gebhart/patrepeval huggingface dataset:
Retroviral Transfer of the nlsLacZ Gene into Human CD34 + Cell Populations and into TF-1 Cells: Future Prospects in Gene Therapy (1994)

Few data are available concerning behavior of reimplanted human hematopoietic cells after autologous stem cell transplantation. This paper reports the possibility to transfer gene markers coding for beta-galactosidase (beta-Gal) activity by retroviral vectors into a human leukemic growth factor-dependent cell line, TF-1, and into human hematopoietic progenitors isolated from peripheral blood or bone marrow. Using various combinations of retroviral vectors and packaging cell lines, we demonstrated high expression of a bacterial beta-Gal activity induced by the LacZ gene, the nlsLacZ gene, or the Sh-ble/LacZ gene, in human hematopoietic cells. The expression of the nlsLacZ construct was stable until the end of the culture in infected CD34+ cell-enriched cell populations, and a slow decrease of transgene expression was observed in a transduced TF-1 cell population during a 1-year long-term culture. Data obtained with the nlsLacZ gene demonstrate that both retroviral transfer and corresponding gene expression were not found to modify the pattern of cell proliferation and differentiation. These results open interesting prospectives for the use of the nlsLacZ gene to mark and follow the fate of progenitor cells isolated from patients with cancers prior to reimplantation.
Vascular Risk Factors for Incident Alzheimer Disease and Vascular Dementia (2006)

Vascular risk factors for Alzheimer disease (AD) and vascular dementia (VaD) have been evaluated; however, few studies have compared risks by dementia subtypes and sex. We evaluated relationships between cardiovascular risk factors (hypertension, high cholesterol, diabetes mellitus, and obesity), events (stroke, coronary artery bypass graft surgery, and myocardial infarction), and subsequent risk of AD and VaD by sex in a community-based cohort of 3264 Cache County residents aged 65 or older. Cardiovascular history was ascertained by self-report or proxy-report in detailed interviews. AD and VaD were diagnosed using standard criteria. Estimates from discrete-time survival models showed no association between self-reported history of hypertension and high cholesterol and AD after adjustments. Hypertension increased the risk of VaD [adjusted hazard ratio (aHR) 2.42, 95% confidence interval (CI) 0.95-7.44]. Obesity increased the risk of AD in females (aHR 2.23, 95% CI 1.09-4.30) but not males. Diabetes increased the risk of VaD in females after adjustments (aHR 3.33, 95% CI 1.03-9.78) but not males. The risk of VaD after stroke was increased in females (aHR 16.90, 95% CI 5.58-49.03) and males (aHR 10.95, 95% CI 2.48-44.78). The results indicate that vascular factors increase risks for AD and VaD differentially by sex. Future studies should focus on specific causal pathways for each of these factors with regard to sex to determine if sex differences in the prevalence of vascular factors have an influence on sex differences in dementia risk.
Cytocompatible SiC/SiOx nanowires for X-ray-excited photodynamic therapy (2015)

The development of innovative nanosystems paves the way to multidisciplinary applications at the frontier between materials science and nanomedicine. In this work we present a novel hybrid nanosystem based on cytocompatible inorganic SiC/SiOx core/shell nanowires conjugated via click-chemistry procedures with an organic photosensitizer belonging to the class of porphyrins. We show that the bare nanowires do not elicit either midterm (72 h) or long-term (10 days) cytotoxic activity leading to irreversible cellular damages or death. The hybrid nanosystem upon irradiation with 6 MV X-Rays at low doses (0.4-2 Gy) is able to generate singlet oxygen, acting therefore as an effective agent for X-Ray-excited photodynamic therapy exploitable to treat deep-seated tumors. In-vitro tests on lung adenocarcinoma cells show that the nanosystem enhances the effects of radiation therapy. As evaluated by clonogenic survival assay 12 days after irradiation at a dose of 2 Gy, the cell population is reduced with respect to control cells by about 75%.
Slim Hole Multiple Radials Drilled with Coiled Tubing (1992)

