gebhart/patrepeval huggingface dataset:
A high density assay format for the detection of novel cytotoxic agents in large chemical libraries (2008)

In response to the need for inexpensive high throughput assays for anti-cancer drug screening, a 1536-well microtiter plate based assay utilizing the Alamar Blue fluorescent dye as a measure of cellular growth was validated in 10 microL assay volume. Its robustness was assessed in a screen against a library of 2000 known bioactives; with an overall Z' value of 0.89 for assay robustness, several known cytotoxic agents were identified including and not limited to anthracyclines, cardiac glycosides, gamboges, and quinones. To further test the sensitivity of the assay, IC50 determinations were performed in both 384-well and 1536-well formats and the obtained results show a very good correlation between the two density formats. These findings demonstrate that this newly developed assay is simple to set up, robust, highly sensitive and inexpensive. It could potentially provide a rapid way to screen established and primary tumor cell lines against large chemical libraries.
LEF1/β-Catenin Complex Regulates Transcription of the Cav3.1 Calcium Channel Gene (Cacna1g) in Thalamic Neurons of the Adult Brain (2010)

β-Catenin, together with LEF1/TCF transcription factors, activates genes involved in the proliferation and differentiation of neuronal precursor cells. In mature neurons, β-catenin participates in dendritogenesis and synaptic function as a component of the cadherin cell adhesion complex. However, the transcriptional activity of β-catenin in these cells remains elusive. In the present study, we found that in the adult mouse brain, β-catenin and LEF1 accumulate in the nuclei of neurons specifically in the thalamus. The particular electrophysiological properties of thalamic neurons depend on T-type calcium channels. Cav3.1 is the predominant T-type channel subunit in the thalamus, and we hypothesized that the Cacna1g gene encoding Cav3.1 is a target of the LEF1/β-catenin complex. We demonstrated that the expression of Cacna1g is high in the thalamus and is further increased in thalamic neurons treated in vitro with LiCl or WNT3A, activators of β-catenin. Luciferase reporter assays confirmed that the Cacna1G promoter is activated by LEF1 and β-catenin, and footprinting analysis revealed four LEF1 binding sites in the proximal region of this promoter. Chromatin immunoprecipitation demonstrated that the Cacna1g proximal promoter is occupied by β-catenin in vivo in the thalamus, but not in the hippocampus. Moreover, WNT3A stimulation enhanced T-type current in cultured thalamic neurons. Together, our data indicate that the LEF1/β-catenin complex regulates transcription of Cacna1g and uncover a novel function for β-catenin in mature neurons. We propose that β-catenin contributes to neuronal excitability not only by a local action at the synapse but also by activating gene expression in thalamic neurons.
The Tetrahymena intervening sequence ribonucleic acid enzyme is a phosphotransferase and an acid phosphatase (1986)

A shortened form of the Tetrahymena intervening sequence (IVS) RNA acts as an enzyme, catalyzing nucleotidyl transfer and hydrolysis reactions with oligo(cytidylic acid) substrates [Zaug, A. J., & Cech, T. R. (1986) Science (Washington, D.C.) 231, 470-475]. These reactions involve phosphodiester substrates. We now show that the same enzyme has activity toward phosphate monoesters. The 3'-phosphate of C5p or C6p is transferred to the 3'-terminal guanosine of the enzyme. The pH dependence of the reaction (optimum at pH 5) indicates that the enzyme has activity toward the dianion and much greater activity toward the monoanion form of the 3'-phosphate of the substrate. Phosphorylation of the enzyme is reversible by C5-OH and other oligo(pyrimidines) such as UCU-OH. Thus, the RNA enzyme acts as a phosphotransferase, transferring the 3'-terminal phosphate of C5p to UCU-OH with multiple turnover. At pH 4 and 5, the phosphoenzyme undergoes slow hydrolysis to yield inorganic phosphate. Thus, the enzyme has acid phosphatase activity. The RNA enzyme dephosphorylates oligonucleotide substrates with high sequence specificity, which distinguishes it from known protein enzymes.
Two tumor necrosis factor-binding proteins purified from human urine. Evidence for immunological cross-reactivity with cell surface tumor necrosis factor receptors. (1990)

