gebhart/patrepeval huggingface dataset:
A comparative study of the thermal stability of oligodeoxyribonucleotides containing 5-substituted 2'-deoxyuridines (1998)

Two series of modified oligonucleotides based on the self-complementary dodecamer d(CGCTAATTAGCG) were synthesized. The first contained the -C identical withCCH2R linker at C5 of deoxyuridine at position 4 (T*) of d(CGCT*AATTAGCG) and the second contained the -SR linker. The goal of the study was to evaluate and compare these two types of side chains for suitability as tethers for linking reporter groups to oligonucleotides. Our primary concern was how these tethers would effect duplex stability. The modified nucleosides were synthesized by palladium-mediated coupling reactions between the substituted alkyne and 5'-(4, 4'-dimethoxytrityl)-5-iodo-2'-deoxyuridine and between a disulfide and 5-chloromercurio-2'-deoxyuridine. The C5 deoxyuridine side chains evaluated included C identical with CCH3, C identical with CCH2NHC(O)CH3, C identical with CCH2N(CH3)2, C identical with CCH2N-HC(O)C5H4N, C identical with CCH2NHC(O)C10H15, SCH3, SC6H5 and SCH2CH2NHC(O)CH3. The nucleosides containing these substituents were incorporated into oligo-deoxyribonucleotides by standard phosphoramidite methodology. Melting studies demonstrated that the sequence containing the C identical with CCH3side chain had the highest T m value (59.1 degrees C) in comparison with the control sequence (T m = 55.2 degrees C) and that any additional substituent on C3 of the propynyl group lowered the T m value relative to propynyl. Nevertheless, even the most destabilizing substituent, adamantylcarbamoyl, yielded an oligodeoxyribonucleotide that dissociated with a T m of 54 degrees C, which is only 1.2 degrees C less than the control sequence. In contrast, the thioether substituents led to lower T m values, ranging from as low as 45.1 degrees C for SPh up to 52.2 degrees C for SMe. Replacing the methyl of the SMe substituent with a CH2CH2NHC(O)CH3 tether led to no further reduction in melting temperature. The T m value of the CH2CH2NHC(O)CH3-containing oligonucleotide was less than the natural sequence by 1.6 degrees C/substituent. This is sufficiently small that it is anticipated that the C5 thioether linkage may be as useful as the acetylenic linkage for tethering reporter groups to oligonucleotides. More importantly, the thioether linkage provides a means to position functional groups to interact specifically with opposing complementary (target) sequences.
A Novel Approach for Nontargeted Data Analysis for Metabolomics. Large-Scale Profiling of Tomato Fruit Volatiles (2005)

To take full advantage of the power of functional genomics technologies and in particular those for metabolomics, both the analytical approach and the strategy chosen for data analysis need to be as unbiased and comprehensive as possible. Existing approaches to analyze metabolomic data still do not allow a fast and unbiased comparative analysis of the metabolic composition of the hundreds of genotypes that are often the target of modern investigations. We have now developed a novel strategy to analyze such metabolomic data. This approach consists of (1) full mass spectral alignment of gas chromatography (GC)-mass spectrometry (MS) metabolic profiles using the MetAlign software package, (2) followed by multivariate comparative analysis of metabolic phenotypes at the level of individual molecular fragments, and (3) multivariate mass spectral reconstruction, a method allowing metabolite discrimination, recognition, and identification. This approach has allowed a fast and unbiased comparative multivariate analysis of the volatile metabolite composition of ripe fruits of 94 tomato (Lycopersicon esculentum Mill.) genotypes, based on intensity patterns of >20,000 individual molecular fragments throughout 198 GC-MS datasets. Variation in metabolite composition, both between- and within-fruit types, was found and the discriminative metabolites were revealed. In the entire genotype set, a total of 322 different compounds could be distinguished using multivariate mass spectral reconstruction. A hierarchical cluster analysis of these metabolites resulted in clustering of structurally related metabolites derived from the same biochemical precursors. The approach chosen will further enhance the comprehensiveness of GC-MS-based metabolomics approaches and will therefore prove a useful addition to nontargeted functional genomics research.
Real time 4D IMRT treatment planning based on a dynamic virtual patient model: Proof of concept (2011)

