gebhart/patrepeval huggingface dataset:
Analysis of gene amplification in archival tissue by differential polymerase chain reaction. (1992)

Oncogene amplification is found in many human tumors, and its detection may have important prognostic value. However, analysis of gene amplification may be hampered by inadequate tissue or poor DNA quality. We have previously described a polymerase chain reaction (PCR)-based procedure called differential PCR that can detect variations in gene dosage using miniscule amounts of tumor DNA [Frye, R.A., Benz, C.C. & Liu, E. (1989). Oncogene, 4, 1153-1157]. We now report the optimization of this technique for the analysis of oncogene amplification in paraffin-embedded archival tissues. We find that differential PCR is able to detect amplification of the HER2 (c-erbB-2) and the epidermal growth factor receptor (EGFR) genes and can be used to arrive at a semiquantitative estimate of gene dosage. Furthermore, our approach can determine gene amplification in samples in which the DNA is significantly degraded. Using differential PCR on paraffin-embedded tissues from cases previously investigated by standard DNA extraction and dot-blot procedures, good correlation between the two methods was found. Approaches are described to overcome technical problems posed by factors that affect the differential PCR, including the method of DNA extraction and extreme fragmentation of the DNA (less than 200 base pairs). Furthermore, the resulting analytical algorithm reported herein has proved effective in detecting oncogene amplification in archival breast cancer specimens from standard pathology laboratories. Thus, differential PCR will be particularly helpful in the analysis of tumor specimens that are archived, small in size or rare in occurrence.
Self-Assembly of Au Nanoparticles on PMMA Template as Flexible, Transparent, and Highly Active SERS Substrates (2014)

We report a simple and rapid method for fabricating a surface-enhanced Raman scattering (SERS) substrate, which offers good flexibility, excellent optical transparency, and high SERS activity. Specifically, the SERS substrate (AuNPs/PMMA film) was obtained through self-assembly of gold nanoparticles (AuNPs) on newborn poly(methyl methacrylate) (PMMA) template. The UV-vis spectroscopy analysis and scanning electron microscopy observation revealed that the gold nanoparticles were closely assembled on the flexible and transparent PMMA template. The fabricated AuNPs/PMMA film SERS substrate allowed detection of model molecule, malachite green isothiocyanate, at a concentration as low as 0.1 nM, and exhibited good reproducibility in the SERS measurement. The Raman enhancement factor (EF) of the AuNPs/PMMA film was found to be as high as (2.4 ± 0.3) × 10(7). In addition, measure of residual malachite green on fish surface was carried out, and the result indicated that the AuNPs/PMMA film had great potential in the in situ ultrasensitive detection of analyte on irregular objects.
Long-Term Pathologic and Behavioral Changes in Mice after Focal Deuteron Irradiation of the Brain (1963)

J. M. Ordy, T. Samorajski, W. Zeman, R. L. Collins, H. J. Curtis, Long-Term Pathologic and Behavioral Changes in Mice after Focal Deuteron Irradiation of the Brain, Radiation Research, Vol. 20, No. 1 (Sep., 1963), pp. 30-42
DNA polymorphisms for the nerve growth factor receptor gene exclude its role in familial dysautonomia. (1986)

Alleles for the single human nerve growth factor receptor gene (NGFR) on chromosome 17q can be distinguished by two polymorphic restriction sites for XmnI and one for HincII. The combined information content for haplotypes is quite high, making the NGFR locus an excellent genetic marker. Two of these polymorphisms were used to follow the inheritance of NGFR alleles in families with two or more members affected with familial dysautonomia. This rare disease is inherited in an autosomal recessive mode in the Ashkenazic Jewish population. Affected individuals show a severe depletion of NGF-dependent nerve populations from birth. Linkage analysis excluded a role for NGFR in this disease with odds of greater than 10(6):1 against the dysautonomia gene being within 1 centiMorgan of the mutation. In a previous study the gene for the beta subunit of NGF (NGFB) was also excluded in this disease. A possible role for other genes involved in NGF action or those coding for other developmentally determining neuronal factors is indicated.
Blind navigation with a wearable range camera and vibrotactile helmet (2011)

