gebhart/patrepeval huggingface dataset:
Focal Adhesion Kinase Controls Aggressive Phenotype of Androgen-Independent Prostate Cancer (2008)

Overexpression of focal adhesion kinase (FAK) has been well correlated with tumor development and/or the maintenance of tumor phenotype. In addition, inappropriate activation of the extracellular regulated kinase (ERK) signaling pathway is common to many human cancers. In the present study, we investigated the interplay between FAK and ERK in androgen-independent prostate cancer cells (PC3 and DU145 cells). We observed that suppression of FAK expression using small interfering RNA-mediated knockdown decreased the clonogenic activity, whereas overexpression of FAK increased it. We also observed that detachment of PC3 and DU145 cells from their substrate induced tyrosine phosphorylation of FAK. ERK knockdown diminished FAK protein levels and tyrosine phosphorylation of FAK as well as FAK promoter-reporter activity. We also tested the effect of MEK inhibitors and small interfering RNA-mediated knockdown of ERK1 and/or ERK2 on cell proliferation, invasiveness, and growth in soft agar of PC3 and DU145 cells. Inhibition of ERK signaling grossly impaired clonogenicity as well as invasion through Matrigel. However, inhibition of ERK signaling resulted in only a modest inhibition of 3H-thymidine incorporation and no effect on overall viability of the cells or increased sensitivity to anoikis. Taken together, these data show, for the first time, a requirement for FAK in aggressive phenotype of prostate cancer cells; reveal interdependence of FAK and ERK1/2 for clonogenic and invasive activity of androgen-independent prostate cancer cells; suggest a role for ERK regulation of FAK in substrate-dependent survival; and show for the first time, in any cell type, the regulation of FAK expression by ERK signaling pathway.
The Regulation of Circadian Period by Phototransduction Pathways in Arabidopsis (1995)

Transgenic Arabidopsis plants expressing a luciferase gene fused to a circadian-regulated promoter exhibited robust rhythms in bioluminescence. The cyclic luminescence has a 24.7-hour period in white light but 30- to 36-hour periods under constant darkness. Either red or blue light shortened the period of the wild type to 25 hours. A phytochrome-deficient mutation lengthened the period in continuous red light but had little effect in continuous blue light, whereas seedlings carrying mutations that activate light-dependent pathways in darkness maintained shorter periods in constant darkness. These results suggest that both phytochrome- and blue light-responsive photoreceptor pathways control the period of the circadian clock.
Analysis of the plasticity of location of the Arg244 positive charge within the active site of the TEM‐1 β‐lactamase (2009)

A large number of beta-lactamases have emerged that are capable of conferring bacterial resistance to beta-lactam antibiotics. Comparison of the structural and functional features of this family has refined understanding of the catalytic properties of these enzymes. An arginine residue present at position 244 in TEM-1 beta-lactamase interacts with the carboxyl group common to penicillin and cephalosporin antibiotics and thereby stabilizes both the substrate and transition state complexes. A comparison of class A beta-lactamase sequences reveals that arginine at position 244 is not conserved, although a positive charge at this structural location is conserved and is provided by an arginine at positions 220 or 276 for those enzymes lacking arginine at position 244. The plasticity of the location of positive charge in the beta-lactamase active site was experimentally investigated by relocating the arginine at position 244 in TEM-1 beta-lactamase to positions 220, 272, and 276 by site-directed mutagenesis. Kinetic analysis of the engineered beta-lactamases revealed that removal of arginine 244 by alanine mutation reduced catalytic efficiency against all substrates tested and restoration of an arginine at positions 272 or 276 partially suppresses the catalytic defect of the Arg244Ala substitution. These results suggest an evolutionary mechanism for the observed divergence of the position of positive charge in the active site of class A beta-lactamases.
Structure-based discovery of an organic compound that binds Bcl-2 protein and induces apoptosis of tumor cells (2000)