The 4D model-based planning, which applies dynamic virtual patient models in IMRT treatment planning, can account for the real time deformable motion of the tumor under different breathing conditions. Under regular motion, the quality of 4DMP plans was comparable with IP and superior to MIP. Under realistic motion in which breathing amplitude and period change, 4DMP gave the best plan quality of the three 4D treatment planning techniques.
Determination of metal cations on miniaturised planar polymeric separation devices using isotachophoresis with integrated conductivity detection (2001)

The feasibility of using miniaturised planar polymeric separation devices for the isotachophoretic separation of metal cations was demonstrated. Devices were produced in silicone rubber using a cast moulding fabrication technique. Detection was performed using an integrated single electrode conductivity detector, a design which offers simple fabrication and high resolution. The electrical characteristics of the devices were found to be suitable for performing electroseparations with a power dissipation of up to 1.5 W m-1 being achieved. The separation of a sample containing a mixture of the four metal ions lithium, lanthanum, dysprosium and ytterbium was reproducibly achieved using miniaturised devices. A comparison with a capillary scale separation of the same mixture was made. The miniaturised separations were achieved in under 600 s, which is less than half the time taken for the capillary scale separations.
Mitigation of CSI Temporal Phase Rotation with B2B Calibration Method for Fine-Grained Motion Detection Analysis on Commodity Wi-Fi Devices (2018)

Limitations of optical devices for motion sensing such as small coverage, sensitivity to obstacles, and privacy exposure result in the need for improvement. As motion sensing based on radio frequency signals is not constrained by the limitation above, channel state information (CSI) from Wi-Fi devices could be used to improve sensing performance under the above circumstances. Unfortunately, CSI phase cannot be practically obtained due to the temporal phase rotation generated from Wi-Fi chips. Therefore, it would be rather complicated to realize motion analysis, especially the direction of motion. To mitigate the issue, this paper proposes a CSI calibration method that employs a back-to-back channel between Wi-Fi transceivers for phase rotation removal while preserving the original CSI phase. Through experiment, calibrated CSI showed a high similarity to the channel without phase rotation measured using a Vector Network Analyzer (VNA). Another experiment was conducted to observe Doppler frequency due to simple hand gestures using the Wavelet transform. A visual analysis revealed that the Doppler frequency of calibrated CSI could correctly capture the motion pattern. To the best of the authors' knowledge, this is the first calibration method that maintains the original CSI and is applicable for in-depth motion analysis.
Synthesis and Conformation of Fluorinated β‐Peptidic Compounds (2012)

Experimental and theoretical data indicate that, for α-fluoroamides, the F-C-C(O)-N(H) moiety adopts an antiperiplanar conformation. In addition, a gauche conformation is favoured between the vicinal C-F and C-N(CO) bonds in N-β-fluoroethylamides. This study details the synthesis of a series of fluorinated β-peptides (1-8) designed to use these stereoelectronic effects to control the conformation of β-peptide bonds. X-ray crystal structures of these compounds revealed the expected conformations: with fluorine β to a nitrogen adopting a gauche conformation, and fluorine α to a C=O group adopting an antiperiplanar conformation. Thus, the strategic placement of fluorine can control the conformation of a β-peptide bond, with the possibility of directing the secondary structures of β-peptides.
What is the Ideal Pulse Frequency for Skeletal Muscle Stimulation After Cardiomyoplasty? (1991)

Routinely the latissimus dorsi (LD) muscle is stimulated with bursts of pulses at 30 pulses/sec after cardiomyoplasty to assist the failing heart. At a lower pulse frequency the contractile force decreases and at higher frequencies the energy demand of the pacemaker increases rapidly. We investigated the effect of the stimulus frequency variation on contractile force in untrained LD muscles and in muscles after 12 weeks of continuous cyclic electrical stimulation. In six dogs, two electrodes (Medtronic SP5528) were implanted in the left LD muscle together with an Itrel muscle stimulator. The LD muscle was stimulated with 30 pulses/sec in bursts to deliver initially 30 and after 10 weeks 80 contractions per minute. Both before and after training of the LD muscle maximum force was observed by stimulating with a frequency of 36 to 130 pulses/sec in a burst. However, training induced a shift in the steep part of the force-frequency relation to lower frequencies. In particular, at 15 pulses/sec 60% of the maximal force was obtained in contrast to 40% before training. A fatigue test of 8 minutes duration was performed specified by 100 bursts/min and a burst duration of 0.25 sec at pulse frequencies of 30, 36, 50, and 85 pulses/sec. The contractile force decreased significantly during the course of the test at all frequencies. However, the force obtained with 30 pulses/sec stimulation was lower during the initial phase and approximately 10% higher at the end of the fatigue test as compared to 36, 50, and 85 pulses/sec stimulation.(ABSTRACT TRUNCATED AT 250 WORDS)
Myocardin is required for cardiomyocyte survival and maintenance of heart function (2009)

