gebhart/patrepeval huggingface dataset:
Greedy Algorithms for Finding a Small Set of Primers Satisfying Cover and Length Resolution Conditions in PCR Experiments. (1997)

Selecting a good collection of primers is very important for polymerase chain reaction (PCR) experiments. Most existing algorithms for primer selection are concerned with computing a primer pair for each DNA sequence. In generalizing the arbitrarily primed PCR, etc., to the case that all DNA sequences of target objects are already known, like about 6000 ORFs of yeast, we may design a small set of primers so that all the targets are PCR amplified and resolved electrophoretically in a series of experiments. This is quite useful because deceasing the number of primers greatly reduces the cost of experiments. Pearson et al. (ISMB 1995: 285-291, 1995; Discrete Appl. Math. 71: 231-246, 1996) consider finding a minimum set of primers covering all given DNA sequences, but their method does not meet necessary biological conditions such as primer amplification and electrophoresis resolution. In this paper, based on the modeling and computational complexity analysis by Doi, we propose algorithms for this primer selection problem. These algorithms do not necessarily minimize the number of primers, but, since basic versions of these problems are shown to be computationally intractable, especially even for approximability with the length resolution condition, this is inevitable. In the algorithms, the amplification condition by a primer pair and the length resolution condition by electrophoresis are incorporated. These algorithms are based on the theoretically well-founded greedy algorithm for the set cover in computer science. Preliminary computational results are presented to show the validity of this approach. The number of computed primers is much less than a half of the number of targets, and hence is less than one forth of the number needed in the multiplex PCR.
Back-side-illuminated image sensor with burst capturing speed of 5.2 Tpixel per second (2013)

We have developed a back-side-illuminated image sensor with a burst capturing speed of 5.2 Tpixels per second. Its sensitivity was 252 V/lux·s (12.7 times that of a front-side-illuminated image sensor) in an evaluation. Sensitivity of a camera system was 2,000 lux F90. The increased sensitivity resulted from optical and time aperture ratios of 100% and also by increasing from a higher optical utilization ratio. The ultrahigh-speed shooting resulted from the use of in-situ storage image sensor. Reducing the wiring resistance and dividing the image area into eight blocks increased the maximum frame rate to 16.7 million frames per second. The total pixel count was 760 horizontally and 411 vertically. The product of the pixel count and maximum frame rate is often used as a figure of merit for high-speed imaging devices, and in this case, 312,360 multiplied by 16.7 million yields 5.2 Tpixels per second. The burst capturing speed is thus 5.2 Tpixels per second, which is the highest speed achieved in high-speed imaging devices to date.
Measurement of Water Flow in Young Grapevines Using the Stem Heat Balance Method (1992)

There are numerous published discussions on the water use and water requirements of grapes (<i>Vitis vinifera</i>, L.), but data on the actual water use of individual plants in an undisturbed field environment are not available. We assessed the applicability of the stem heat balance method, using commercially available gauges, to determine the daily and seasonal water use of three-year-old Chardonnay plants in New Deal, TX. We first evaluated the gauges in the field by simultaneously measuring the hourly and daily water use of a potted three-year-old Cabernet Sauvignon plant gravimetrically and with a stem flow gauge. Second, we measured, over a period of 100 days between anthesis and harvest, starting on 17 May 1990, the daily sap flow of five Chardonnay plants in a vineyard that was irrigated by flooding. Our results show that the stem flow gauges were accurate within 5% to 10% of the daily value of transpiration as measured gravimetrically. The mean cumulative sap flow of the plants in the field over the entire measurement period was 461 ± 44 kg/plant or 124 ± 12 mm on an area basis. When the total sap flow for each plant was normalized by its leaf area, the variability among plants was greatly reduced. The mean cumulative evapotranspiration (ET) over the 100-day period was measured as 528 ± 13 mm, implying that soil evaporation was 77% of ET. We conclude: <i>(1)</i> that the stem heat balance method is capable of accurately measuring the daily water use of grape plants in the field; <i>(2)</i> that for our experimental conditions, the water use by the grape plants was low compared to the total water loss from the field, to the water use of other field crops in the same area, and to the calculated potential ET of 870 mm.
High frequency characteristics of MCM decoupling capacitors (2002)

