular resistance, mainly mediated by the expression of the MDR phenotype or by microtubule alterations. However, the remarkable relevance of paclitaxel and docetaxel in clinical oncology stimulated intensive efforts in the last decade to identify new derivatives endowed with improved activities towards resistant tumor cells, resulting in a huge number of novel natural and synthetic taxanes. Among them, several structurally different derivatives were found to exhibit a promising behavior against the MDR phenotype in terms of either MDR inhibiting properties, or enhanced cytotoxicity compared to parental drugs, or both. On the other hand, only in more recent years have the first taxanes retaining activity against resistant cancer cells bearing alterations of the tubulin/microtubule system emerged. This review describes the main molecular mechanisms of resistance to paclitaxel and docetaxel identified so far, focusing on the advances achieved in the development of new taxanes potentially useful for the treatment of resistant tumors.
Removal of sparse-excitation artifacts in CELP (2002)

In CELP, the use of codebooks with entries with only a few non-zero samples provides high speech quality and facilitates fast computation. With decreasing bit-rate, the intervals between the pulses increase, and the quality of the reconstructed signal begins to suffer from a particular type of artifact, which is strongest for noise-like segments. In this paper we describe experiments which show that the perceived artifacts are mainly concentrated at frequencies above 3 kHz, and this is consistent with our understanding of auditory theory. Our analysis leads to simple strategies to eliminate the artifacts, even at lower bit rates. We describe both a non-adaptive and an adaptive post-processing method to remove the artifacts. The methods are demonstrated to be efficient when used in the ACELP algorithm. A closed-loop method for ACELP is also described.
Exogenous Hydrogen Sulfide Inhibits Superoxide Formation, NOX-1 Expression and Rac<sub>1</sub> Activity in Human Vascular Smooth Muscle Cells (2008)

The activity of NADPH oxidase (NOX) is blocked by nitric oxide (NO). Hydrogen sulfide (H(2)S) is also produced by blood vessels. It is reasonable to suggest that H(2)S may have similar actions to NO on NOX. In order to test this hypothesis, the effect of sodium hydrosulfide (NaHS) on O(2)(-) formation, the expression of NOX-1 (a catalytic subunit of NOX) and Rac(1) activity (essential for full NOX activity) in isolated vascular smooth muscle cells (hVSMCs) was investigated. hVSMCs were incubated with the thromboxane A(2) analogue U46619 +/- NaHS for 1 or 16 h, and O(2)(-) formation, NOX-1 expression and Rac(1) activity were assessed. The possible interaction between H(2)S and NO was also studied by using an NO synthase inhibitor, L-NAME, and an NO donor, DETA-NONOate. The role of K(ATP) channels was studied by using glibenclamide. NaHS inhibited O(2)(-) formation following incubation of 1 h (IC(50), 30 nM) and 16 h (IC(50), 20 nM), blocked NOX-1 expression and inhibited Rac(1) activity. These inhibitory effects of NaHS were mediated by the cAMP-protein-kinase-A axis. Exogenous H(2)S prevents NOX-driven intravascular oxidative stress through an a priori inhibition of Rac(1) and downregulation of NOX-1 protein expression, an effect mediated by activation of the adenylylcyclase-cAMP-protein-kinase-G system by H(2)S.
Synthesis of (3S,5R)-Carbapenam-3-carboxylic Acid and Its Role in Carbapenem Biosynthesis and the Stereoinversion Problem (2003)

(5R)-Carbapenem-3-carboxylic acid is the simplest structurally among the naturally occurring carbapenem beta-lactam antibiotics. It is the produced from (3S,5S)-carbapenam-3-carboxylic acid utilizing a remarkable stereoinversion/desaturation process by CarC (carbapenem synthase), an alpha-ketoglutarate dependent non-heme iron oxygenase. In this communication, we demonstrate for the first time that the epimeric (3S,5R)-carbapenam-3-carboxylic acid is an intermediate in the overall catalytic cycle to the carbapenem antibiotic. The role of alpha-ketoglutarate in the stereoinversion and desaturation processes is also examined.
Prostate cancer targeting motifs: Expression of ανβ3, neurotensin receptor 1, prostate specific membrane antigen, and prostate stem cell antigen in human prostate cancer cell lines and xenografts (2011)

The regulation of mRNA and protein expression of the cell-surface target proteins α(ν) β(3), NTSR1, PSMA, and PSCA, in prostate cancer cells with different tumorigenic potential, was influenced by factors of the microenvironment, differing between cell cultures and murine xenotransplants. Integrin α(ν) β(3), NTRS1 and PSCA mRNA expression increased with tumorigenic potential, but mRNA expression levels for these proteins do not translate directly to equivalent expression levels of membrane bound protein.
Comparative Study of 2D and 3D Micromechanical Discrete Element Modeling of Indirect Tensile Tests for Asphalt Mixtures (2018)

Based on imaging and the discrete element method (DEM), this study mainly aims to compare the two-dimensional (2D) and three-dimensional (3D) micromechanical modeling of the indirect tensile (IDT) tests for asphalt mixtures. The 2D and 3D microstructure-based discrete element models for the IDT test were established by a discrete element program. The strengths and stresses at low temperatures were simulated based on these models. The obtained results were compared and verified by an actual IDT test. The effects of stiffness and bond strength on the 3D simulation were also analyzed. Results show that the 3D discrete element simulation results are more stable and more reliable than the 2D discrete element simulation results. The model parameters influence the 3D discrete element simulation results, and different model parameters influence the strength and stress with respect to the IDT test at low temperatures to different extents.
New route to monoorganotin oxides and alkoxides from trialkynylorganotins (1998)