Abstract Two methods of combining water jet drilling and coiled tubing, the Ultrashort Radius Radial System (URRS) and the Quick Radial System (QRS), are described. Both provide multiple horizontal radials on a single horizon from a single vertical wellbore to penetrate near wellbore damage. The URRS requires section milling of the casing and underreaming of a cavity. The QRS penetrates the casing with abrasives. Typical field production results with both light and heavy oil are discussed.
Estimating shadow prices for Colombia in an input-output table framework (1979)

The purpose of this paper is to explain the calculation of shadow prices at the national level using the so-called Input-Output Table technique. In contrast to previous estimates of shadow prices in World Bank work, which are limited to only a few aggregate shadow prices for commodities and for labor, the new estimation technique, herein applied to the Colombian economy, permits the easy calculation of many more such prices. The larger set of pre-calculated National Accounting Prices, derived on the basis of information contained in a country's Input-Output Table, should save project economists' time while at the same time improving appraisal results. The present paper follows largely this approach as far as efficiency pricing is concerned, i.e., considering price distortions owing to export and import duties and subsidies and distribution margins biased by them. In the case of social shadow pricing, i.e., considering criteria of growth and income distribution, we follow the approach developed by Lyn Squire and Herman G. van der Tak traditionally used in World Bank work.
Are matrix metalloproteinases the missing link (2005)

It is more and more evident that the matrix metalloproteinase (MMP) system is not a characteristicfeature of vertebrate animals only, as it can also be found in many invertebrate organisms. Thisendopeptidase family has been widely studied since its first member was described 40 years agoduring metamorphosis in tadpole tails. Many researches have been carried out in mammals in order toelucidate and analyze the several and important roles these endopeptidases play, both inphysiological pathways and in pathological processes. The evolving researches of these multifacetedenzymes enter the very interesting and fascinating world of the invertebrates, where these enzymesseem to be in the front line during important biological events. MMP-like enzymes and their inhibitorshave been found in insects, crustaceans, mussels, sea urchins and also in organisms as simple ashydra. In these species MMPs partake in several fundamental processes, such as extracellular matrix(ECM) remodelling, embryonic development, cell growth and differentiation and also in defensemechanisms thus highlightening their intriguing and unexpected functional importance in invertebratelife too.
Genetic inactivation of mitochondria-targeted redox enzyme p66ShcA preserves neuronal viability and mitochondrial integrity in response to oxidative challenges (2012)

Mitochondria are essential to neuronal viability and function due to their roles in ATP production, intracellular calcium regulation, and activation of apoptotic pathways. Accordingly, mitochondrial dysfunction has been indicated in a wide variety of neurodegenerative diseases, including Alzheimer's disease (AD), Huntington's disease, amyotrophic lateral sclerosis, stroke, and multiple sclerosis (MS). Recent evidence points to the permeability transition pore (PTP) as a key player in mitochondrial dysfunction in these diseases, in which pathologic opening leads to mitochondrial swelling, rupture, release of cytochrome c, and neuronal death. Reactive oxygen species (ROS), which are inducers of PTP opening, have been prominently implicated in the progression of many of these neurodegenerative diseases. In this context, inactivation of a mitochondria-targeted redox enzyme p66ShcA (p66) has been recently shown to prevent the neuronal cell death leading to axonal severing in the murine model of MS, experimental autoimmune encephalomyelitis (EAE). To further characterize the response of neurons lacking p66, we assessed their reaction to treatment with stressors implicated in neurodegenerative pathways. Specifically, p66-knockout (p66-KO) and wild-type (WT) neurons were treated with hydrogen peroxide (H(2)O(2)) and nitric oxide (NO), and assessed for cell viability and changes in mitochondrial properties, including morphology and ROS production. The results showed that p66-KO neurons had greater survival following treatment with each stressor and generated less ROS when compared to WT neurons. Correspondingly, mitochondria in p66-KO neurons showed diminished morphological changes in response to these challenges. Overall, these findings highlight the importance of developing mitochondria-targeted therapeutics for neurodegenerative disorders, and emphasize p66, mitochondrial ROS, and the PTP as key targets for maintaining mitochondrial and neuronal integrity.
Compact, “Clickable” Quantum Dots Photoligated with Multifunctional Zwitterionic Polymers for Immunofluorescence and In Vivo Imaging (2020)

