gebhart/patrepeval huggingface dataset:
ANTISENSE OLIGONUCLEOTIDES: FROM DESIGN TO THERAPEUTIC APPLICATION (2006)

1. An antisense oligonucleotide (ASO) is a short strand of deoxyribonucleotide analogue that hybridizes with the complementary mRNA in a sequence-specific manner via Watson-Crick base pairing. Formation of the ASO-mRNA heteroduplex either triggers RNase H activity, leading to mRNA degradation, induces translational arrest by steric hindrance of ribosomal activity, interferes with mRNA maturation by inhibiting splicing or destabilizes pre-mRNA in the nucleus, resulting in downregulation of target protein expression. 2. The ASO is not only a useful experimental tool in protein target identification and validation, but also a highly selective therapeutic strategy for diseases with dysregulated protein expression. 3. In the present review, we discuss various theoretical approaches to rational design of ASO, chemical modifications of ASO, ASO delivery systems and ASO-related toxicology. Finally, we survey ASO drugs in various current clinical studies.
Ro (SS‐A) antibody and antigen in a patient with congenital complete heart block (1985)

Congenital complete heart block is closely associated with the presence of anti-Ro (SS-A) autoantibodies. Quantitative solid-phase assays for Ro (SS-A) autoantigen and autoantibody have established the presence of Ro (SS-A) in cardiac tissues and have been used to evaluate an informative pedigree. The propositus we describe here had complete congenital heart block and showed anti-Ro (SS-A) binding of 13-fold less than his normal HLA-identical twin sister. Both had identical titers of antinuclear antibody. These data support the hypothesis that anti-Ro (SS-A) may be directly involved in the pathogenesis of congenital complete heart block.
Characterization of the Class IV Homeodomain-Leucine Zipper Gene Family in Arabidopsis (2006)

The Arabidopsis (Arabidopsis thaliana) genome contains 16 genes belonging to the class IV homeodomain-Leucine zipper gene family. These include GLABRA2, ANTHOCYANINLESS2, FWA, ARABIDOPSIS THALIANA MERISTEM LAYER1 (ATML1), and PROTODERMAL FACTOR2 (PDF2). Our previous study revealed that atml1 pdf2 double mutants have severe defects in the shoot epidermal cell differentiation. Here, we have characterized additional members of this gene family, which we designated HOMEODOMAIN GLABROUS1 (HDG1) through HDG12. Analyses of transgenic Arabidopsis plants carrying the gene-specific promoter fused to the bacterial beta-glucuronidase reporter gene revealed that some of the promoters have high activities in the epidermal layer of the shoot apical meristem and developing shoot organs, while others are temporarily active during reproductive organ development. Expression profiles of highly conserved paralogous gene pairs within the family were found to be not necessarily overlapping. Analyses of T-DNA insertion mutants of these HDG genes revealed that all mutants except hdg11 alleles exhibit no abnormal phenotypes. hdg11 mutants show excess branching of the trichome. This phenotype is enhanced in hdg11 hdg12 double mutants. Double mutants were constructed for other paralogous gene pairs and genes within the same subfamily. However, novel phenotypes were observed only for hdg3 atml1 and hdg3 pdf2 mutants that both exhibited defects in cotyledon development. These observations suggest that some of the class IV homeodomain-Leucine zipper members act redundantly with other members of the family during various aspects of cell differentiation. DNA-binding sites were determined for two of the family members using polymerase chain reaction-assisted DNA selection from random oligonucleotides with their recombinant proteins. The binding sites were found to be similar to those previously identified for ATML1 and PDF2, which correspond to the pseudopalindromic sequence 5'-GCATTAAATGC-3' as the preferential binding site.
A Blockchain-Based Framework for Secure Log Storage (2019)

Logs are critical data, which can help us to troubleshoot and identify the person in charge of an unexpected accident. Log systems have been widely used for log storage. However, the traditional log system can't prevent the log from being tampered. Centralized servers are more vulnerable to be attacked. Those who have permission to operate records can easily tamper with logs. Blockchain is a disruptive technology in recent years, which has the advantages of decentralization, tamper-proof and traceability. Given its decentralization and tamper-proof properties, the paper proposed a blockchain-based framework for secure log storage. However, the cost of storing big files in the blockchain is very high. Thus, the paper utilized the InterPlanetary File System(IPFS) to store log files instead of a blockchain. Besides, the paper adopted Ethereum blockchain to store the hash of log files and a smart contract to create an index for log files. The solution is not only applicable to log but also other scenarios requiring secure data storage and efficient retrieval.
Direct current superposed dual-frequency capacitively coupled plasmas in selective etching of SiOCH over SiC (2011)

