gebhart/patrepeval huggingface dataset:
Flavopiridol Inactivates P-TEFb and Blocks Most RNA Polymerase II Transcription in Vivo (2001)

Flavopiridol (L86-8275, HMR1275) is a cyclin-dependent kinase (Cdk) inhibitor in clinical trials as a cancer therapy that has been recently shown to block human immunodeficiency virus Tat transactivation and viral replication through inhibition of positive transcription elongation factor b (P-TEFb). Flavopiridol is the most potent P-TEFb inhibitor reported and the first Cdk inhibitor that is not competitive with ATP. We examined the ability of flavopiridol to inhibit P-TEFb (Cdk9/cyclin T1) phosphorylation of both RNA polymerase II and the large subunit of the 5, 6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) sensitivity-inducing factor and found that the IC(50) determined was directly related to the concentration of the enzyme. We concluded that the flavonoid associates with P-TEFb with 1:1 stoichiometry even at concentrations of enzyme in the low nanomolar range. These results indicate that the apparent lack of competition with ATP could be caused by a very tight binding of the drug. We developed a novel immobilized P-TEFb assay and demonstrated that the drug remains bound for minutes even in the presence of high salt. Flavopiridol remained bound in the presence of a 1000-fold excess of the commonly used inhibitor DRB, suggesting that the immobilized P-TEFb could be used in a simple screening assay that would allow the discovery or characterization of compounds with binding properties similar to flavopiridol. Finally, we compared the ability of flavopiridol and DRB to inhibit transcription in vivo using nuclear run-on assays and concluded that P-TEFb is required for transcription of most RNA polymerase II molecules in vivo.
Antennas in Matter: Fundamentals, Theory, and Applications (1981)

The volume provides an introduction to antennas and probes embedded within or near material bodies such as the earth, the ocean, or a living organism. After a fundamental analysis of insulated and bare antennas, an advanced treatment of antennas in various media is presented, including a detailed study of the electromagnetic equations in homogeneous isotropic media, the complete theory of the bare dipole in a general medium, and a rigorous analysis of the insulated antenna as well as bare and insulated loop antennas. Finally, experimental models and measuring techniques related to antennas and probes in a general dissipative or dielectric medium are examined.
A trauma‐like elevation of plasma cytokines in humans in response to treadmill running (1998)

1. Elevated levels of cytokines, especially interleukin (IL)-6 and IL-1ra, can be measured in the plasma of athletes after exhaustive long term exercise. 2. The present study investigates the kinetics of several cytokines and chemokines in ten male athletes before, during and after 2.5 h of treadmill running at 75 % of maximal oxygen consumption (VO2,max). Blood was sampled before, every half-hour during running and every hour in the following 6 h recovery period. 3. The plasma concentration of IL-6 increased after 30 min of running, and peaked at the end of running with a 25-fold increase compared with the pre-exercise value. IL-1ra increased only after running, and peaked after 2 h of rest with an 18-fold increase compared with the pre-exercise value. No changes were found in the concentrations of IL-1beta, tumour necrosis factor (TNF)alpha, IL-15 and macrophage inflammatory protein (MIP)-1beta, and the concentrations of IL-8 and MIP-1alpha were below detection limits. 4. The results suggest that very early events in exercise trigger the release of IL-6, and that the cytokine response to exercise has similarities to that observed after trauma.
Growth of high quality Ge∕Si1−xGex on nano-scale patterned Si structures (2005)

Heteroepitaxial growth of thick (∼6μm) Ge∕3μm SixGe1−x layers on nano-scale patterned Si substrates has been investigated. These nm scale structures are fabricated using interferometric lithography with reactive ion and wet-chemical etching techniques. The quality of the growth on the nanopatterned substrates was compared to growth on planar substrates. The quality of the epitaxial layers was characterized using scanning electron microscopy, transmission electron microscopy, high-resolution x-ray diffraction and etch pit density measurements. We demonstrated the nanopatterned structures produce significantly superior quality heteroepitaxial epilayers in comparison with unpatterned Si surfaces. The dislocation density of Ge epilayers on the nanopatterned Si was ∼ three orders magnitude lower than on planar Si. Growth on nanopatterned surfaces also reduced surface roughness and eliminated crosshatch patterns characterstic of planar surfaces.
Using an Animal Model of Deficient Sensorimotor Gating to Study the Pathophysiology and New Treatments of Schizophrenia (1998)