We detail the preparation of highly fluorescent quantum dots (QDs), surface-engineered with multifunctional polymer ligands that are compact and readily compatible with strain-promoted click conjugation, and the use of these nanocrystals in immunofluorescence and <i>in vivo</i> imaging. The ligand design combines the benefits of mixed coordination (i.e., thiol and imidazole) with zwitterion motifs, yielding sterically-stabilized QDs that present a controllable number of azide groups, for easy conjugation to biomolecules <i>via</i> the selective click chemistry. The polymer coating was characterized using NMR spectroscopy to extract estimates of the diffusion coefficient, hydrodynamic size, and ligand density. The azide-functionalized QDs were conjugated to anti-tropomyosin receptor kinase B antibody (α-TrkB) or to the brain-derived neurotrophic factor (BDNF). These conjugates were highly effective for labeling the tropomyosin receptor kinase B (TrkB) in pyramidal neurons within cortical tissue and for monitoring the BDNF induced activation of TrkB signaling in live neuronal cells. Finally, the polymer-coated QDs were applied for <i>in vivo</i> imaging of <i>Drosophila melanogaster</i> embryos, where the QDs remained highly fluorescent and colloidally stable, with no measurable cytotoxicity. These materials would be of great use in various imaging applications, where a small size, ease of conjugation, and great colloidal stability for <i>in vivo</i> studies are needed.
Reversible Microwave-Assisted Cycloaddition of Aziridines to Carbon Nanotubes (2007)

We report a new approach that uses microwaves to rapidly functionalize carbon nanotubes by using 1,3-dipolar cycloaddition of aziridines, well-known precursors to azomethine ylides, in solvent-free conditions. The efficiency of our microwave-mediated protocol is confirmed by comparison to a similar protocol in classical conditions for the azomethine ylides in DMF. Under these latter conditions, the reaction proceeds in 5 days (against 1 h under microwave irradiation), and the functionalization degree is much lower, as confirmed by thermogravimetric analysis and Raman spectroscopy. With our procedure, we easily scale-up the reaction up to 250 mg of functionalized MWNT in 1 h. We also provide an indirect proof of the covalent sidewall functionalization of the tubes.
A Transient Interaction between the Phosphate Binding Loop and Switch I Contributes to the Allosteric Network between Receptor and Nucleotide in Gαi1 (2014)

Receptor-mediated activation of the Gα subunit of heterotrimeric G proteins requires allosteric communication between the receptor binding site and the guanine nucleotide binding site, which are separated by >30 Å. Structural changes in the allosteric network connecting these sites are predicted to be transient in the wild-type Gα subunit, making studies of these connections challenging. In the current work, site-directed mutants that alter the energy barriers between the activation states are used as tools to better understand the transient features of allosteric signaling in the Gα subunit. The observed differences in relative receptor affinity for intact Gαi1 subunits versus C-terminal Gαi1 peptides harboring the K345L mutation are consistent with this mutation modulating the allosteric network in the protein subunit. Measurement of nucleotide exchange rates, affinity for metarhodopsin II, and thermostability suggest that the K345L Gαi1 variant has reduced stability in both the GDP-bound and nucleotide-free states as compared with wild type but similar stability in the GTPγS-bound state. High resolution x-ray crystal structures reveal conformational changes accompanying the destabilization of the GDP-bound state. Of these, the conformation for Switch I was stabilized by an ionic interaction with the phosphate binding loop. Further site-directed mutagenesis suggests that this interaction between Switch I and the phosphate binding loop is important for receptor-mediated nucleotide exchange in the wild-type Gαi1 subunit.
Two block-based motion compensation methods for video coding (1996)

