gebhart/patrepeval huggingface dataset:
Effect of manganese ions on the incorporation of dideoxynucleotides by bacteriophage T7 DNA polymerase and Escherichia coli DNA polymerase I. (1989)

Incorporation of dideoxynucleotides by T7 DNA polymerase and Escherichia coli DNA polymerase I is more efficient when Mn2+ rather than Mg2+ is used for catalysis. Substituting Mn2+ for Mg2+ reduces the discrimination against dideoxynucleotides approximately 100-fold for DNA polymerase I and 4-fold for T7 DNA polymerase. With T7 DNA polymerase and Mn2+, dideoxynucleotides and deoxynucleotides are incorporated at virtually the same rate. Mn2+ also reduces the discrimination against other analogs with modifications in the furanose moiety, the base, and the phosphate linkage. A metal buffer, isocitrate, expands the MnCl2 concentration range effective in catalyzing DNA synthesis. The lack of discrimination against dideoxynucleoside triphosphates using T7 DNA polymerase and Mn2+ results in uniform terminations of DNA sequencing reactions, with the intensity of adjacent bands on polyacrylamide gels varying in most instances by less than 10%.
The PRC2-binding long non-coding RNAs in human and mouse genomes are associated with predictive sequence features (2017)

Recently, long non-coding RNAs (lncRNAs) have emerged as an important class of molecules involved in many cellular processes. One of their primary functions is to shape epigenetic landscape through interactions with chromatin modifying proteins. However, mechanisms contributing to the specificity of such interactions remain poorly understood. Here we took the human and mouse lncRNAs that were experimentally determined to have physical interactions with Polycomb repressive complex 2 (PRC2), and systematically investigated the sequence features of these lncRNAs by developing a new computational pipeline for sequences composition analysis, in which each sequence is considered as a series of transitions between adjacent nucleotides. Through that, PRC2-binding lncRNAs were found to be associated with a set of distinctive and evolutionarily conserved sequence features, which can be utilized to distinguish them from the others with considerable accuracy. We further identified fragments of PRC2-binding lncRNAs that are enriched with these sequence features, and found they show strong PRC2-binding signals and are more highly conserved across species than the other parts, implying their functional importance.
Cutting Edge: TLR2-Deficient and MyD88-Deficient Mice Are Highly Susceptible to Staphylococcus aureus Infection (2000)

Toll-like receptor (TLR) family acts as pattern recognition receptors for pathogen-specific molecular patterns. We previously showed that TLR2 recognizes Gram-positive bacterial components whereas TLR4 recognizes LPS, a component of Gram-negative bacteria. MyD88 is shown to be an adaptor molecule essential for TLR family signaling. To investigate the role of TLR family in host defense against Gram-positive bacteria, we infected TLR2- and MyD88-deficient mice with Staphylococcus aureus. Both TLR2- and MyD88-deficient mice were highly susceptible to S. aureus infection, with more enhanced susceptibility in MyD88-deficient mice. Peritoneal macrophages from MyD88-deficient mice did not produce any detectable levels of cytokines in response to S. aureus. In contrast, TLR2-deficient macrophages produced reduced, but significant, levels of the cytokines, and TLR4-deficient macrophages produced the same amounts as wild-type cells, indicating that S. aureus is recognized not only by TLR2, but also by other TLR family members except for TLR4.
Polycrystalline silicon films on ceramic substrates by aluminium-induced crystallisation process (2003)

Growth of polycrystalline silicon layers on ceramic substrates using the aluminium induced crystallisation (AIC) process of amorphous silicon is presented. Alumina and mullite ceramics were used as substrates as well as thermally-oxidized silicon for comparison. We have found a faster layer exchange process and therefore smaller grains in the final continuous poly-Si seed film on mullite and alumina. Raman spectroscopy confirmed the high crystalline quality of this AIC layer. Silicon epitaxy on the AIC seed layers by high temperature CVD is also reported, thanks to the ceramic substrate.
Non-high-density lipoprotein cholesterol as a risk factor: addressing risk associated with apolipoprotein B-containing lipoproteins (2004)

