gebhart/patrepeval huggingface dataset:
Organic films deposited on Si p-n junctions: Accurate measurements of fluorescence internal efficiency, and application to luminescent antireflection coatings (1996)

Ultraviolet (UV) optical pumping followed by fluorescence wavelength downconversion of thin film organic light emitting materials deposited directly on the surface of Si p-n junction diodes is found to be an accurate and rapid means to determine the film internal fluorescence efficiency. By measuring the photoresponse of the Si detectors in the UV, we find that the organic light emitting films of aluminum tris-(8-hydroxyquinoline) (Alq3), N,N′-diphenyl-N,N′-bis-(3-methylphenyl)- 1,1′-biphenyl-4,4′-diamine, and bis-(8-hydroxyquinaldine)-chlorogallium (Gaq2′Cl), have internal fluorescence efficiencies of 0.30±0.05, 0.35±0.03, and 0.36±0.03, respectively. It has also been found that the organic films can be grown to a thickness which optimizes UV light conversion and can, at the same time, serve as antireflection coatings in the visible spectral region, thereby resulting in enhanced Si photodiode sensitivity extending from the UV to the infrared.
High-Frequency Epigenetic Repression and Silencing of Retroviruses Can Be Antagonized by Histone Deacetylase Inhibitors and Transcriptional Activators, but Uniform Reactivation in Cell Clones Is Restricted by Additional Mechanisms (2007)

Integrated retroviral DNA is subject to epigenetic gene silencing, but the viral and host cell properties that influence initiation, maintenance, and reactivation are not fully understood. Here we describe rapid and high-frequency epigenetic repression and silencing of integrated avian sarcoma virus (ASV)-based vector DNAs in human HeLa cells. Initial studies utilized a vector carrying the strong human cytomegalovirus (hCMV) immediate-early (IE) promoter to drive expression of a green fluorescent protein (GFP) reporter gene, and cells were sorted into two populations based on GFP expression [GFP(+) and GFP(-)]. Two potent epigenetic effects were observed: (i) a very broad distribution of GFP intensities among cells in the GFP(+) population as well as individual GFP(+) clones and (ii) high-frequency GFP reporter gene silencing in GFP(-) cells. We previously showed that histone deacetylases (HDACs) can associate with ASV DNA soon after infection and may act to repress viral transcription at the level of chromatin. Consistent with this finding, we report here that treatment with the histone deacetylase inhibitor trichostatin A (TSA) induces GFP activation in GFP(-) cells and can also increase GFP expression in GFP(+) cells. In the case of the GFP(-) populations, we found that after removal of TSA, GFP silencing was reestablished in a subset of cells. We used that finding to enrich for stable GFP(-) cell populations in which viral GFP reporter expression could be reactivated by TSA; furthermore, we found that the ability to isolate such populations was independent of the promoter driving the GFP gene. In such enriched cultures, hCMV IE-driven, but not the viral long terminal repeat-driven, silent GFP reporter expression could be reactivated by the transcriptional activator prostratin. Microscopy-based studies using synchronized cells revealed variegated reactivation in cell clones, indicating that secondary epigenetic effects can restrict reactivation from silencing. Furthermore we found that entry into S phase was not required for reactivation. We conclude that HDACs can act rapidly to initiate and maintain promoter-independent retroviral epigenetic repression and silencing but that reactivation can be restricted by additional mechanisms.
Gene Birth, Death, and Divergence: The Different Scenarios of Reproduction-Related Gene Evolution1 (2009)