Bcl-2 and related proteins are key regulators of apoptosis or programmed cell death implicated in human disease including cancer. We recently showed that cell-permeable Bcl-2 binding peptides could induce apoptosis of human myeloid leukemia in vitro and suppress its growth in severe combined immunodeficient mice. Here we report the discovery of HA14-1, a small molecule (molecular weight = 409) and nonpeptidic ligand of a Bcl-2 surface pocket, by using a computer screening strategy based on the predicted structure of Bcl-2 protein. In vitro binding studies demonstrated the interaction of HA14-1 with this Bcl-2 surface pocket that is essential for Bcl-2 biological function. HA14-1 effectively induced apoptosis of human acute myeloid leukemia (HL-60) cells overexpressing Bcl-2 protein that was associated with the decrease in mitochondrial membrane potential and activation of caspase-9 followed by caspase-3. Cytokine response modifier A, a potent inhibitor of Fas-mediated apoptosis, did not block apoptosis induced by HA14-1. Whereas HA14-1 strongly induced the death of NIH 3T3 (Apaf-1(+/+)) cells, it had little apoptotic effect on Apaf-1-deficient (Apaf-1(-/-)) mouse embryonic fibroblast cells. These data are consistent with a mechanism by which HA14-1 induces the activation of Apaf-1 and caspases, possibly by binding to Bcl-2 protein and inhibiting its function. The discovery of this cell-permeable molecule provides a chemical probe to study Bcl-2-regulated apoptotic pathways in vivo and could lead to the development of new therapeutic agents.
Aminolysis and Polymerization of 3‐(p‐Toluenesulfonoxy)Hydantoin (1969)

Abstract Aminolysis of 3‐(p‐toluenesulfonoxy)hydantoin (I) through two alternative routes led to the formation of series of both methylene‐diurea derivatives(II) and ω‐arylsemicarbazido (N‐arylacetamides) (III). 3‐(p‐Toluenesulfonoxy)hydantoin was found to undergo a novel kind of polymerization reaction induced by triethylamine, yielding a new polymer structure which consists of hydantoin groups combined by a hydrazinic linkage. 5‐Isopropyl‐3‐(p‐toluenesulfonoxy) hydantoin (IV) was prepared here from α‐isopropylmalonic acid diethyl ester, via α‐isopropylmalonohydroxamic acid (V); properties of this compound were also studied.
Timing of the first cleavage post‐insemination affects cryosurvival of in vitro–produced bovine blastocysts (1999)

The time of the first cleavage of bovine zygotes during in vitro culture can affect the rate of development and cell number of the blastocysts. The aim of this work was to study the effect of the timing of first cleavage on the cryosurvival of the resulting blastocysts. Following standard IVM and IVF, zygotes were cultured in modified synthetic oviduct fluid (SOF), with 10% fetal calf serum (FCS) added 48 hr post insemination, in a humidified atmosphere of 5% CO 2, 5% O 2 and 90% N 2 . Embryos which cleaved by 24, 27 30, 33, or 36 hr after insemination (IVF) were harvested and further cultured to the blastocyst stage (day 7 or day 8 post IVF). All developing blastocysts on days 7 and 8 were classified into three groups and were cryopreserved by vitrification. Group A consisted of blastocysts (150 m, small blastocysts); group B consisted of expanded or hatching blastocysts (150 m, large blastocysts); and group C consisted of morphologically poor quality blastocysts. The vitrification solution consisted of 6.5 M glycerol and 6% bovine serum albumin in PBS (VS3a). Thawed embryos were cultured further and survival was defined as the re-expansion and maintenance of the blastocoel over 24, 48, and 72 hr, respectively. Overall survival and hatching at 72 hr post-thawing was higher in blastocysts formed by day 7 than those formed by day 8 (60% vs. 40% survival; 63% vs. 45% hatching). Large blastocysts from day-7 and day-8 groups survived significantly better than small or poor quality blastocysts (76% vs. 63% and 31%; 72% vs. 30% and 26%, respectively; P 0.05). Day-7 blastocysts from the 27-and 30-hr cleavage groups survived significantly better than those from the 36-hr group (63% and 66% vs. 25%, P 0.05). Day-8 blastocysts from later cleaved (30 hr) zygotes had a higher survival than the 27-hr cleavage groups (52% vs. 26%, P 0.05). These results indicate that the day of blastocyst appearance, developmental stage, and timing of the first cleavage post-insemination can influence the cryosurvival of bovine blastocysts following vitrification.
Perceived time and temporal structure: Neural entrainment to isochronous stimulation increases duration estimates (2016)

