gebhart/patrepeval huggingface dataset:
Desmin gene expression in cardiac myocytes is responsive to contractile activity and stretch (1996)

Experiments were performed to assess the ability of mechanical stimuli, experienced by ventricular cardiac myocytes during the progression of hypertrophic and dilated pathology, to increase the expression of desmin in cultured neonatal rat cardiac myocytes. Results indicate that both contractile activity and load due to passive stretch increase desmin content in neonatal rat cardiac myocytes through increased desmin gene transcription. Western blot analysis demonstrated that contraction induced a selective increase in desmin protein content in neonatal rat cardiac myocytes above increases observed in the content of total cellular protein. Northern blot analysis indicated that desmin mRNA content increased in response to contraction as well as to alpha-adrenergic stimulation. Desmin mRNA content also increased in cultured neonatal myocytes in response to stretch. Angiotensin II (ANG II) treatment of contracting neonatal cardiac myocytes further increased desmin mRNA content, whereas similar treatment in arrested neonatal cardiac myocytes further increased desmin mRNA content, whereas similar treatment in arrested neonatal cardiac myocytes failed to increase desmin mRNA. This contraction-dependent responsiveness to ANG II is not a function of increases in the density or relative subtype composition of ANG II receptors. Treatment of contracting neonatal rat cardiac myocytes with actinomycin D prevented increases in desmin mRNA content, suggesting regulation of transcription of the desmin gene by contraction. Nuclear run-on experiments indicate that contraction. Nuclear run-on experiments indicate that contraction increases transcription of the desmin gene in cardiac myocytes. These results are consistent with the modulation of desmin gene expression secondarily to changes in the mechanical environment that occur in cardiac tissue undergoing dilation or hypertrophy.
Interfering with Resistance to Smoothened Antagonists by Inhibition of the PI3K Pathway in Medulloblastoma (2010)

The malignant brain cancer medulloblastoma is characterized by mutations in Hedgehog (Hh) signaling pathway genes, which lead to constitutive activation of the G protein (heterotrimeric guanosine triphosphate-binding protein)-coupled receptor Smoothened (Smo). The Smo antagonist NVP-LDE225 inhibits Hh signaling and induces tumor regression in animal models of medulloblastoma. However, evidence of resistance was observed during the course of treatment. Molecular analysis of resistant tumors revealed several resistance mechanisms. We noted chromosomal amplification of Gli2, a downstream effector of Hh signaling, and, more rarely, point mutations in Smo that led to reactivated Hh signaling and restored tumor growth. Analysis of pathway gene expression signatures also, unexpectedly, identified up-regulation of phosphatidylinositol 3-kinase (PI3K) signaling in resistant tumors as another potential mechanism of resistance. Probing the relevance of increased PI3K signaling, we demonstrated that addition of the PI3K inhibitor NVP-BKM120 or the dual PI3K-mTOR (mammalian target of rapamycin) inhibitor NVP-BEZ235 to the initial treatment with the Smo antagonist markedly delayed the development of resistance. Our findings may be useful in informing treatment strategies for medulloblastoma.
Systemic Delivery of Bone Marrow–Derived Mesenchymal Stem Cells to the Infarcted Myocardium (2003)

Systemic intravenous delivery of BM-MSCs to rats after MI, although feasible, is limited by entrapment of the donor cells in the lungs. Direct left ventricular cavity infusion enhances migration and colonization of the cells preferentially to the ischemic myocardium.
Holonomic Quantum Computation in Decoherence-Free Subspaces (2005)

We show how to realize, by means of non-Abelian quantum holonomies, a set of universal quantum gates acting on decoherence-free subspaces and subsystems. In this manner we bring together the quantum coherence stabilization virtues of decoherence-free subspaces and the fault tolerance of all-geometric holonomic control. We discuss the implementation of this scheme in the context of quantum information processing using trapped ions and quantum dots.
Fluorescence Quenching by Pyridine and Derivatives Induced by Intermolecular Hydrogen Bonding to Pyrrole-Containing Heteroaromatics (2002)

