gebhart/patrepeval huggingface dataset:
Correlates of Peripheral Blood Mitochondrial DNA Content in a General Population (2015)

Accumulation of mitochondrial DNA (mtDNA) mutations leads to alterations of mitochondrial biogenesis and function that might produce a decrease in mtDNA content within cells. This implies that mtDNA content might be a potential biomarker associated with oxidative stress and inflammation. However, data on correlates of mtDNA content in a general population are sparse. Our goal in the present study was to describe in a randomly recruited population sample the distribution and determinants of peripheral blood mtDNA content. From 2009 to 2013, we examined 689 persons (50.4% women; mean age = 54.4 years) randomly selected from a Flemish population (Flemish Study on Environment, Genes, and Health Outcomes). Relative mtDNA copy number as compared with nuclear DNA was measured by quantitative real-time polymerase chain reaction in peripheral blood. There was a curvilinear relationship between relative mtDNA copy number and age. mtDNA content slightly increased until the fifth decade of life and declined in older subjects (Page (2) = 0.0002). mtDNA content was significantly higher in women (P = 0.007) and increased with platelet count (P < 0.0001), whereas it was inversely associated with white blood cell count (P < 0.0001). We also observed lower mtDNA content in women using estroprogestogens (P = 0.044). This study demonstrated in a general population that peripheral blood mtDNA content is significantly associated with sex and age. Blood mtDNA content is also influenced by platelet and white blood cell counts and estroprogestogen intake. Further studies are required to clarify the impact of chronic inflammation and hormone therapy on mitochondrial function.
A Review of CYP3A Drug-Drug Interaction Studies: Practical Guidelines for Patients Using Targeted Oral Anticancer Drugs (2021)

Many oral anticancer drugs are metabolized by CYP3A. Clinical drug-drug interaction (DDI) studies often only examine the effect of strong CYP3A inhibitors and inducers. The effect of moderate or weak inhibitors or inducers can be examined using physiologically based pharmacokinetic simulations, but data from these simulations are not always available early after approval of a drug. In this review we provide recommendations for clinical practice on how to deal with DDIs of oral anticancer drugs if only data from strong CYP3A inhibitors or inducers is available. These recommendations were based on reviewed data of oral anticancer drugs primarily metabolized by CYP3A and approved for the treatment of solid tumors from January 1st, 2013 to December 31st, 2015. In addition, three drugs that were registered before the new EMA guideline was issued (i.e., everolimus, imatinib, and sunitinib), were reviewed. DDIs are often complex, but if no data is available from moderate CYP3A inhibitors/inducers, a change in exposure of 50% compared with strong inhibitors/inducers can be assumed. No <i>a priori</i> dose adaptations are indicated for weak inhibitors/inducers, because their interacting effect is small. In case pharmacologically active metabolites are involved, the metabolic pathway, the ratio of the parent to the metabolites, and the potency of the metabolites should be taken into account.
Varicella-Zoster Virus ORF47 Protein Serine Kinase: Characterization of a Cloned, Biologically Active Phosphotransferase and Two Viral Substrates, ORF62 and ORF63 (2001)

Varicella-zoster virus (VZV) codes for a protein serine kinase called ORF47; the herpes simplex virus (HSV) homolog is UL13. No recombinant alphaherpesvirus serine kinase has been biologically active in vitro. We discovered that preservation of the intrinsic kinase activity of recombinant VZV ORF47 required unusually stringent in vitro conditions, including physiological concentrations of polyamines. In this assay, ORF47 phosphorylated two VZV regulatory proteins: the ORF62 protein (homolog of HSV ICP4) and the ORF63 protein (homolog of HSV ICP22). Of interest, ORF47 kinase also coprecipitated ORF63 protein from the kinase assay supernatant.
A time-frequency algorithm for the simulation of the initial transient response of oscillators (2002)

The paper presented here deals with a novel algorithm for calculating the initial transient response of an oscillator circuit. The method is based on reformulating the original system ordinary differential-algebraic equations (DAEs) by a system similar to partial differential equations (PDEs). The time-scales of the solution of the PDEs are unlike the original DAEs not widely separated. The PDE approach is therefore much better suited for CAD. Unlike existing methods the novel algorithm has a sound mathematical basis.
Global Warming: No Nuclear Quick Fix (1990)

