gebhart/patrepeval huggingface dataset:
Testosterone (T) Enhances Apoptosis-Related Damage in Human Vascular Endothelial Cells (2002)

Androgens may contribute to higher cardiovascular risk in men via deleterious effects on vascular endothelial cells (EC). We examined the effects of androgens on male human umbilical vein EC (EA.hy926) in culture. [(3)H]Thymidine incorporation assays showed that after 24-h serum deprivation, testosterone (T) (but not dehydroepiandrosterone nor 17beta-E2) induced significant dose-dependent decreases in DNA synthesis (10-16% at 1-100 nmol/liter); the AR antagonist flutamide (100 nmol/liter) abolished this effect of T. After 48-h serum deprivation, typical apoptotic DNA patterns were detected in agarose gels, and the number of floating cells indicative of severe damage was significantly greater after T treatment for 48 and 72 h (13.7 +/- 0.5% and 30.2 +/- 2.5%, respectively) than the control values (9.7 +/- 1.05% and 23.7 +/- 3.0%). Analysis of attached cells by annexin V-fluorescein isothiocyanate/propidium iodide staining showed that after 48-h serum deprivation, T significantly increased the number of cells in the early (16.0 +/- 1.1%) and late (8.3 +/- 0.3%) stages of apoptosis compared with control (6.8 +/- 1.0% and 4.0 +/- 0.2%, respectively); such increases in apoptosis-related damage were also observed, to a lesser degree, in serum-enriched culture. Western blotting showed that B cell leukemia/lymphoma-2 protein (Bcl-2) expression decreased significantly in serum-deprived EC treated with T. Thus, T reduces DNA synthesis and enhances apoptosis after serum deprivation in EC, possibly related to reduced Bcl-2 expression.
A Mechanistic Framework for the Second Step of Splicing Catalyzed by the Tetrahymena Ribozyme (1996)

A simple model system is described which mimics the second step of splicing and reverse cyclization reactions of the self-splicing intron from Tetrahymena thermophila. This model is based on the L-21 Sca I catalyzed ligation reaction between exogenously added oligomers: cucu + UCGa L-21 Sca I cucua + UCG. Steady-state kinetics for the forward and reverse direction were measured at 15 degrees C to find oligonucleotides that exhibit Michaelis-Menten behavior with acceptable KMS. CUCU and UCGA fit both criteria and were chosen for further studies. Steady-state kinetics reveal a lag that appears to be an RNA folding step that is eliminated by preincubation of the ribozyme with 2 mM and higher [Mg2+] and by UCGA. At constant ionic strength, the Mg2+ dependence of steady-state rates exhibits a sharp maximum near 5 mM Mg2+. Pre-steady-state and steady-state kinetics, along with active-site titrations, explain the Mg2+ profile: the rate of reaction up to and including chemistry increases with Mg2+ concentration, while the fraction of active ribozyme and the rate of postchemistry steps decrease with Mg2+ concentration. The rate-limiting step at 5 mM Mg2+ for the reaction mimicking the second step of splicing is either chemistry or a conformational change before chemistry involving ribozyme bound with substrates. The rate-limiting step at 50 mM Mg2+ appears to be a postchemistry conformational change of the ribozyme or product release. At 50 mM Mg2+, single-turnover experiments support ordered binding of substrates with 5'-exon mimic binding before 3'-splice site mimic. Moreover, the 3'-splice site mimic binds and reacts in the presence of 5'-exon mimics predocked into the catalytic core. Results also indicate that Mg2+ ions associate with the ribozyme upon docking.
Genetic construction and characterization of the diphtheria toxin-related interleukin 15 fusion protein DAB389 sIL-15 (1995)

A gene fusion encoding DAB389 sIL-15 was constructed in which the catalytic and transmembrane domains of native diphtheria toxin (DAB389) are genetically linked to the N-terminus of simian interleukin 15 (sIL-15). It was demonstrated that the cytotoxic action of DAB389 sIL-15 is mediated through the IL-15 receptor. Since toxicity may be blocked with chloroquine, it was concluded that following binding to the IL-15 receptor, the fusion toxin is internalized by receptor-mediated endocytosis and must pass through an acidic compartment in order to facilitate the delivery of the catalytic domain to the cytosol of target cells. As a non-toxic control, the ADP-ribosyltransferase defective mutant DA(E149S)B389 sIL-15 was constructed. It was demonstrated that both sIL-15 and DA(E149S)B389 sIL-15 stimulate protein and DNA synthesis in IL-15 receptor-positive CTLL-2 cells in vitro.
Processing of Laminin-5 and Its Functional Consequences: Role of Plasmin and Tissue-type Plasminogen Activator (1998)

