gebhart/patrepeval huggingface dataset:
Inference of gene regulatory model by genetic algorithms (2002)

Presents an application of genetic algorithms (GAs) to the gene network inference problem; this is one of the active topics in recent bioinformatics. The objective is to predict a regulating network structure of the interacting genes from the observed outcome, i.e. expression pattern. The task consists of modeling the rules of regulation and inferring the network structure from the observed data. The GA is applied to training the model with observed data in order to predict the regulatory pathways, represented as an influence matrix. We have implemented a reverse engineering method based on GAs in a quantitative and linear biological framework. The merit of this approach is that it can be applied with a small amount of data, it can optimize large numbers of parameters simultaneously and it can be applied to nonlinear models. The GA implementation includes multi-stage evolution and matrix chromosomes. This method has been applied to both simulated and experimentally observed gene expression patterns. In this research, we used the knowledge of designing an electric circuit by a GA.
Offset-compensated switched-capacitor integrators (2002)

The performance of several switched-capacitor (SC) integrators is compared, and a description representation is introduced. Offset-compensated circuits which reduce the capacitance spread in very large time-constant SC integrators are presented. The theoretical equations are derived for all SC circuits and are then confirmed by simulations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Self-Motions of General 3-<i><u>R</u>PR</i> Planar Parallel Robots (2008)

We study the kinematic geometry of general 3-RPR planar parallel robots with actuated base joints. These robots, while largely overlooked, have simple direct kinematics and large singularity-free workspace. Furthermore, their kinematic geometry is the same as that of a newly developed parallel robot with SCARA-type motions. Starting from the direct and inverse kinematic model, the expressions for the singularity loci of 3-RPR planar parallel robots are determined. Then, the global behavior at all singularities is geometrically described by studying the degeneracy of the direct kinematic model. Special cases of self-motions are then examined and the degree of freedom gained in such special configurations is kinematically interpreted. Finally, a practical example is discussed and experimental validations performed on an actual robot prototype are presented.
A Microchannel Neuroprosthesis for Bladder Control After Spinal Cord Injury in Rat (2013)

A severe complication of spinal cord injury is loss of bladder function (neurogenic bladder), which is characterized by loss of bladder sensation and voluntary control of micturition (urination), and spontaneous hyperreflexive voiding against a closed sphincter (detrusor-sphincter dyssynergia). A sacral anterior root stimulator at low frequency can drive volitional bladder voiding, but surgical rhizotomy of the lumbosacral dorsal roots is needed to prevent spontaneous voiding and dyssynergia. However, rhizotomy is irreversible and eliminates sexual function, and the stimulator gives no information on bladder fullness. We designed a closed-loop neuroprosthetic interface that measures bladder fullness and prevents spontaneous voiding episodes without the need for dorsal rhizotomy in a rat model. To obtain bladder sensory information, we implanted teased dorsal roots (rootlets) within the rat vertebral column into microchannel electrodes, which provided signal amplification and noise suppression. As long as they were attached to the spinal cord, these rootlets survived for up to 3 months and contained axons and blood vessels. Electrophysiological recordings showed that half of the rootlets propagated action potentials, with firing frequency correlated to bladder fullness. When the bladder became full enough to initiate spontaneous voiding, high-frequency/amplitude sensory activity was detected. Voiding was abolished using a high-frequency depolarizing block to the ventral roots. A ventral root stimulator initiated bladder emptying at low frequency and prevented unwanted contraction at high frequency. These data suggest that sensory information from the dorsal root together with a ventral root stimulator could form the basis for a closed-loop bladder neuroprosthetic.
Antimicrobial and Chemopreventive Properties of Herbs and Spices (2004)