Abstract Superpositioning of negative dc bias in dual-frequency capacitively coupled plasmas (dc-superposed (DS)-CCP) was realized for the selective etching of carbon-doped silicon oxide (SiOCH) films over carbon-doped amorphous silicon (SiC) films, while the dc bias exceeded about −800 V. When a dc bias of −1200 V was superposed on 60 MHz VHF power on the top electrode opposed to a wafer on the bottom electrode biased with 13.56 MHz power, a selectivity of above 50 for SiOCH over SiC was obtained. From characterization of the plasma density and various chemical species in the gaseous phase, such as CF 2 , CF and atomic N, the density of CF 2 significantly decreased with the application of dc bias ranging from −800 to −1200 V. This indicated that CF 2 radicals were consumed at the surface of the counter electrode which was made of silicon. The bulk densities of the species including CF 2 were decreased, especially due to excess surface loss caused by the bombardment of highly energetic ions accelerated by the superposed dc bias, as well as the rf sheath for the superposition of the negative dc bias. The DS-CCP technology is thus concluded to be indispensable for yielding highly selective etching of SiOCH over SiC.
Projection display throughput: Efficiency of optical transmission and light-source collection (1998)

The optical system for a projection display based on three miniature reflective spatial light modulators (SLMs) is described. The total projection display light throughput is a function not only of the optical system efficiency but also of the light-collection and light-coupling efficiency referred to here as the lamp-SLM coupling. The optical system efficiency is the transmission of the optical components in the projection display. These are examined in detail through measurements and estimates of the components in the system. The various optical components include UV-IR filtering, illumination optics, polarization optics, color separation and recombination optics, SLM efficiency, and projection optics. The lamp-SLM coupling, which is the amount of usable light that can be collected from a particular lamp coupled to the projection optical system, is determined by the light-source luminance, the efficiency of the light-collection optics, and the optical system étendue. For small SLMs, less than 50 mm diagonal, for example, the lamp-SLM coupling efficiency falls off rapidly with SLM size and optical system f-number. The dependence of this coupling efficiency on SLM size is determined from measurements of the light-collection efficiency as a function of aperture size, where the apertures are used to simulate SLMs of the same dimensions. A variety of arc lamps were investigated for use in the projection display based on IBM reflective SLM devices. The lamp-SLM coupling dependence on arc gap was determined. The measurements are used to compare various lamps and to estimate directly the throughput for the complete projection system. The SLMs used in the projection display are liquid crystal devices which utilize only one polarization of light while discarding the second. Converting the discarded polarization into useful light can in principle double the throughput of the projector. However, polarization conversion results in doubling of the size of the light source and thus produces less efficient lamp-SLM coupling, particularly for long-arc-gap lamps. Measurements and analysis of throughput enhancement by polarization conversion are presented, and the dependence on arc gap and optical system étendue is discussed.
Induction of Autophagy by Second-Fermentation Yeasts during Elaboration of Sparkling Wines (2006)

Autophagy is a transport system mediated by vesicles, ubiquitous in eukaryotic cells, by which bulk cytoplasm is targeted to a lysosome or vacuole for degradation. In the yeast Saccharomyces cerevisiae, autophagy is triggered by nutritional stress conditions (e.g., carbon- or nitrogen-depleted medium). In this study we showed that there is induction of autophagy in second-fermentation yeasts during sparkling wine making. Two methods were employed to detect autophagy: a biochemical approach based on depletion of the protein acetaldehyde dehydrogenase Ald6p and a morphological strategy consisting of visualization of autophagic bodies and autophagosomes, which are intermediate vesicles in the autophagic process, by transmission electron microscopy. This study provides the first demonstration of autophagy in second-fermentation yeasts under enological conditions. The correlation between autophagy and yeast autolysis during sparkling wine production is discussed, and genetic engineering of autophagy-related genes in order to accelerate the aging steps in wine making is proposed.
On‐Line runaway detection in batch reactors using chaos theory techniques (1999)