Two proteins which specifically bind tumor necrosis factor (TNF) were isolated from human urine by ligand (TNF)-affinity purification, followed by reversed phase high performance liquid chromatography. The molecular weights of the two proteins, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, were similar (about 30,000). Both proteins provided protection against the cytocidal effect of TNF in vitro and both bound TNF-alpha more effectively than TNF-beta. Antibodies raised against each of the proteins had an inhibitory effect on the binding of TNF to cells, suggesting that both proteins are structurally related to the TNF receptors. However, the two proteins differed in NH2-terminal amino acid sequences: Asp-Ser-Val-Cys-Pro- in one and Val-Ala-Phe-Thr-Pro- in the other. The NH2-terminal sequence of the former protein was invariable, while that of the latter was truncated to varying degrees. The two proteins were also immunologically distinct. The relative efficacy of anti-sera against the two proteins in inhibiting the binding of TNF to cells varied markedly from one line of cells to another. Evidence has been presented recently for the existence of two distinct molecular species of cell surface receptors for TNF and for differential expression of those two receptors by cells of different lines. The findings presented in this study are consistent with the notion that the urinary TNF-binding proteins constitute soluble forms of the two molecular species of the cell surface TNF receptors.
Isoosmolar Enemas Demonstrate Preferential Gastrointestinal Distribution, Safety, and Acceptability Compared with Hyperosmolar and Hypoosmolar Enemas as a Potential Delivery Vehicle for Rectal Microbicides (2013)

Rectally applied antiretroviral microbicides for preexposure prophylaxis (PrEP) of HIV infection are currently in development. Since enemas (rectal douches) are commonly used by men who have sex with men prior to receptive anal intercourse, a microbicide enema could enhance PrEP adherence by fitting seamlessly within the usual sexual practices. We assessed the distribution, safety, and acceptability of three enema types-hyperosmolar (Fleet), hypoosmolar (distilled water), and isoosmolar (Normosol-R)-in a crossover design. Nine men received each enema type in random order. Enemas were radiolabeled [(99m)Tc-diethylene triamine pentaacetic acid (DTPA)] to assess enema distribution in the colon using single photon emission computed tomography/computed tomography (SPECT/CT) imaging. Plasma (99m)Tc-DTPA indicated mucosal permeability. Sigmoidoscopic colon tissue biopsies were taken to assess injury as well as tissue penetration of the (99m)Tc-DTPA. Acceptability was assessed after each product use and at the end of the study. SPECT/CT imaging showed that the isoosmolar enema had greater proximal colonic distribution (up to the splenic flexure) and greater luminal and colon tissue concentrations of (99m)Tc-DTPA when compared to the other enemas (p<0.01). Colon biopsies also showed that only the hyperosmolar enema caused sloughing of the colonic epithelium (p<0.05). In permeability testing, the hypoosmolar enema had higher plasma (99m)Tc-DTPA 24-h area under the concentration-time curve and peak concentration compared to the hyperosmolar and isoosmolar enemas, respectively. Acceptability was generally good with no clear preferences among the three enema types. The isoosmolar enema was superior or similar to the other enemas in all categories and is a good candidate for further development as a rectal microbicide vehicle.
Biological effects of enzymatic deprivation of L-methionine in cell culture and an experimental tumor. (1973)

Summary An enzyme, which degrades l-methionine to methanethiol, ammonia and α-ketobutyric acid (l-methionine-α-deamino-γ-mercaptomethane-lyase or l-methioninase), isolated from Clostridium sporogenes, was found to inhibit growth of P815 cell cultures and Walker carcinosarcoma 256 of the rat. Compared with a methionine-free diet, this enzyme had greater growth-inhibiting activity and yet resulted in negligible toxicity when evaluated by weight loss of the host. One hr after a single i.v. injection of 250 units of semipurified l-methioninase the plasma levels of methionine fell rapidly to below 8% of the control but recovered almost completely within 24 hr. The half-life of the active enzyme was about 4 hr. The ratios of maximal plasma levels of active enzyme after i.v., i.p., and s.c. injection of 250 units of the enzyme per kg were 100:30:2. The ratios of maximal levels (units/g tissue) reached in liver, kidney, and spleen after a single i.v. injection were 100:50:5.
Extracellular Superoxide Dismutase Overexpression Improves Behavioral Outcome from Closed Head Injury in the Mouse (2001)