The increased frequency operation of CMOS microprocessors and other circuitry places severe demands on power distribution systems to supply stable, noise-free power. Particularly in MCMs, where short signal line lengths allow fast off-chip switching, improved decoupling capacitors are required for short-term charge storage to reduce dI/dt noise. This paper examines the relative parasitic contributions of off-chip connections, MCM power distribution planes, and decoupling capacitors, and the effect of these parasitics on power distribution integrity. It is shown that the effect of the inductances of chip-to-substrate interconnections can be minimized by using multiple interconnections and careful design both in a wirebond or in a flip chip environment. Similarly, the intrinsic inductance and resistance of power distribution planes, either solid, perforated, or the new IMPS (Interconnected Mesh Power System), is extremely low and does not determine the effectiveness of power distribution.
Radioresistant cervical cancer shows upregulation of the NHEJ proteins DNA-PKcs, Ku70 and Ku86 (2009)

Our results show that cervical carcinoma surviving radiotherapy have an increased DNA-PK expression. Studies on larger patient cohorts are needed to allow an interpretation that an upregulation of DNA-PK function may be part of a radioresistance mechanism within this tumour type.
An evaluation of the neuroprotective effects of melatonin in an in vitro experimental model of age‐induced neuronal apoptosis (2009)

The neuroprotective effects of melatonin in an experimental model of aging-induced apoptosis have been examined. Cerebellar granule neurons show characteristics of apoptosis after 17 days in culture (DV). The addition of melatonin to neuronal cell cultures (100-500 mum) resulted in neuroprotective and antiapoptotic effects, which were revealed by nuclear condensed cell counting. In a thorough analysis by Western-blot of the potential pathways responsible for melatonin's neuroprotective effects, we found an increase in the activation of prosurvival Akt. Subsequently GSK3beta inhibition and an increase in p-FOXO1 phosphorylation occurred. In this model of aging, apoptosis was associated with an elevated DNA damage, as demonstrated by an increase in the activation of ataxia telangiectasia muted (ATM). Subsequently, downstream targets such as p53 were activated. Furthermore, the process of DNA damage was coupled to an increase in the expression of certain proteins involved in cell cycle regulation; these were cyclin D and the proapoptotic transcription factor E2F-1. We conclude that the antiapoptotic effects of melatonin were mediated by two potential mechanisms: by increasing the activity of prosurvival pathways via Akt and by the prevention of DNA damage (via ATM inhibition) followed by the reduction of cell cycle re-entry.
Golf Ballistics (1949)

The trajectory of a golf ball is determined by the force with which the club strikes the ball and by the forces which act on the ball during its flight through air.
Production of Chimeras Derived from Murine Embryonic Stem Cells (2003)

Embryonic stem cells are undifferentiated cells derived from early mouse embryos, which under appropriate culture conditions proliferate continuously in vitro. ES cells have been demonstrated to be pluripotent in vivo from their capacity to form teratocarcinomas and germ-line chimeric mice, dependent on the environment into which the stem cells are introduced. When ES cells are introduced under the kidney capsule, in vivo differentiation is chaotic with the teratocarcinoma composed of a wide variety of different cell types. If, however, the stem cells are returned into a preimplantation mouse embryo, in vivo differentiation proceeds in a normal and organized manner, and the ES cells colonize the three primary cell lineages of the developing embryo: the primitive ectoderm, endoderm, and mesoderm. This leads to the formation of chimeric offspring composed of cells of two different genetic constitutions: the host embryonic cells and those derived from the ES cells. The ES cells are capable of contributing to every tissue in the fetus, including the primordial germ cells. Furthermore, the trophectodermal and primitive endodermal derivatives in the extraembryonic tissues of the conceptus may also be colonized by ES cells. Recent studies have shown that murine ES cells are capable of supporting complete fetal development, following the aggregation of stem cells with tetraploid-cleavage-stage embryos.
Targeted Degradation of the AML1/MDS1/EVI1 Oncoprotein by Arsenic Trioxide (2006)