Reproductive genes are known to evolve more rapidly than genes expressed in other organs. In this paper we present an overview and bring some new data on the evolutionary study of reproduction-related genes by integrating phylogeny with gene genomic localization. We focus on the gene evolutionary processes of gene birth, death, and divergence. We show that phylogenetic gene birth is confirmed by gene location in genomes, which definitively localized the "place of birth" of new genes (such as Obox and KHDC1/DPPA5/ECAT1/OOEP gene families). By finding their "place of death" in genomes, it also demonstrates that ZP genes TGM4 and OVGP1 have been lost in certain species during vertebrate evolution. Moreover, in the case of gene divergence, comparison of gene locations across different genomes establishes orthologous relationships that are weakly supported by the phylogenetic tree. Specifically, genomic localization demonstrates that the fish and bird mtnr1c (Mel1C) receptor is orthologous to mammalian GPR50, and that ungulate genomes contain new seminal vesicle-specific BSP genes that are not present in other species. Overall, the phylogenomic approach to gene evolution presented in this paper offers more insight into gene function, such as species-specific duplications for speciation, changes in gene expression due to gene divergence, and functional loss by gene death.
Conception et realisation de circuits mmic a base de transistors bipolaires a heterojonction appliques a la boucle a verrouillage de phase (1994)

Ce travail montre la demarche suivie pour concevoir et realiser des circuits mmic a base de transistor bipolaire a heterojonction. Le tbh gaas/gaa1as est presente d'un point de vue theorique, en decrivant les phenomenes physiques intervenant lors de son fonctionnement. Le transistor est modelise dans les domaines lineaires et non-lineaire pour la conception des mmic. Les circuits radiofrequences intervenant dans les radiotelephones de 2 generation, et les circuits rapides des liaisons a haut debit par fibre optique sont decrits. Le principe de la pll et ses applications pour la synthese de frequence et la recuperation d'horloge sont ensuite presentes. La filiere technologique mmic tbh a ete specifie et optimise de maniere a realiser en seulement 12 etapes des fonctions analogiques, numeriques et de puissance. Nous avons optimise et mesure un ensemble de 8 mmic pour les applications a 1,8 ghz (radiotelephone) et a 10 ghz (communications optiques haut debit). Nous avons realise 4 diviseurs de frequence fonctionnant entre 1 et 18,5 ghz ; un melangeur large bande ayant un gain de conversion positif jusqu'a 18,5 ghz ; deux vco fonctionnant dans les bandes 1,4-1,8 ghz et 8-11 ghz ; un synthetiseur de frequence en bande l. Les resultats obtenus demontrent l'interet du tbh pour ce type d'application
EPR Optical Detection of F Centre Pairs in Alkali Halides I. Pumping Cycle Kinetics and Characteristics of the Resonances (1972)

Abstract The electron paramagnetic resonance of F centres in the ground and excited states has been optically detected in the following alkali halide crystals: NaCl, KF, KCl, KBr, KI, RbBr, and RbI. A decrease of the radiative quantum efficiency of the F centre luminescence is observed when microwave transitions are induced between the spin levels. The mechanism responsible for this effect is an electronic tunnelling through the crystal field potential; the electron in the relaxed excited state of an F centre (F̃*) is transfered non radiatively to another nearby F centre in its ground state (F 0 ), and leads to the momentary formation of an α and an F′ centre. Such a process is a function of the total spin of the F̃*‐F 0 pair. The role played by the paired centres is confirmed by measurements at different F centre concentration. Moreover at high optical excitation pumping rate the population of the intermediate complexes (F′‐α) is large enough to allow an estimation of the rate of the reverse process F′ + α → F 0 + F 0 .
An ENDOR analysis of a diatomic sulphur defect in RbI (1995)

In this article, an ENDOR analysis of the S-2(-) defect in Rbl is presented. A complete angular variation of one set of Rb-85 and Rb-87 ENDOR transitions is measured. The corresponding hyperfine and nuclear quadrupole coupling tensors are determined. The orientation of the principal axes of these tensors is in good agreement with the overall D-2h symmetry of the S-2(-) ion in the lattice. The ENDOR results clearly lead to a monovacancy model, wherein the S-2(-) ion is replacing one I- ion on a lattice site. The linewidth of the EPR signals can be explained using the ENDOR data A comparison with previous ENDOR studies of O-2(-) and S-2(-) defects in rubidium halides is made.
The Fingernails of Mary Sullivan: Developing Reliable Methods for Selectively Isolating Endogenous and Exogenous DNA from Evidence (2003)