Oxidative stress is known to play an important role in the response of brain to traumatic insults. We tested the hypothesis that increased extracellular superoxide dismutase (EC-SOD) expression can reduce injury in a mouse model of closed head injury. Neurologic, cognitive, and histologic outcomes were compared between transgenic mice exhibiting a fivefold increase in EC-SOD activity and wild-type littermate controls. Severe or moderate transcranial impact was induced in anesthetized and physiologically controlled animals. After severe impact, transgenic mice had better neurological outcome at 24 hr postinjury (p = 0.038). Brain water content was increased, but there was no difference between groups. Moderate impact resulted in predominantly mild neurologic deficits in both groups at both 24 hr and 14 days postinjury. Morris water maze performance, testing cognitive function at 14-17 days after trauma, was better in EC-SOD overexpressors (p = 0.018). No differences were observed between groups for histologic damage in hippocampal CA1 and CA3. We conclude that EC-SOD has a beneficial effect on behavioral outcome after both severe and moderate closed head injury in mice. Because EC-SOD is believed to be predominantly located in the extracellular space, these data implicate an adverse effect of extracellular superoxide anion on outcome from closed head injury.
Distribution and function of EGFR in human tissue and the effect of EGFR tyrosine kinase inhibition. (2004)

From immunohistochemical and ligand-binding studies, it is known that the epidermal growth factor receptor (EGFR), a member of the erbB family of receptors, is expressed in tissues of epithelial, mesenchymal and neuronal origin and plays a major role in normal cellular processes such as proliferation, differentiation and development. EGFR is highly expressed in a number of solid tumours and its expression correlates with tumour progression, resistance to chemotherapy and a poor prognosis; it is consequently an attractive target for the rational design of novel anticancer agents. Knowledge of the role of EGFR in normal tissues will help the understanding of the adverse events associated with such agents. Studies in knockout mice and preclinical toxicology studies have shown that the major effects of inhibiting the EGFR are skin and gastrointestinal toxicities. Clinical studies with inhibitors of EGFR, such as gefitinib, cetuximab and erlotinib, have shown a favourable adverse-event profile, primarily consisting of skin and gastrointestinal toxicities, as predicted from the mechanism-based effects observed in preclinical studies.
A Simple and Efficient Synthesis of RAFT Chain Transfer Agents via Atom Transfer Radical Addition−Fragmentation (2009)

A simple, versatile, and one-step atom transfer radical addition−fragmentation (ATRAF) technique is reported for the synthesis of chain transfer agents (CTA) containing dithio groups (dithiobenzoate, dithiocarbamate, and xanthate), with various alkyl substituents, in the presence of copper catalyst, alkyl halide, and bis(thiocarbonyl) disulfide. The ATRAF procedure is efficient and selective, leading to almost quantitative conversion of alkyl halide initiators and formation of CTAs in high isolated yield under stoichiometric conditions as well as in the presence of catalytic amounts of copper(I) species. The CTAs synthesized by this process were used for reversible addition−fragmentation chain transfer (RAFT) polymerizations of styrene and methyl methacrylate without any further column purification, producing well-controlled polymers with low polydispersity, thereby demonstrating the effectiveness of ATRAF. Moreover, a simple one-pot, two-step RAFT polymerization was successful, starting from CTA synthesized in situ via ATRAF, followed directly by the addition of a monomer.
Clinical comparison of preanaesthetic intramuscular medetomidine and dexmedetomidine in domestic sheep. (2001)

