gebhart/patrepeval huggingface dataset:
Making Sense of Optogenetics (2015)

This review, one of a series of articles, tries to make sense of optogenetics, a recently developed technology that can be used to control the activity of genetically-defined neurons with light. Cells are first genetically engineered to express a light-sensitive opsin, which is typically an ion channel, pump, or G protein-coupled receptor. When engineered cells are then illuminated with light of the correct frequency, opsin-bound retinal undergoes a conformational change that leads to channel opening or pump activation, cell depolarization or hyperpolarization, and neural activation or silencing. Since the advent of optogenetics, many different opsin variants have been discovered or engineered, and it is now possible to stimulate or inhibit neuronal activity or intracellular signaling pathways on fast or slow timescales with a variety of different wavelengths of light. Optogenetics has been successfully employed to enhance our understanding of the neural circuit dysfunction underlying mood disorders, addiction, and Parkinson's disease, and has enabled us to achieve a better understanding of the neural circuits mediating normal behavior. It has revolutionized the field of neuroscience, and has enabled a new generation of experiments that probe the causal roles of specific neural circuit components.
<title>Structural outlier detection for automatic landmark extraction</title> (2001)

The aim of this paper is to introduce a structural dissimilarity measure which allows to detect outliers in automatically extracted landmark pairs in two images. In previous work, to extract landmarks automatically, candidate points have been defined using invariance criteria coming from differential geometry such as maximum curvature; or they are statistical entities such as gravity centers of confiners, where the confiners are defined as the connected components of the level sets. After a first estimation of the semi-rigid transformation (representing translation, rotation, and scaling) relating the candidate point sets, outliers are detected applying the euclidian distance between corresponding points. However, this approach does not allow to distinguish between real deformations and outliers coming from noise or additional features in one of the images. In this paper, we define a structural dissimilarity measure which we use to decide if two associated candidate points come from two corresponding confiners. We select landmarks pairs with a dissimilarity value smaller than a given threshold and we calculate the affine transformation relating best all selected landmark pairs. We evaluated our technique on successive slices of a MRI image of the human brain and show that we obtain a significantly sharper error diminution using the new dissimilarity measure instead of the euclidian distance for outlier rejection.
Individually tuned color enhancements for imagery interpretation by color-impaired users (2002)

Experiments have been performed with software to allow color-impaired users to tune and save their own enhancement scales for image interpretation. An interactive technique that enabled image users to define and save their own scales was developed. Color-impaired subjects were recruited and asked to develop scales to assist them in feature recognition on a set of three images, including both infrared and visual data. Example images that are enhanced by using scales tuned to several different types of color impairment are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Antigen-presenting cells and tolerance induction (2002)

T cell tolerance induction to foreign and self-antigens has occupied research since the beginning of the understanding of the immune system. Much controversy still exists on this question even though new methods became available to investigate immunoregulatory mechanisms. Antigen-presenting cells play a pivotal role in transferring information from the periphery of the organism to lymphoid organs. There, they initiate not only the activation of naive T cells but seem to deliver important signals which result in T cell unresponsiveness with antigen-specific tolerance induction.
Spectroelectrochemistry of a Photochromic [2.2]Paracyclophane-Bridged Imidazole Dimer: Clarification of the Electrochemical Behavior of HABI (2012)

The photochromic behavior of the imidazole dimers can be attributable to the photoinduced homolytic cleavage of the C-N bond between the two imidazole rings. On the other hand, although the simultaneous formation of the imidazolyl radical and imidazole anion by the one-electron reduction of an imidazole dimer was reported, no definitive evidence for this electrochemical reaction has been demonstrated. We report the first direct evidence for the electrochemical generation of the imidazolyl radical from the radical anion of the imidazole dimer by conducting the UV-vis-NIR spectroelectrochemical analysis of the [2.2]paracyclophane-bridged imidazole dimer.
The Masking Breakdown Point of Multivariate Outlier Identification Rules (1997)