(1990). Global Warming: No Nuclear Quick Fix. Bulletin of the Atomic Scientists: Vol. 46, No. 5, pp. 31-34.
S phase entry causes homocysteine-induced death while ataxia telangiectasia and Rad3 related protein functions anti-apoptotically to protect neurons (2010)

A major phenotype seen in neurodegenerative disorders is the selective loss of neurons due to apoptotic death and evidence suggests that inappropriate re-activation of cell cycle proteins in post-mitotic neurons may be responsible. To investigate whether reactivation of the G1 cell cycle proteins and S phase entry was linked with apoptosis, we examined homocysteine-induced neuronal cell death in a rat cortical neuron tissue culture system. Hyperhomocysteinaemia is a physiological risk factor for a variety of neurodegenerative diseases, including Alzheimer's disease. We found that in response to homocysteine treatment, cyclin D1, and cyclin-dependent kinases 4 and 2 translocated to the nucleus, and p27 levels decreased. Both cyclin-dependent kinases 4 and 2 regained catalytic activity, the G1 gatekeeper retinoblastoma protein was phosphorylated and DNA synthesis was detected, suggesting transit into S phase. Double-labelling immunofluorescence showed a 95% co-localization of anti-bromodeoxyuridine labelling with apoptotic markers, demonstrating that those cells that entered S phase eventually died. Neurons could be protected from homocysteine-induced death by methods that inhibited G1 phase progression, including down-regulation of cyclin D1 expression, inhibition of cyclin-dependent kinases 4 or 2 activity by small molecule inhibitors, or use of the c-Abl kinase inhibitor, Gleevec, which blocked cyclin D and cyclin-dependent kinase 4 nuclear translocation. However, blocking cell cycle progression post G1, using DNA replication inhibitors, did not prevent apoptosis, suggesting that death was not preventable post the G1-S phase checkpoint. While homocysteine treatment caused DNA damage and activated the DNA damage response, its mechanism of action was distinct from that of more traditional DNA damaging agents, such as camptothecin, as it was p53-independent. Likewise, inhibition of the DNA damage sensors, ataxia-telangiectasia mutant and ataxia telangiectasia and Rad3 related proteins, did not rescue apoptosis and in fact exacerbated death, suggesting that the DNA damage response might normally function neuroprotectively to block S phase-dependent apoptosis induction. As cell cycle events appear to be maintained in vivo in affected neurons for weeks to years before apoptosis is observed, activation of the DNA damage response might be able to hold cell cycle-induced death in check.
Indica Rice (<i>Oryza sativa</i>, BR29 and IR64) (2006)

Rice is the world's most important food crop. Indica-type rice provides the staple food for more than half of the world population. To satisfy the growing demand of the ever-increasing population, more sustained production of indica-type rice is needed. In addition, because of the high per capita consumption of indica rice, improvement of any traits including its nutritive value may have a significant positive health outcome for the rice-consuming population. Rice yield productivity is greatly affected by different biotic stresses, like diseases and insect pests, and abiotic stresses like drought, cold, and salinity. Attempts to improve resistance in rice to these stresses by conventional breeding through introgression of traits have limited success owing to a lack of resistance germplasm in the wild relatives. Gene transfer technology with genes from other sources can be used to make rice plants resistant or tolerant to insect pests, diseases, and different environmental stresses. For improving the nutritional value of the edible endosperm part of the rice, genes for increasing iron, beta-carotene, or better quality protein can be introduced in rice plants by genetic engineering. Different crops have been transformed using various gene transfer methods, such as protoplast transformation, biolistic, and Agrobacterium-mediated transformation. This chapter describes the Agrobacterium-mediated transformation protocol for indica-type rice. The selectable marker genes used are hygromycin phosphotransferase (hpt), neomycin phosphotransferase (nptII), or phosphomannose isomerase (pmi), and, accordingly, the selection agents are hygromycin, kanamycin (G418), or mannose, respectively.
Audio Denoising by Time-Frequency Block Thresholding (2008)

Removing noise from audio signals requires a nondiagonal processing of time-frequency coefficients to avoid producing ldquomusical noise.rdquo State of the art algorithms perform a parameterized filtering of spectrogram coefficients with empirically fixed parameters. A block thresholding estimation procedure is introduced, which adjusts all parameters adaptively to signal property by minimizing a Stein estimation of the risk. Numerical experiments demonstrate the performance and robustness of this procedure through objective and subjective evaluations.
Nail growth. Thirty-five years of observation (1980)