Certain animal models can greatly enhance our understanding of the neurobiology of schizophrenia and can be used to predict the antipsychotic activity of compounds. Prepulse inhibition (PPI), the reduction in startle produced by a prepulse stimulus, is diminished in schizophrenia patients. Theoretically, deficient PPI in schizophrenia patients is a measure of the loss of sensorimotor gating that may lead to sensory flooding and cognitive fragmentation. In rats, PPI is disrupted by systemic administration of dopamine agonists, serotonin agonists, or glutamate antagonists and by a variety of surgical or pharmacological manipulations of neural circuitry linking the limbic cortex, striatum, pallidum, and pontine reticular formation. This article describes several different ways the loss of PPI in rats can be used as a model for studying the pathophysiology and neurobiology of impaired sensorimotor gating in schizophrenia patients and for predicting antipsychotic activity in novel compounds. First, new experimental strategies may be used to distinguish behavioral profiles of "typical" versus "atypical" antipsychotics. Second, this paradigm can be used to study the effects of early developmental insults--including neonatal lesions and isolated rearing--on the adult emergence of deficient sensorimotor gating. Third, using different animal strains and species, as well as gene "knockout" strategies, greatly increases our ability to understand specific genetic or receptor contributions to the regulation of deficient PPI. Each of these uses of the PPI paradigm is enhanced by studies of the basic brain substrates that regulate PPI in rats and by the increasingly sophisticated assessments of PPI and related measures in schizophrenia spectrum patients.
Toll‐like receptors 7, 8, and 9: linking innate immunity to autoimmunity (2007)

Toll-like receptors (TLRs) detect infections by highly conserved components of pathogens that are either not present in our own cells or are normally sequestered in cellular compartments that are inaccessible to the TLRs. Most TLRs are expressed on the cell surface, where they have been shown to detect pathogen-expressed molecules such as lipopolysaccharides and lipopeptides. A subset of TLRs, including TLR3, TLR7, TLR8, and TLR9, are expressed intracellularly within one or more endosomal compartments and detect nucleic acids. Because pathogen and host nucleic acids have very similar structures, these endosomal TLRs may face an extra challenge to induce anti-pathogen immune responses while avoiding the induction of autoimmune diseases. With the rapid growth in understanding of the biology of the TLRs has come an increasing awareness of their effects on autoimmunity, several aspects of which are the focus of this review. First, recent studies have revealed an inappropriate activation of TLR7, TLR8, and TLR9 in systemic lupus erythematosus and several other autoimmune diseases. Secondly, the potential for therapeutic development of TLR antagonists is considered. Finally, with the rapid progress in the development of therapeutic agonists for the TLRs, there is accompanying attention to the theoretical possibility that such therapy may induce autoimmunity or autoimmune diseases.
Concentrated Pomegranate Juice Improves Lipid Profiles in Diabetic Patients with Hyperlipidemia (2004)