Despite intense investigation over the past century, the molecular mechanisms that regulate maintenance and adaptation of the heart during postnatal development are poorly understood. Myocardin is a remarkably potent transcriptional coactivator expressed exclusively in cardiac myocytes and smooth muscle cells during postnatal development. Here we show that myocardin is required for maintenance of cardiomyocyte structure and sarcomeric organization and that cell-autonomous loss of myocardin in cardiac myocytes triggers programmed cell death. Mice harboring a cardiomyocyte-restricted null mutation in the myocardin gene (Myocd) develop dilated cardiomyopathy and succumb from heart failure within a year. Remarkably, ablation of the Myocd gene in the adult heart leads to the rapid-onset of heart failure, dilated cardiomyopathy, and death within a week. Myocd gene ablation is accompanied by dissolution of sarcomeric organization, disruption of the intercalated disc, and cell-autonomous loss of cardiomyocytes via apoptosis. Expression of myocardin/serum response factor-regulated myofibrillar genes is extinguished, or profoundly attenuated, in myocardin-deficient hearts. Conversely, proapoptotic factors are induced and activated in myocardin-deficient hearts. We conclude that the transcriptional coactivator myocardin is required for maintenance of heart function and ultimately cardiomyocyte survival.
AA1, a newly synthesized monovalent lipophilic cation, expresses potent in vivo antitumor activity. (1994)

Certain lipophilic cations have been reported to display anticarcinoma activities because of their selective uptake and retention by mitochondria of cancer cells. Thus, these agents may comprise a unique class of agents directed against carcinoma. After screening more than 1000 lipophilic cations, we found that the monovalent lipophilic cation, 2,6-bis(4-amino-phenyl)-4-[4-(dimethylamino)phenyl]thiopyrylium chloride (AA1), displayed remarkable anticarcinoma activity both in vitro and in vivo. Unlike most other lipophilic cations, AA1 is stable and displays minimal light sensitivity. In vitro testing showed that AA1 was 10 times more toxic to the carcinoma cell line CX-1 than to the normal epithelial cell line CV-1. In vivo animal experiments showed that AA1 significantly prolonged the survival of mice implanted with tumors. For C57BL x DBA/2 F1 mice implanted with the mouse bladder carcinoma cell line, MB49, the treated:control ratio was 344%. For Swiss nu/nu mice implanted i.p. with the human melanoma cell line, LOX, the treated:control ratio was 341%. The most significant observation was obtained with Swiss nu/nu mice that were implanted i.p. with the human ovarian cell line, OVCAR-III. The treated:control ratio in this situation was greater than 450%. In all these tumor models, AA1 produced minimal toxicities. AA1 exhibited little inhibition of electron transport in isolated rat liver mitochondria; however, it inhibited mitochondrial ATPase with 50% inhibitory concentration of 6 microM. Compared with previously reported anticarcinoma lipophilic cations such as rhodamine 123 and dequalinium chloride, AA1 appeared to display more effective in vivo anticarcinoma activity. Thus, AA1 could be considered for further clinical development as a candidate for anticarcinoma chemotherapy.
Transport of endocannabinoids across the plasma membrane and within the cell (2013)