• A 35-year observation of the growth of my nails indicates the slowing of growth with increasing age. The average daily growth of the left thumbnail, for instance, has varied from 0.123 mm a day during the first part of the study when I was 32 years of age to 0.095 mm a day at the age of 67. (<i>Arch Intern Med</i>140:73-76, 1980)
Determination of 8-hydroxydeoxyguanosine by an immunoaffinity chromatography-monoclonal antibody-based ELISA (1995)

The postulated importance of oxidative damage to DNA in aging and age-related degenerative pathologies such as cancer has prompted efforts to develop sensitive quantitation methods. 8-Hydroxy-2'-deoxyguanosine (8-OHdG) is a widely used marker for oxidative damage to DNA. To develop an immunoassay for quantitation of 8-OHdG, two monoclonal antibodies have been developed and characterized by competitive enzyme-linked immunosorbent assay (ELISA). Antibody 1F7 has 50% inhibition at 5 pmol 8-OHdG and 1 x 10(5) pmol dG, while antibody 1F11 has 50% inhibition at 2.5 pmol 8-OHdG and 2000 pmol dG. Both antisera crossreact with guanosine and several structurally related derivatives, including 6- and 8-mercaptoguanosine, 8-bromoguanosine, 8-methylguanine, and 7-methylguanosine. Immunoaffinity columns were prepared with antibody 1F7, which exhibits higher selectivity than 1F11, to isolate 8-OHdG from DNA hydrolyzates followed by ELISA quantitation with antibody 1F11. This method allows the analysis of approximately one 8-OHdG/10(5) dG using 100 micrograms DNA. To validate the assay, DNA extracted from human placental tissues were assayed by both ELISA and HPLC with electrochemical detection. Values by both methods correlated well (r = 0.87, p < 0.001), but the levels determined by ELISA were approximately sixfold higher than those determined by HPLC. This may be due to oligonucleotides detected by the ELISA but not the HPLC method or crossreactivity with other damaged bases present in the immunoaffinity purified material. Placental samples from current smokers had significantly higher 8-OHdG by ELISA than those from nonsmokers (p < 0.05). The method of immunoaffinity purification combined with ELISA quantitation has sufficient sensitivity for detecting 8-OHdG in human DNA samples. Although absolute values are higher than those determined by HPLC, the method provides a good alternative to the HPLC-EC method for monitoring relative oxidative damage in molecular epidemiological studies.
Functional Pace-Mapping Responses for Identification of Targets for Catheter Ablation of Scar-Mediated Ventricular Tachycardia (2012)

During pace-mapping, electrograms that exhibit MES and PMI may be specific for sites critical to reentry. These functional responses hold promise for identifying important sites for catheter ablation of VT.
Characterization of some potentially probiotic Lactobacillus strains isolated from Iranian native chickens (2014)

The objective of the present study was to isolate, identify and characterize new LAB strains with high probiotic potentials from Iranian (Isfahan) indigenous chickens. From 90 isolated LABs, 11 isolates had high growth rate under different stress conditions, including acid (pH 2.5), bile (0.5% oxgall), salt (6-15%) and temperatures 15 and 45°C, and their aggregation time was less than 120 min. Based on the molecular identification using 16S rDNA sequencing and phylogenetic analysis, the isolates belonged to two Lactobacillus salivarius and L. reuteri species. The isolates showed different tolerance to 16 clinically and veterinary relevant antibiotics, and most of them were resistant to or semi-tolerant of 7-15 different studied antibiotics. The Es11, Es12, Es3 and Es13 strains with resistance to or semi-tolerance of 15, 14 and 13 different antibiotics, respectively, were the most tolerant strains. The selected isolates showed a wide range of antimicrobial activity against 7 different pathogenic strains. All the isolates exhibited antagonistic activity against E. coli, Enterococcus hirae, Salmonella enterica and Staphylococcus aureus. The isolates Es6 and Es11 with high antagonistic activity and resistance against 6 of the studied pathogens were the most powerful antagonistic isolates. The values and types of adhesion to the Caco-2 cell cultures were significantly different (0-40 bacteria/Caco-2 cell), and the maximum adhesion was observed for the isolates Es6 and Es13 with 35 and 40 bacteria adhesion/cell, respectively. Finally, based on all the experiments, 7 strains, including Es1, Es6, Es7, Es11, Es12 and Es13, were selected for the further in vivo assays and possible use in the poultry industry.
Estimation of Local Attenuation and Its Application to Rationalized Gain Control (2007)