Arsenic trioxide (ATO) has been found to be an effective treatment for acute promyelocytic leukemia patients and is being tested for treating other hematologic malignancies. We have previously shown that AML1/MDS1/EVI1 (AME), a fusion gene generated by a t(3;21)(q26;q22) translocation found in patients with chronic myelogenous leukemia during blast phase, myelodysplastic syndrome, or acute myelogenous leukemia (AML), impairs hematopoiesis and eventually induces an AML in mice. Both fusion partners of AME, AML1 and MDS1/EVI1, encode transcription factors and are also targets of a variety of genetic abnormalities in human hematologic malignancies. In addition, aberrant expression of ectopic viral integration site 1 (EVI1) has also been found in solid tumors, such as ovarian and colon cancers. In this study, we examined whether ATO could target AME and related oncoproteins. We found that ATO used at therapeutic levels degrades AME. The ATO treatment induces differentiation and apoptosis in AME leukemic cells in vitro as well as reduces tumor load and increases the survival of mice transplanted with these cells. We further found that ATO targets AME via both myelodysplastic syndrome 1 (MDS1) and EVI1 moieties and degrades EVI1 via the ubiquitin-proteasome pathway and MDS1 in a proteasome-independent manner. Our results suggest that ATO could be used as a part of targeted therapy for AME-, AML1/MDS1-, MDS1/EVI1-, and EVI1-positive human cancers.
Matching fluid simulation elements to surface geometry and topology (2010)

We introduce an Eulerian liquid simulation framework based on the Voronoi diagram of a potentially unorganized collection of pressure samples. Constructing the simulation mesh in this way allows us to place samples anywhere in the computational domain; we exploit this by choosing samples that accurately capture the geometry and topology of the liquid surface. When combined with high-resolution explicit surface tracking this allows us to simulate nearly arbitrarily thin features, while eliminating noise and other artifacts that arise when there is a resolution mismatch between the simulation and the surface---and allowing a precise inclusion of surface tension based directly on and at the same resolution as the surface mesh. In addition, we present a simplified Voronoi/Delaunay mesh velocity interpolation scheme, and a direct extension of embedded free surfaces and solid boundaries to Voronoi meshes.
Ultrahigh-Power Single-Mode Fiber Lasers from 1.065 to 1.472 µm using Yb-doped Cladding-Pumped and Cascaded Raman Lasers (1997)

We report Yb-doped cladding-pumped fiber lasers with two fiber Bragg gratings and a cascaded Raman laser that yield unprecedented power levels (16.4 W at 1065 nm, 20.4 W at 1101 nm, and 8.5 W at 1472 nm) in a single-mode fiber.
Die Beeinflussung von Desinfektions‐Wirkstoffen durch nichtionische Tenside (1974)

Abstract Auf die Nachteile für die Anwendung nicht‐grenzflächenaktiver Desinfektionswirkstoffe (sog. Oberflächen‐Desinfektionsmittel) wird hingewiesen. Anschließend wird an drei Produktmöglichkeiten dargestellt, welche Auswirkung der Einsatz nichtionogener Tenside auf die praktische Verwendbarkeit oder die Desinfektionswirkung der desinfektionswirksamen Substanzen hat. Zu diesen Desinfektionsmittel‐Gruppen gehören die auf Basis Jod (Jodophore), quartäre Ammoniumverbindungen sowie Enzyme und quartäre Ammoniumverbindungen aufgebauten Produkte.
Nonlinear optical waveguide fabrication by direct electron-beam irradiation and thermal development using a high Tg polymer (1997)