There is increasing interest in the use of non-high-density lipoprotein (non-HDL-C) cholesterol as a marker of coronary heart disease risk. Non-HDL-C provides a measure of all apolipoprotein B-containing lipoproteins, including very-low-density lipoprotein (VLDL), intermediate-density lipoprotein (IDL), LDL (including small, dense LDL) and lipoprotein(a), all of which have the potential to deliver cholesterol into the arterial wall. This measure thus reflects atherogenic risk not captured by low-density lipoprotein cholesterol (LDL-C) measurement alone, particularly in the context of elevated triglycerides – a setting in which there are increased concentrations of VLDL and atherogenic VLDL remnants. In patients requiring lipid-lowering therapy, non-HDL-C is currently recommended for use as a secondary outcome measure, after LDL-C, in patients with elevated triglycerides. Statins are the most effective agents for reducing levels of atherogenic lipoproteins. Consistent with its distinct pharmacologic properties compared with earlier members of the statin class, rosuvastatin reduces LDL-C significantly more than other statins and produces marked attenuation in atherogenic lipid profiles at a low dose across a wide range of dyslipidaemic phenotypes and patient subpopulations. A recent randomised, double-blind, crossover trial assessed the effects of rosuvastatin 40 mg in hypercholesterolaemic patients with normal triglyceride levels (type IIa dyslipidaemia) or elevated triglyceride levels (type IIb dyslipidaemia). In hypertriglyceridaemic patients, rosuvastatin reduced VLDL1 by 46%, VLDL2 by 42%, IDL by 54%, LDL by 58% and small, dense LDL by 69%. In normotriglyceridaemic patients, who have lower VLDL and remnant concentrations, rosuvastatin reduced VLDL1 by 18%, VLDL2 by 26%, IDL by 57%, LDL by 52% and small, dense LDL by 44%. Rosuvastatin thus has the ability to correct substantially the atherogenic lipoprotein profile across a wide range of phenotypes even when elevated concentrations of atherogenic lipoproteins are present as VLDL.
Effect of food or antacid on pharmacokinetics and pharmacodynamics of febuxostat in healthy subjects (2007)

Even though food caused a decrease in the rate and extent of absorption of febuxostat, this decrease was not associated with a clinically significant change in febuxostat pharmacodynamic effect. Despite a decrease in the absorption rate of febuxostat, antacid had no effect on the extent of febuxostat absorption. Therefore, febuxostat can be administered regardless of food or antacid intake.
Viral Vector-Based Therapeutic Cancer Vaccines (2011)

Most viruses are naturally immunogenic and can be engineered to express tumor antigen transgenes. Moreover, many types of recombinant viruses have been shown to infect professional antigen-presenting cells, specifically dendritic cells, and express their transgenes. This enhanced presentation of tumor antigens to the immune system has led to an increase in the frequency and avidity of cytotoxic T lymphocytes that target tumor cells expressing the tumor antigen(s) encoded in the vaccine vector. Logistically, recombinant viruses can be produced, administered, and quality controlled more easily compared with other immunotherapy strategies. The intrinsic properties of each virus have distinct advantages and disadvantages, which can determine their applicability in a particular therapeutic setting. The disadvantage of some vectors is the development of host-induced neutralizing antibodies to the vector itself, thus limiting its continued use. The "off-the-shelf" nature of viral vaccine platforms renders them exceptionally suitable for multicenter randomized trials. This review described and discussed the strategies used and results using viral-based vaccines, with emphasis on phases II and III clinical trials. Future directions will involve the evaluation of viral-based vaccines in the adjuvant and neoadjuvant settings, in patients with low burden metastatic disease, and in combination with other forms of therapy including immunotherapy.
Orthogonal‐plane fluorescence optical sectioning: Three‐dimensional imaging of macroscopic biological specimens (1993)

An imaging technique called orthogonal-plane fluorescence optical sectioning (OPFOS) was developed to image the internal architecture of the cochlea. Expressions for the three-dimensional point spread function and the axial and lateral resolution are derived. Methodologies for tissue preparation and for construction, alignment, calibration and characterization of an OPFOS apparatus are presented. The instrument described produced focused, high-resolution images of optical sections of an intact, excised guinea-pig cochlea. The lateral and axial resolutions of the images were 10 and 26 microns, respectively, within a 1.5-mm field of view.
Direct observation of the triplet lifetime quenching of single dye molecules by molecular oxygen (2001)

