gebhart/patrepeval huggingface dataset:
Compilation of DNA strand exchange sites for non-homologous recombination in somatic cells (1988)

DNA sequences of 496 somatic cell illegitimate crossing over regions were compiled and analyzed. Sites for non-homologous recombination on linear DNAs transfected into mammalian cells (Transfected Linear DNAs; TLD) were analyzed separately from the remaining illegitimate recombination regions (IRR). Trinucleotides that are preferentially cleaved by rat liver topoisomerase I in vitro (CAT, CTY, GTY, RAT where R = purine, Y = pyrimidine) were present in the 10 base pair (bp) vicinity of the cross-over sites in 92% of IRR and 93% of TLD. Multiple repeats of these trinucleotides have been observed in 39% of IRR and 38% of TLD. Runs of five or more contiguous purines (or pyrimidines on the complementary strand) were found in 26% of IRR and 14% of TLD. Adenine-Thymine rich regions of five or more bases were found in 14% of IRR and 21% of TLD. Alternating purine-pyrimidine tracks longer than four nucleotides in length were found in 11% of IRR, though only in 4% of TLD. I discuss the possible biological significance of these findings and present an appendix containing the sequences in the 10 bp vicinity of the non-homologous recombination sites analyzed.
Distributed algorithm for downlink resource allocation in multicarrier small cell networks (2012)

In small cell networks (SCNs) co-channel interference is an important issue, and necessitates the use of interference mitigation strategies that allocate resources efficiently. This work discusses a distributed utility-based algorithm for downlink resource allocation (i.e., power and scheduling weights per carrier) in multicarrier SCNs. The proposed distributed downlink resource allocation (DDRA) algorithm aims to maximize the sum utility of the whole system. To achieve this goal, each base station (BS) selects the resource allocation strategy to maximize a surplus function comprising both, own cell utility and interference prices (that reflect the interference that is caused to neighboring cells). Two different utility functions are considered: max-rate and proportional fair-rate. For performance evaluation, a SCN deployed in a single story WINNER office building is considered. Simulation results show that the proposed algorithm is effective in enhancing not only the sum data rate of a SCN, but also the degree of fairness in resource sharing among users.
Exact solutions of electromagnetic fields in both near and far zones radiated by thin circular-loop antennas: a general representation (1997)

This paper presents an alternative vector analysis of the electromagnetic (EM) fields radiated from thin circular-loop antennas of arbitrary radius a. This method, which employs the dyadic Green's function in the derivation of the EM radiated fields, makes the analysis more general, compact, and straightforward than those two methods published recently by Werner (1996) and Overfelt (1996). Both near and far zones are considered so that the EM radiated fields are expressed in terms of the vector-wave eigenfunctions. Not only the exact solution of the EM fields in the near and far zones outside the region (where r>a) is derived by the use of the spherical Hankel function of the first kind, but also the closed-series form of the EM fields radiated in the near zone inside the region 0/spl les/r<a is obtained in series of the spherical Bessel functions of the first kind. As an example, a Fourier cosine series is used to expand an arbitrary current distribution along the loop and the exact representations of the EM radiated fields due to the loop everywhere are obtained in closed form. The closed form reduces to those for the sinusoidal current loop and further for the uniform current loop. Validity of the approximate formulas is discussed and clarified. Error analysis based on numerical computations of the radiated fields is also given to show the accuracy of the limiting cases.
Generation and detection of millimeter waves by picosecond photoconductivity (1983)

Picosecond photoconductors in the form of dielectric resonators have been used to generate and detect extremely short bursts of millimeter wave radiation at 55 GHz with a repetition rate of 100 MHz. Both the generator and detector are tuned to a frequency which is determined by the length of the photoconducting dielectric resonators. The detector, which is phase coherent, has an estimated noise equivalent power of only 4×10−11 W for an integration bandwidth of 1 Hz, and is capable of resolving time intervals corresponding to a small fraction of one millimeter-wave cycle.
Fluorescence resonance energy transfer between donor‐acceptor pair on two oligonucleotides hybridized adjacently to DNA template (2003)