The laminin-5 component of the extracellular matrices of certain cultured cells such as the rat epithelial cell line 804G and the human breast epithelial cell MCF-10A is capable of nucleating assembly of cell- matrix adhesive devices called hemidesmosomes when other cells are plated upon them. These matrices also impede cell motility. In contrast, cells plated onto the laminin-5-rich matrices of pp126 epithelial cells fail to assemble hemidesmosomes and are motile. To understand these contradictory phenomena, we have compared the forms of heterotrimeric laminin-5 secreted by 804G and MCF-10A cells with those secreted by pp126 cells, using a panel of laminin-5 subunit-specific antibodies. The alpha3 subunit of laminin-5 secreted by pp126 cells migrates at 190 kD, whereas that secreted by 804G and MCF-10A cells migrates at 160 kD. The pp126 cell 190-kD alpha3 chain of laminin-5 can be specifically proteolyzed by plasmin to a 160-kD species at enzyme concentrations that do not apparently effect the laminin-5 beta and gamma chains. After plasmin treatment, pp126 cell laminin-5 not only impedes cell motility but also becomes competent to nucleate assembly of hemidesmosomes. The possibility that plasmin may play an important role in processing laminin-5 subunits is supported by immunofluorescence analyses that demonstrate colocalization of laminin-5 and plasminogen in the extracellular matrix of MCF-10A and pp126 cells. Whereas tissue-type plasminogen activator (tPA), which converts plasminogen to plasmin, codistributes with laminin-5 in MCF-10A matrix, tPA is not present in pp126 extracellular matrix. Treatment of pp126 laminin-5-rich extracellular matrix with exogenous tPA results in proteolysis of the laminin-5 alpha3 chain from 190 to 160 kD. In addition, plasminogen and tPA bind laminin-5 in vitro. In summary, we provide evidence that laminin-5 is a multifunctional protein that can act under certain circumstances as a motility and at other times as an adhesive factor. In cells in culture, this functional conversion appears dependent upon and is regulated by tPA and plasminogen.
Linkage analysis of quantitative traits: increased power by using selected samples. (1991)

Although a number of methods have been developed for linkage analysis of quantitative traits, power is relatively poor unless there is a single major locus of very large effect. Here it is demonstrated that the use of selected samples (i.e., ascertainment of a proband with an extreme score on the quantitative measure) can dramatically increase power, especially when proband selection is performed on the tail of a distribution with an infrequent recessive gene. Depending on gene action and allele frequency, selected samples permit detection of a major locus that accounts for as little as 10%-20% of the phenotypic variation. The judicious use of selected samples can make an appreciable difference in the feasibility of linkage studies for quantitative traits.
Mode Coupling Effects in Graded-Index Optical Fibers (1975)

Mode coupling theory is applied to the study of multimode optical fibers with graded-index cores. For coupling caused by random bends in the waveguide axis, the results predict the dependence of the induced losses on the fiber's characteristics. The impulse response is determined for fibers with random bends having several different power spectra. The results are used to predict the transmitted power, the delay time, and the rms pulse width in fibers with graded-index cores.
Capillary Electrophoresis for Sampling Single Nerve Cells (1991)

Two micro-capillary electrophoresis techniques are underdevelopment to acquire and determine catecholamines in single nerve cells. The first method involves the analysis of neurotransmitters in a portion of cytoplasm withdrawn from a single cell, and the second method involves the determination of neurotransmitters in a whole nerve cell. Amperometric detection can be used to determine the easliy oxidized species in both of these methods. A large dopamine-containing cell in the brain of the pond snail, Planorbis corneus, has been used as a model system to evaluate both of these microsampling techniques. Results for both the acquisition and separation of neurotransmitters in whole nerve cells as well as the analysis of small portions of single cell cytoplasm are presented here.
Tinigible Body Macrophages in Regulation of Germinal Center Reactions (1997)