In this paper, we consider one-step outlier identifiation rules for multivariate data, generalizing the concept of so-called alpha outlier identifiers, as presented in Davies and Gather (1993) for the case of univariate samples. We investigate, how the finite-sample breakdown points of estimators used in these identification rules influence the masking behaviour of the rules.
Isolation and partial characterization of the reduction-modifiable protein of Neisseria gonorrhoeae. (1986)

We have isolated and purified the reduction-modifiable protein (protein III) from several strains of Neisseria gonorrhoeae. We have found them to be basic proteins (pI 8.6) and virtually identical. A similar but not identical protein was isolated from a meningococcal strain. Antibodies raised against this purified protein would absorb to whole bacteria, confirming that the protein is exposed on the surface of the organism.
Understanding Formic Acid Decomposition as a Corrosion Inhibitor Intensifier in Strong Acid Environments (2007)

Abstract For many years formic acid has been used to intensify, or aid in, the performance of acid corrosion inhibitors in hydrochloric acid-based fluids used for stimulation procedures in the oilfield industry. Even so, the picture of how formic acid accomplishes this and under what conditions it functions is incomplete. One theory for how formic acid aids in inhibition is that it undergoes a dehydration reaction to form water and carbon monoxide (CO), a known corrosion inhibitor.HCOOH→CO+H2O This paper confirms that CO is produced by decomposition of formic acid in strong acids under downhole conditions. In addition, the conditions for the release of CO were found to be dependent on several variables, including temperature, acid strength, and alloy. Delineation of these conditions is important for effective implementation of formic acid as a corrosion inhibitor intensifier.
Genetic and agronomic approaches to decreasing acrylamide precursors in crop plants (2007)

Progress in developing genetic and agronomic approaches for reducing the levels of the principal precursors of acrylamide, asparagine and sugars in crop plants is reviewed. The factors that affect asparagine and sugar accumulation, particularly in cereal seeds and potato tubers, are described. Asparagine levels appear to be the key parameter in determining acrylamide formation in processed wheat flour and agronomic strategies for reducing asparagine accumulation in wheat grain are reviewed. Sulphur availability has been shown to be particularly important, with sulphur deprivation causing a dramatic increase in grain asparagine levels and acrylamide risk. Nitrogen availability is also a factor, with increasing nitrogen availability causing grain asparagine levels and acrylamide risk to rise. In potato, attention has been focused on sugars, and there has been some success in reducing sugar accumulation in stored potatoes by genetic modification, with a resultant reduction in acrylamide formation. However, the wisdom or otherwise of this dogma is discussed. Other possible genetic targets for manipulation or development as genetic markers in breeding programmes are reviewed. Plant breeders and farmers are encouraged to exploit the varietal differences in acrylamide risk that have already been identified and to develop good agronomic practice to reduce the levels of acrylamide precursors in cereals and potato.
Changes in miR-143 and miR-21 Expression and Clinicopathological Correlations in Pancreatic Cancers (2012)

Deregulation of miR-143 and miR-21 may reflect histological features and biological behavior of different PCs. Association data with clinical parameters might indicate a prognostic significance for miR-143 and miR-21 in PCs.
<i>Sleeping Beauty</i>transposition: from biology to applications (2016)

Sleeping Beauty (SB) is the first synthetic DNA transposon that was shown to be active in a wide variety of species. Here, we review studies from the last two decades addressing both basic biology and applications of this transposon. We discuss how host-transposon interaction modulates transposition at different steps of the transposition reaction. We also discuss how the transposon was translated for gene delivery and gene discovery purposes. We critically review the system in clinical, pre-clinical and non-clinical settings as a non-viral gene delivery tool in comparison with viral technologies. We also discuss emerging SB-based hybrid vectors aimed at combining the attractive safety features of the transposon with effective viral delivery. The success of the SB-based technology can be fundamentally attributed to being able to insert fairly randomly into genomic regions that allow stable long-term expression of the delivered transgene cassette. SB has emerged as an efficient and economical toolkit for safe and efficient gene delivery for medical applications.
A novel pulse power supply for magnetron using high voltage capacitor embedded high frequency transformer (2004)