We use fluorescein as the energy donor and rhodamine as the acceptor to measure the efficiency of fluorescence resonance energy transfer (FRET) in a set of hybridized DNA constructs. The two fluorophores are covalently attached via linkers to two separate oligonucleotides with fluorescein at the 3' end of one oligonucleotide and rhodamine at the 5' end or in the middle of another nucleotide. For the FRET analysis both fluorophore-labeled oligonucleotides are hybridized to adjacent sections of the same DNA template to form a three-component duplex with a one base gap between the two labeled oligonucleotides. A similar configuration is implemented for a quantitative real-time polymerase chain reaction (PCR) with LightCycler technology, where a 1-5 base separation between donor and acceptor is recommended to optimize energy transfer efficiencies. Our constructs cover donor-acceptor separations from 2 to 17 base pairs (approximately 10-70 A). The results show that, when the two fluorophores are located at close distances (less than 8 base separation), FRET efficiencies are above 80%, although there may be ground-state interactions between fluorophores when the separation is under about 6 bases. Modeling calculations are used to predict the structure of these three-component constructs. The duplex mostly retains a normal double helical structure, although slight bending may occur near the unpaired base in the DNA template. Stable and reproducible energy transfer is also observed over the distance range investigated here in real-time thermal cycling. The study identifies important parameters that determine FRET response in applications such as real-time PCR.
Designing and constructing thick holographic optical elements (1978)

Previously, holographic optical elements have been constructed with two spherical waves. Better image quality and efficiency can be achieved by constructing thick HOE's with spherically aberrated wavefronts. We include an exact lens equivalent for a HOE to allow computer optimization of such systems. The effect of changes in the index of refraction and thickness of the emulsion are considered along with the quality of the substrate. Optical systems to construct such HOE's are discussed and analytically described. Many examples are presented.
Inherited variation in the PARP1 gene and survival from melanoma (2014)

We report the association of an inherited variant located upstream of the poly(adenosine diphosphate-ribose) polymerase 1 (PARP1) gene (rs2249844), with survival in 11 BioGenoMEL melanoma cohorts. The gene encodes a protein involved in a number of cellular processes including single-strand DNA repair. Survival analysis was conducted for each cohort using proportional hazards regression adjusting for factors known to be associated with survival. Survival was measured as overall survival (OS) and, where available, melanoma-specific survival (MSS). Results were combined using random effects meta-analysis. Evidence for a role of the PARP1 protein in melanoma ulceration and survival was investigated by testing gene expression levels taken from formalin-fixed paraffin-embedded tumors. A significant association was seen for inheritance of the rarer variant of PARP1, rs2249844 with OS (hazard ratio (HR) = 1.16 per allele, 95% confidence interval (CI) 1.04-1.28, p = 0.005, eleven cohorts) and MSS (HR = 1.20 per allele, 95% CI 1.01-1.39, p = 0.03, eight cohorts). We report bioinformatic data supportive of a functional effect for rs2249844. Higher levels of PARP1 gene expression in tumors were shown to be associated with tumor ulceration and poorer OS.
Weld Plume Emissions During Nd:YAG Laser Welding (2005)

Most of the emitted light appears to be temperature radiation and only a few weak emission lines are visible.It can thus be concluded that the weld plume is only weakly ionized.Since the measurements were not calibrated and the wavelength dependant emissivity is unknown, no quantitative conclusions can be drawn from these measurements.In the CuNI90/10 and the FeP04 spectra the measurement angle is closer to the sample normal.Apparently these welding processes behave more like a specular reflector than a diffuse reflector. AA5182 reflects the most Nd:YAG radiation, followed by CuNi90/10 and then FeP04. The weld plume is weakly ionized. For FeP04 and CuNi90/10 the weld pool behaves like a specular reflector. The presented spectral data can aid greatly in the design of a monitoring system 1.
Regulatory levels for the transport of ammonium in plant roots (2004)

Ammonium is an attractive nitrogen form for root uptake due to its permanent availability and the reduced state of the nitrogen. On the other hand, ammonium fluxes are difficult to control because ammonium represents an equilibrium between NH4+ and NH3, which are two N forms with different membrane permeabilities. There is increasing evidence that AMT-type ammonium transporters represent the major entry pathways for root uptake of NH4+. Since excess uptake of ammonium might cause toxicity and since ammonium is also released from catabolic processes within the cell, ammonium uptake across the root plasma membrane has to be tightly regulated. To take over a function in cellular ammonium homeostasis, various AMT transporters are synthesized that differ in their biochemical properties, their localization, and in their regulation at the transcriptional level. At the same time, AMT-driven transport is subject to control by the nitrogen status of a local root portion as well as of the whole plant. In this review, the focus is on the different levels at which AMT-dependent ammonium uptake is regulated and the gaps in current knowledge are highlighted.
[The fluorescein angiographic picture of hereditary colloid bodies (author's transl)]. (1976)

The authors present five patients with dominant hereditary colloid bodies of the retinal centre from two family trees. Their fluoroangiographical pictures confirm the variable clinical manifestations and ophthalmological findings which because of the special colloid bodies arrangement show a resemblance to the Hutchinson-Tay, Holthouse-Batton, Doyne and Klaingutti cases, also within the framework of a single family tree. With the help of the angiogram the type and development stage can be followed, while this disease passes from functionally and ophthalmologically unimportant lesions into the final stage of atrophy and the fibrous conversion of the whole rear eye pole.
Visualization of <i>Pseudomonas</i> genomic structure by abundant 8–14mer oligonucleotides (2009)