Medetomidine and its active d-enantiomer, dexmedetomidine, are highly selective alpha-2 agonists with potent sedative, anaesthetic-sparing and analgesic effects. These properties make them an ideal pre-anaesthetic medication for noxious surgical procedures. However, sheep can develop adverse hypoxaemic effects after intravenous alpha-2 agonists. Objective of the present study was to compare intramuscular injection of medetomidine or dexmedetomidine at equipotent doses as preanaesthetic medication prior to isoflurane anaesthesia in sheep. Nineteen healthy, adult, non-pregnant, female sheep of various breeds were used. The study was carried out as a randomised, blind trial. Group A received 15 micrograms/kg bwt dexmedetomidine and group B received 30 micrograms/kg bwt medetomidine intramuscularly (i.m.) 30 minutes prior to induction of anaesthesia. Anaesthesia was induced with ketamine (2.0 mg/kg bwt i.v.) and maintained with isoflurane in 100% oxygen. End expired anaesthetic concentration (FEiso), respiratory frequency (fR), direct arterial blood pressures and heart rates (HR) were measured. Arterial blood samples were taken at intervals. Data were averaged over time (sum of measurements/number of measurements) and tested for differences between groups by independent t-tests, and ANOVA for repeated measures followed by Bonferroni corrected t-tests. There were no differences in demographic data between the groups. Duration of anaesthesia [A: 170 (42) minutes, B: 144 (33) minutes] and duration of surgery [A: 92 (32) minutes, B: 85 (31) minutes] were similar in both groups. Average FEiso concentrations required to maintain a surgical plane of anaesthesia were not significantly different between groups [A: 0.82 (0.14)%; B: 1.00 (0.25)%]. Mean average fR, did not differ between groups [A: 31 (14), B: 37 (15)]. Heart rates were significantly lower in group B over the course of the anaesthesia. Mean arterial blood pressures (MAP) were not significantly different between the groups. The PaO2 was less variable in group A than in group B. Individual minimum values were 19.1 kPa and 7.9 kPa in group A and B, respectively. There were no significant differences in PaCO2 and paH between the groups and over time. In conclusion, intramuscular application of dexmedetomidine at 15 micrograms/kg bwt and medetomidine at 30 micrograms/kg bwt prior to isoflurane anaesthesia induced similar changes in clinically monitored cardiorespiratory parameters. The observed differences (heart rates, PaO2) between dexmedetomidine and medetomidine at the chosen dose relationship can be considered clinically not significant. At the chosen dose rates individual animals responded with a transient drop in blood oxygenation, therefore careful monitoring is required. In addition, in compromised sheep medetomidine and dexmedetomidine should be used carefully.
ChemInform Abstract: Atropisomerism and Axial Chirality in Heteroaromatic Compounds (2012)

Abstract Review: ca. 800 refs.
Apoptosis of uninfected cells induced by HIV envelope glycoproteins (2004)

Apoptosis, or programmed cell death, is a key event in biologic homeostasis but is also involved in the pathogenesis of many human diseases including human immunodeficiency virus (HIV) infection. Although multiple mechanisms contribute to the gradual T cell decline that occurs in HIV-infected patients, programmed cell death of uninfected bystander T lymphocytes, including CD4+ and CD8+ T cells, is an important event leading to immunodeficiency. The HIV envelope glycoproteins (Env) play a crucial role in transducing this apoptotic signal after binding to its receptors, the CD4 molecule and a coreceptor, essentially CCR5 and CXCR4. Depending on Env presentation, the receptor involved and the complexity of target cell contact, apoptosis induction is related to death receptor and/or mitochondria-dependent pathways. This review summarizes current knowledge of Env-mediated cell death leading to T cell depletion and clinical complications and covers the sometimes conflicting studies that address the possible mechanisms of T cell death.
Role of calcium-dependent protease(s) in globulization of isolated rat lens cortical fiber cells. (2001)

Elevation of calcium in the medium results in a proportionate increase in [Ca(2+)](i) and the proteolytic activity in isolated lens fiber cells. The increase in the proteolytic activity is accompanied by an increase in the rate of globulization of the fiber cells. Inhibition of the proteolytic activity by leupeptin increases T:(g) without affecting the gain in [Ca(2+)](i). These results suggest that globulization of isolated fiber cells in physiological salt solutions is mediated by Ca(2+)-activated protease(s).
Clinical Features of Nipah Virus Encephalitis among Pig Farmers in Malaysia (2000)

Nipah virus causes a severe, rapidly progressive encephalitis with a high mortality rate and features that suggest involvement of the brain stem. The infection is associated with recent contact with pigs.
Osteopontin is a ligand for the α4β1 integrin (1998)