Herbs and spices have been used for generations by humans as food and to treat ailments. Scientific evidence is accumulating that many of these herbs and spices do have medicinal properties that alleviate symptoms or prevent disease. A growing body of research has demonstrated that the commonly used herbs and spices such as garlic, black cumin, cloves, cinnamon, thyme, allspices, bay leaves, mustard, and rosemary, possess antimicrobial properties that, in some cases, can be used therapeutically. Other spices, such as saffron, a food colorant; turmeric, a yellow colored spice; tea, either green or black, and flaxseed do contain potent phytochemicals, including carotenoids, curcumins, catechins, lignan respectively, which provide significant protection against cancer. This review discusses recent data on the antimicrobial and chemopreventive activities of some herbs and spices and their ingredients.
SELECTED PROPERTIES OF VANADIUM ALLOYS FOR REACTOR APPLICATION (1957)

formation were found at 1600 deg K. An attempt was made to interpret these quantities in terms of the various configurational, vibrational, and magnetic changes that occur in this system on alloying. (auth)
Growth of AlGaN/GaN based electronic device structures with semi‐insulating GaN buffer and AlN interlayer (2005)

Heterostructures of GaN/AlGaN for power applications are grown by metal organic vapor phase epitaxy in a multiwafer reactor on sapphire and SiC substrates. The insulating properties of the GaN buffer and the influence of an AlN interlayer on the two-dimensional electron gas transport properties of high electron mobility transistor structures have been studied. By optimizing the growth conditions the resistivity could be increased to 1011 Ωcm. For GaN/AlGaN heterostructures on sapphire with a 1 nm AlN interlayer a room temperature mobility of 1780 cm2/Vs and an electron sheet carrier density of 1.2 ×1013 cm–2 were achieved. Power devices were fabricated on s.i. SiC showing a power density of 4.9 W/mm at 10 GHz for a multifinger transistor with a gate width of 1 mm. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Stem Cell Factor Enhances the Survival of Murine Intestinal Stem Cells after Photon Irradiation (1995)

Recombinant rat stem cell factor (SCF) has been shown to decrease lethality in mice exposed to total-body irradiation (TBI) in the lower range of lethality through radioprotection of hematopoietic stem cells and acceleration of bone marrow repopulation. This study evaluates the effect of SCF on the survival of the intestinal mucosal stem cell after TBI. This non-hematopoietic stem cell is clinically relevant. Gastrointestinal toxicity is common during and after abdominal and pelvic radiation therapy and limits the radiation dose in these regions. As observed with bone marrow, the administration of SCF to mice prior to TBI enhanced the survival of mouse duodenal crypt stem cells. The maximum enhancement of survival was seen when 100 micrograms/kg of SCF was given intraperitoneally 8 h before irradiation. This regimen increased the survival of duodenal crypt stem cells after 12.0 Gy TBI from 22.5 +/- 0.7 per duodenal cross section for controls to 30.0 +/- 1.7 after treatment with SCF (P = 0.03). The TBI dose producing 50% mortality at 6 days (LD50/6) was increased from 14.9 Gy for control mice to 19.0 Gy for mice treated with SCF (dose modification factor = 1.28). These findings demonstrate that SCF has radioprotective effects on a non-hematopoietic stem cell population and suggest that SCF may be of clinical value in preventing radiation injury to the intestine.
Digital subtraction angiographic imaging of coronary flow reserve. (1987)

Recent studies have demonstrated that subjective assessment of the severity of coronary artery stenoses results in poor interobserver concordance and poor correlation with physiologic significance as determined by Doppler measurements of coronary flow reserve. Use of the coronary flow reserve as an integrated measure of the effect of stenosis geometry has been emphasized within the context of quantitative cinemetric analysis. The comparison of two parametric digital subtraction angiographic flow images obtained before and after hyperemic intervention has led to calculation of flow reserve values that correlate well with electromagnetic flowmeter data in dogs. By means of a similar model relating blood flow and image variables, single flow ratio images have been formed. These parametric images provide a two-dimensional display of the ratio of hyperemic flow to baseline flow. Linear temporal interpolation of data from a sequence of cardiac phase-matched subtraction images is used to improve the resolution of the displayed flow ratios. Summation of flow variables measured within the perfusion bed was used to calculate a value for the overall coronary flow reserve and to characterize the significance of isolated lesions in an open-chest canine preparation. A linear regression calculation relating parametric image flow ratio values to electromagnetic flowmeter measurements resulted in a linear fit of y = .96x - 0.19 with a correlation coefficient of .90. The direct visual representation of flow ratio distribution provided by the parametric imaging method may aid in the interpretation of multiple complex lesions as well as of single lesions.
DNA Methylation Profiles in Precancerous Tissue and Cancers: Carcinogenetic Risk Estimation and Prognostication Based on DNA Methylation Status (2010)