Abstract In this work nonlinear time‐series analysis using delay coordinate embedding was applied to simulated temperature data from isoperibolic batch reactors to develop an early‐warning detection system of the runaway. In the first part of this study an early‐warning detection criterion, that is, when the divergence of the system becomes positive on a segment of the reaction path, was developed and compared with previous criteria. This criterion has the property of being preserved under phase‐space reconstruction and, hence, it is possible to calculate it when only temperature data are available. This reconstructed divergence is compared with the theoretically calculated divergence using temperature and conversion data. The comparison demonstrates the validity of such an approach finding a new path, lying between the simple use of measured variables and the complex model‐based reconstruction techniques, to assess in advance hazardous situations in chemical reactors.
Mast cells and mastocytosis (2008)

Mast cells have been recognized for well over 100 years. With time, human mast cells have been documented to originate from CD34+ cells, and have been implicated in host responses in both innate and acquired immunity. In clinical immunology, they are recognized for their central role in IgE-mediated degranulation and allergic inflammation by virtue of their expression of the high-affinity receptor for IgE and release of potent proinflammatory mediators. In hematology, the clinical disease of mastocytosis is characterized by a pathologic increase of mast cells in tissues, often associated with mutations in KIT, the receptor for stem cell factor. More recently, and with increased understanding of how human mast cells are activated through receptors including the high-affinity receptor for IgE and KIT, specific tyrosine kinase inhibitors have been identified with the potential to interrupt signaling pathways and thus limit the proliferation of mast cells as well as their activation through immunoglobulin receptors.
Ethology of Sleep Studied with Time-Lapse Photography: Postural Immobility and Sleep-Cycle Phase in Humans (1978)

Human sleep is characterized by episodes of immobility punctuated by major postural shifts. The organization of this motor activity was shown with a combination of photographic and electroencephalographic recording to be periodic and related to the electroencephalographic sleep cycle. The amount of immobility as measured photographically was positively related to subjective estimates of the goodness of sleep.
Integrated waveguide circuits for optical quantum computing (2011)

Although practical realisation of a fully functioning quantum computer is still a long way off, recent progress both experimentally and theoretically is paving the way for possible implementations. One of the leading approaches is quantum optics, where photons are used as carriers of quantum information, and are manipulated in both linear and non-linear optical circuits. More recently, advances in integrated quantum photonics are enabling the realisation of compact and stable quantum gates and circuits. This approach provides routes to enhancing the complexity of quantum optic experiments, and ultimately towards the development of advanced quantum technologies. This study presents an overview of recent developments in the field of integrated waveguide quantum circuits. Key building blocks required for the realisation of quantum circuits are presented, and a rudimentary version of Shor&apos;s quantum factoring algorithm is demonstrated. Planar waveguide quantum circuits provide a high-performance platform from which quantum technologies and experimental quantum physics using single photons can be developed, and a new generation of quantum information and computing devices can be monolithically integrated onto a single optical chip.
Imaging of mRNA in Live Cells Using Nucleic Acid-Templated Reduction of Azidorhodamine Probes (2009)

Nucleic acid-templated reactions leading to a fluorescent product represent an attractive strategy for the detection and imaging of cellular nucleic acids. Herein we report the use of a Staudinger reaction to promote the reduction of profluorescent azidorhodamine. The use of two cell-permeable GPNA probes, one labeled with the profluorescent azidorhodamine and the other with trialkylphosphine, enabled the detection of the mRNA encoding O-6-methylguanine-DNA methyltransferase in intact cells.
The small leucine‐rich proteoglycan biglycan modulates BMP‐4‐induced osteoblast differentiation (2004)

Biglycan (bgn) is a small leucine-rich proteoglycan enriched in extracellular matrices of skeletal tissues. Bgn-deficient mice develop age-related osteopenia with a phenotype that resembles osteoporosis and premature arthritis. In the present study, we have examined the differentiation of bgn-deficient osteoblasts from neonatal murine calvariae and found that the absence of bgn caused less BMP-4 binding, which reduced the sensitivity of osteoblasts to BMP-4 stimulation. The loss of sensitivity resulted in a reduction of Cbfa1 expression, which ultimately led to a defect in the differentiation of osteoblasts. However, the response of bgn-deficient osteoblasts to BMP-4 was completely rescued by reintroduction of biglycan by viral transfection. We propose that biglycan modulates BMP-4-induced signaling to control osteoblast differentiation.
Self-assembled monolayers of alkanethiols on gold: the adsorption and wetting properties of monolayers derived from two components with alkane chains of different lengths (1992)