The fingernails of Mary Sullivan, the last victim of the Boston Strangler, were examined to determine if any genetic information about the murderer could be obtained. The nails were extremely friable necessitating the development of new techniques for isolating and purifying DNA. DNA yields from nails were optimized by using a NaOH-based preparation technique, which was simple, efficient, and minimized handling. Methods for selectively and thoroughly removing exogenous material on nails were also developed through use of a species-specific PCR assay, wherein mitochondrial DNA from the nail could easily be differentiated from DNA of contaminating cells.
Multiple Choice Test Questions for LU Decomposition of Solving Simultaneous Linear Equations (2003)

Take a test on LU Decomposition of Solving Simultaneous Linear Equations. The test is based on six levels of Bloom's Taxonomy
Hydrophobic Core Repacking in a Coiled-Coil Dimer via Phage Display:  Insights into Plasticity and Specificity at a Protein−Protein Interface (2004)

The coiled-coil, which consists of two or more interwoven amphiphilic alpha-helices, is formed by sequences that have a characteristic heptad repeat (abcdefg) where a and d are hydrophobic residues. Most efforts to elucidate the origins of coiled-coil pairing selectivity have focused on electrostatic interactions among side chains that flank the core (positions e and g) and on polar side chains that occur occasionally at core positions. We have used phage display to explore another source of coiled-coil specificity: steric matching among nonpolar side chains in the core. We introduced a destabilizing Leu-->Ala mutation into the core of one helix in a known heterodimer and then screened a phage-based library of potential partner helices in search of compensating mutations. We identified a new heterodimer pair (30 residues/helix) that is comparable in stability to the GCN4-p1 homodimer (33 residues/helix). Furthermore, the Leu-->Ala mutant shows specificity for its phage-derived partner over the original partner despite their similar sequences. These results show that a phage-based approach can provide unique insights on coiled-coil pairing preferences that should facilitate both the analysis of natural sequences and the development of specific dimerization motifs that are orthogonal to one another.
Electronic structure of GaN measured using soft-x-ray emission and absorption (1996)

The electronic structure of thin-film wurtzite GaN has been studied using a combination of soft-x-ray absorption and emission spectroscopies. We have measured the elementally and orbitally resolved GaN valence and conduction bands by recording Ga $L$ and N $K$ spectra. We compare the x-ray spectra to the partial density of states from a recent ab initio calculation and find good overall agreement. The x-ray emission spectra confirm that the top of the valence band is dominated by N $2p$ states whereas they reveal that there is only weak hybridization between Ga $4s$ and N $2p$ states. Surprisingly, we found a weak feature in the N $K$ emission at approximately 19.5 eV below the valence-band maximum that arises from hybridization between N $2p$ and Ga $3d$ states. X-ray absorption spectra show that the bottom of the conduction band is a mixture of Ga $4s$ and N $2p$ states, again in very good agreement with the theory.
Complete momentum analysis of multi-photon photo-double ionization of xenon by XUV and infrared photons (2008)

Photo-double ionization (PDI) of xenon by the Ti:Sapphire laser fundamental frequency combined to its 19th and 25th harmonics has been studied by means of a momentum imaging spectrometer. The measurement of the two emitted photoelectrons' momenta and their energy and angular correlations gives insight into the various mechanisms leading to PDI. Although the conditions for non-sequential direct photo-double ionization are fulfilled in the experiment, it is found that the two-step processes dominate.
High-temperature superconductivity in ultrathin films of Y1Ba2Cu3O7−x (1989)

We have grown ultrathin films of Y1Ba2Cu3O7−x in situ on (001) SrTiO3 by pulsed laser deposition. The zero resistance transition temperature (Tc0) is &amp;gt;90 K for films &amp;gt;300 Å thick. The critical current density (Jc at 77 K) is 0.8×106 A/cm2 for a 300 Å film and 4–5×106 A/cm2 for a 1000 Å film. The Tc0 and Jc deteriorate rapidly below 300 Å, reaching values of 82 K and 300 A/cm2 at 77 K, respectively, for a 100 Å film. Films only 50 Å thick exhibit metallic behavior and possible evidence of superconductivity without showing zero resistance to 10 K. These results are understood on the basis of the defects formed at the film-substrate interface, the density of which rapidly decreases over a thickness of 100 Å. We have studied these defects by ion channeling measurements and cross-section transmission electron microscopy. Our results suggest that the superconducting transport in these films is likely to be two dimensional in nature, consistent with the short coherence length along the c axis of the crystals.
Information storage across a microbial community using universal RNA memory (2023)