Functional monoorganotin oxides and alkoxides are synthesised in high yield by hydrolysis or alcoholysis of the corresponding trialkynylorganotins; the hydrolytic behaviour of trialkynylorganotins is the same as for trialkoxyorganotins.
Codon usage in twelve species of Drosophila (2007)

Overall, these results suggest that natural selection has acted on codon usage in the genus Drosophila, at least often enough to leave a footprint of selection in modern genomes. However, there is evidence in the data that random forces (drift and mutation) have also left patterns in the data, especially in genes under weak selection for codon usage for example genes in regions of low recombination. The documentation of codon usage patterns in each of these twelve genomes also aids in ongoing annotation efforts.
New Genes from Old: Redeployment of dUTPase by Herpesviruses (2005)

Published work (D. J. McGeoch, Nucleic Acids Res. 18:4105-4110, 1990; J. E. McGeehan, N. W. Depledge, and D. J. McGeoch, Curr. Protein Peptide Sci. 2:325-333, 2001) has indicated that evolution of dUTPase in the class of herpesviruses that infect mammals and birds involved capture of a host gene followed by a duplication event that resulted in a coding region comprising two fused dUTPase domains. Some of the conserved residues required for enzyme activity were then lost, resulting in a dUTPase containing a single active site with different elements contributed by each half of the protein. Further conserved residues were lost in one subfamily (the Betaherpesvirinae), yielding a protein that is related to herpesvirus dUTPases but has a different and as yet unrecognized function. Evidence from sequence similarities and structural predictions now indicates that several additional genes were derived from the herpesvirus dUTPase gene, probably by duplication. These are UL31, UL82, UL83, and UL84 in human cytomegalovirus (and counterparts in other members of the Betaherpesvirinae) and ORF10 and ORF11 in human herpesvirus 8 (and counterparts in other members of the Gammaherpesvirinae). The findings clarify the evolutionary history of these genes and provide novel insights for structural and functional studies.
The Visualization Toolkit: An Object-Oriented Approach to 3-D Graphics (1997)

From the Publisher:
Visualization is a part of every day life. From weather map generation of financial modelling to MRI technology in medicine to 3D graphics used in movies like Jurassic Park, examples of visualization abound. The book/CD package offers readers the opportunity to practice visualization using a complete C++ programming environment developed by the authors.
Maximal Flow Through a Network (1956)

Introduction. The problem discussed in this paper was formulated by T. Harris as follows: “Consider a rail network connecting two cities by way of a number of intermediate cities, where each link of the network has a number assigned to it representing its capacity. Assuming a steady state condition, find a maximal flow from one given city to the other.”
Metabolic engineering of proanthocyanidins by ectopic expression of transcription factors in Arabidopsis thaliana (2005)

Genetic transformation of Arabidopsis thaliana with the Arabidopsis TT2 MYB transcription factor resulted in ectopic expression of the BANYULS gene, encoding anthocyanidin reductase, AHA10 encoding a P-type proton-pump and TT12 encoding a transporter involved in proanthocyanidin biosynthesis. When coupled with constitutive expression of PAP1, a positive regulator of anthocyanin biosynthesis, TT2 expression in Arabidopsis led to accumulation of proanthocyanidins, but only in a subset of cells in which the BANYULS promoter is naturally expressed. Ectopic expression of the maize Lc MYC transcription factor weakly induced AHA10 but did not induce BANYULS, TT12 or accumulation of proanthocyanidins. However, high-level combined expression of TT2, PAP1 and Lc resulted in proanthocyanidin synthesis throughout young leaves and cotyledons, followed by death of the plants 1 to 2 weeks after germination. We discuss these results in relation to engineering proanthocyanidins to improve the quality of food and forage plants.
Lipids and Lipoprotein Changes After Heart and Liver Transplantation in a Patient with Homozygous Familial Hypercholesterolemia (1988)

Changes in lipids and lipoprotein fractions were studied 6 months after a combined heart and liver transplantation in a patient with terminal ischemic heart disease due to homozygous familial hypercholesterolemia. The double transplant was followed by striking decreases in total and low-density-lipoprotein cholesterol levels (-71% and -79%) and content of apolipoprotein B in the low-density-lipoprotein fraction (-74%). There was also an increase in high-density-lipoprotein cholesterol (+7.8%). These changes are greater than those reported with portacaval shunt or plasma exchange. Liver transplantation may be considered in selected patients with homozygous familial hypercholesterolemia.
Synthesis Of Labeled Glycosyl Phosphatidyl Inositol (GPI) Anchors (1999)

The exploration of the molecular and structural basis for the sorting of GPI-anchored proteins is based on labeled partial structures of GPI′s which can be incorporated into the GPI anchor biosynthesis and cellular transport systems. To this end, from mannosyl donor 6 and the D-glucosaminyl-(1→6)-D-myo-inositol derivative 7 as acceptor, the pseudotrisaccharide 8 was prepared. Compound 8 was transformed into the GPI partial structures 5a,b which contain the pseudotrisaccharide ligated to two different phosphatidyl residues. Compounds 5a,b have Boc protection at the 2-amino group of the glucosamine residue (2b-position) and a free amino group at the 6b-position. The 6b-amino group was used for the ligation of the 3-(7-nitrobenzofurazan-4-yl)-aminopropanoyl group as a fluorescent label, the 5-azido-2-nitrobenzoyl and 4-azidophenylaminothiocarbonyl groups as photolabels, and the 4-azido-2-hydroxybenzoyl group as a radiolabel after the introduction of radioactive iodine by an electrophilic aromatic substitution. Thus, after acid-catalyzed removal of the protective groups, the unprotected target molecules 1–4 were obtained.