Summary Under‐ and over‐represented mono‐ to hexanucleotides are signatures of bacterial genomes, but the compositional biases of octa‐ to tetradecanucleotides have not yet been explored. Thirteen completely sequenced genomes of the Pseudomonas genus were searched for highly overrepresented 8–14mers. Between 59–989 overrepresented 8–14mers were found to exceed the applied threshold value. All genomic data sets of the 13 strains showed a consistent pattern, with individual oligomers clustering in either non‐coding or coding regions. Non‐coding oligonucleotides were typically part of longer repeats. Coding oligonucleotides were evenly distributed in the core genome, preferred one reading frame and matched with the local tetranucleotide usage patterns. Genomic islands were recognized by the depletion of overrepresented oligonucleotides. Several mainly coding 8–14mers occurred in genomes on average every 10 000 bp or less. Such frequently occurring 8–14mers could become useful markers for species identification. In the future of next‐generation ultra‐high throughput DNA sequencing, the composition of bacterial metagenomes may be quantified by scanning the primary sequence reads for these 8–14mer markers.
Pinching with finger tips in humanoid robot hand (2006)

It is difficult to generate the action of stably pinching paper or needle, etc. with the finger tips, which is one of the important functions to be realized by humanoid robot hands. In this paper, the authors firstly propose a small-sized and light-weight robotic hand designed according to the concept of extracting required minimum motor functions and implementing them to the robot, and secondly propose a new robot hand capable of properly realizing a pinching motion with finger tips, by adding the minimum required degree of supplementary freedom which can be realized only with a machine. In the new robot hand, the authors mainly focus on additions of the degrees of freedom of independent motion to the terminal fingers and the degree of freedom of twisting motion to the thumb. Experiments were carried out to investigate force control characteristics of the finger tip joint. The results showed that providing the finger tip with a joint rich in force control performance even with weak maximum generated force is effective for securing delicate control characteristics finger tip force
La tributación indirecta del contrato de concesión de obras públicas a la luz de la Ley 30/2007, de contratos del sector público, y de la reciente doctrina de la Dirección General de Tributos (2008)

El presente trabajo tiene por objeto el análisis de la tributación indirecta del contrato de concesión de obras públicas, incidiendo fundamentalmente en los efectos que, en el Impuesto sobre el Valor Añadido y en el Impuesto sobre Transmisiones Patrimoniales Onerosas, tendrán las distintas alternativas de colaboración público-privada a través de las cuales es posible instrumentar tanto la ejecución como el mantenimiento y explotación de las infraestructuras públicas. A estos efectos, se toma como referente la doctrina de la Dirección General de Tributos relativa al contrato de concesión de obras públicas, plasmada en su reciente Resolución de 5 de noviembre de 2007.
High Density Optical Interconnects Integrated with Lasers, Optical Modulators and Photodetectors on a Single Silicon Chip (2013)

Silicon optical interposers for inter-chip interconnects, integrated with lasers, an optical splitter, optical modulators and germanium photodetectors on a single silicon substrate were demonstrated. A 12.5-Gbps error-free data transmission and 6.6-Tbps/cm2 transmission density were achieved.
Optical properties of gold-silica-gold multilayer nanoshells (2008)

The spectral and angular radiation properties of gold-silica-gold multilayer nanoshells are investigated using Mie theory for concentric multilayer spheres. The spectral tunability of multilayer nanoshells is explained and characterized by a plasmon hybridization model and a universal scaling principle. A thinner intermediate silica layer, scaled by particle size, red shifts the plasmon resonance. This shift is relatively insensitive to the overall particle size and follows the universal scaling principle with respect to the resonant wavelength of a conventional silica-gold core-shell nanoshell. The extra tunability provided by the inner core further shifts the extinction peak to longer wavelengths, which is difficult to achieve on conventional sub-100 nm nanoshells due to limitations in synthesizing ultrathin gold coatings. We found multilayer nanoshells to be more absorbing with a larger gold core, a thinner silica layer, and a thinner outer gold shell. Both scattering intensity and angular radiation pattern were found to differ from conventional nanoshells due to spectral modulation from the inner core. Multilayer nanoshells may provide more backscattering at wavelengths where silica-gold core-shell nanoshells predominantly forward scatter.
Beneficial Effects of Chronic Pharmacological Manipulation of β-Adrenoreceptor Subtype Signaling in Rodent Dilated Ischemic Cardiomyopathy (2004)

These results provide proof of concept for the efficacy of chronic beta2AR stimulation in this DCM model.
EXPERIMENTAL STUDIES ON URINARY INCONTINENCE (1989)