Tingible body macrophages (TBM), long thought simply as scavengers of apoptotic lymphocytes, are located in the unique microenvironment of germinal centers in close proximity to antigen-retaining follicular dendritic cells (FDC). Observations that TBM endocytose FDC-iccosomal (immune-complex coated bodies) antigen suggested that TBM might present this antigen and help regulate the germinal center reaction. To test for antigen presentation, the ovalbumin (OVA)-specific T(H) hybridoma, 3DO-54.8, which produces IL-2 on receiving effective presentation of OVA, were used as responders to OVA-bearing TBM. Results showed that OVA-bearing TBM failed to induce IL-2 production. Furthermore, addition of TBM to IL-2-inducing positive controls (B cells) not only failed to augment IL-2 production, but rather TBM significantly (55-90%) reduced B-cell induction of IL-2. We found that TBM were rich in prostaglandin by comparison with other nongerminal center lymph node macrophages and that addition of indomethacin to the cultures reversed the inhibitory effect of TBM. Depletion of TBM from enriched preparations, prior to addition to positive control cultures, also abrogated the inhibitory effect on IL-2 production. These data support the concept that TBM, within the unique microenvironment of germinal centers, may be specialized to downregulate the germinal center reaction.
Tadalafil for Prevention of Erectile Dysfunction After Radiotherapy for Prostate Cancer (2014)

clinicaltrials.gov Identifier: NCT00931528.
High density, high aspect ratio through-wafer electrical interconnect vias for mems packaging (2003)

A novel micro-electromechanical system (MEMS) package has been developed based on modular, reconfigurable components such as substrate, cap, bond region and through-wafer electrical interconnect (TWEI). The paper presents the details of the process for the fabrication of high density, high aspect ratio TWEIs that includes deep dry etching holes through the substrate, depositing an insulation layer and depositing a conductive layer. Two different processes to make the TWEI have been developed: Post-Process where the TWEI is fabricated after the fabrication of MEMS devices and Pre-Process where the TWEI is fabricated before the fabrication of MEMS device. For both processes, the interconnect holes are created by an anisotropic etching process-inductively coupled plasma (ICP) etching. For the post-process, a silicon dioxide layer was deposited in a plasma enhanced chemical vapor deposition (PECVD) chamber to insulate the interconnect holes. For the pre-process, the PECVD process was replaced with a thermal oxide growth step to ensure a more conformal oxide coating. Three different ways to deposit a conductive layer after deposition of an insulation layer have been practiced: sputtering Cu, electroplating Cu and low-pressure chemical vapor deposition (LPCVD) of phosphorus doped polysilicon. The electrical performance of the TWEIs achieved in each way was measured, analyzed and discussed.
The inducible transcription factor NF-κB: structure-function relationship of its protein subunits (1993)

Research Article| March 01 1993 The inducible transcription factor NF-κB: structure-function relationship of its protein subunits S Grimm; S Grimm 1Laboratory for Molecular Biology of the Ludwig-Maximilians University Munich, Gene Center, Am Klopferspitz 18a, D-8033 Martinsried, Federal Republic of Germany Search for other works by this author on: This Site PubMed Google Scholar P A Baeuerle P A Baeuerle 1Laboratory for Molecular Biology of the Ludwig-Maximilians University Munich, Gene Center, Am Klopferspitz 18a, D-8033 Martinsried, Federal Republic of Germany Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1993) 290 (2): 297–308. https://doi.org/10.1042/bj2900297 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 S Grimm, P A Baeuerle; The inducible transcription factor NF-κB: structure-function relationship of its protein subunits. Biochem J 1 March 1993; 290 (2): 297–308. doi: https://doi.org/10.1042/bj2900297 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 Journal Search Advanced Search © 1993 The Biochemical Society, London1993 Article PDF first page preview Close Modal You do not currently have access to this content.
High resolution footprinting ofEcoRI and distamycin with Rh(phi)2(bpy)3+, a new photofootprinting reagent (1989)