We present a way finding system that uses a range camera and an array of vibrotactile elements which we built into a helmet.
Efficient FLP recombination in mouse ES cells and oocytes (2001)

We report an improved vector, pCAGGS-FLPe, for transient expression of the enhanced FLP recombinase in mouse ES cells and oocytes. In standard transfection experiments, about 6% of total ES colonies showed FLP recombination, albeit with mosaicism within each colony. After microinjection of pCAGGS-FLPe into oocytes, about one-third of heterozygotic mice born showed complete FLP recombination. Thus pCAGGS-FLPe presents two practical options for removal of FRT cassettes in mice.
<i>Bacillus thuringiensis</i>: a century of research, development and commercial applications (2011)

Bacillus thuringiensis (Bt) is a soil bacterium that forms spores during the stationary phase of its growth cycle. The spores contain crystals, predominantly comprising one or more Cry and/or Cyt proteins (also known as δ-endotoxins) that have potent and specific insecticidal activity. Different strains of Bt produce different types of toxin, each of which affects a narrow taxonomic group of insects. Therefore, Bt toxins have been used as topical pesticides to protect crops, and more recently the proteins have been expressed in transgenic plants to confer inherent pest resistance. Bt transgenic crops have been overwhelmingly successful and beneficial, leading to higher yields and reducing the use of chemical pesticides and fossil fuels. However, their deployment has attracted some criticism particularly with regard to the potential evolution of pest-resistant insect strains. Here, we review recent progress in the development of Bt technology and the countermeasures that have been introduced to prevent the evolution of resistant insect populations.
Evaporation of Brine: A Field Study on the Bonneville Salt Flats, Utah (1970)

Evaporation rates were determined for seven brines whose average specific gravities varied from 1.207 to 1.333. Evaporation of the brines ranged from 70% to 9.5%, respectively, of the freshwater evaporation rate. The field data agree exceptionally well with differential vapor pressures over Great Salt Lake brine, measured in the laboratory by Dickson et al. [1965]. Water occasionally condenses on the heavier brines because of an inverted vapor pressure gradient.
Cell cycle regulation of DNA replication initiation proteins in mammalian cells (1999)

Genomic DNA has to be replicated completely and only once during a single cell cycle in order to maintain integrity. Eukaryotes have developed highly regulated machinery for precisely replicating genomic DNA that is fragmented into multiple chromosomes. Our knowledge of such mechanisms largely depends on findings with budding yeast, since identification of specific DNA sequences acting as replication origins, autonomously replicating sequences, has allowed extensive analyses of the initiation of DNA replication. Several factors essential for regulation of initiation have been identified, including ORC, CDC6 and MCM. Subsequent work has suggested that the fundamental machinery for DNA replication may be conserved in metazoan embryonic cells in which replication occurs sequence-independently, and also in mammalian nonembryonic cells, where replication origins are more specific. However, there are specific differences. In this review, information on function and regulation of mammalian initiation factors, ORC, CDC6 and MCM, is summarized, and yeast and embryonic systems are compared. A hypothetical model for the state of prereplication chromatin in mammalian cell nuclei and regulation during the cell cycle is also proposed.
Procyanidins are not bioavailable in rats fed a single meal containing a grapeseed extract or the procyanidin dimer B<sub>3</sub> (2002)

Flavanols are the most abundant flavonoids in the human diet where they exist as monomers, oligomers and polymers. In the present study, catechin, the procyanidin dimer B 3 and a grapeseed extract containing catechin, epicatechin and a mixture of procyanidins were fed to rats in a single meal. After the meals, catechin and epicatechin were present in conjugated forms in both plasma and urine. In contrast, no procyanidins or conjugates were detected in the plasma or urine of any rats. Procyanidins were not cleaved into bioavailable monomers and had no significant effects on the plasma levels or urinary excretion of the monomers when supplied together in the grapeseed extract. We conclude that the nutritional effects of dietary procyanidins are unlikely to be due to procyanidins themselves or monomeric metabolites with the intact flavonoid-ring structure, as they do not exist at detectable concentrations in vivo . Future research should focus on other procyanidin metabolites such as phenolic acids and on the effects of the unabsorbed oligomers and polymers on the human gastrointestinal tract.
The two faces of the inflammasome adaptor ASC in epithelial skin carcinogenesis. (2015)