Alterations in DNA methylation, which are associated with DNA methyltransferase abnormalities and result in silencing of tumor-related genes and chromosomal instability, are involved even in precancerous changes in various organs. DNA methylation alterations also account for the histological heterogeneity and clinicopathological diversity of human cancers. Therefore, we have analyzed DNA methylation on a genome-wide scale in clinical tissue samples. Our approach using the bacterial artificial chromosome array-based methylated CpG island amplification method has revealed that DNA methylation alterations correlated with the future development of more malignant cancers are already accumulated at the precancerous stage in the kidney, liver and urinary tract. DNA methylation profiles at precancerous stages are basically inherited by the corresponding cancers developing in individual patients. Such DNA methylation alterations may confer vulnerability to further genetic and epigenetic alterations, generate more malignant cancers, and thus determine patient outcome. On the basis of bacterial artificial chromosome array-based methylated CpG island amplification data, indicators for carcinogenetic risk estimation have been established using liver tissue specimens from patients with hepatitis virus infection, chronic hepatitis and liver cirrhosis or histologically normal urothelia, and for prognostication using biopsy or surgically resected specimens from patients with renal cell carcinoma, hepatocellular carcinoma and urothelial carcinoma. Such genome-wide DNA methylation profiling has now firmly established the clinical relevance of translational epigenetics.
Fast convergence of the backpropagation learning algorithm by using adaptive accuracy of weights (2003)

The authors investigate increase in the speed of convergence for the standard backpropagation learning algorithm by adapting the accuracy used to represent the weights during the learning process, instead of using a fixed weight accuracy. The change of the accuracy is determined adaptively from the learning process itself, using statistical measures of the error function. Simulations were performed and results are presented for a XOR problem, relating to seven-segment liquid crystal diode coding and a 8-5-8 encoder. Simulation results show that convergence speed can be increased drastically.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Effects of age and diabetes mellitus on the solubility and nonenzymatic glucosylation of human skin collagen. (1981)

Collagen from human skin was fractionated into neutral salt-soluble, acid-soluble, pepsin-released, and insoluble fractions. No age-related changes were observed in the proportion of collagen extracted by neutral salt. A significant age-related decrease in the proportion of acid-soluble collagen was found. A highly significant (P less than 0.001) age-related decrease in the amount of collagen released by pepsin digestion was observed, with a concomitant age-related increase in the fraction of insoluble collagen. The amount of ketoamine-linked glucose bound to this insoluble collagen also increased significantly with age. Skin collagen from three juvenile onset diabetics (JOD) and one young maturity onset diabetic (MOD) appeared to have undergone accelerated aging. JOD and the young MOD had significantly less collagen released by pepsin digestion and significantly more insoluble collagen than would be predicted by their ages. The collagen released by pepsin digestion of the diabetic samples had more high molecular weight components than similar fractions obtained from age-matched nondiabetic controls. There was also more ketoamine-linked glucose bound to the insoluble collagen of JOD than to that fraction from comparably aged control subjects. The apparent acceleration of collagen aging in diabetes mellitus may play a role in complications of diabetes that occur in collagen-rich tissues.
Alkaline hydrolysis of acetonitrile and its impact in GE FASTlab synthesis of [18F]Fluciclovine and [18F]FDG (2011)