The complex bis(phenanthrenequinone diimine)(bipyridyl)rhodium(III), Rh(phi)2(bpy)3+, cleaves DNA efficiently in a sequence-neutral fashion upon photoactivation so as to provide a novel, high resolution, chemical photofootpring reagent. Photofootprinting of two crystallographically characterized DNA-binding agents, distamycin, a small natural product which binds to DNA in the minor groove, and the endonuclease EcoRI, which binds in the major groove, gave respectively a 5-7 base pair footprint for the drug at its A6 binding site and a 10-12 base pair footprint for the enzyme centered at its recognition site (5'-GAATTC-3'). Both footprints agree closely with the crystallographic results. The photocleavage reaction can be performed using either a high intensity lamp or, conveniently, a simple transilluminator box, and the photoreaction is not inhibited by moderate concentrations of reagents which are sometimes required for examining interactions of molecules with DNA. When compared with other popular footprinting agents, the rhodium complex shows a number of distinct advantages: sequence-neutrality, high resolution, ability to footprint major as well as minor groove-binding ligands, applicability in the presence of additives such as Mg2+ or glycerol, ease of handling, and a sharply footprinted pattern. Light activated footprinting reactions furthermore offer the possibility of examining DNA-binding interactions with time resolution and within the cell.
Non-Invasive Glucose Monitoring Techniques: A review and current trends (2008)

Diabetes mellitus is a complex group of syndromes that have in common a disturbance in the body's use of glucose, resulting in an elevated blood sugar. Once detected, sugar diabetes can be controlled by an appropriate regimen that should include diet therapy, a weight reduction program for those persons who are overweight, a program of exercise and insulin injections or oral drugs to lower blood glucose. Blood glucose monitoring by the patient and the physician is an important aspect in the control of the devastating complications (heart disease, blindness, kidney failure or amputations) due to the disease. Intensive therapy and frequent glucose testing has numerous benefits. With ever improving advances in diagnostic technology, the race for the next generation of bloodless, painless, accurate glucose instruments has begun. In this paper, we reviewed various methods, techniques and approaches successfully demonstrated for measuring or monitoring blood glucose. Invasive, minimally invasive and noninvasive techniques available in literature are summarised.
Recurrent bacterial meningitis in patients with genetic defects of terminal complement components. (1980)

Isolated genetic deficiencies of complement components in man are rare. We describe two kindreds with inborn deficiencies of either C5 or C6 in which both propositi presented with recurrent bacterial meningitis. Neisseria meningitidis was isolated from the cerebrospinal fluid of the C5-deficient patient and bactericidal activity against his autologous meningococcus was absent from whole fresh patients' serum despite a rising titre of complement-fixing antibody. The stimulated movement of normal leucocytes was impaired in the presence of C5-deficient serum but not in the presence of C6-deficient serum; neither deficiency reduced significantly the complement-dependent opsonization of Saccharomyces cerevisiae. HLA typing and complement component phenotyping showed no segregation with the complement defect in either the C5- or C6-deficient families. Normal individuals and apparent heterozygotes with approximately half the normal levels of the relevant component were found in both families, in keeping with an autosomal codominant inheritance of the defects.
New Regiosymmetrical Dioxopyrrolo- and Dihydropyrrolo-Functionalized Polythiophenes (2004)

[structure: see text] We present the synthesis of two N-alkylated poly(dioxopyrrolothiophene)s and two N-alkylated poly(dihydropyrrolothiophene)s with potential application in the field of conducting polymers. The polymers are synthesized from the corresponding 2,5-dibromothiophenes by an Ullmann-type polymerization and a Stille-type polymerization, respectively. The two N-alkylated poly(dihydropyrrolothiophene)s are the first examples of amino-functionalized polythiophenes built from regiosymmetrical thiophene monomers.
Identification of NVP-TAE684, a potent, selective, and efficacious inhibitor of NPM-ALK (2006)

Constitutive overexpression and activation of NPM-ALK fusion protein [t(2:5)(p23;q35)] is a key oncogenic event that drives the survival and proliferation of anaplastic large-cell lymphomas (ALCLs). We have identified a highly potent and selective small-molecule ALK inhibitor, NVP-TAE684, which blocked the growth of ALCL-derived and ALK-dependent cell lines with IC(50) values between 2 and 10 nM. NVP-TAE684 treatment resulted in a rapid and sustained inhibition of phosphorylation of NPM-ALK and its downstream effectors and subsequent induction of apoptosis and cell cycle arrest. In vivo, NVP-TAE684 suppressed lymphomagenesis in two independent models of ALK-positive ALCL and induced regression of established Karpas-299 lymphomas. NVP-TAE684 also induced down-regulation of CD30 expression, suggesting that CD30 may be used as a biomarker of therapeutic NPM-ALK kinase activity inhibition.
Narcolepsy: clinical features, co-morbidities & treatment. (2010)