The effects of various alpha-adrenergic agonists and antagonists on the contractile properties of the isolated urethra of male and female rabbits were examined and the population of alpha 1- and alpha 2-adrenoceptors, using radioligand receptor binding techniques, was also quantified to define the functional role of postsynaptic alpha-adrenoceptors in urethral smooth muscle. Norepinephrine, epinephrine (non-specific alpha-adrenergic agonists) and phenylephrine (alpha 1-adrenergic agonists) induced increases in contractile force in both the male and female urethra. Clonidine (alpha 2-adrenergic agonist) caused a relatively large contractile response in the female urethra but only a small contractile response in the male urethra. Receptor binding studies indicated that the male urethra contains almost equal amounts of alpha 1- and alpha 2-adrenoceptors (32 vs. 34 fmol/mg protein, respectively) whereas the female urethra contains a significantly greater density of alpha 2- than alpha 1-adrenoceptors (122 vs. 34 fmol/mg protein, respectively). Our studies have indicated that: (1) both alpha 1-and alpha 2-adrenoceptors cause contractile responses in male and female rabbit urethra; (2) the greater response to alpha 2-agonist in female than male urethra is correlated with a higher density of alpha 2-adrenoceptors in this tissue.
Influence of the Bridging Atom on the Performance of a Low‐Bandgap Bulk Heterojunction Solar Cell (2009)

Replacing a carbon atom with silicon (see figure) on the main chain of a conjugated polythiophene gives a polysilole with higher crystallinity, improved charge transport, reduced bimolecular recombination, and reduced formation of charge transfer complexes when blended with a fullerene derivative. Optimized bulk heterojunction solar cells using this blend give certified efficiencies of 5.2% under AM1.5 illumination.
About the application of the van Cittert-Zernike theorem in ultrasonic imaging (1995)

The specific circumstances under which the van Cittert-Zernike theorem applies in ultrasonic imaging systems are examined through analysis and computations. Expressions are obtained for the mutual coherence function of an incoherent source when the signals are discrete in time and space and have finite lengths. Expressions are also obtained for statistics and effective signal-to-noise ratios that describe the error in the assumption of an incoherent source with finite signal lengths. Images of a one-dimensional source are reconstructed for different signal lengths and different pulse windows. The results show that ultrasonic signals with a relatively long effective length are needed to satisfy the incoherence requirement for image reconstruction based on the van Cittert-Zernike theorem. Consequently, although the van Cittert-Zernike theorem may be used to estimate the coherence length of ultrasonic signals in the aperture of an imaging system, special data acquisition techniques are needed for satisfactory reconstruction of ultrasonic images when depth resolution like that in current b-scans is required.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Combining virtual and augmented reality to improve the mechanical assembly training process in manufacturing (2012)

Nowadays, the industrial sector and specially manufacturing companies, have a huge challenge trying to train the workforce while maintaining up to date with the technology, machinery and manufacturing techniques involved in the production process. For that reason this sector claims for effective, in time and quality, training methodologies that do not interrupt or interfere with the continuous workflow of the company or its technological evolution.

Virtual reality offers an alternative that has been successfully implemented in other industries. Virtual reality based training systems have numerous advantages over the conventional methodologies, however, for some applications, virtual reality cannot replace the whole training process because it may be incapable of sufficiently transferring the skills to real world. On the contrary, augmented reality operates in a real environment, providing computer-generated aids to the user in order to enhance the real world; therefore, augmented reality based training systems may transfer skills in a greater extent compared to virtual reality. However, augmented reality does not provide all the advantages that virtual reality does, as it makes extensive use of resources like traditional methodologies do. This paper proposes a new methodology that combines virtual and augmented reality; a complete and robust process that fits more complex and demanding training needs of manufacturing companies.
Fluorescence of Aromatic Amines and Their Fluorescamine Derivatives for Detection of Explosive Vapors (2006)

Nitroaromatics (such as dinitrotoluene, trinitrotoluene, and nitrobenzene) found in explosive vapors from buried landmines can be reduced to aminoaromatics by a novel process involving Pd metal nanocatalysts prepared in supercritical fluid carbon dioxide and supported on multi-walled carbon nanotubes. These aminoaromatics are fluorescent and, if desired, the fluorescence yield can be increased and the fluorescence maxima shifted further toward the red by reaction with appropriate derivatizing agents such as fluorescamine. Corrected spectra for these chemicals and their derivatives are included. Subpicomolar detection limits have already been achieved using a laboratory spectrofluorometer with a 150 W Xe arc lamp. Using lasers as excitation sources, this approach has the potential for developing a field sensor competitive with other methods currently used for detecting explosive vapors from land mines.