This study assessed the effect of concentrated pomegranate juice (CPJ) consumption on lipid profiles of type II diabetic patients with hyperlipidemia (cholesterol ≥5.2 mmol/L or triacylglycerol ≥2.3 mmol/L). In this quasi-experimental study 22 otherwise healthy diabetic patients, 14 women (63.6%) and eight men (36.4%), were recruited from among patients referred to the Iranian Diabetes Society. The patients were followed for 8 weeks to establish a baseline for normal dietary intake before beginning the CPJ intervention. During the pre-study period a 24-hour food recall and food records (recording flavonoid-rich foods) were completed every 10 days. At the end of the eighth week, anthropometric and biochemical assessments were done. Thereafter the patients consumed 40 g/day of CPJ for 8 weeks, during which time dietary assessment was continued. After completing the study, anthropometric and blood indices were again evaluated. The Wilcoxon signed test was used for statistical analysis. A value of P < .05 was considered significant. Mean (± SD) age, weight, and duration of diabetes were 52.5 ± 5.2 years, 71.5 ± 10.3 kg, and 7.9 ± 6.6 years, respectively. After consumption of CPJ, significant reductions were seen in total cholesterol (P < .006), low-density lipoprotein (LDL)-cholesterol (P < .006), LDLcholesterol/ high-density lipoprotein (HDL)-cholesterol (P < .001), and total cholesterol/HDL-cholesterol (P < .001). But, there were no significant changes in serum triacylglycerol and HDL-cholesterol concentrations. Anthropometric indices, physical activity, kind and doses of oral hypoglycemic agents, and the intakes of nutrients and flavonoid-rich foods showed no change during the CPJ consumption period. It is concluded that CPJ consumption may modify heart disease risk factors in hyperlipidemic patients, and its inclusion therefore in their diets may be beneficial.
Asymmetric synthesis catalyzed by chiral ferrocenylphosphine-transition metal complexes. 5. Palladium-catalyzed asymmetric allylation of active methine compounds (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAsymmetric synthesis catalyzed by chiral ferrocenylphosphine-transition metal complexes. 5. Palladium-catalyzed asymmetric allylation of active methine compoundsTamio Hayashi, Koichi Kanehira, Toshiya Hagihara, and Makoto KumadaCite this: J. Org. Chem. 1988, 53, 1, 113–120Publication Date (Print):January 1, 1988Publication History Published online1 May 2002Published inissue 1 January 1988https://doi.org/10.1021/jo00236a023RIGHTS & PERMISSIONSArticle Views1399Altmetric-Citations173LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (1009 KB) Get e-Alerts Get e-Alerts
Synthesis and biological activity of tetragastrin analogues modifying the tryptophan residue. (1977)

Three analogues of tetragastrin, in which the tryptophan residue was substituted by 3-(1-naphthyl)-L-alanine, 3-(2-naphthyl)-L-alanine or 1, 2, 3, 4-tetrahydro-β-carboline-3-carboxylic acid, were synthesized and evaluated for their gastric juice stimulating activity. The results suggest that the indolyl NH function in the tryptophan residue plays an important role and that the role of the tryptophan residue in an interaction between tetragastrin and its receptor is different from that in the case of luteinizing hormonereleasing hormone.
A 16-bit oversampling A-to-D conversion technology using triple-integration noise shaping (1987)

A highly stable triple-integration noise-shaping technology which permits greater accuracy for monolithic audio A/D converters is discussed. Based on this technology, a 16-bit 24-kHz bandwidth A-D converter LSI with digital filters was successfully fabricated in 2-/spl mu/m CMOS technology. An SNR (S/(N+THD)) of 91 dB and a total harmonic distortion (THD) of 0.002% at full-scale input were attained.
Transformations of steroidal neopentyl systems. VII. Mechanism of the transformation of (19R)-(19)-hydroxy-19-methyl-3-oxo-5.alpha.- to 3.alpha.-hydroxy-19-methyl-19-oxo-5.alpha.-analogs (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTransformations of steroidal neopentyl systems. VII. Mechanism of the transformation of (19R)-(19)-hydroxy-19-methyl-3-oxo-5.alpha.- to 3.alpha.-hydroxy-19-methyl-19-oxo-5.alpha.-analogsJerzy Wicha and Eliahu CaspiCite this: J. Org. Chem. 1973, 38, 7, 1280–1283Publication Date (Print):April 1, 1973Publication History Published online1 May 2002Published inissue 1 April 1973https://doi.org/10.1021/jo00947a006Request reuse permissionsArticle Views52Altmetric-Citations5LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (586 KB) Get e-Alertsclose Get e-Alerts
Concise Review: Stem Cell‐Derived Erythrocytes as Upcoming Players in Blood Transfusion (2012)