465 Objectives [18F]Fluciclovine and [18F]FDG are under development and in use as PET imaging tracers. The FASTlab synthesizer traps [18F]fluoride on a QMA column followed by elution with a carbonate salt in an MeCN-H2O mixture. Formation of acetamide and acetate at mg/ml levels can take place when alkaline eluent solutions with MeCN are stored. The objective of this study was to assess the impact of acetamide and acetate on the synthesis of [18F]Fluciclovine and [18F]FDG and to develop an alternative eluent without MeCN. Methods Stability studies with eluent formulations of K222, K2CO3 in MeCN:H2O at different temp and pH was performed and were analyzed for acetamide and acetate at pre-determined timepoints. Spiking studies were performed where acetamide and ammonium acetate was added to freshly made eluent used in synthesis of [18F]fluciclovine and [18F]FDG. An eluent in which MeCN was replaced with MeOH was developed. Results Stability studies showed formation of acetamide (0.2-14.8 mg/ml) and acetate at (0.05-3.5 mg/m) after 14 days. Storage temp of 5-50 oC were of major importance. Spiking studies showed negative correlation between ammonium acetate and radiochemical yields for both tracers, most pronounced for [18F]Fluciclovine (18 % decrease with 3.5 mg/ml a acetate in 1.1ml eluent). Acetamide was efficiently removed (>99.9 %) during FASTlab synthesis and had no effect on radiochemical yield or purity. Replacing MeCN with MeOH in the eluent removed any formation of acetamide & acetate and gave same radiochemical yields as freshly made eluent with MeCN. Conclusions Acetamide and ammonium acetate were generated through alkaline hydrolysis of MeCN in the eluent formulation upon storage. Ammonium acetate did affect the radiochemical yields in synthesis of both [18F]FDG and [18F]Fluciclovine, while acetamide had no effect. A new eluent in which MeCN was replaced by MeOH was successfully developed
Endoplasmic reticulum signaling as a determinant of recombinant protein expression (2002)

Generation of functional recombinant proteins requires efficient and undisturbed functioning of the ER-Golgi secretory pathway in host cells. In large-scale production, where target proteins are highly overexpressed, this pathway can be easily congested with unfolded or misfolded proteins. Accumulating evidence suggests that, in addition to responsibility for protein processing, ER is also an important signaling compartment and a sensor of cellular stress. Two ER responses have been described to arise from the overaccumulation of proteins: unfolded protein response (UPR) and ER overload response (EOR). UPR and EOR employ various mechanisms at the transcriptional and the translational levels to deal efficiently and appropriately with encountered stress. This review will outline the molecular bases of ER functioning and stress response, highlight the relevance of ER signaling to the large-scale cell culture productivity and discuss possible approaches to the improvement of the secretion capacities of recombinant cells.
Relaxation of guinea‐pig tracheal smooth muscle to arachidonate is converted to contraction following epithelium removal (1987)

1 The effect of epithelium removal on responses of guinea-pig isolated trachealis to sodium arachidonate has been examined. 2 Arachidonate (100 microM) caused relaxation of epithelium-intact preparations, but following epithelium removal, the response to arachidonate was converted to contraction. In the presence of indomethacin (1 microM), arachidonate caused contraction in intact and denuded trachea. 3 Arachidonate also produced concentration-dependent effects, the qualitative nature of which varied with the presence or absence of the epithelium. In the presence of indomethacin, tracheal strips contracted in a concentration-dependent manner whether or not the epithelium had been removed. 4 Nordihydroguaiaretic acid (NDGA; 10 microM) markedly inhibited the contractile response of denuded strips to arachidonate. In intact tissues this lipoxygenase inhibitor converted the arachidonate-induced relaxation to a concentration-dependent contraction. The contraction to arachidonate, in the presence of NDGA, was epithelium-dependent. In the presence of both indomethacin and NDGA, responses to arachidonate were abolished. 5 It is concluded that the relaxation of guinea-pig trachea to arachidonic acid is epithelium-dependent and is mediated by an inhibitory product of the cyclo-oxygenase metabolic pathway. The contraction in denuded trachea, and trachea in the presence of indomethacin, may be mediated by lipoxygenase products of arachidonic acid metabolism, i.e. peptidoleukotrienes. The mediator of the epithelium-dependent contraction in NDGA-treated tissues is unknown.
Automatic dissolve and fade detection for video sequences (2003)