The influence of oxygen on the photophysical properties of individual DiI18 molecules has been investigated by means of both wide field and confocal scanning optical fluorescence microscopy. Excited close to saturation intensity, single-molecule fluorescence detected in wide field by a charge-coupled device camera showed a dramatic increase at exposure to air compared to the fluorescence when the sample was protected from oxygen by nitrogen flush. The change of the triplet lifetime of individual dye molecules due to oxygen quenching was measured in real time by means of time resolved single photon counting. In the presence of oxygen, the triplet state lifetime decreases from several tens of milliseconds down to fractions of a millisecond, whereas no changes of the intersystem crossing quantum yield and the fluorescence lifetime are observed. The triplet lifetimes in the presence and absence of oxygen, respectively, are anti-correlated indicative of heterogeneity of the polymer surrounding the dye molecules.
Presenilin 1 associates with glycogen synthase kinase-3β and its substrate tau (1998)

Families bearing mutations in the presenilin 1 (PS1) gene develop Alzheimer's disease. Previous studies have shown that the Alzheimer-associated mutations in PS1 increase production of amyloid beta protein (Abeta1-42). We now show that PS1 also regulates phosphorylation of the microtubule-associated protein tau. PS1 directly binds tau and a tau kinase, glycogen synthase kinase 3beta (GSK-3beta). Deletion studies show that both tau and GSK-3beta bind to the same region of PS1, residues 250-298, whereas the binding domain on tau is the microtubule-binding repeat region. The ability of PS1 to bring tau and GSK-3beta into close proximity suggests that PS1 may regulate the interaction of tau with GSK-3beta. Mutations in PS1 that cause Alzheimer's disease increase the ability of PS1 to bind GSK-3beta and, correspondingly, increase its tau-directed kinase activity. We propose that the increased association of GSK-3beta with mutant PS1 leads to increased phosphorylation of tau.
Role of Mucosal Immunity in Herpes Simplex Virus Infection (1998)

This study evaluates whether the vaginal mucosal surface of immunized mice can prevent invasion by herpes simplex virus (HSV) and aims to identify immune components that affect immunity after challenge at the vaginal mucosa. Despite the induction of both IgA and IgG vaginal Ab following immunization with recombinant vaccinia virus vectors expressing either glycoproteins B or D, viral infection occurred in most animals even after minimal viral dose challenge. Challenged immune animals, including those genetically unable to generate anti-HSV Ab, survived and showed few if any clinical signs of infection. Experiments with T cell subtype knockout animals and depletion with T cell subset-specific MAb indicated that immunity following vaginal challenge was principally dependent on the function of CD4+ T cells. Our results indicate that anti-HSV vaccines may not provide barrier immunity at the vaginal mucosal site but may be adequate to minimize clinical expression of disease.
Advances in cryogenic engineering. Volume 33 - Proceedings of the Cryogenic Engineering Conference, Saint Charles, IL, June 14-18, 1987 (1988)

Papers are presented on superconductivity applications including magnets, electronics, rectifiers, magnet stability, coil protection, and cryogenic techniques. Also considered are insulation, heat transfer to liquid helium and nitrogen, heat and mass transfer in He II, superfluid pumps, and refrigeration for superconducting systems. Other topics include cold compressors, refrigeration and liquefaction, magnetic refrigeration, and refrigeration for space applications. Papers are also presented on cryogenic applications, commercial cryogenic plants, the properties of cryogenic fluids, and cryogenic instrumentation and data acquisition.
Restriction fragment length polymorphisms mapped in spontaneously hypertensive rats using kallikrein probes (1989)