Blood transfusions have become indispensable to treat the anemia associated with a variety of medical conditions ranging from genetic disorders and cancer to extensive surgical procedures. In developed countries, the blood supply is generally adequate. However, the projected decline in blood donor availability due to population ageing and the difficulty in finding rare blood types for alloimmunized patients indicate a need for alternative red blood cell (RBC) transfusion products. Increasing knowledge of processes that govern erythropoiesis has been translated into efficient procedures to produce RBC ex vivo using primary hematopoietic stem cells, embryonic stem cells, or induced pluripotent stem cells. Although in vitro-generated RBCs have recently entered clinical evaluation, several issues related to ex vivo RBC production are still under intense scrutiny: among those are the identification of stem cell sources more suitable for ex vivo RBC generation, the translation of RBC culture methods into clinical grade production processes, and the development of protocols to achieve maximal RBC quality, quantity, and maturation. Data on size, hemoglobin, and blood group antigen expression and phosphoproteomic profiling obtained on erythroid cells expanded ex vivo from a limited number of donors are presented as examples of the type of measurements that should be performed as part of the quality control to assess the suitability of these cells for transfusion. New technologies for ex vivo erythroid cell generation will hopefully provide alternative transfusion products to meet present and future clinical requirements.
Anthrax pathogen evades the mammalian immune system through stealth siderophore production (2006)

Systemic anthrax, caused by inhalation or ingestion of Bacillus anthracis spores, is characterized by rapid microbial growth stages that require iron. Tightly bound and highly regulated in a mammalian host, iron is scarce during an infection. To scavenge iron from its environment, B. anthracis synthesizes by independent pathways two small molecules, the siderophores bacillibactin (BB) and petrobactin (PB). Despite the great efficiency of BB at chelating iron, PB may be the only siderophore necessary to ensure full virulence of the pathogen. In the present work, we show that BB is specifically bound by siderocalin, a recently discovered innate immune protein that is part of an antibacterial iron-depletion defense. In contrast, neither PB nor its ferric complex is bound by siderocalin. Although BB incorporates the common 2,3-dihydroxybenzoyl iron-chelating subunit, PB is novel in that it incorporates the very unusual 3,4-dihydroxybenzoyl chelating subunit. This structural variation results in a large change in the shape of both the iron complex and the free siderophore that precludes siderocalin binding, a stealthy evasion of the immune system. Our results indicate that the blockade of bacterial siderophore-mediated iron acquisition by siderocalin is not restricted to enteric pathogenic organisms and may be a general defense mechanism against several different bacterial species. Significantly, to evade this innate immune response, B. anthracis produces PB, which plays a key role in virulence of the organism. This analysis argues for antianthrax strategies targeting siderophore synthesis and uptake.
Graphene morphology on Ni single-crystal surfaces: Experimental and theoretical investigation (2009)

Experimental investigation and computer simulation of a graphite monolayer (graphene) on different Ni single-crystal surfaces have been performed. In contrast to graphene on Ni(111), which forms a solid coating with a (1 × 1) structure, graphene on Ni(110) forms a complex crystal structure which is substantially distorted by interaction with the substrate. The calculations showed that the strong chemical interaction of carbon with nickel leads to a significant bending of the graphene layer (up to few angstroms). The calculated model made it possible to predict the main result of studying graphene on faceted surfaces, which revealed the graphene ability to coat geometrically nonuniform surfaces with a curved continuous film.
Franki makes piling history on GFIP bridges : on the cover (2009)

Big structures, like towers, skyscrapers and bridges attract a great deal of attention. The Eiffel Tower, the Empire State Building, the Sydney Harbour Bridge, the Burj Dubai and, closer to home, the Sentech (Brixton) Tower and the Nelson Mandela Bridge are iconic in their representation of what architects, engineers and contractors can accomplish. But the awe of these structures is confined to their visual spectacle. Little thought is given to those critical feats of engineering where the end product is hidden, quite literally, beneath the surface. This is the domain in which Franki Africa works. The company's ingenious foundation solutions for a wide variety of structures, including its work on numerous bridges for the Gauteng Freeway Improvement Project (GFIP), have earned Franki the respect of its professional peers. While the structures themselves are dramatic, only a few will take note of the world-class geotechnical solutions provided by Franki, including, on some of them, a unique Franki solution - the Odex Percussion or Rotapile.
SiPep: a system for the prediction of tissue‐specific minor histocompatibility antigens (2006)