Two new motion compensation methods for video coding are presented. The first method named motion-partitioned adaptive block matching algorithm (MPA-BMA) uses motion boundary information as the sub-dividing or merging criteria to form variable-size matching blocks. The second method named predictive block matching algorithm (PBMA) eliminates the need of sending motion data by predicting motion vectors from previously transmitted pixels. The performance evaluation of both algorithms are given in the experiments.
Dome: Distributed Object Migration Environment (1994)

Dome is an object based parallel programming environment for heterogeneous distributed networks of machines. This paper gives a brief overview of Dome. We show that Dome programs are easy to write. A description of the load balancing performed in Dome is presented along with performance measurements on a cluster of DEC Alpha workstations connected by a DEC Gigaswitch. A Dome program is compared with a sequential version and one written in PVM. We also present an overview of architecture independent checkpoint and restart in Dome.
Application of Pharmacophore Fingerprints to Structure‐Based Design and Data Mining (2006)

This chapter contains sections titled: Introduction Applications of 3D Pharmacophore Fingerprints Focused/Diverse Library Design Using Pharmacophore Fingerprints Analyzing Protein-Ligand Interactions Using Pharmacophore Fingerprints Virtual High-throughput Screen (vHTS) and Protein Selectivity Application of FLIP Technology Conclusion Acknowledgments References
Control of three phase power supplies for ultra low THD (2002)

Current regulators are proposed and investigated for high-power three-phase power supplies with ultra-low total harmonic distortion (THD) (less than 0.5%). Two valid approaches to realize three-phase power supplies can be proposed. In the first approach, current regulated pulse-width-modulated (PWM) inverters along with high bandwidth voltage control loops are proposed. In the second approach, an internal voltage synthesizer under closed loop current control is used. Both approaches have mechanisms to decouple the LC filter interactions and to lower the THD. The tradeoffs of these two basic approaches are investigated. The influence of different current regulators in case of the current-regulated PWM (CRPWM) converter is investigated as well as different approaches to control the voltage synthesizer under current control. The study compares the effectiveness of these current regulator in soft-switching PWM inverters and describes a method to measure accurately ultra-low THDs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Abstract 2551: New understanding of cancer induction by ionizing radiation (2012)

Abstract Ionizing radiation is a unique carcinogen that provides an opportunity to vary the location of biological damage within a cell nucleus. For example, electron and x-ray beams deposit dose uniformly and randomly, while energetic heavy ions deposit dose in densely packed straight lines along the ion paths. Cancer yields for these 2 radiations vary as follows: upward curvature with dose rate sparing for random and linearity and no dose rate sparing for heavy ions. Dose rate sparing has long been assumed to be based on biological repair, but it has never been explained why dose responses should differ between these radiation or why repair should be ineffective for heavy ions. To understand this better, consider how the distribution of a typical molecular lesion, DNA double strand breaks (DSBs), varies with the type of radiation. For heavy ions at a specific energy, DSBs are expected to be lined up at random intervals along each track, their number being proportional to average track length in each nucleus, i.e. DSBs per nucleus are proportional to radiation dose (D). Increased charge on the heavy ion causes increased lineal energy transfer (L), i.e. DSBs are also proportional to L. Similarly for heavy ions fusions between DSBs would also be proportional to D and L. The comparable scenario for randomly deposited radiation differs in that the DSBs are distributed randomly with the nuclei. Their number remains proportional to radiation dose, but now fusions would exhibit proportionality to dose-squared as a direct result of the randomness of the DSBs. Moreover randomness eliminates simultaneity. Consequently DSBs can be eliminated before second ones occur close enough to fuse, which automatically gives rise to dose rate sparing. DSB fusion yields based on the above considerations would have the form Yfusions = CfLD + BfD2 with no dose rate sparing for the first term and positive dose rate sparing for the second term. If fusions are the initial lesion of radiation carcinogenesis, then Ycancer = CcaLD + BcaD2. Extensive cancer data in rat skin based on radiations with very different L values (56Fe (L = 150 keV/µ), 40Ar (L = 125 keV/ µ), 29Ne (L = 26 keV/ µ), 1H (L = 0.34 keV/ µ).) and doses are presented that confirm the existence of independent linear and dose-squared terms and that dose rate sparing only applies to the dose-squared term. The data support the proposition that DSB fusions could be the initial lesion of radiation carcinogenesis in the rat skin model. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2551. doi:1538-7445.AM2012-2551
[Glutathione and N-acetylcysteine in the prevention of free-radical damage in the initial phase of septic shock]. (2002)