The development of tumours is a multistep process during which cells acquire the capability to sustain proliferation, evade growth suppressors and/or resist cell death. One factor, which is increasingly recognised to influence tumour progression, is the inflammatory environment of the tumour. The responsible molecular mechanisms and signalling pathways are only beginning to emerge. One major pathway able to induce potent inflammation is the activation of the inflammasome and the subsequent secretion of the pro-inflammatory cytokines IL-1β and IL-18. Both these cytokines have been implicated in tumour-genesis/progression. However, evidence for the role of inflammasomes in this process is still scarce and mainly derived from murine colitis associated tumour models. In this short review we discuss current knowledge on the role of inflammasomes in epithelial cancer of the gut and skin with a special focus on the complex role of the inflammasome adaptor ASC in epithelial skin carcinogenesis.
Scheduling of real-time messages in optical broadcast-and-select networks (2001)

We consider broadcast-and-select networks based on optical passive stars. In these single-hop networks, communicating pairs can exchange messages directly, without the need to store information at intermediate nodes for later forwarding. Messages are transmitted in a packetized way, and each message has an associated deadline. In order to guarantee the message reception timeliness, we ask that all the messages are received within their corresponding deadline. We show that this scheduling problem is strong NP-complete, even in a very restricted case. Then, we turn our attention to fast approximating heuristics. We present four of them, assess their average performance by means of computer simulation, and give their worst-case performance bounds. Such bounds can be effectively used to test the success of the schedule before generating it.
Customer value elasticity, equi-value curves and value vectors: implications for customer behaviour and strategic marketing. (2009)

The analysis presented in the paper uses algebraic and geometric methods to explore the implications of the two different specifications of the customer's value equation, the ratio approach and the subtractive approach, for customer behaviour and strategic marketing decisions. Three key concepts are defined and investigated for each specification of the customer's value equation: customer value elasticity, equi-value curves (or "iso-values"), and value vectors. Customer value elasticity measures the sensitivity of customer value to small changes in customer perceived benefits and sacrifices. Equi-value curves are functions connecting points of equal customer perceived value. Value vectors are customer-value-based marketing strategies which have a specific directional orientation with respect to equi-value curves. The analysis of customer value elasticity and of equi-value curves suggests a number of important hypotheses for subsequent empirical testing. The analysis of value vectors suggests that there are eight feasible customer-value-based marketing strategies available to business organisations.
Spirastrellolide B: The Synthesis of Southern (C<sub>9</sub>−C<sub>25</sub>) Region (2008)

A combination of "chiron" and "asymmetric" approaches is utilized to construct the southern (C 9-C 25) region of marine natural product spirastrellolide B. The key functionalities are derived from d-glucose and Sharpless asymmetric epoxidation and dihydroxylation.
Thermoelectric micro power generator utilizing self-standing polysilicon-metal thermopile (2002)

A prototype self-standing polysilicon-metal junction thermopile has been developed. In order to realize ideal higher thermal isolation, a thermopile without a membrane and having self-standing structure is proposed. The hot and cold contacts in the proposed thermopile are reversible. The thermocouple is composed of an n-type polysilicon and an Au junction. The thermopile was fabricated by MICS (Micromachine Integrated Chip Service: three polysilicon layers structure) organized by the Cooperative Research Committee for Standardization of Micromachines in IEE of Japan. Output characteristics were measured as a function of distance between hot contact of the thermocouple and the radiation source, in order to confirm performance of the proposed thermopile as a micro power generator. Experimental results were in good agreement with the calculations.
Robust Time Optimal Obstacle Avoidance Problem for Constrained Discrete Time Systems (2006)

This paper presents algorithms for the computation of the set of states that can be robustly steered in a finite number of steps via state feedback control to a given target set while avoiding pre–specified zones or obstacles. The paper therefore extends standard results in (robust) time optimal control. A general procedure is given for the case when the system is discrete-time, nonlinear and time-invariant, and subject to constraints on the state and input. Furthermore, the paper shows how the necessary set computations may be performed using polyhedral algebra, linear programming and computational geometry software, when the system is piecewise affine with additive state disturbances.
Synthesis and quantitative structure-activity relationships of antihyperlipaemic 2-substituted thieno[3,2-d]pyrimidin-4(3H)-ones. (1996)