Photophysical studies of a series of over 20 compounds based on pyrrole, indole, and carbazole chromophores were carried out in protic, nonpolar, and polar solvents. Absorption spectra revealed the formation of ground-state hydrogen bonding with protic solvent partners. The equilibrium constants were determined by spectrophotometric titration. Strong fluorescence quenching was observed when azaaromatic proton acceptors, pyridine and quinoline, were used as protic solvents. No quenching occurs for nonaromatic protic partners such as dimethyl sulfoxide, morpholine, and piperidine, even though the ground-state equilibrium constants are not smaller. The rates of quenching in pyridine solutions at 293 K span a range from 1.2 × 109 to 5.9 × 1010 s-1 and are sensitive to minor structural variations. The mechanism of quenching involves an electron transfer from a photoexcited chromophore to a hydrogen-bonded partner, followed by a rapid internal conversion (back electron transfer) to the ground state. The quenching rates are larger for systems with stronger hydrogen bonds. This model was confirmed by theoretical time-dependent DFT and semiempirical studies, in which the pattern of excited states of an isolated chromophore was compared with that of a hydrogen-bonded pyridine complex. For the latter, low-lying charge transfer (CT) states were predicted, with an electron transferred to pyridine.
Properties and Application of a Thermostable Maltogenic Amylase Produced by a Strain of Bacillus Modified by Recombinant‐DNA Techniques (1984)

Abstract During a screening programme for amylase producing microorganisms a strain of Bacillus was isolated which produced a maltogenic amylase which had possible industrial potential. Unlike the microbial β‐amylases from B. cereus, B. megaterium, B. polymyxa and B. circulans this enzyme was characterized by being stable at 60–70°C at pH 4.5.‐5.5. Unfortunately the microorganism proved to be difficult to cultivate. Using recombinant‐DNA techniques it was possible to transfer the gene, which coded for the enzyme, to a host organism which was easier to cultivate, thus making industrial production a viable proposition. The enzyme is suitable for producing high maltose syrups from liquefied starch. When used together with an amylopectin debranching enzyme such as pullulanase, more than 75% maltose can be obtained at 30% D. S.
High-Resolution Mapping of Probes near the X-Linked Lymphoproliferative Disease (XLP) Locus (1993)

Fluorescence in situ hybridization (FISH) was employed in high-resolution mapping of probes near the X-linked lymphoproliferative disease (XLP) locus. The map includes the DXS42, DXS12, DXS6, DXS982, DXS739, DXS75, DXS100, DXS10, and DXS177 loci. Metaphase analysis showed that DXS12 and DXS42 mapped to proximal Xq25, while DXS10 and DXS177 mapped to proximal Xq26.1. DXS6, DXS982, DXS739, DXS75, and DXS100 were in Xq25. The order of probes deduced from interphase FISH was: Xq24-(DXS12, DXS42)-DXS6-DXS982-DXS739-DXS75-DXS100+ ++-DXS10-DXS177-Xq26.2. We estimate that the entire region between DXS12 and DXS177 is about 7 Mb. Our previous study indicated that all three XLP deletions (63-3, 66-1, and 43-4) lacked DXS739. We now report that DXS75 and DXS982 are also missing in these deletions. Using interphase FISH measurements, we estimate that 2 Mb are absent in 63-3, and 4 Mb are absent in 66-1 and 43-4. This FISH map confines the XLP candidate gene region to a 2-Mb interval between DXS6 and DXS100 and places DXS100 distal to the XLP locus. This study also demonstrates that small probes (0.6 to 3.6 kb) can be utilized in FISH.
Photochemical control of biological processes (2006)

Photochemical regulation of biological processes offers a high level of control to study intracellular mechanisms with unprecedented spatial and temporal resolution. This report summarizes the advances made in recent years, focusing predominantly on the in vivo regulation of gene function using irradiation with UV light. The majority of the described applications entail the utilization of photocaging groups installed either on a small molecule modulator of biomolecular function or directly on a biological macromolecule itself.
The importance of injecting vaccines into muscle (2000)

Most vaccines should be given via the intramuscular route into the deltoid or the anterolateral aspect of the thigh. This optimises the immunogenicity of the vaccine and minimises adverse reactions at the injection site. Recent studies have highlighted the importance of administering vaccines correctly.1–3 Clinical practice needs to reflect considerations about the right length and gauge of needles used to ensure that those vaccinated get the immunological benefit of the vaccines without local side effects.