Distortions of perceived duration can give crucial insights into the mechanisms that underlie the processing and representation of stimulus timing. One factor that affects duration estimates is the temporal structure of stimuli that fill an interval. For example, regular filling (isochronous interval) leads to an overestimation of perceived duration as compared to irregular filling (anisochronous interval). In the present article, we use electroencephalography (EEG) to investigate the neural basis of this subjective lengthening of perceived duration with isochrony. In a two-interval forced choice task, participants judged which of two intervals lasts longer - one always being isochronous, the other one anisochronous. Response proportions confirm the subjective overestimation of isochronous intervals. At the neural level, isochronous sequences are associated with enhanced pairwise phase consistency (PPC) at the stimulation frequency, reflecting the brain's entrainment to the regular stimulation. The PPC over the entrainment channels is further enhanced for isochronous intervals that are reported to be longer, and the magnitude of this PCC effect correlates with the amount of perceptual bias. Neural entrainment has been proposed as a mechanism of attentional selection, enabling increased neural responsiveness toward stimuli that arrive at an expected point in time. The present results support the proposed relationship between neural response magnitudes and temporal estimates: An increase in neural responsiveness leads to a more pronounced representation of the individual stimuli filling the interval and in turn to a subjective increase in duration.
Endothelial cell expression of vasoconstrictors and growth factors is regulated by smooth muscle cell-derived carbon monoxide. (1995)

CO is produced in vascular smooth muscle cells (VSMC) by heme oxygenase-1 (HO-1). CO increases cGMP levels in VSMC; however, its possible additional roles in the vasculature have not been examined. We report that a product of HO, released from VSMC and inhibited by hemoglobin, has paracrine effects on endothelial cells: it increases endothelial cGMP content and decreases the expression of the mitogens, endothelin-1 (ET-1) and platelet-derived growth factor-B (PDGF-B). This product has the characteristics of CO, and its production is increased sevenfold under hypoxia. The VSMC-derived CO caused a fourfold rise in endothelial cell cGMP. In addition, it inhibited the hypoxia-induced increases in mRNA levels of the ET-1 and PDGF-B genes. Inhibitors of HO, and hemoglobin, a scavenger of CO, prevented the rise in cGMP and also restored the hypoxic response of these genes. The inhibition of ET-1 and PDGF-B mRNA by CO resulted in decreased production of these endothelial-derived mitogens, and in turn, inhibition of VSMC proliferation. These findings suggest an important physiologic role for VSMC-derived CO in modulating cell-cell interaction and cell proliferation in the vessel wall during hypoxia.
Cytokine secretion by genetically modified nonimmunogenic murine fibrosarcoma. Tumor inhibition by IL-2 but not tumor necrosis factor (1993)

Recent investigations have demonstrated that the in vivo growth of weakly immunogenic murine tumors can be inhibited by genetic manipulations that enable them to secrete a variety of cytokines. Inasmuch as most human tumors fail to elicit a detectable host immune response we questioned whether the growth of a nonimmunogenic murine tumor could be inhibited by the secretion of cytokines. We have thus inserted the cDNA encoding for human IL-2 or TNF into the nonimmunogenic murine fibrosarcoma MCA 102. Tumor cells secreting IL-2 failed to grow in vivo despite normal in vitro growth. This growth inhibition required an intact immune system as tumors grew progressively in mice sublethally irradiated before tumor injection. Tumor inhibition was abrogated by the in vivo depletion, by specific mAb before tumor injection, of either CD8+ T cells or NK cells, but not CD4+ T cells. IL-2 secretion by tumor afforded a significant survival benefit to the animal, and IL-2-secreting tumor limited the growth of admixed nonsecreting parental tumor. Histologic evidence and FACS analyses revealed a dense lymphocytic infiltration of IL-2-secreting tumors composed of both CD4+ and CD8+ T cells. In contrast, secretion of TNF failed to inhibit the growth of MCA 102, and similar lymphocyte subset depletions, or administration of specific anti-TNF mAb had no effect on the growth of TNF secreting MCA 102. In summary, these investigations demonstrated that the host response to this nonimmunogenic tumor can be markedly enhanced by the genetic manipulation of the tumor cells to secrete IL-2, but not TNF. This strategy has potential application for the development of immunotherapies for nonimmunogenic tumors.
A self-correcting projector (2005)