Approximately 50 years ago it was found that inbred strains of mice were able to reject tumours and skin grafts from major histocompatibility complex (MHC) identical donors. They proposed that additional transplantation antigens must exist outside the MHC. These were described as minor histocompatibility antigens (mHAgs). Since then, related studies in humans have identified 16 human mHAgs. The aim of this work is to increase the number of known mHAgs by prediction of candidate minor histocompatibility loci by identifying coding single nucleotide polymorphisms (SNPs) where the amino acid variation lies within an MHC-binding peptide and alters the ability of that peptide to bind. We have developed an algorithm called SiPep which uses peptide sequences derived from the flanking regions of known non-synonymous SNPs, various MHC-binding and proteolytic cleavage evaluation methods and protein expression data to predict mHAgs. We have processed 45094 SNPs using the SiPep algorithm and have stored the results in a database called SNPBinder. The facilities to process submitted proteins through the SiPep algorithm as well as the SNPBinder database are available to the public. A set of peptides that are predicted as possible mHAgs by the SiPep algorithm have been tested using refolding assays and gel filtration and the results are presented in this paper. The SiPep tools and SNPBinder database are available free of charge via the internet. An HTML interface providing search facilities can be found at the following address: http://www.sipep.org/.
Prevalence of sleep deprivation in patients with chronic neck and back pain: a retrospective evaluation of 1016 patients (2012)

Sleep disturbance should be assessed when treating patients with CNP or CLBP, especially in patients with higher pain intensity, failed back surgery syndrome, and a migrational background. Further research is needed to explore the complex relationship of sleep disturbance and chronic pain.
Kinetics ofα2-macroglobulin andα1-acid glycoprotein in rats subjected to repeated acute inflammatory stimulation (2009)

The kinetics of alpha(2)-macroglobulin (alpha2M) and alpha(1)-acid glycoprotein (AAG) in rats repeatedly stimulated with intramuscular injections of turpentine oil at doses 0.05 and 0.4 mL/rat were investigated. Mean serum levels of alpha2M peaked at 48 h after the first turpentine oil injection, reaching 1.74 and 2.36 mg/mL at 0.05 and 0.4 mL/rat, respectively. AAG peaks were also observed at 48 h after injection, and the mean values were 2.02 and 2.53 mg/mL, respectively. These peak values of alpha2M and AAG differed significantly between the 0.05 and 0.4 mL/rat injection groups. Mean serum levels of interleukin-6 (IL-6) at 0.05 mL/rat were 52.61 pg/mL at 12 h, 48.86 pg/mL at 36 h and 81.93 pg/mL at 84 h after the first injection. Mean IL-6 serum levels at 0.4 mL/rat were 215.24 pg/mL at 12 h, 56.33 pg/mL at 36 h and 39.25 pg/mL at 84 h after the first injection. Mean serum levels of cytokine-induced chemoattractant-1 (CINC-1) at a dose of 0.05 mL/rat were 5.70 ng/mL at 12 h, 5.58 ng/mL at 36 h and 4.58 ng/mL at 84 h after the first injection. Mean serum levels of CINC-1 after injection at 0.4 mL/rat were 11.57 ng/mL at 12 h, 4.68 ng/mL at 36 h and 4.42 ng/mL at 84 h. Serum levels of IL-6 differed significantly at 12, 24, 72 and 84 h, while those of CINC-1 differed significantly at 12, 24, 48 and 96 h between the 0.05 and 0.4 mL/rat injection groups. Differences in peak serum levels in the 0.05 and 0.4 mL/rat groups were attributed to differences in the production of IL-6 and CINC-1, which are thought to contribute to alpha2M and AAG production.