The hyperproduction of oxygen free radicals (OFR) and the weakening of natural scavenging mechanisms are implicated in endothelial damage and in multiple organ failure during septic shock. Many authors have proposed the use of antioxidants to decrease OFR damage. Glutathione (GSH) is one of the most important endogenous antioxidants. It plays the role of a sulphydryl group provider for scavenging reactions. N-Acetylcysteine (NAC) is an artificial precursor of GSH which both increases GSH levels and acts as OFR scavenger. The authors carried out a clinical trial to confirm the capacity of high doses of GSH and NAC to cooperate in reducing lipoperoxidative damage in patients with early septic shock. Patients were divided into three groups who received shock therapy only or shock therapy plus GSH or shock therapy plus GSH plus NAC. OFR damage was evaluated by measuring expired ethane, plasma malondialdehyde, complement activation and clinical scores. The study demonstrated that the group who received GSH and NAC showed a significant decrease in peroxidative indexes and an improvement of the clinical scores if compared with the other two groups. In conclusion the administration of high doses of NAC added to GSH significantly decreases the peroxidative stress of patients with early septic shock.
A borehole-model-derived algorithm for estimating QP logs from full-waveform sonic logs (2007)

Abstract We develop a processing algorithm to estimate the intrinsic seismic attenuation QP−1 from P head waves of full-waveform sonic logs. The algorithm, based on an extended version of the amplitude spectral ratio (ASR) method, corrects the apparent attenuation for the effects of multiple raypaths within the borehole, geometric spreading of head waves, and formation inhomogeneity. The algorithm is derived from two ray models. The first model simulates the interaction among rays reflected within the borehole and rays reflected from layer interfaces. This model removes these reflections and extracts the leading borehole wavelet. The second model uses a single-ray model for the borehole head wave in layered formations. This model provides the transmission coefficients across the layer interfaces between the source depth and the receiver depth with sectional geometric spreading within these layers. We use these two models to simultaneously separate, correct for, and normalize the effects of the borehole, geometric spreading, and layering. Then we test the accuracy and limits of the models using the finite-difference solution of a point source in a fluid-filled borehole surrounded by uniform and layered formations. In 255 tested cases, the absolute difference between the estimated and exact divided by the exact QP−1 is within 3% for more than half of the cases and 5% for more than two-thirds of the cases. The lower accuracy in the remaining cases is associated mainly with certain receiver locations with regard to the layer interfaces and is caused by the limitations of the ray models.
Synthesis of N-Hydroxy Peptides:  Chemical Ligation of O-Acyl Hydroxamic Acids (2000)

[process--see text] A novel chemical ligation process is described that results in the construction of N-hydroxy peptides.
Capillary Gas Chromatographic Drug Screen for Use in Forensic Toxicology (1994)

A screening method is presented involving the use of capillary gas chromatography using a BP-5 column and nitrogen-phosphorous detection. This method is a quick yet reliable procedure for a large range of neutral and basic drugs and uses 1 mL or less of blood. Running standards that contain a number of commonly observed drugs with each batch of cases allows for more accurate tentative identifications of likely drugs in unknown cases and also provides a measure of quality assurance. This method is suitable for postmortem and clinical blood samples as well as plasma and serum.
A Multicenter, Double-Blind, Placebo-Controlled Trial of Aprotinin for Reducing Blood Loss and the Requirement for Donor-Blood Transfusion in Patients Undergoing Repeat Coronary Artery Bypass Grafting (1995)

This study demonstrates that high- and low-dose aprotinin significantly reduces the requirement for donor-blood transfusion in repeat CABG patients without increasing the risk for perioperative MI.