ABSTRACT Biological recorders can code information in DNA, but they remain challenging to apply in complex microbial communities. To program microbiome information storage, a synthetic catalytic RNA (cat-RNA) was used to write information in ribosomal RNA (rRNA) about gene transfer host range. By reading out native and modified rRNA using amplicon sequencing, we find that 140 out of 279 wastewater microbial community members from twenty taxonomic orders participate in conjugation and observe differences in information storage across amplicon sequence variants. Twenty of the variants were only observed in modified rRNA amplicons, illustrating information storage sensitivity. This autonomous and reversible RNA-addressable memory (RAM) will enable biosurveillance and microbiome engineering across diverse ecological settings and studies of environmental controls on gene transfer and cellular uptake of extracellular materials. One-Sentence Summary Ribosomal RNA sequencing detects cellular events recorded across a wastewater microbial community using synthetic biology.
Influence of Human Serum Albumin on Photodegradation of Folic Acid in Solution (2006)

It has been proposed that photodegradation of folates may be the reason for the pigmentation of races living under high fluence rates of ultraviolet radiation. The photodegradation of folic acid (FA) induced by ultraviolet-A (UV-A) radiation, in solution and in the presence of human serum albumin (HSA), was studied with absorption and fluorescence spectroscopy. FA photodegradation, with formation of p-aminobenzoyl-l-glutamic acid, 6-formylpterin and pterin-6-carboxylic acid, was found to follow an exponential trend. A scheme of FA photodegradation, which involves photosensitization of FA degradation by its photoproducts, was proposed. The rate of FA photodegradation decreased drastically in the presence of HSA, whereas the spectral characteristics of the photoproducts remained constant. The reduction of the FA photodegradation rate by HSA was accompanied by degradation of tryptophan in HSA. Tryptophan, when added to solutions of FA, had a similar effect as HSA. In solutions of FA and HSA the FA photoproducts cause photodamage mainly to HSA rather than to FA itself. The oxygen dependence of FA photodegradation and the inhibition of this process by sodium azide indicate that singlet oxygen may participate in the photosensitizing activity of FA photoproducts.
Promotion of Plant Growth by Bacterial ACC Deaminase (2007)

To date, there has been only limited commercial use of plant growth-promoting bacteria in agriculture, horticulture, and silviculture. However, with recent progress toward understanding the mechanisms that these organisms utilize to facilitate plant growth, the use of plant growth-promoting bacteria is expected to continue to increase worldwide. One of the key mechanisms employed by plant growth-promoting bacteria to facilitate plant growth is the lowering of plant ethylene levels by the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase. This article reviews the published work on this enzyme, with an emphasis on its biochemistry, protein structure, genes, and regulation. In addition, this article provides some initial insights into the changes in both plants and ACC deaminase-containing plant growth-promoting bacteria as a consequence of plant-microbe interactions. Finally, a brief discussion of how bacterial ACC deaminase and indoleacetic acid (IAA) together modulate plant growth and development is included.
Some macrophages kill Listeria monocytogenes while others do not (1997)

It is not known why some macrophages can kill certain microbes, such as the facultative intracellular bacterium Listeria monocytogenes (L. monocytogenes), while other macrophages cannot. Perhaps listericidal activity is a property of macrophages at specific stages of differentiation; may be the ability to kill this bacterium is regulated by the microenvironment of the cell: or it is possible that other regulatory forces are important. We describe here three characteristics that distinguish macrophages which can kill L. monocytogenes from those which cannot. First, listericidal macrophages must have neither too much nor too little intracellular iron-they must have an intermediate amount. Second, the receptor a macrophage uses to phagocytose L. monocytogenes seems to influence the intracellular fate of this bacterium. And third, macrophages which have cell-surface interleukin-10 (IL-10), a known downregulator of macrophage function, cannot kill L. monocytogenes. These traits of macrophages and their effects on listericidal activity are reviewed here, and the possibility that these properties might interact to control macrophage bactericidal activity is discussed.
Removing depth map coding distortion by using post filter set (2013)