This paper described that novel high voltage capacitor (HVC) embedded high frequency transformer and novel inverter power supply topology for driving magnetron in microwave oven. This transformer is used to achieve down-sizing, low-cost and efficiency improvement. Proposed transformer has HVC in its secondary winding. Therefore, this transformer does not need external high voltage capacitor which used in conventional power supply. As use of this transformer, output voltage is shifted from ground to above 2000 [V] and efficiency of microwave oven can be improved. The weight of proposed transformer is about one sixth of conventional one and efficiency is improved by seven percent compared to the efficiency of the conventional system.
Healing response associated with balloon-dilated ePTFE (1998)

Deployment of endovascular grafts composed of a metallic stent surrounded by expanded polytetrafluoroethylene (ePTFE) stretches the polymer beyond its original dimensions, altering the structural characteristics of the ePTFE. We hypothesized this structural modification would alter the healing response associated with the implant. In this study, 4 mm i.d. of ePTFE (30 microns internodal distance) vascular grafts were balloon dilated using angioplasty balloons having final diameters of 6 (1.5X), 8 (2X), 10 (2.5X), 12 (3X), and 18 (4.5X) mm. Following balloon dilatation of the ePTFE, a circular punch (6 mm in diameter) was used to prepare polymer samples for implantation. The ePTFE circular patches were implanted within subcutaneous tissue and epididymal fat pads of male Sprague-Dawley rats. After 5 weeks, the implants were removed and analyzed for fibrous capsule formation, inflammation, and neovascularization associated with the material. Histological analysis revealed the formation of fibrous capsules only with control subcutaneous implants. The inflammatory response associated with subcutaneously implanted ePTFE was decreased significantly following balloon dilatation to at least 2.5 times the original diameter of the graft. In contrast, ePTFE implanted within adipose tissue demonstrated a significantly greater inflammatory response following balloon dilatation when compared to control implants. Only ePTFE balloons dilated to 6 mm and implanted within adipose tissue demonstrated neovascularization to any extent. These data suggest the structural modifications incurred by ePTFE following balloon dilatation dramatically affect the inflammatory response associated with an implant. Therefore, polymeric materials used for endovascular graft technology require designs that consider changes in polymer healing inherent to device design.
Etretinate absorption in the <i>in situ</i> perfused intestinal lumen: Preliminary studies in the rat (1991)

The absorption characteristics of etretinate were examined in the Sprague-Dawley rat with the use of the in situ intestinal lumen perfusion model. Intestinal segments of 15-50 cm were cannulated and perfused with etretinate solutions of 178-1405 micrograms ml-1 in a single-pass manner at flow rates of 0.15-0.96 ml min-1. The intestinal effluent was collected and analyzed by HPLC for etretinate, as was blood that was drawn from the jugular vein. Despite its lipophilic nature, etretinate does not appear to be well absorbed from the rat intestine; the maximum fraction disappearing from the intestinal lumen was approximately 0.35. The absorption of etretinate appeared to be controlled by the aqueous diffusion layer. There was no evidence that the uptake of etretinate by the gastrointestinal membrane involved an active transport system.
A therapeutic role for targeting c-Myc/Hif-1- dependent signaling pathways (2010)