We describe a calibration and rendering technique for a projector that can render rectangular images under keystoned position. The projector utilizes a rigidly attached camera to form a stereo pair. We describe a very easy to use technique for calibration of the projector-camera pair using only black planar surfaces. We present an efficient rendering method to pre-warp images so that they appear correctly on the screen, and show experimental results.
Interferon induces tryptophanyl-tRNA synthetase expression in human fibroblasts. (1991)

A cDNA clone complementary to an interferon (IFN)-induced mRNA was isolated and used to characterize the regulation of expression of its RNA by the IFNs and to identify the protein its RNA encodes. This cDNA hybridizes to IFN-induced 3.1- and 2.3-kilobase mRNAs that are synthesized in response to both IFN-alpha and IFN-gamma. IFN-gamma induces the sustained accumulation of these mRNAs while IFN-alpha induces their transient accumulation. Cycloheximide (50 micrograms/ml) failed to inhibit the induction of these mRNAs by either IFN-alpha or IFN-gamma, suggesting that their induction does not require de novo protein synthesis. DNA sequence analysis of this cDNA reveals that it encodes a protein of Mr 53,168 that has sequence homology with and the biological activity of a tryptophanyl-tRNA synthetase, an enzymatic activity that has been demonstrated to play a role in and be modulated by the growth of cells. Elevated levels of this enzyme may be involved in the cell growth inhibitory activity of the IFNs.
Lock allocation (2007)

We introduce lock allocation , an automatic technique that takes a multi-threaded program annotated with atomic sections (that must be executed atomically), and infers a lock assignment from global variables to locks and a lock instrumentation that determines where each lock should be acquired and released such that the resulting instrumented program is guaranteed to preserve atomicity and deadlock freedom (provided all shared state is accessed only within atomic sections). Our algorithm works in the presence of pointers and procedures, and sets up the lock allocation problem as a 0-1 ILP which minimizes the conflict cost between atomic sections while simultaneously minimizing the number of locks. We have implemented our algorithm for both C with pthreads and Java, and have applied it to infer locks in 15K lines of AOLserver code. Our automatic allocation produces the same results as hand annotations for most of this code, while solving the optimization instances within a second for most programs.
Homing Viruses (1998)

Everyone who uses mammalian cell cultures must have a silent envy of colleagues who make their living studying processes in simple organisms. Systems like yeast offer robust molecular genetic tools that allow creation of informative mutants at any defined locus. From total gene knockouts to subtle missense alleles to large chromosomal deletions, a genetically manipulatable system can yield a wealth of useful data with a modest amount of effort.
A Prospective Study of Dehydroepiandrosterone Sulfate, Mortality, and Cardiovascular Disease (1986)

It has been postulated that dehydroepiandrosterone (DHEA) and its sulfate ester, dehydroepiandrosterone sulfate (DHEAS), the major secretory products of the human adrenal gland, may be discriminators of life expectancy and aging. We examined the relation of base-line circulating DHEAS levels to subsequent 12-year mortality from any cause, from cardiovascular disease, and from ischemic heart disease in a population-based cohort of 242 men aged 50 to 79 years at the start of the study. Mean DHEAS levels decreased with age and were also significantly lower in men with a history of heart disease than in those without such a history. In men with no history of heart disease at base line, the age-adjusted relative risk associated with a DHEAS level below 140 micrograms per deciliter was 1.5 (P not significant) for death from any causes, 3.3 (P less than 0.05) for death from cardiovascular disease, and 3.2 (P less than 0.05) for death from ischemic heart disease. In multivariate analyses, an increase in DHEAS level of 100 micrograms per deciliter was associated with a 36 percent reduction in mortality from any causes (P less than 0.05) and a 48 percent reduction in mortality from cardiovascular disease (P less than 0.05), after adjustment for age, systolic blood pressure, serum cholesterol level, obesity, fasting plasma glucose level, cigarette smoking status, and personal history of heart disease. Our conclusions are limited by the single determination of DHEAS levels, but the data suggest that the DHEAS concentration is independently and inversely related to death from any cause and death from cardiovascular disease in men over age 50.
Directly modeling speech waveforms by neural networks for statistical parametric speech synthesis (2015)