This paper describes the preparation and wetting properties of two-component self-assembled monolayers (SAMs) obtained by the competitive adsorption of one short-chain (HS(CH2)10Sh) and one long-chain (HS(CH2)21Lg) alkanethiol onto gold from dilute ethanolic solutions. The four possible combinations of the tail groups CH3 and CH2OH were investigated: Sh = CH3/Lg = CH2OH, Sh = CH2OH/Lg = CH3, Sh = CH2OH/Lg = CH2OH, and Sh = CH3/Lg = CH,. The compositions of these SAMs are not the same as the compositions of the solutions from which they were formed. Although the relationship between the composition of the SAM and the composition of the solution suggests that some phase separation may be occurring within the SAM, contact angles with water and hexadecane show that significant disorder still remains in the interfacial region.
Public key infrastructure: how it works (2001)

A variety of authentication methods to verify the identity of valid users can be implemented with IPSec (IP security), including shared secret, token cards and digital certificates. For a large extranet implementation, the easiest method is public key infrastructure (PKI) using digital certificates. This article gives telecommunications managers, network planners and engineers a more detailed look at how PKI works in a virtual private network (VPN) environment.
ColoType: a forty gene signature for consensus molecular subtyping of colorectal cancer tumors using whole-genome assay or targeted RNA-sequencing (2020)

Colorectal cancer (CRC) tumors can be partitioned into four biologically distinct consensus molecular subtypes (CMS1-4) using gene expression. Evidence is accumulating that tumors in different subtypes are likely to respond differently to treatments. However, to date, there is no clinical diagnostic test for CMS subtyping. In this study, we used novel methodology in a multi-cohort training domain (n = 1,214) to develop the ColoType scores and classifier to predict CMS1-4 based on expression of 40 genes. In three validation cohorts (n = 1,744, in total) representing three distinct gene-expression measurement technologies, ColoType predicted gold-standard CMS subtypes with accuracies 0.90, 0.91, 0.88, respectively. To accommodate for potential intratumoral heterogeneity and tumors of mixed subtypes, ColoType was designed to report continuous scores measuring the prevalence of each of CMS1-4 in a tumor, in addition to specifying the most prevalent subtype. For analysis of clinical specimens, ColoType was also implemented with targeted RNA-sequencing (Illumina AmpliSeq). In a series of formalin-fixed, paraffin-embedded CRC samples (n = 49), ColoType by targeted RNA-sequencing agreed with subtypes predicted by two independent methods with accuracies 0.92, 0.82, respectively. With further validation, ColoType by targeted RNA-sequencing, may enable clinical application of CMS subtyping with widely-available and cost-effective technology.
Prognostic and Warning System for Power-Electronic Modules in Electric, Hybrid Electric, and Fuel-Cell Vehicles (2008)

Reliability of power-electronic modules is of paramount importance for the commercial success of various types of electric vehicles. In this paper, we study the technical feasibility of detecting and utilizing early symptoms and warning signs of power-module degradation due to thermomechanical stress and fatigue and develop a prognostic system that can monitor the state of health of the power modules in electric, hybrid, and fuel-cell vehicles. A special degradation trace on the V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CEsat</sub> of the insulated-gate bipolar-transistor modules was observed by a power-cycling accelerated test, which was not reported in literatures. A prognostic system based on utilizing the aforementioned trace is then developed. The system consists of the hardware architecture and current adaptive-algorithm-based software architecture. In addition, this prognostic system hardly increases the hardware cost on existing vehicle-driver system. An extensive simulation based on MATLAB/Simulink verifies the developed prognostic system.
Neurotrophic Action of Interleukin 3 and Granulocyte-Macrophage Colony-Stimulating Factor on Murine Sympathetic Neurons (2000)