Deregulated c-Myc occurs in approximately 30% of human cancers. Similarly, hypoxia-inducible factor (HIF) is commonly overexpressed in a variety of human malignancies. Under physiologic conditions, HIF inhibits c-Myc activity; however, when deregulated oncogenic c-Myc collaborates with HIF in inducing the expression of VEGF, PDK1 and hexokinase 2. Most of the knowledge of HIF derives from studies investigating a role of HIF under hypoxic conditions, however, HIF-1alpha stabilization is also found in normoxic conditions. Specifically, under hypoxic conditions HIF-1-mediated regulation of oncogenic c-Myc plays a pivotal role in conferring metabolic advantages to tumor cells as well as adaptation to the tumorigenic micromilieu. In addition, our own results show that under normoxic conditions oncogenic c-Myc is required for constitutive high HIF-1 protein levels and activity in Multiple Myeloma (MM) cells, thereby influencing VEGF secretion and angiogenic activity within the bone marrow microenvironment. Further studies are needed to delineate the functional relevance of HIF, MYC, and the HIF-MYC collaboration in MM and other malignancies, also integrating the tumor microenvironment and the cellular context. Importantly, early studies already demonstrate promising preclinical of novel agents, predominantly small molecules, which target c-Myc, HIF or both.
An investigation of the clique problem in FlexRay (2008)

Distributed, time-triggered communication based on FlexRay is likely to become an enabler for future safety related applications in the automotive domain. Prior to series deployment, however, confidence has to be established that all mechanisms work as expected. One particular issue in this regard is the clique problem. Cliques are groups of nodes connected to the same bus which are only able to communicate with the members of the same clique, but not with members from another one. In time-triggered systems cliques might be caused, for instance, by Byzantine faults leading to a different view of the global time. In constrast to other hard real-time systems, FlexRay lacks explicit protocol support for detecting and resolving cliques. Thus, in this paper we investigate the clique problem in a real FlexRay system. We explain the different types of cliques and give examples how they might emerge and look like. One focus is the experimental study of the behavior of a real FlexRay cluster with existing cliques. In particular, we investigate the integration behavior of nodes into a system with present cliques as well as the behavior of the system when it is in a clique state. After a presentation of the results, we conclude by giving some directions about some protocol features which might be used for implementing clique avoidance or clique detection mechanisms.
Chimeric Erythropoietin-Interferon γ Receptors Reveal Differences in Functional Architecture of Intracellular Domains for Signal Transduction (1997)

Binding of interferon gamma (IFN-gamma) causes oligomerization of the two interferon gamma receptor (IFN-gammaR) subunits, receptor chain 1 (IFN-gammaR1, the ligand-binding chain) and the second chain of the receptor (IFN-gammaR2), and causes activation of two Jak kinases (Jak1 and Jak2). In contrast, the erythropoietin receptor (EpoR) requires only one receptor chain and one Jak kinase (Jak2). Chimeras between the EpoR and the IFN-gammaR1 and IFN-gammaR2 chains demonstrate that the architecture of the EpoR and the IFN-gammaR complexes differ significantly. Although IFN-gammaR1 alone cannot initiate signal transduction, the chimera EpoR/gammaR1 (extracellular/intracellular) generates slight responses characteristic of IFN-gamma in response to Epo and the EpoR/gammaR1. EpoR/gammaR2 heterodimer is a fully functional receptor complex. The results demonstrate that the configuration of the extracellular domains influences the architecture of the intracellular domains.
Phenomenological theory of a single domain wall in uniaxial trigonal ferroelectrics: Lithium niobate and lithium tantalate (2005)

A phenomenological treatment of domain walls based on the Ginzburg-Landau-Devonshire theory is developed for uniaxial trigonal ferroelectrics, lithium niobate and lithium tantalate. The contributions to the domain-wall energy from polarization and strain as a function of orientation are considered. Analytical expressions are developed that are analyzed numerically to determine the minimum polarization, strain, and energy configurations of domain walls. It is found that hexagonal $y$ walls are preferred over $x$ walls in both materials. This agrees well with experimental observation of domain geometries in stoichiometric composition crystals.
Fluorescent labelling of sequencing primers for automated oligonucleotide synthesis (1992)