The synthesis, antihyperlipaemic evaluation and quantitative structure-activity relationships (QSAR) of two series of thieno[3,2-d]pyrimidin-4-one derivatives are reported. While most of the compounds in these series were found to exhibit antihyperlipaemic activity, the QSAR study of these two series indicated a positive influence of only the electronic nature of the 2-substitutents on the biological activity. The lipophilic and the steric parameters did not appear to be significant.
Mechanism of Thiolate−Disulfide Interchange Reactions in Biochemistry (2007)

Both density functional theory (DFT) (B3LYP) and CCSD ab initio calculations were employed in a theoretical investigation of the mechanism of thiolate-disulfide exchange reactions. The reaction pathway for degenerate thiolate-disulfide exchange reactions with dimethyl disulfide has been shown to proceed through a SN2-like transition structure that is very close in energy to the corresponding trisulfur anionic intermediate ([delta-S-S-Sdelta(-)]). When relatively small substituents are involved, the level of theory must be increased to CCSD to make this rather subtle mechanistic distinction. With the more sterically hindered exchange reaction involving t-butyl mercaptide and di-t-butyl disulfide, the potential energy surface exhibits a distinct preference for the S(N)2 displacement pathway with an activation barrier of 9.8 kcal/mol. When corrections for solvent polarity are included (COSMO), an S(N)2 mechanism is also implicated in both polar and nonpolar solvents. DFT studies on thiolate-disulfide exchange, when the substituent is a model peptide, strongly support the intermediacy of a trisulfur intermediate that lies 10.7 kcal/mol below isolated reactants. A well depth of this magnitude should provide a sufficient lifetime of the intermediate to accommodate the requisite conformational adjustments that accompanies formation of the new disulfide bond.
Automated generation of core test description file for hierarchical test (2016)

Most of modern system-on-chip (SoC) contain multiple hierarchy levels. This imposes specific requirements on the test solution, test access mechanism (TAM), and porting of core test patterns. Another challenge for multi-core hierarchical SoCs is the test integration time and automated generation of hierarchical test network and TAM. This paper presents a method for automated generation of core test description. The core test description file transfers the core test information required for automated generation of hierarchical test system. The test description file can contain bulky core-specific information on core test features necessary for hierarchical test. Automated generation of core test description allows drastically reduce hierarchical system generation and integration time.
THE SELECTIVE ADENOSINE A2A RECEPTOR AGONIST CGS 21680 REDUCES JNK MAPK ACTIVATION IN OLIGODENDROCYTES IN INJURED SPINAL CORD (2009)

Permanent functional deficit after spinal cord injury (SCI) arises from both mechanical injury and from secondary tissue reactions involving inflammation. Adenosine is an important regulator of inflammatory mechanisms. Although functional studies indicate a protective effect of adenosine A2A receptor agonists in SCI, the basic molecular mechanisms accounting for the their protective effects from SCI have to be fully elucidated. In this study, we investigated if the selective A2A receptor agonist 2-[p-(2-carboxyethyl)-phenethylamino]-5'-N-ethylcarboxamidoadenosine (CGS 21680) administered after SCI has protective effects against tissue damage, motor deficit, and different inflammatory readouts. Spinal cord injury was induced in mice by extradural compression of a section of the SC exposed via a four-level T5-T8 laminectomy. CGS 21680, administered by subcutaneously implanted osmotic minipumps after SCI, clearly reduced motor deficit for up to 19 days after operation. The drug repeatedly administered intraperitoneally after SCI reduced tissue damage, influx of myeloperoxidase-positive leukocytes, nuclear factor-kappaB activation and iNOS expression in injured spinal cord tissue 24 h after SCI. Enhanced immunoreactivity of microglia, astrocytes, and oligodendrocytes (stained by anti-CD11/B, anti-glial fibrillary acidic protein, and anti-Olig2 antibodies, respectively) was also observed 24 h after SCI. Neurons lose immunoreactivity in the nucleus. c-Jun amino-terminal kinase (JNK) mitogen-activated protein kinase, quantified by Western blot, was definitely activated in injured tissue. CGS 21680 treatment significantly reduced JNK phosporylation. Phospho-JNK mitogen-activated protein kinase was de novo expressed selectively in oligodendrocytes. CGS 21680 reduced phospho-JNK immunostaining in oligodendrocytes. Data indicate that protection by the A2A agonist is secondary to reduced leukocyte recruitment in the damaged area. A reducing effect of JNK activation in oligodendrocytes might account for protective effect of the A2A agonist against SCI-induced demyelination.
Cysteinyl Leukotriene Levels in Esophageal Mucosal Biopsies of Children with Eosinophilic Inflammation: Are They All the Same? (2006)