We have explored the role of kallikrein-kinin system in essential hypertension using spontaneously hypertensive rats (SHR) as an animal model. A rat tissue kallikrein complementary (c) DNA (RSK 1105) was used as a probe in Southern blot hybridization to detect restriction fragment length polymorphisms (RFLPs) in SHR. Using 23 different restriction endonucleases, we have identified five RFLPs involving alterations in restriction fragment lengths for the restriction enzymes Bgl II, Dra I, Nde I, Sph I, and Bcl I. Three of the enzymes, Nde I, Sph I, and Bgl II, generate multiple polymorphic fragments. We have further mapped these RFLPs with two additional probes, both from the rat renal kallikrein gene RSKG 7. The 5' probe, consisting of sequences approximately 2000 base pair (bp) 5' of the first exon, recognizes RFLPs in DNA digested with Bcl I and Sph I. The 3' probe, approximately 4400 bp away from the fifth exon, recognizes polymorphic fragments in DNA digested with Bcl I, Dra I and Nde I. These findings indicate possible differences in tissue kallikrein genes or their regulatory regions in SHR that could contribute to the pathogenesis of hypertension in this animal model.
T Cell Development in TCRβ Enhancer-Deleted Mice: Implications for αβ T Cell Lineage Commitment and Differentiation (2000)

T cell differentiation in the mouse thymus is an intricate, highly coordinated process that requires the assembly of TCR complexes from individual components, including those produced by the precisely timed V(D)J recombination of TCR genes. Mice carrying a homozygous deletion of the TCR beta transcriptional enhancer (E beta) demonstrate an inhibition of V(D)J recombination at the targeted TCR beta locus and a block in alpha beta T cell differentiation. In this study, we have characterized the T cell developmental defects resulting from the E beta-/- mutation, in light of previously reported results of the analyses of TCR beta-deficient (TCR beta-/-) mice. Similar to the latter mice, production of TCR beta-chains is abolished in the E beta-/- animals, and under these conditions differentiation into cell-surface TCR-, CD4+CD8+ double positive (DP) thymocytes depends essentially on the cell-autonomous expression of TCR delta-chains and, most likely, TCR gamma-chains. However, contrary to previous reports using TCR beta-/- mice, a minor population of TCR gamma delta+ DP thymocytes was found within the E beta-/- thymi, which differ in terms of T cell-specific gene expression and V(D)J recombinase activity, from the majority of TCR-, alpha beta lineage-committed DP thymocytes. We discuss these data with respect to the functional role of E beta in driving alpha beta T cell differentiation and the mechanism of alpha beta T lineage commitment.
Clinical experience with intravenous zoledronic acid in the treatment of male osteoporosis: evidence and opinions (2013)

Osteoporosis frequently remains underrecognized and undertreated in men. Most osteoporosis-related fractures could be prevented if men at risk would be diagnosed, treated, and remained compliant with therapy. Bisphosphonates, the mainstay of osteoporosis treatment, are potent antiresorptive agents that inhibit osteoclast activity, suppress in vivo markers of bone turnover, increase bone mineral density, decrease fractures, and likely improve survival in men with osteoporosis. The focus of the article is on intravenous zoledronic acid, which may be a preferable alternative to oral bisphosphonate therapy in patients with cognitive dysfunction, the inability to sit upright, polypharmacy, significant gastrointestinal pathology or suspected medication noncompliance. Zoledronic acid is approved in the United States (US) and European Union (EU) as an annual 5 mg intravenous infusion to treat osteoporosis in men. The zoledronic acid 4 mg intravenous dose has been studied in the prevention of bone loss associated with androgen deprivation therapy. This article reviews the evidence for zoledronic acid, currently the most potent bisphosphonate available for clinical use, and its therapeutic effects in the treatment of men with osteoporosis.
Photochemical crosslinked electrospun collagen nanofibers: Synthesis, characterization and neural stem cell interactions (2010)