Recent work has shown that osteopontin expression is upregulated at sites of cardiovascular injury. It has been hypothesized that osteopontin provides an adhesive matrix for endothelial and smooth muscle cells during remodeling of the vascular wall following injury. Osteopontin has also been found to be synthesized by monocytes and macrophages within injury sites. Here, we present data showing that osteopontin can promote leukocyte adhesion through the alpha4beta1 integrin. In the presence of physiologic concentrations of Mg2+ and Ca2+, osteopontin purified from bovine milk promoted cell-substrate adhesion of HL-60 and Ramos cells, two model leukocyte cell lines. As with other adhesive ligands, adhesion to osteopontin required leukocyte activation. Under these conditions, no adhesion to control substrates such as bovine serum albumin was observed. Leukocyte adhesion was inhibited by anti-integrin antibodies directed at either the alpha4 or beta1 integrin subunits but not by control antibodies directed to other integrins. Further adhesion experiments revealed that leukocyte binding to osteopontin was completely inhibited by an alpha4beta1-binding peptide containing the leucine-aspartate-valine (LDV) sequence, while a control, non-binding peptide containing leucine-glutamate-valine (LEV) had minimal effects. Affinity chromatography using either surface labeled HL-60 or Ramos cell extracts revealed that the alpha4beta1 integrin specifically bound to osteopontin. Immunoprecipitation of eluted fractions from these columns positively identified the alpha4beta1 integrin. In order to localize potential alpha4beta1-binding sites within osteopontin, the protein was proteolytically cleaved with thrombin. A 30 kDa N-terminal osteopontin fragment purified using fast protein liquid chromatography promoted alpha4beta1 dependent leukocyte adhesion in a manner similar to that of the intact protein. These data collectively demonstrate that the alpha4beta1 integrin is a new adhesion receptor for osteopontin and that an alpha4beta1 binding site exists in the NH2-terminal thrombin fragment of osteopontin.
The purinosome, a multi-protein complex involved in the de novo biosynthesis of purines in humans (2013)

Purine nucleotides are ubiquitous molecules that play vital roles in all kingdoms of life, not only as components of nucleic acids, but also participating in signaling and energy storage. Cellular pools of purines are maintained by the tight control of several complementary and sometimes competing processes including de novo biosynthesis, salvage and catabolism of nucleotides. While great strides have been made over the past sixty years in understanding the biosynthesis of purines, we are experiencing a renaissance in this field. In this feature article we discuss the most recent discoveries relating to purine biosynthesis, with particular emphasis upon the dynamic multi-protein complex called the purinosome. In particular we highlight advances made towards understanding the assembly, control and function of this protein complex and the attempts made to exploit this knowledge for drug discovery.
T Cell-specific Expression of the MurineCD3δ Promoter (2002)

T cell-specific expression of human and mouse CD3delta is known to be governed by an enhancer element immediately downstream from the gene. Here we demonstrate by transgenic and in vitro studies that the murine CD3delta (mCD3delta) promoter prefers to be expressed in cells of the T lineage. Deletion analyses of a promoter segment (-401/+48 bp) followed by transient transfections indicate that upstream elements between -149 and -112 bp contribute to full expression of the gene. Furthermore, a core promoter region -37/+29 appears to contribute to a T cell specificity. Using substitution mutant scanning, four positive and one negative regulatory elements were found within the mCD3delta core promoter. The first two positive elements comprise two classical initiator-like sites, which recruit TFII-I, whereas a third contains a functional Ets binding site. Immediately adjacent to the observed transcription start site is a negative element that utilizes the transcription regulator YY1. The last positive regulatory element contains a potentially functional CREB binding site and the minor transcriptional start site. Because NERF-2, Elf-1, and Ets-1 are expressed preferentially in lymphocytes and because, in addition, YY1 represses the promoter activity strongly in non-T cells, we conclude that the combination of these transcription factors contributes to the T cell-specific expression pattern of mouse CD3delta.
The role of high-temperature island coalescence in the development of stresses in GaN films (2001)

The formation of dislocations and stress in GaN layers grown by metalorganic vapor phase epitaxy on sapphire is investigated with regard to the average grain diameter. The grain diameter was determined by monitoring the high-temperature GaN island coalescence process during growth using reflectometry. It is found that the density of edge threading dislocations decreases and the compressive stress measured after cooling to room temperature increases when the coalescence thickness and the grain diameter increase. The data are consistent with models of development of tensile stress due to island coalescence during growth.