This paper proposes a novel approach for directly-modeling speech at the waveform level using a neural network. This approach uses the neural network-based statistical parametric speech synthesis framework with a specially designed output layer. As acoustic feature extraction is integrated to acoustic model training, it can overcome the limitations of conventional approaches, such as two-step (feature extraction and acoustic modeling) optimization, use of spectra rather than waveforms as targets, use of overlapping and shifting frames as unit, and fixed decision tree structure. Experimental results show that the proposed approach can directly maximize the likelihood defined at the waveform domain.
Heritability of illicit drug use and transition to dependence in Southwest California Indians (2007)

These findings suggest that heritability of the initiation of substance use, in Southwest California Indians, may be similar to other population samples. In this population, however, high rates of dependence on marijuana, opiates, and stimulants are seen once initiation of the use of the substance has occurred.
Neural Transplantation for Neurodegenerative Diseases: Past, Present, and Futurea (1993)

After almost 100 years of sporadic, and marginally successful, studies of neural transplantation in animals, we are now on the threshold of a clinical treatment of the damaged brain. The initial studies of neural transplantation have focused on Parkinson's disease, primarily as a model for a more general strategy of "repair by cellular replacement." Parkinson's is known to result from the loss of a small population of cells that produce the essential neuromodulator, dopamine, for much of the brain. Further, the disease is improved significantly, during the early part of its course, by chemical augmentation of dopamine activity through drug therapies, such as L-dopa. Finally, the disease is often fatal in spite of the best medical treatments, therefore justifying more radical therapeutic experiments. If transplantation of brain cells can be accomplished successfully in humans, as it has been in animals, then replacement of a small population of dopamine-producing cells in Parkinson's disease should have important functional effects and possibly reverse the course and symptoms of the disease. Other useful applications will surely follow for conditions affecting millions of people for whom medicine now has only palliative and ineffective treatments. Just as Parkinson's disease is a model clinical condition for testing cellular replacements, fetal neural tissue transplants are also a first step for a broader strategy of molecular and cellular therapies. Fetal cells are, in many respects, the best replacements one could imagine, since precursor cells have the capacity to develop into every cell found in the adult. So, the best replacement for a dopamine neuron would likely be a precursor dopamine neuron or "neuroblast." Animal research through 1985 had demonstrated the unique properties of such fetal cells, but survivability after transplantation had not been attained with primate or human neural tissue. Our programs developed techniques to transplant monkey fetal neural tissue, to cryopreserve it, and to reverse functional effects of the neurotoxin, MPTP, in monkeys. This technique was applied to the collection and preservation of human tissue, and preliminary successful results have been obtained in patients with idiopathic Parkinson's disease. Others have reported success with different techniques in two MPTP-Parkinsonian patients and a small number of patients with idiopathic disease. If the most dramatic improvements can be replicated consistently and the benefits last for a reasonable period without complications, a clinical treatment might develop using "random-source" fetal cadaver cells.
Beam Shaping for Advanced Laser Materials Processing (2015)

Abstract For recent industrial materials processing with advanced high power lasers, beam shaping optics are utilized as a key technology. Aspheric or diffractive beam shapers transform a Gaussian intensity profile of a single mode (TEM 00 ) laser beam into a flattop one. While an aspheric beam shaper can make a circular flattop, a diffractive one can realize much flexibility in output beam shapes, like square, rectangular, linear, or other complex beam shapes. The beam shaping is often combined with a scanning optical system, consisting of galvanometric mirrors and an f‐theta lens. Those beam shapers are used for either pulsed or CW single mode laser applications, i. e. ablation, cutting, drilling, scribing, annealing, etc. of thin films or bulk materials. This article describes principles, design concepts and specification examples of those optical systems used in practical applications.
CEP: a conformational epitope prediction server (2005)

CEP server (http://bioinfo.ernet.in/cep.htm) provides a web interface to the conformational epitope prediction algorithm developed in-house. The algorithm, apart from predicting conformational epitopes, also predicts antigenic determinants and sequential epitopes. The epitopes are predicted using 3D structure data of protein antigens, which can be visualized graphically. The algorithm employs structure-based Bioinformatics approach and solvent accessibility of amino acids in an explicit manner. Accuracy of the algorithm was found to be 75% when evaluated using X-ray crystal structures of Ag-Ab complexes available in the PDB. This is the first and the only method available for the prediction of conformational epitopes, which is an attempt to map probable antibody-binding sites of protein antigens.