Endocannabinoids are readily accumulated from the extracellular space by cells. Although their uptake properties have the appearance of a process of facilitated diffusion, it is by no means clear as to whether there is a plasma membrane transporter dedicated to this task. Intracellular carrier proteins that shuttle the endocannabinoid anandamide from the plasma membrane to its intracellular targets such as the metabolic enzyme, fatty acid amide hydrolase, have been identified. These include proteins with other primary functions, such as fatty-acid-binding proteins and heat shock protein 70, and possibly a fatty acid amide hydrolase-like anandamide transporter protein. Thus, anandamide uptake can be adequately described as a diffusion process across the plasma membrane followed by intracellular carrier-mediated transport to effector molecules, catabolic enzymes and sequestration sites, although it is recognized that different cells are likely to utilize different mechanisms of endocannabinoid transport depending upon the utility of the endocannabinoid for the cell in question.
Development of a sensitive, stable and EGFR‐specific molecular imaging agent for surface enhanced Raman spectroscopy (2015)

We created and studied a novel nanoprobe for spectroscopic molecular imaging of the epidermal growth factor (EGF) receptor, whose over‐expression is a hallmark of a wide range of cancers. Silver nanoparticles (AgNPs) of 45 nm diameter were synthesized and coupled to EGF by α ‐lipoic acid, a short ligand that exhibits excellent silver binding affinity. Time‐of‐flight mass spectroscopy demonstrates formation of the protein complex. Enzyme‐linked immunosorbent assay verifies the protein complex is 100% active for the EGF receptor, alone and, following conjugation to silver nanoparticles. Compared with its monosulfide analog, 6‐mercaptohexanoic acid, α ‐lipoic acid is stabilized by binding to silver with a total energy that is lower by 1.38 eV, as found from Density Functional Theory (DFT)/natural bond analysis calculations. A Highest Occupied Molecular Orbital (HOMO)‐Lowest Unoccupied Molecular Orbital (LUMO) gap energy of 5.25 (spin‐up electrons) and 5.74 eV (spin‐down electrons) was obtained for the silver‐ α ‐lipoic acid complex. This is the first report of silver nanoparticles being attached to EGF, and the first theoretical and experimental report on the surface enhanced Raman spectroscopy spectral interpretation of α ‐lipoic acid bound to silver. These nanoprobes exhibit surface enhanced Raman spectroscopy, when aggregated in solution, at picomolar concentrations and have the necessary properties – specificity, sensitivity and stability – to serve as molecular imaging agents. Copyright © 2015 John Wiley & Sons, Ltd.
Independent Component Analysis of Real Data (2009)

Independent component analysis (ICA) is a statistical method used to discover hidden factors (sources or features) from a set of measurements or observed data such that the sources are maximally independent. The ICA algorithms are able to separate the sources according to the distribution of the data. The original Infomax algorithm for blind separation is better suited to estimation of super-Gaussian sources. FastICA can separate the sources having non-Gaussian distributions. Real data (e.g. functional magnetic resonance imaging (fMRI) data and speech signal obtained at cocktail party problem) is having Gaussian and non-Gaussian distributions. So existing ICA algorithms such as the Infomax, FastICA can not separate the independent components from the real data. For proper separation of independent components we have tried with different ICA algorithms. Recently developed Combi ICA can separate the independent components from real data faithfully. Because the Combi ICA can separate the sources having non-Gaussian and Gaussian distributions. In this paper, we find the independent components by a number of ICA algorithms from which Efficient FastICA and Combi ICA are found to be good because the accuracy in terms of the variance of the gain matrix (Amari Performance Index) is more as compared to others. In our work we 1) used the kurtosis and negentropy to know the distribution of data 2) review the analysis methods for finding independent components from real data (specially fMRI data), 3) comparison of different ICA algorithms. The purpose of this work is to have an idea about the problems, challenges and methods about analysis of independent components from real data.
Suppression of growth in vitro and tumorigenicity in vivo of human carcinoma cell lines by transfectedp16INK4 (1996)