We propose a fast post filter set for removing coding distortions of depth maps. Lossy coding generates various distortions, such as mosquito and block noises, edge blurs, and over quantization. These distortions seriously deteriorate image quality of synthesized views in free viewpoint image rendering. Thus, we propose the post filter set which includes median filter, Gaussian filter, min-max blur remove filer, and binary weighted range filter to remove these noises. In experiments, we use various codecs, which are JPEG, JPEG-LS, JPEG2000, and H.264/AVC, for depth map coding, and synthesize views with the coded depth maps. Experimental results show that our post filter set can improves every codecs performance. Improvement of PSNR is larger than the conventional post filter, and especially JPEG is large. The computational time of the filter set, which is implemented by C++ with SIMD optimization, is within 5.2 ms at high bit rate cases, and within 15.3 ms at low bit rate cases.
Roles for motility in bacterial–host interactions (1997)

The ability to move in a directed manner may confer distinct advantages upon host-adapted prokaryotes. Potential benefits of motility include increased efficiency of nutrient acquisition, avoidance of toxic substances, the ability to translocate to preferred hosts and access optimal colonization sites within them, and dispersal in the environment during the course of transmission. The costs of motility also may be significant. These include the metabolic burden of synthesizing flagellar components, the energetic expense of fuelling flagellar motors and the presentation of polymeric and highly antigenic targets to the immune system. It is therefore not surprising that synthesis of the motility apparatus is usually subject to strict control. Studies of a variety of bacterial-host interactions demonstrate roles for motility, and its regulation, at points throughout the infectious cycle.
Segmentation Based Online Word Recognition: A Conditional Random Field Driven Beam Search Strategy (2013)

We propose a segmentation based online word recognition approach which uses a Conditional Random Field (CRF) driven beam search strategy. An efficient trie-lexicon directed, breadth-first beam search algorithm is employed in a combined segmentation-and-recognition framework to accomplish real-time recognition of online handwritten cursive English words. This framework is developed by building a candidate lattice of primitive segments obtained through over segmentation of the word pattern. The search space for the lattice is expanded by synchronously matching the lattice nodes to likely character patterns from a trie-dictionary constructed out of the target lexicon. The probable paths are evaluated by integrating character recognition scores with physical and spatial characteristics of the handwritten segments in a CRF (conditional random field) model and a beam search strategy is used to prune the set of likely paths. This approach has been benchmarked on the new IBM_UB_1 dataset as well as on the UNIPEN dataset for comparison.
Determining EMC Test Levels for Implantable Devices in Bipolar Lead Configuration (2021)

Certain low-frequency magnetic fields cause interference in implantable medical devices. Electromagnetic compatibility (EMC) standards prescribe injecting voltages into a device under evaluation to simplify testing while approximating or simulating real-world exposure situations to low-frequency magnetic fields. The EMC standard ISO 14117:2012, which covers implantable pacemakers and implantable cardioverter defibrillators (ICDs), specifies test levels for the bipolar configuration of sensing leads as being one-tenth of the levels for the unipolar configuration. The committee authoring this standard questioned this testing level difference and its clinical relevance. To evaluate this issue of EMC test levels, we performed both analytical calculations and computational modeling to determine a basis for this difference. Analytical calculations based upon Faraday's law determined the magnetically induced voltage in a 37.6-cm lead. Induced voltages were studied in a bipolar lead configuration with various spacing between a distal tip electrode and a ring electrode. Voltages induced in this bipolar lead configuration were compared with voltages induced in a unipolar lead configuration. Computational modeling of various lead configurations was performed using electromagnetic field simulation software. The two leads that were insulated, except for the distal and proximal tips, were immersed in a saline-conducting media. The leads were parallel and closely spaced to each other along their length. Both analytical calculations and computational modeling support continued use of a one-tenth amplitude reduction for testing pacemakers and ICDs in bipolar mode. The most recent edition of ISO 14117 includes rationale from this study.