This is the first study to examine CysLT levels in esophageal mucosal biopsies of children with AEE and normal children. CysLT levels in AEE patients are similar to those in controls, and independent of the severity of inflammation. While this would argue against the use of CysLT antagonists in the treatment of AEE, further studies into the expression of the CysLT receptor itself are needed.
Stability Analysis of Load Sharing Control for Distributed Generation Systems (2007)

This paper discusses the small-signal stability analysis of the combined droop and average power method for load sharing control of multiple distributed generation systems (DGS) in a stand-alone ac supply mode. The small-signal model is developed and its accuracy is verified from simulations of the original nonlinear model. It is shown that the small-signal model accurately predicts the stability of the parallel systems.
Aged Non‐Human Primates: An Animal Model of Age‐Associated Neurodegenerative Disease (1991)

Aged non-human primates develop age-associated behavioral and brain abnormalities similar to those that occur in aged humans and, to a greater extent, in individuals with Alzheimer's disease. Declines in performance on cognitive and memory tasks begin at the monkey equivalent of late-middle life. As occurs in elderly humans, significant differences have been demonstrated in levels of performance between animals within older age groups. The brains of old monkeys show degenerative changes in neurons, abnormal axons and neurites (particularly in telencephalic areas), and deposits of amyloid in senile plaques and around blood vessels. Moreover, in some older animals, decrements occur in markers of specific neurotransmitter circuits, including the basal forebrain cholinergic system. It has been suggested that alterations in these cholinergic neurons contribute to the memory deficits that occur in older individuals. Because axotomy-induced retrograde degeneration of these neurons can be prevented by the administration of nerve growth factor, we have begun studies to determine whether administration of nerve growth factor improves performance of aged animals on memory tasks. This review describes the complementary nature of studies of non-human primates and human subjects, illustrating how these investigations can clarify factors that influence behavior and brain biology in age-associated diseases.
A new beam-scanning technique by controlling the coupling angle in a coupled oscillator array (1998)

The authors present a new technique for electronic beam scanning of a coupled oscillator array. A constant phase progression in a coupled oscillator array is achieved by controlling the coupling phase of the outermost coupling circuits only, while that of the innermost coupling circuits is zero and all free-running frequencies of the oscillators are the same. Analytical solution of nonlinear phase dynamic equations changes periodically as a piecewise-linear function of coupling phase only. The theory developed here is verified using a four-element oscillator array operating at 6.16 GHz. The full scan range is measured to be -17/spl deg/ to 18/spl deg/ off broadside. This scan range is very close to the theoretically achievable scan range of -19.2/spl deg/ to 19.2/spl deg/ for this array.
Aldeburgh Festival, 2003 (2003)

Mauricio Kagel's Eine Brise , a ‘fleeting action’ for 111 cyclists, was one of the signature events of the Aldeburgh Festival this year, a bizarre procession along the beach front, creating an evanescent, mobile performance of honking, whistling, and singing. It was a brilliantly absurdist gesture – and typical Kagel, you might think. But Eine Brise , composed in 1996, was the exception in Aldeburgh's focus on Kagel's recent music. Their mini-retrospective of his music of the last couple of decades revealed how the surrealist master of the 1960s and 70s has developed into a more complex figure, at once more conventional and more elusive.