Narcolepsy is a neurologic illness that typically begins in the second and third decades of life. It is chronic in nature and negatively impacts the quality of life of affected patients. The classic presentation is a tetrad of excessive daytime sleepiness, cataplexy, sleep paralysis, and hypnagogic hallucinations. The exact cause remains unknown, but there is significant evidence that hypocretin deficiency plays an integral role. Some primary conditions that result in secondary narcolepsy include traumatic brain injury, congenital disorders, tumours, and strokes. Some medical and psychiatric disorders share characteristics of narcolepsy, at times leading to diagnostic inaccuracy. Other sleep disorders are commonly co-morbid. Diagnosis relies on patient history and objective data gathered from polysomnography and multiple sleep latency testing. Treatment focuses on symptom relief through medication, education, and behavioural modification. Both classic pharmacological treatments as well as newer options have significant problems, especially because of side effects and abuse potential. Novel modalities are being examined to expand options for treatment.
Modification of Si field emitter surfaces by chemical conversion to SiC (1994)

Silicon field emitters have been modified by coating with a thin SiC film through a chemical conversion process. Silicon carbide was formed on Si emitter surfaces by reacting with ethylene gas at temperatures between 850 and 950 °C using pressures as high as 5×10−3 Torr. The thickness of the coatings ranged from 2 to 500 nm, determined by a combination of reaction time, pressure, and temperature. Stable emission currents above 10 μÅ were measured from individual SiC coated emitters.
Furin/PACE/SPC1: A convertase involved in exocytic and endocytic processing of precursor proteins (1996)

One of the most exciting breakthroughs of the 90's in the fields of biochemistry, cell biology and neuroendocrinology is the identification of a novel family of proteolytic enzymes called mammalian subtilisin-like convertases. This family is comprised so far of seven distinct endoproteases responsible for the proteolytic excision of biologically active polypeptides from inactive precursor proteins. Six years after the initial observation of a structural conservation between a characterized yeast enzyme (kexin) and a human gene product (furin), it is now well accepted that one of these convertases, furin, has the enzymatic capabilities to efficiently and correctly process a great variety of precursors. Furin's ability to cleave precursors within both the exocytic and endocytic pathways will require sustained efforts in order to delineate all of its physiological roles.
Methylated Tumor-Specific DNA as a Plasma Biomarker in Patients with Glioma (2006)

Patients with high grade gliomas have large amounts of DNA in the plasma. Of these primary brain tumors, 90 percent contained methylated gene promoters, and in over 60 percent of these patients the same methylated promoters present in the tumor also were found in the plasma. This represents the first step to developing a quantitative plasma biomarker that could be used to monitor glioma status.
The RGD-containing domain of exogenous HIV-1 Tat inhibits the engulfment of apoptotic bodies by dendritic cells (1997)

Our results support a role for HIV-1 Tat in decreasing the function of dendritic cells, possibly impairing antigen presentation.
FPGAs in the Cloud: Booting Virtualized Hardware Accelerators with OpenStack (2014)

We present a new approach for integrating virtualized FPGA-based hardware accelerators into commercial-scale cloud computing systems, with minimal virtualization overhead. Partially reconfigurable regions across multiple FPGAs are offered as generic cloud resources through OpenStack (opensource cloud software), thereby allowing users to “boot” custom designed or predefined network-connected hardware accelerators with the same commands they would use to boot a regular Virtual Machine. We propose a hardware and software framework to enable this virtualization. This is a first attempt at closely fitting FPGAs into existing cloud computing models, where resources are virtualized, flexible, and have the illusion of infinite scalability. Our system can set up and tear down virtual accelerators in approximately 2.6 seconds on average, much faster than regular virtual machines. The static virtualization hardware on the physical FPGAs causes only a three cycle latency increase and a one cycle pipeline stall per packet in accelerators when compared to a non-virtualized system. We present a case study analyzing the design and performance of an application-level load balancer using a fully implemented prototype of our system. Our study shows that FPGA cloud compute resources can easily outperform virtual machines, while the system's virtualization and abstraction significantly reduces design iteration time and design complexity.