Injecting a vaccine into the layer of subcutaneous fat, where poor vascularity may result in slow mobilisation and processing of antigen, is a cause of vaccine failure1—for example in hepatitis B,2 rabies, and influenza vaccines.3 Compared with intramuscular administration, subcutaneous injection of hepatitis B vaccine leads to significantly lower seroconversion rates and more rapid decay of antibody response.1

Traditionally the buttocks were thought to be an appropriate site for vaccination, but …
Dynamic Light Scattering Of Biopolymers And Biocolloid (1977)

Widespread applications of dynamic light scattering techniques to the study of macromolecular Brownian motion have yielded not only a valuable store of factual information concerning solution conformations and conformational changes, but have also provided an important window through which to view the dynamics of internal modes of motion. These techniques have coincided with a resurgence of interest in the solution physical chemistry of macromolecules, including hydrodynamic properties, and the profound effect of intermolecular interactions on both the disposition and dynamics of macromolecules in solution.
Proposal of a near-field optical head using a new solid immersion mirror (1999)

The near field optical recording technologies using a solid immersion lens (SIL) or solid immersion mirror (SIM) have been proposed as promising candidates to overcome the density limit of conventional optical recordings with far field optics. These devices are also suitable for the OAM (optically-assisted magnetic) recording technologies with avoiding the super paramagnetic problem in HDD.
FETAL NUCLEIC ACIDS IN MATERNAL PLASMA (2006)

Prenatal diagnosis is now an established part of modern obstetrical practice around the world. While the current definitive methods for prenatal diagnosis rely mainly on invasive procedures such as chorionic villus sampling and amniocentesis, such procedures carry a low but definite risk of fetal loss. As a consequence of the procedure-associated risk of miscarriage, prenatal diagnosis is currently limited to pregnant women with an increased likelihood of bearing an abnormal fetus. To extend the application of prenatal diagnosis to all pregnant women, it has been a long-sought goal of researchers worldwide to introduce safer methods for prenatal diagnosis, towards noninvasive prenatal diagnosis.
Electrospray‐ionization mass spectrometry of intact intrinsic membrane proteins (1998)

Membrane proteins drive and mediate many essential cellular processes making them a vital section of the proteome. However, the amphipathic nature of these molecules ensures their detailed structural analysis remains challenging. A versatile procedure for effective electrospray-ionization mass spectrometry (ESI-MS) of intact intrinsic membrane proteins purified using reverse-phase chromatography in aqueous formic acid/isopropanol is presented. The spectra of four examples, bacteriorhodopsin and its apoprotein from Halobacterium and the D1 and D2 reaction-center subunits from spinach thylakoids, achieve mass measurements that are within 0.01% of calculated theoretical values. All of the spectra reveal lesser quantities of other molecular species that can usually be equated with covalently modified subpopulations of these proteins. Our analysis of bovine rhodopsin, the first ESI-MS study of a G-protein coupled receptor, yielded a complex spectrum indicative of extensive molecular heterogeneity. The range of masses measured for the native molecule agrees well with the range calculated based upon variable glycosylation and reveals further heterogeneity arising from other covalent modifications. The technique described represents the most precise way to catalogue membrane proteins and their post-translational modifications. Resolution of the components of protein complexes provides insights into native protein/protein interactions. The apparent retention of structure by bacteriorhodopsin during the analysis raises the potential of obtaining tertiary structure information using more developed ESI-MS experiments.
Characterization of an amyloid beta precursor protein that binds heparin and contains tyrosine sulfate. (1989)

A secreted form of the amyloid beta protein precursor was isolated from the growth conditioned medium of the PC12 sympathetic nerve-like cell line. This protein is recognized by an antiserum that detects a protein of 140 kDa and a less abundant species of 115 kDa on NaDodSO4/acrylamide gels. The amyloid precursor proteins contain O-linked sugars and tyrosine sulfate and bind to the glycosaminoglycan heparin. These results suggest a role for extracellular sulfated glycoproteins in the pathogenesis of Alzheimer disease.
gp180, a Host Cell Glycoprotein That Binds Duck Hepatitis B Virus Particles, Is Encoded by a Member of the Carboxypeptidase Gene Family (1995)

Duck hepatitis B virus particles bearing the L and S envelope proteins bind a cellular glycoprotein of 180 kDa (gp180) with high affinity and specificity. Binding is mediated by the pre-S region of the L protein and is blocked by neutralizing but not by non-neutralizing monoclonal antibodies to the virus. These and other properties have suggested that gp180 may be a component of the viral entry machinery. Here we report the purification of gp180 from duck liver and the isolation and characterization of cDNA encoding it. DNA sequence analysis of this cDNA indicates that gp180 is a novel member of the basic carboxypeptidase gene family.
Antibody Prophylaxis and Therapy against West NileVirus Infection in Wild-Type and ImmunodeficientMice (2003)