The function of p16INK4 as a putative tumor suppressor gene was examined by investigating its ability to inhibit the growth of cancer cell lines in vitro and tumor formation in vivo. A p16INK4 cDNA expression vector was transfected into five human cancer cell lines that varied in their p16INK4 and retinoblastoma (Rb) status. Suppression of colony-forming efficiency was seen in four cell lines. Of two cell lines wild type for p16INK4 but null for Rb protein expression, one (Hep 3B) showed inhibition of colony formation, whereas the other (Saos-2) did not. This observation may demonstrate involvement of p16INK4 independent of Rb. The transfected p16INK4 gene was frequently selected against and lost during continued growth in vitro. When compared to the colon carcinoma cell line (DLD-1),p16INK4-transfected DLD-1 clone 1 cells were less tumorigenic in athymic nude mice. Tumors arising from p16INK4-transfected DLD-1 clones, which were growth suppressed in vitro, either lost the integrated exogenous p16INK4 or expressed reduced amounts of p16INK4 protein. Therefore, p16INK4 was also selected against during tumor formation in vivo. These data are consistent with the hypothesis that p16INK4 is a tumor suppressor gene.
CARE: cache guided deterministic replay for concurrent Java programs (2014)

Deterministic replay tools help programmers debug concurrent programs. However, for long-running programs, a replay tool may generate huge log of shared memory access dependences. In this paper, we present CARE, an application-level deterministic record and replay technique to reduce the log size. The key idea of CARE is logging read-write dependences only at per-thread value prediction cache misses. This strategy records only a subset of all exact read-write dependences, and reduces synchronizations protecting memory reads in the instrumented code. Realizing that such record strategy provides only value-deterministic replay, CARE also adopts variable grouping and action prioritization heuristics to synthesize sequentially consistent executions at replay in linear time. We implemented CARE in Java and experimentally evaluated it with recognized benchmarks. Results showed that CARE successfully resolved all missing read-write dependences, producing sequentially consistent replay for all benchmarks. CARE exhibited 1.7--40X (median 3.4X) smaller runtime overhead, and 1.1--309X (median 7.0X) smaller log size against state-of-the-art technique LEAP.
Comparison of manual and autopilot breakout maneuvers with three closely spaced parallel runway approaches (2009)

This study used a high-fidelity flight simulator to explore approach operations for three closely-spaced parallel runways using autopilot and manually flown breakout procedures. An initial study investigated the concept under manual control mode only. The concept aimed to achieve visual meteorological conditions capacities under instrument meteorological conditions when landing aircraft on runways as close as 750 ft apart. This investigation studied procedures related to autopilot breakout maneuvers for triple parallel aircraft flying in an echelon formation and compared them to the manual procedures investigated earlier. All of the data collection runs had an off-nominal situation, which was either caused by the wake of the lead aircraft drifting too close to the center and trailing aircraft, or the lead aircraft deviating from its course and blundering towards the center and trailing aircraft. The location of the off-nominal situation (high/low altitude) and the position of the ownship (center or right runway) were also manipulated. Statistically significant results showed that autopilot breakout maneuvers were flown more accurately than manual breakout maneuvers. Some improved lateral separation was also observed between the paired aircraft while the autopilot was used, which could be attributed to the improved accuracies with which the breakout maneuver was flown using autopilot. On the subjective ratings, pilots experienced reduced workload, a similar level of situation awareness, and a reduced level of situational demands under the autopilot condition. Objective and subjective data from the current study extends the results from the previous research, with some evidence to suggest further improvement in these factors when autopilot breakout procedures are used.
DNA and Free Radicals (1993)

Oxidants are major contributors to cancer and aging. Part 1 Chemistry and measurement of damage to DNA by reactive oxygen species: chemistry of free radical damage to DNA and nucleoproteins DNA damage induced by photosensitization oxidative damage - meaning and measurement. Part 2 Mechanism of DNA damage by oxidative stress: hydrogen peroxide and DNA damage oxidative stress and calcium homeostasis lipid peroxidation and cancer the role of organic peroxyl radicals carcinogenesis. Part 3 Consequences of oxidative DNA damage: enzymes that repair oxidative damage to DNA sex as a response to oxidative DNA damage oxidative stress and cell proliferation in vitro ornithine decarboxylase and tumour promotion - a role for oxidants. Part 4 Pro-oxidants and DNA damage: redox cycling drugs and DNA damage role of reactive oxygen species the mutagenicity of complex mixtures of plant origin mineral fibres, cigarette smoke and oxidative DNA damage use of DNA damage as a measure of pro-oxidant actions of antioxidant food additives and nutrient components.