We investigated neurotrophic effects of interleukin 3 (IL-3) and granulocyte-macrophage colony-stimulating factor (GM-CSF) on cultured sympathetic neurons obtained from mouse superior cervical ganglia. After 1 day of culture with physiological concentrations of mouse recombinant IL-3 and GM-CSF, the numbers of process-bearing neurons were increased. Maximum responses were elicited by 10 U/ml IL-3 and 1 U/ml GM-CSF, which were equivalent to the action of a submaximal dose (5 ng/ml) of nerve growth factor (NGF). The effects of IL-3 and GM-CSF were completely blocked by their corresponding antibodies, but not by anti-NGF, indicting their action is specific and completely independent of NGF. IL-3 and, to a lesser extent, GM-CSF were also able to protect NGF-differentiated neurons from apoptotic cell death caused by NGF withdrawal. The mitogen-activated protein (MAP) kinase signal transduction pathway is known to be involved in action of IL-3 and GM-CSF on hemopoietic cells, and thus we examined the participation of this pathway in the neurotrophic activities of IL-3 and GM-CSF. IL-3 and GM-CSF stimulation of the differentiated neurons was found to result in a rapid elevation of MAP kinase activity, and PD98059, an inhibitor of MAP kinase kinase activity, blocked both the neuritogenic and neuroprotective effects of IL-3 and GM-CSF. Immunocytochemical studies showed that IL-3 and GM-CSF receptors were present on the differentiated neurons. Thus, IL-3 and GM-CSF appear to be able to stimulate sympathetic nerve growth, via specific cytokine receptors on neurons, which lead to activation of the MAP kinase pathway that then mediates the observed neurotrophic effects.
Alpha Interferon Suppresses the Cyclin D3 and cdc25A Genes, Leading to a Reversible G 0 -Like Arrest (1996)

Alpha interferon is a potent growth inhibitor of Daudi Burkitt's lymphoma cells. We show here that alpha-interferon signaling interacted simultaneously with several components of the basic cell cycle machinery, causing cells to enter into a state that had many features characteristic of the G0 state. Within a few hours after alpha-interferon treatment, cyclin D3 mRNA and protein levels dropped to undetectable levels and, in parallel, the activities of cyclin A- and cyclin E-associated kinases were significantly reduced. The latter resulted from the rapid alpha-interferon-mediated elimination of cdc25A, a phosphatase that is required for antagonism of negative tyrosine phosphorylation of cdk2 in cyclin-cdk complexes. This regulation represents a novel mechanism through which an external inhibitory cytokine interacts with the cell cycle machinery. At later time points after alpha-interferon treatment, the levels of the 55-kDa slowly migrating hyperphosphorylated form of cyclin E and of cyclin A were also reduced. The antiproliferative effects were reversible, and cultures from which alpha interferon was removed reentered S phase after a lag that typically corresponded to approximately two doubling times. During this lag period, the expression of cyclin D3 and cyclin A, as well as of the cdc25A phosphatase, continued to be switched off, in spite of the removal of alpha interferon from the cell surface. In contrast, c-myc, which represents another downstream target gene that is subjected to negative regulation by alpha interferon, was relieved from suppression much earlier, concomitant with the decay in early signaling of the cytokine. The delayed pattern of cyclin reexpression provides evidence that alpha-interferon signaling imposes a G0-like state on this system.
Antibody to Platelet/Endothelial Cell Adhesion Molecule-1 Reduces Myocardial Infarct Size in a Rat Model of Ischemia-Reperfusion Injury (1996)

These results demonstrate that blocking PECAM-1 exerts a significant protective effect in a rat model of myocardial ischemia-reperfusion injury via blockade of neutrophil accumulation in the myocardium.
Synthese und Eigenschaften einiger 1,2,4‐Thiadiazolyl‐sulfenylchloride (1972)

Abstract Aus dem Dikaliumsalz der N‐Cyano‐imidodithiokohlensäure entsteht mit Chlor 3‐Chlor‐1,2,4‐thiadiazol‐5‐sulfenylchlorid, welches sich an feuchter Luft zum Bis‐ 3‐chlor‐1,2,4‐thiadiazolyl‐(5)‐ ‐disulfid ( 9 ) zersetzt; mit Brom reagiert 1 zum Bis‐ 3‐brom‐1,2,4‐thiadiazolyl‐(5)‐ ‐disulfid, letzteres mit primären Aminen zu entsprechenden Sulfenamiden.