West Nile virus (WNV) is a mosquito-borne Flavivirus that causes encephalitis in a subset of susceptible humans. Current treatment for WNV infections is supportive, and no specific therapy or vaccine is available. In this study, we directly tested the prophylactic and therapeutic efficacy of polyclonal antibodies against WNV. Passive administration of human gamma globulin or mouse serum prior to WNV infection protected congenic wild-type, B-cell-deficient ( micro MT), and T- and B-cell-deficient (RAG1) C57BL/6J mice. Notably, no increased mortality due to immune enhancement was observed. Although immune antibody completely prevented morbidity and mortality in wild-type mice, its effect was not durable in immunocompromised mice: many micro MT and RAG1 mice eventually succumbed to infection. Thus, antibody by itself did not completely eliminate viral reservoirs in host tissues, consistent with an intact cellular immune response being required for viral clearance. In therapeutic postexposure studies, human gamma globulin partially protected against WNV-induced mortality. In micro MT mice, therapy had to be initiated within 2 days of infection to gain a survival benefit, whereas in the wild-type mice, therapy even 5 days after infection reduced mortality. This time point is significant because between days 4 and 5, WNV was detected in the brains of infected mice. Thus, passive transfer of immune antibody improves clinical outcome even after WNV has disseminated into the central nervous system.
Inhibition of Diacylglycerol Acyltransferase by Alkamides Isolated from the Fruits of Piper longum and Piper nigrum (2006)

Pharmacological inhibition of acyl CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) has emerged as a potential therapy for the treatment of obesity and type 2 diabetes. Bioassay-guided isolation of CHCl3 extracts of the fruits of Piper longum and Piper nigum (Piperaceae), using an in vitro DGAT inhibitory assay, lead to isolation of a new alkamide named (2E,4Z,8E)-N-[9-(3,4-methylenedioxyphenyl)-2,4,8-nonatrienoyl]piperidine (2), together with four known alkamides: retrofractamide C (1), pipernonaline (3), piperrolein B (4), and dehydropipernonaline (5). Compounds 2-5 inhibited DGAT with IC50 values of 29.8 (2), 37.2 (3), 20.1 (4), and 21.2 (5) microM, respectively, but the IC50 value for 1 was more than 900 microM. This finding indicates that compounds possessing piperidine groups (2-5) can be potential DGAT inhibitors.
SEEING THE ROAD AHEAD : GPS-AUGMENTED REALITY AIDS DRIVERS (2003)

This article describes an augmented reality (AR) driver-assistance system which combines Global Positioning System (GPS)/inertial measurements with real-time road video footage. Known as the Intelligent Navigation Aid (INA), the system is designed to display highlighted road boundaries and up-to-date positions of surrounding vehicles. This allows for drivers to be alerted when their vehicles drift off the road or into a lane of oncoming traffic. The system uses a multi-antenna array of dual frequency GPS receivers for determining driver perspective and position. It overlays highlighted road boundaries from digitally stored information onto real-time road imagery.
Anti-Gal-mediated targeting of human B lymphoma cells to antigen-presenting cells: a potential method for immunotherapy using autologous tumor cells. (2005)

This study suggests that immunization with irradiated autologous lymphoma cells processed to express alpha-gal epitopes will result in anti-Gal-mediated, in vivo targeting of the autologous tumor vaccine to APC.
Diverse gene sequences are overexpressed in werner syndrome fibroblasts undergoing premature replicative senescence. (1991)