The aim of this paper is to provide a local attenuation estimation algorithm from ultrasound images. Using the computed attenuation coefficients locally, we define a 2-D table for tissue attenuation compensation in the sense of a rationalized gain control. To handle the frequency shift in the broadband system, we use nonlinear least squares (NLS) data fitting directly to the local amplitude changes due to the tissue attenuation. By looking at the convergence of the NLS method, e.g., the Levenberg-Marquardt algorithm, we proposed a technique to test the possible tissue heterogeneity locally. Algorithms have been verified both in phantom and in vivo images. Results showed that the proposed method can have at most 4% relative error in estimating attenuation coefficients of phantom images in a broadband system. It also showed a uniform in vivo image after the proposed rationalized gain control.
Pulsed power performance of PBFA Z (2002)

PBFA Z is a new 60 TW/5 MJ electrical driver located at Sandia National Laboratories. The authors use PBFA Z to drive Z pinches. The pulsed power design of PBFA Z is based on a conventional single-pulse Marx generator, water-line pulse-forming technology used on the earlier Saturn and PBFA II accelerators. PBFA Z stores 11.4 MJ in its 36 Marx generators, couples 5 MJ in a 60 TW/105 ns pulse to the output water transmission lines, and delivers 3.0 MJ and 50 TW of electrical energy to the Z-pinch load. Depending on the initial load inductance and the implosion time, one attains peak currents of 16-20 MA with a rise time of 105 ns. Current is fed to the Z-pinch load through self magnetically-insulated transmission lines (MITLs). Peak electric fields in the MITLs exceed 2 MV/cm. The current from the four independent conical-disk MITLs is combined together in a double post-hole vacuum convolute with an efficiency greater than 95%. The authors achieved X-ray powers of 200 TW and X-ray energies of 1.9 MJ from a tungsten wire-array Z-pinch loads.
Pharmacological classes that extend lifespan of Caenorhabditis elegans (2015)

Recent progress in the field of aging has resulted in ever increasing numbers of compounds that extend lifespan in Caenorhabditis elegans. Lifespan extending compounds include metabolites and synthetic compounds, as well as natural products. For many of these compounds, mammalian pharmacology is known, and for some the actual targets have been experimentally identified. In this review, we explore the data available in C. elegans to provide an overview of which pharmacological classes have potential for identification of further compounds that extend lifespan.
A simple method for extracting the natural beauty of hair (1992)

A simple differential equation method is proposed for modeling the aesthetic features of human hair. In the method, a simplified cantilever beam simulation is employed for hairstyle modeling, which allows hairdressing variations with volumetric and realistic appearance. In order to describe the dynamical behavior of hair in an animation, one-dimensional projective differential equations of angular momenta for linked rigid sticks are also derived. For the problem of collision detection between hair and a human head, the "rough" approximate solution is provided, which gives visually satisfactory results by solving the projective equations under a ps~udo-force field. The hair's pliability can be controlled by using a set of stiffness parameters in the method. In addition, a fast rendering technique for anisotropic reflection is introduced, which is derived from Blirm's specular model. The efficiency of the proposed method is illustrated by the still images and short animations obtained.
Investigation of Treatment Failure in Neonatal Echovirus 7 Infection (2006)

We describe a case of fatal neonatal enteroviral infection caused by echovirus 7. Multiple treatments, including specific antiviral therapy, were attempted and failed. Studies of the viral isolate, maternal plasma, intravenous immunoglobulin preparations and pleconaril were performed to identify potential causes for treatment failure.
SU‐E‐T‐640: Proton Modulated Arc Therapy Using Scanned Pencil Beams (2015)