Currently available crosslinking methods for electrospun collagen nanofibers do not preserve the fibrous architecture over prolonged periods of time. In addition, electrospinning of collagen often involves solvents that lead to extensive protein denaturation. In this study, we demonstrate the advantage of acetic acid over 1,1,1,3,3,3 hexafluoroisopropanol (HFP) in preventing collagen denaturation. A novel photochemical crosslinking method using rose bengal as the photoinitiator is also introduced. Using circular dichorism analyses, we demonstrate the fraction of collagen helical structure to be significantly greater in acetic acid-spun fibers than HFP-spun fibers (28.9 +/- 5.9% vs. 12.5 +/- 2.0%, p < 0.05). By introducing 0.1% (w/v) rose bengal into collagen fibers and subjecting these scaffolds to laser irradiation at a wavelength of 514 nm for 100 sec, biodegradable crosslinked scaffolds were obtained. Scaffold degradation as evaluated by soaking crosslinked collagen scaffolds in PBS at 37 degrees C, indicated a mass loss of 47.7 +/- 7.4% and 68.9 +/- 24.7% at day 7 and day 15, respectively. However, these scaffolds retained fibrous architecture for at least 21 days under physiological conditions. Neural stem cell line, C17.2, cultured on crosslinked collagen scaffolds proliferated after 7 days by forming a confluent layer of cells with extensive cellular projections that were indicative of neurite outgrowth. Taken together, these findings support the potential of acetic acid-electrospun photochemical crosslinked collagen nanofibers for neural tissue engineering.
Effect of low‐power laser irradiation on bony implant sites (2002)

This study was designed to examine the effects of low-energy laser irradiation on osteocytes and bone resorption at bony implant sites. Five male baboons with a mean age of 6.5 years were used in the study. Four holes for accommodating implants were drilled in each iliac crest. Sites on the left side were irradiated with a 100 mW low-energy laser (690 nm) for 1 min (6 Joule) immediately after drilling and insertion of four sandblasted and etched (Frialit-2 Synchro) implants. Five days later, the bone was removed en bloc and was evaluated histomorphometrically. The mean osteocyte count per unit area was 109.8 cells in the irradiated group vs. 94.8 cells in the control group. As intra-individual cell counts varied substantially, osteocyte viability was used for evaluation. In the irradiated group, viable osteocytes were found in 41.7% of the lacuna vs. 34.4% in the non-irradiated group. This difference was statistically significant at P < 0.027. The total resorption area, eroded surface, was found to be 24.9% in the control group vs. 24.6% in the irradiated group. This difference was not statistically significant. This study showed that osteocyte viability was significantly higher in the samples that were subjected to laser irradiation immediately after implant site drilling and implant insertion, in comparison to control sites. This may have positive effects on the integration of implants. The bone resorption rate, in contrast, was not affected by laser irradiation.
Influence of molecular weight on fatigue behavior of polyethylene and polystyrene (1977)

Abstract Fatigue tests in reversed tension‐compression have been carried out on samples of polyethylene and polystyrene of widely varying molecular weights, extending up to 2, 000, 000. All tests on polystyrene specimens were made at 1600 rpm. For polyethylene, tests speeds had to be reduced to 100 rpm in order to avoid serious temperature effects. For both materials, increasing molecular weight leads to improved resistance to alternating loading. For polystyrene, this improvement in ultimate properties even continued well beyond molecular weight values where T g , becomes effectively independent of molecular weight. For polyethylene, samples of high molecular weight did not fail even after 10 7 cycles of alternating loading at a stress level of 3000 psi.
Seismic time-frequency spectral decomposition by matching pursuit (2006)

Abstract A seismic trace may be decomposed into a series of wavelets that match their time-frequency signature by using a matching pursuit algorithm, an iterative procedure of wavelet selection among a large and redundant dictionary. For reflection seismic signals, the Morlet wavelet may be employed, because it can represent quantitatively the energy attenuation and velocity dispersion of acoustic waves propagating through porous media. The efficiency of an adaptive wavelet selection is improved by making first a preliminary estimate and then a localized refining search, whereas complex-trace attributes and derived analytical expressions are also used in various stages. For a constituent wavelet, the scale is an important adaptive parameter that controls the width of wavelet in time and the bandwidth of the frequency spectrum. After matching pursuit decomposition, deleting wavelets with either very small or very large scale values can suppress spikes and sinusoid functions effectively from the time-frequency spectrum. This time-frequency spectrum may be used in turn for lithological analysis—for instance, detection of a gas reservoir. Investigation shows that the low-frequency shadow associated with a carbonate gas reservoir still exists, even high-frequency amplitudes are compensated by inverse-Q filtering.