Genes that play a role in the senescent arrest of cellular replication are likely to be overexpressed in human diploid fibroblasts (HDF) derived from subjects with Werner syndrome (WS) because these cells have a severely curtailed replicative life span. To identify some of these genes, a cDNA library was constructed from WS HDF after they had been serum depleted and repleted (5 days in medium containing 1% serum followed by 24 h in medium containing 20% serum). Differential screening of 7,500 colonies revealed 102 clones that hybridized preferentially with [32P]cDNA derived from RNA of WS cells compared with [32P]cDNA derived from normal HDF. Cross-hybridization and partial DNA sequence determination identified 18 independent gene sequences, 9 of them known and 9 unknown. The known genes included alpha 1(I) procollagen, alpha 2(I) procollagen, fibronectin, ferritin heavy chain, insulinlike growth factor-binding protein-3 (IGFBP-3), osteonectin, human tissue plasminogen activator inhibitor type I, thrombospondin, and alpha B-crystallin. The nine unknown clones included two novel gene sequences and seven additional sequences that contained both novel segments and the Alu class of repetitive short interspersed nuclear elements; five of these seven Alu+ clones also contained the long interpersed nuclear element I (KpnI) family of repetitive elements. Northern (RNA) analysis, using the 18 sequences as probes, showed higher levels of these mRNAs in WS HDF than in normal HDF. Five selected mRNAs studied in greater detail [alpha 1(I) procollagen, fibronectin, insulinlike growth factor-binding protein-3, WS3-10, and WS9-14] showed higher mRNA levels in both WS and late-passage normal HDF than in early-passage normal HDF at various intervals following serum depletion/repletion and after subculture and growth from sparse to high-density confluent arrest. These results indicate that senescence of both WS and normal HDF is accompanied by overexpression of similar sets of diverse genes which may play a role in the senescent arrest of cellular replication and in the genesis of WS, normal biological aging, and attendant diseases.
Usefulness of immunotherapy in patients with severe summer hay fever uncontrolled by antiallergic drugs. (1991)

Immunotherapy is effective in patients with severe summer hay fever, but immediate anaphylactic reactions limit its use to specialised centres. Patient selection is extremely important, and chronic perennial asthma should be specifically excluded. As serious reactions occur within minutes a two hour wait for all patients after each injection seems unnecessary.
Purification and characterization of heme oxygenase from chick liver (1990)

A major inducible form of heme oxygenase (EC 1.14.99.3) was purified from liver microsomes of chicks pretreated with cadmium chloride. The purification involved solubilization of microsomes with Emulgen 913 and sodium cholate, followed by DEAE-Sephacel, carboxymethyl-cellulose (CM-52) and hydroxyapatite chromatography, and FPLC through Superose 6 and 12 columns operating in series. The final product gave a single band on silver-stained SDS/polyacrylamide gels (Mr = 33,000). Optimal conditions for measurement of activity of solubilized heme oxygenase were studied. In a reconstituted system containing purified heme oxygenase, NADPH-cytochrome reductase, biliverdin reductase and NADPH, the Km for free heme was 3.8 +/- 0.5 microM; for heme in the presence of bovine serum albumin (5 mol heme/3 mol albumin) the Km was 5.0 +/- 0.8 microM; and the Km for NADPH was 6.1 +/- 0.4 microM (all values mean +/- SD, n = 3). Oxygen concentration as low as 15 microM, with saturating concentrations of heme and NADPH, did not affect the reaction rate, indicating that the supply of oxygen is not involved in the physiological regulation of activity of the enzyme. The pH optimum of the reaction was 7.4; at 37 degrees C, the apparent Vmax was 580 +/- 44 nmol biliverdin.(mg protein)-1.min-1 and the molecular activity was 19.2 min-1. Biliverdin IXa was the sole biliverdin isomer formed. In the presence of purified biliverdin reductase, biliverdin was converted quantitatively to bilirubin. Addition of catalase to the reconstituted system decreased the breakdown of heme to non-biliverdin products and led to nearly stoichiometric conversion of heme to biliverdin. Activity of the enzyme in the reconstituted system was inhibited by metalloporphyrins in the following order of decreasing potency: tin mesoporphyrin greater than tin protoporphyrin greater than zinc protoporphyrin greater than manganese protoporphyrin greater than cobalt protoporphyrin. Protoporphyrin (3.3 or 6.6 microM) (and several other porphyrins) and metallic ions (100 microM) alone had little if any inhibitory effect, except for Hg2+ which inhibited by 67% at 10 microM and totally at 15 microM. Following partial cleavage, fragments of the purified enzyme were sequenced. Comparison of sequences to those derived from cDNA sequences for the major inducible rat and human heme oxygenase showed 69% and 76% similarities, respectively. The histidine residue at position 132 of rat heme oxygenase-1 and the residues (Lys128-Arg136) flanking His132 were conserved in all three enzymes, as well as in the corresponding portion of a fourth less highly similar rat enzyme, heme oxygenase-2.(ABSTRACT TRUNCATED AT 400 WORDS)
Putative synaptic genes defined from a Drosophila whole body developmental transcriptome by a machine learning approach (2015)

The utility of our approach is that it reduces the number of genes to be tested through hypothesis-driven experimentation.