Due to the enormous amount of information contained in multimedia databases, the design of automatic tools to allow content-based analysis, browsing, and retrieval is of paramount importance. We present an algorithm tailored to the detection of editing effects such as dissolve and fade, which are widely used in television and movie production. A computationally inexpensive, although effective, correlation based algorithm is presented. The experimental results highlight the effectiveness of the proposed method.
Studies on Agents with Vasodilator and .BETA.-Blocking Activities. I. (1994)

A series of hydrazinopyridazine derivatives combined with a beta-blocking side chain were synthesized. When they were given intravenously to anesthetized rats, some of them exhibited both hypotensive and beta-blocking activities. Their structure-activity relationships for hypotensive and beta-blocking activities are discussed. Compound 11c had the best profile and was selected for further study.
Efficient Use of Variation in Evolutionary Optimization (2010)

Evolutionary algorithms face a fundamental trade-off between exploration and exploitation. Rapid performance improvement tends to be accompanied by a rapid loss of diversity from the population of potential solutions, causing premature convergence on local rather than global optima. However, the rate at which diversity is lost from a population is not simply a function of the strength of selection but also its efficiency, or rate of performance improvement relative to loss of variation. Selection efficiency can be quantified as the linear correlation between objective performance and reproduction. Commonly used selection algorithms contain several sources of inefficiency, some of which are easily avoided and others of which are not. Selection algorithms based on continuously varying generation time instead of discretely varying number of offspring can approach the theoretical limit on the efficient use of population diversity.
Structural Perspective on Enzymatic Halogenation (2008)

Simple halogen substituents frequently afford key structural features that account for the potency and selectivity of natural products, including antibiotics and hormones. For example, when a single chlorine atom on the antibiotic vancomycin is replaced by hydrogen, the resulting antibacterial activity decreases by up to 70% ( Harris , C. M. ; Kannan , R. ; Kopecka , H. ; Harris , T. M. J. Am. Chem. Soc. 1985 , 107 , 6652 - 6658 ). This Account analyzes how structure underlies mechanism in halogenases, the molecular machines designed by nature to incorporate halogens into diverse substrates. Traditional synthetic methods of integrating halogens into complex molecules are often complicated by a lack of specificity and regioselectivity. Nature, however, has developed a variety of elegant mechanisms for halogenating specific substrates with both regio- and stereoselectivity. An improved understanding of the biological routes toward halogenation could lead to the development of novel synthetic methods for the creation of new compounds with enhanced functions. Already, researchers have co-opted a fluorinase from the microorganism Streptomyces cattleya to produce (18)F-labeled molecules for use in positron emission tomography (PET) ( Deng , H. ; Cobb , S. L. ; Gee , A. D. ; Lockhart , A. ; Martarello , L. ; McGlinchey , R. P. ; O'Hagan , D. ; Onega , M. Chem. Commun. 2006 , 652 - 654 ). Therefore, the discovery and characterization of naturally occurring enzymatic halogenation mechanisms has become an active area of research. The catalogue of known halogenating enzymes has expanded from the familiar haloperoxidases to include oxygen-dependent enzymes and fluorinases. Recently, the discovery of a nucleophilic halogenase that catalyzes chlorinations has expanded the repertoire of biological halogenation chemistry ( Dong , C. ; Huang , F. ; Deng , H. ; Schaffrath , C. ; Spencer , J. B. ; O'Hagan , D. ; Naismith , J. H. Nature 2004 , 427 , 561 - 565 ). Structural characterization has provided a basis toward a mechanistic understanding of the specificity and chemistry of these enzymes. In particular, the latest crystallographic snapshots of active site architecture and halide binding sites have provided key insights into enzyme catalysis. Herein is a summary of the five classes of halogenases, focusing on the three most recently discovered: flavin-dependent halogenases, non-heme iron-dependent halogenases, and nucleophilic halogenases. Further, the potential roles of halide-binding sites in determining halide selectivity are discussed, as well as whether or not binding-site composition is always a seminal factor for selectivity. Expanding our understanding of the basic chemical principles that dictate the activity of the halogenases will advance both biology and chemistry. A thorough mechanistic analysis will elucidate the biological principles that dictate specificity, and the application of those principles to new synthetic techniques will expand the utility of halogenations in small-molecule development.