A nonlinear optical waveguide fabrication process for use with dye doped polymer is described. The ridge-type channel waveguide containing the chromophores was fabricated by direct electron-beam irradiation. The electron beam with an energy of 25 kV and dose of 1000 μC/cm2 was exposed directly onto the dye doped polymer film, and then thermal development and corona-poling were performed simultaneously. We could also demonstrate the periodically poled nonlinear optical polymer waveguide on the basis of this new process.
A single amino acid change restores DNA Cytosine methyltransferase activity in a cloned chlorella virus pseudogene (1992)

The chlorella virus PBCV-1 contains an open reading frame, named P17-ORF4, which differs by eight amino acids from a DNA cytosine methyltransferase, M.CviJI, encoded by a different chlorella virus IL-3A. Whereas IL-3A expresses M.CviJI, which methylates the central cytosine in (A/G)GC(T/C/G) sequences, P17-ORF4 is non-functional. Gene fusions between P17-ORF4 and M.CviJI and site-directed point mutations revealed that changing Gln188 to Lys188 abolishes M.CviJI methyltransferase activity. Conversely, changing Lys188 in P17-ORF4 to Gln188 results in M.CviJI activity. The other altered seven amino acids do not appear to affect M.CviJI activity.
Polyamides, Plastics (2001)

Abstract Polyamides (nylons) are important engineering plastics as well as being well known for fiber applications. This article covers the properties, manufacture, processing, and use of polyamide plastics together with information on specifications, sales, pricing, and suppliers. Materials discussed include nylon‐6,6, nylon‐6, nylon‐6,9, nylon‐6,12, nylon‐11, nylon‐12, nylon‐4,6, amorphous nylon, and other semiaromatic nylons. Physical properties described are crystallinity, thermal properties, moisture absorption, electrical properties, and flammability. Chemical properties are hydrolysis/polycondensation, thermal degradation, oxidation, uv aging, and effect of chemicals and solvents. Manufacture is described including solid‐state polymerization, compounding, and pultrusion. Compounding also includes a review of additives and modifications covering lubricants, nucleants, stabilizers, impact modifiers, flame retardants, plasticizers, reinforcements, nanocomposites, and polymer blends. The following processing routes are detailed: injection molding, extrusion, film, tubing and pipe, monofilament, rods and profiles, wire and cable coating, blow molding, rotomolding, reaction injection molding, powder coating, and also assembly techniques. Uses and automotive, electrical/electronic, consumer, and industrial applications are described. A discussion of recycling is followed by a summary of economic aspects including suppliers, sales, and pricing. Specifications, standards, and quality control are also reviewed with an indication of appropriate test methods.
Contextual Augmentation of Ontology for Recognizing Sub-events (2011)

With the advances in technology and proliferation of cheap storage, high rate of digital multimedia interaction signifies the increasing need of computer users for a decent application to organize personal media in a meaningful way. In this paper, we want to organize personal media in terms of the sub-events they cover. A semantic gap exists between media, and people's perception of the events and memories associated with this media. A framework is needed to address such gap. This paper describes a novel model-based approach for partitioning and organizing personal photo archive in terms of high-level subevents that capture and represent human experience. Since photos are the most ubiquitous and prolific form of user generated content, we focus on the automatic annotation of personal photo collection in this paper. We introduce ROntology (Recognition-Ontology) that is a context-aware model with concrete contextual information for subevent recognition. Currently our approach utilizes the mereological, spatial and temporal properties of modeled-events in R-Ontology. Personal media will then populate R-Ontology. We tested this approach using our personal photo archive describing two different scenarios: Trip and Indianwedding.
Decoupling research on a car suspension using principal coordinate of oscillation equations (2011)

Under research on principal coordinate of oscillation equations of multiple-degree-of-freedoms, if the relation between sprung mass of a whole car suspension and four sprung masses supported by four wheel systems is determined, the mass distribution coefficient in automotive theory would be enriched. In this paper, based on vertical and lateral excitations under the wheels, a traditional car model with fifteen degree of freedoms is adopted as research background. With the help of force analysis of sprung mass in space and investigations on vertical, lateral, pitch angle, roll angle and yaw angle motions, the principal coordinate equations of a whole car from vertical and lateral sides are obtained. The ratio relations of coupling dynamics between a whole suspension and four quarter suspensions are deduced and achieved. The results obtained in this paper found the theoretical basis for future studies on vibration control of suspension system, steering and running stability in vehicle field.
A fully multiple‐criteria implementation of the Sobol′ method for parameter sensitivity analysis (2012)