Purpose: Rotational proton radiotherapy would be an interesting treatment modality if it proves to produce dose distributions that conform to the target as well or better than currently available treatment modalities, while reducing the dose to the surrounding organs at risk. A treatment planning study is presented, showing how this objective can be achieved using a single or small number of scanned mono‐energetic pencil beams delivered while the proton gantry rotates at the same time that they may deliver faster and more biologically effective treatments than current proton modalities.Methods Proton treatment using single‐ (SFO) and multi‐field optimized (MFO) PBS plans are compared with PMAT plans in phantoms of different shape and uniformity as well as on a brain case. The method followed in ECLIPSE to produce PMAT plans is presented and the feasibility is discussed. Results Table 1 shows that the conformity and uniformity of the PMAT plans is of similar order than those of the SFO and MFO plans. However, in the brain case, the DVHs shown in Figure 1 indicate a significant reduction of the dose to the OARs when PMAT is used. Similarly, the use of PMAT increases the LET in the treatment area, which could translate into a more biologically effective treatment.Conclusions PMAT could provide dose distributions as conformal as current PBS plans but could also offer faster beam delivery and more biologically effective proton plans.
Low voltage FE-STEM for characterization of state-of-the-art silicon SRAM (2002)

Low voltage (30 kV) field emission scanning transmission electron microscopy (FE-STEM) has been employed in the characterization of state-of-the-art semiconductor static random access memory (SRAM) using specimens prepared at several different thicknesses (70-180 nm). A focused ion beam (FIB) system, a FIB-SEM compatible specimen holder and an in-lens FE-SEM have been employed for alternating between FIB milling and SEM/ STEM imaging. As a result, ion implanted atom damage during manufacturing, grains in aluminium interconnects, poly silicon gates, thin metal barriers and a thin gate oxide layer were observed by low voltage FE-STEM. STEM, in-lens FESEM, FIB
Kinetics of the gas‐phase reactions of Cl atom with selected C2–C5 unsaturated hydrocarbons at 283 < T < 323 K (2000)

The reaction of Cl atoms with a series of C2–C5 unsaturated hydrocarbons has been investigated at atmospheric pressure of 760 Torr over the temperature range 283–323 K in air and N2 diluents. The decay of the hydrocarbons was followed using a gas chromatograph with a flame ionization detector (GC-FID), and the kinetic constants were determined using a relative rate technique with n-hexane as a reference compound. The Cl atoms were generated by UV photolysis (λ ≥ 300 nm) of Cl2 molecules. The following absolute rate constants (in units of 10−11 cm3 molecule−1 s−1, with errors representing ±2σ) for the reaction at 295 ± 2 K have been derived from the relative rate constants combined to the value 34.5 × 10−11 cm3 molecule−1 s−1 for the Cl + n-hexane reaction: ethene (9.3 ± 0.6), propyne (22.1 ± 0.3), propene (27.6 ± 0.6), 1-butene (35.2 ± 0.7), and 1-pentene (48.3 ± 0.8). The temperature dependence of the reactions can be expressed as simple Arrhenius expressions (in units of 10−11 cm3 molecule−1 s−1): kethene = (0.39 ± 0.22) × 10−11 exp{(226 ± 42)/T}, kpropyne = (4.1 ± 2.5) × 10−11 exp{(118 ± 45)/T}, kpropene = (1.6 ± 1.8) × 10−11 exp{(203 ± 79)/T}, k1-butene = (1.1 ± 1.3) × 10−11 exp{(245 ± 90)/T}, and k1-pentene = (4.0 ± 2.2) × 10−11 exp{(423 ± 68)/T}. The applicability of our results to tropospheric chemistry is discussed. © 2000 John Wiley & Sons, Inc. Int J Chem Kinet 32: 478–484, 2000
TFD: The transcription factors database (1992)

Journal Article TFD: The transcription factors database Get access David Ghosh David Ghosh National Center for Biotechnology InformationNLM, NIH, Bethesda, MD 20894, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 20, Issue suppl, 11 May 1992, Pages 2091–2093, https://doi.org/10.1093/nar/20.suppl.2091 Published: 11 May 1992
New fully differential variable gain instrumentation amplifier based on a DDA topology (2003)

A two-stage Fully differential Differential Difference Amplifier (FDDA) cell is presented. The input linear transconductance ports and the two stage topology are referred and the open-loop characteristics discussed. Based on this fully differential analogue cell, a new fully differential variable gain instrumentation amplifier is proposed. This new topology is based on the previous described FDDA cell, with a voltage-controlled differential transconductance cell used on the feedback loop of the amplifier to control the amplifier's gain. The gains can be continuously tuned within one decade variation range by a controlling voltage V/sub g/. This decade range is set by two equal feedback resistors R/sub g/. Simulation results are discussed and applications of these analogue building blocks in a modular architecture for smart sensor development are referred to.