A fluorescein derivative is described which can be used as a normal phosphoramidite in oligonucleotide synthesis, giving high yields of fluorescein labelled sequencing primers. The labelled primers were used in automated DNA-sequence analysis without modification of existing protocols, the computer-processed sequences being reproducibly readable up to 400 bases. The procedure described makes the fluorescent labelling of oligonucleotides much easier, and the time of labelling can be significantly reduced. It speeds up the "primer walking" approach of automated DNA sequencing.
VSB demodulator ASIC design and development for HDTV system (2002)

In this paper, we present ASIC design and implementation of vestigial sideband (VSB) demodulator for high definition television (HDTV) system employing the VSB modulation technique. We present three ASIC chips for VSB demodulator implementation.
Subcritical co‐solvents extraction of lipid from wet microalgae pastes of <i>Nannochloropsis</i> sp. (2011)

In this paper subcritical co-solvents extraction (SCE) of algal lipid from wet pastes of Nannochloropsis sp. is examined. The influences of five operating parameters including the ratio between ethanol to hexane, the ratio of mixed solvents to algal biomass (dry weight), extraction temperature, pressure, and time were investigated. The determined optimum extraction conditions were 3:1 (hexane to ethanol ratio), 10:1 ratio (co-solvents to microalgae (dry weight) ratio), 90°C, 1.4 MPa, and 50 min, which could produce 88% recovery rate of the total lipids. In addition, electron micrographs of transmission electron microscopy (TEM) and scanning electron microscopy (SEM) were conducted to show that the algal cell presented shrunken, collapsed with some wrinkles and microholes after SCE extraction. The main composition of total lipids extracted under the optimum conditions was TAG which represented more than 80%. And the fatty acid profile of triglycerides revealed that C16:0 (35.67 ± 0.2%), C18:1 (26.84 ± 0.044%) and C16:1 (25.96 ± 0.011%) were dominant. PRACTICAL APPLICATIONS: The reported method could save energy consumption significantly through avoiding deep dewatering (for example drying). The composition of the extracted lipid is suitable for the production of high quality biodiesel.
Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae (2018)

Molecular combing and gel electrophoretic studies revealed endogenous nicks with free 3'OH ends at ∼100 kb intervals in the genomic DNA (gDNA) of unperturbed and G1-synchronized Saccharomyces cerevisiae cells. Analysis of the distribution of endogenous nicks by Nick ChIP-chip indicated that these breaks accumulated at active RNA polymerase II (RNAP II) promoters, reminiscent of the promoter-proximal transient DNA breaks of higher eukaryotes. Similar periodicity of endogenous nicks was found within the ribosomal rDNA cluster, involving every ∼10th of the tandemly repeated 9.1 kb units of identical sequence. Nicks were mapped by Southern blotting to a few narrow regions within the affected units. Three of them were overlapping the RNAP II promoters, while the ARS-containing IGS2 region was spared of nicks. By using a highly sensitive reverse-Southwestern blot method to map free DNA ends with 3'OH, nicks were shown to be distinct from other known rDNA breaks and linked to the regulation of rDNA silencing. Nicks in rDNA and the rest of the genome were typically found at the ends of combed DNA molecules, occasionally together with R-loops, comprising a major pool of vulnerable sites that are connected with transcriptional regulation.
Thermal Expansion Coefficients of High-T<sub>c</sub> Superconductors (1988)

High- T c superconducting oxides were confirmed to have much higher thermal expansion coefficients than various substrate materials. The difference in thermal expansion between superconductor and substrate materials corresponded well with the crack size formed in the film. Thermal expansion of Ba 2 YCu 3 O 7-δ abruptly changes at about 350°C and 650°C, which reflects the change of oxygen concentration and the phase transition, respectively. The expansion pattern varied considerably by the substitution of yttrium by ytterbium, suggesting a difference in the kinetics of oxygen uptake and secession between the two superconductors.