We present a novel rank‐based fully multiple‐criteria implementation of the Sobol′ variance‐based sensitivity analysis approach that implements an objective strategy to evaluate parameter sensitivity when model evaluation involves several metrics of performance. The method is superior to single‐criterion approaches while avoiding the subjectivity observed in “pseudo” multiple‐criteria methods. Further, it contributes to our understanding of structural characteristics of a model and simplifies parameter estimation by identifying insensitive parameters that can be fixed to default values during model calibration studies. We illustrate the approach by applying it to the problem of identifying the most influential parameters in the Simple Biosphere 3 (SiB3) model using a network of flux towers in Brazil. We find 27–31 (out of 42) parameters to be influential, most (∼78%) of which are primarily associated with physiology, soil, and carbon properties, and that uncertainties in the physiological properties of the model contribute most to total model uncertainty in regard to energy and carbon fluxes. We also find that the second most important model component contributing to the total output uncertainty varies according to the flux analyzed; whereas morphological properties play an important role in sensible heat flux, soil properties are important for latent heat flux, and carbon properties (mainly associated with the soil respiration submodel) are important for carbon flux (as expected). These distinct sensitivities emphasize the need to account for the multioutput nature of land surface models during sensitivity analysis and parameter estimation. Applied to other similar models, our approach can help to establish which soil‐plant‐atmosphere processes matter most in land surface models of Amazonia and thereby aid in the design of field campaigns to characterize and measure the associated parameters. The approach can also be used with other sensitivity analysis procedures that compute at least two model performance metrics.
A Surrogate for Topical Delivery in Human Skin: Silicone Membranes (2013)

We have identified, for any surrogate membrane and human skin in vitro, the maximum flux through the membrane (output) should be measured if a correlation between the two is to be obtained. We also identified from an analysis of the passive permeation process that molecular weight, lipid and aqueous solubilities (which are easily measured) constitute the physicochemical properties of the active (input), upon which prediction of flux through the surrogate membrane and through skin in vitro should be based. Besides providing the bases for predicting flux, changes in these physicochemical properties can be easily implemented by those wishing to optimize new cosmetics or topical products. Maximum flux values through silicone membrane (n = 70) and through human skin in vitro (n = 52) have been collected and a good correlation between the flux through human skin in vitro and flux through silicone membrane (for the same molecules) was found.
Serum Steroid Levels in Two Old Men with Alzheimer's Disease (AD) Before, During, and After Oral Administration of Dehydroepiandrosterone (DHEA). Pregnenolone Synthesis May Become Rate-Limiting in Agin (1990)

Serum Steroid Levels in Two Old Men with Alzheimer's Disease (AD) Before, During, and After Oral Administration of Dehydroepiandrosterone (DHEA). Pregnenolone Synthesis May Become Rate-Limiting in Agin was published in The Biologic Role of Dehydroepiandrosterone (DHEA) on page 43.
Comparison of urban propagation models with CW-measurements (2003)

The European research committee COST 231 has developed a propagation model for the estimation of urban transmission loss in cellular mobile radio. This model considers the diffraction loss due to equidistantly spaced buildings along the direct radio path and the diffraction and scatter losses from the rooftop down to the mobile. CW measurements in the 900- and 1800-MHz bands were performed in the cities of Mannheim and Darmstadt, Germany. Mannheim can be characterized as a homogeneously structured urban area with a rectangular street grid. The land cover in Darmstadt, on the other hand, is characterized by an inhomogeneous structure. The influences of base station antenna height, radio frequency, and street orientation are analyzed in detail. The quality of path-loss estimation and the shortcomings of the COST-231 model are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>