gebhart/patrepeval huggingface dataset:
Topology of three-way junctions in folded RNAs (2005)

The three-way junctions contained in X-ray structures of folded RNAs have been compiled and analyzed. Three-way junctions with two helices approximately coaxially stacked can be divided into three main families depending on the relative lengths of the segments linking the three Watson-Crick helices. Each family has topological characteristics with some conservation in the non-Watson-Crick pairs within the linking segments as well as in the types of contacts between the segments and the helices. The most populated family presents tertiary interactions between two helices as well as extensive shallow/minor groove contacts between a linking segment and the third helix. On the basis of the lengths of the linking segments, some guidelines could be deduced for choosing a topology for a three-way junction on the basis of a secondary structure. Examples and prediction bas'ed on those rules are discussed.
Dissociation between syncytia formation and HIV spreading. Suppression of syncytia formation does not necessarily reflect inhibition of HIV infection (1991)

In this study, we have observed that a dissociation may occur in vitro between syncytia formation and HIV spreading. Efficient HIV spreading and virus replication occurred either in HIV-infected LFA-1+ lymphocytes treated with anti-LFA-1 mAb or in HIV-infected lymphocytes genetically deficient in LFA-1, despite the fact that syncytia formation was completely suppressed. Therefore, these results indicate that syncytia formation cannot be used as the sole parameter to evaluate the spread of HIV in vitro.
Chimeric crRNAs with 19 DNA residues in the guide region show the retained DNA cleavage activity of Cas9 with potential to improve the specificity (2019)

We demonstrated that 19 out of 20 RNA residues in the guide region of crRNA can be replaced with DNA residues with high GC-contents. The cellular activity of the chimeric crRNAs to disrupt the target gene was comparable to that of the native crRNA.
Dipole moments and dielectric properties of fluorine substituted nematic liquid crystals (1989)

Abstract The effect of lateral fluorine substituents on the dielectric properties of a range of nematic liquid crystals is reported. Measurements of dipole moments and electric permittivities have been made and used to calculate Kirkwood correlation factors over a range of temperature. The results show that the extent and nature of dipole correlations are important considerations in determining the magnitude of the dielectric anisotropy in these materials. Correlation factors up to 1.4 are found, providing good evidence for the presence of parallel dipole associations.
Method of constructing exactly solvable chaos (1997)

We present a systematic method of constructing rational mappings as ergodic transformations with nonuniform invariant measures on the unit interval I=[0,1]. As a result, we obtain a two-parameter family of rational mappings that have a special property in that their invariant measures can be explicitly written in terms of algebraic functions of parameters and a dynamical variable. Furthermore, it is shown here that this family is the most generalized class of rational mappings possessing the property of exactly solvable chaos on I, including the Ulam--von Neumann map y=4x(1-x). Based on the present method, we can produce a series of rational mappings resembling the asymmetric shape of the experimentally obtained first return maps of the Beloussof-Zhabotinski chemical reaction, and we can match some rational functions with other experimentally obtained first return maps in a systematic manner.
The SHADE cipher: an efficient hash-function-based Feistel network (2002)

We propose SHADE, a balanced Feistel network (H. Feistel, 1973; H. Feistel et al., 1975) that uses a modified hash function that accepts two fixed size inputs (each of which is the size of the function output) as the round function. This new hash function blends many of the concepts of MD5 and SHA-1, with some modifications and extensions. A complete description of the SHADE cipher, including key schedule, blocksize, round (hash) function, and number of rounds, is presented.
Near Wellbore Stimulation by Acoustic Waves (2003)

Abstract Reduced well productivity or injectivity is often caused by near-wellbore formation damage due to the interaction of reservoir formation with drilling and completion fluids. The problem can be further compounded by production induced formation damage. A prime example is fines migration and fines plugging of rock pores or gravel packs. High frequency sonic waves, especially ultrasonic waves have been used in many industrial applications to remove contaminants like dirt, oil, and grease from parts immersed in fluids. An obvious extension of this application is the removal of wellbore impairment by exposing it to high frequency acoustic waves. Although the concept is old, successful large-scale application of acoustic well stimulation is not common. Greater understanding of the technology's applicability and limitations are essential in order to design effective downhole acoustic tool and guide successful field implementation. To this end, we have embarked on a dedicated project to mature the technology, which includes dedicated experimentation and tool design. In this paper, we focus on some key experimental results and discuss potential applications in production engineering.
Regulation of Somatic-Cell Therapy and Gene Therapy by the Food and Drug Administration (1993)

Scientific advances in the past decade have made the clinical testing of somatic-cell therapy and gene therapy a reality. Early trials in humans suggest that important new diagnostic and therapeutic tools are on the horizon. The objectives of this article are to examine the regulation of somatic-cell and gene therapy by the Food and Drug Administration (FDA) in the context of the agency's traditional role in the development of biologic products and to stimulate discussion in areas in which policy is still being formulated. The technology of somatic-cell and gene therapy has moved from the bench to clinical evaluation with . . .
Propofol inhibits neuronal differentiation of mouse embryonic stem cells in vitro (2013)

Propofol (2,6-diisopropylphenol) is a general intravenous anesthetic which plays roles in the central neural system by binding GABAA receptors (GABAARs) and enhancing the chloride channels of the neurons.1 Previous studies mainly focused on the effects of anesthetics on mature neurons,but little attention was paid to their role in early neural differentiation or neural stem cells.Therefore,in the present study,we choose the widely used mouse embryonic cells (ES) cells as the model to investigate the potential effect ofpropofol on neuronal differentiation.
A 3D Freehand Ultrasound System for Multi-view Reconstructions from Sparse 2D Scanning Planes (2011)

Multi-view 3D reconstruction from sparse 2D freehand B-mode images leads to more accurate volume quantification compared to single view systems. The flexibility and low-cost of the proposed system allow for fine control of the image acquisition planes for optimal 3D reconstructions from multiple views.
Modular Multiplication for Public Key Cryptography on FPGAs (2009)

All public key cryptosystems, though being highly secure, have a common drawback: They require heavy computational effort. This is due to the reliance on modular multiplication of large operands (1024 bits or higher). The same problem arises in data encryption/decryption and digital signature schemes. Examples of such cryptosystems are RSA, DSA, and ECC. Now considering embedded platforms for applications of smart cards and smart tokens, the overall time performance of the cipher system becomes very slow. This refers to the limited computational power of the embedded processors. This paper introduces an enhanced architecture for computing the modular multiplication of large operands. The proposed design can act as a co-processor for embedded general purpose CPUs. The proposed design is compared with three previous architectures depending on carry save adders and look up tables, and scoring 69 MHz of maximum frequency. Look up tables should be loaded with a set of pre-computed values. Our proposed architecture replaces both look up tables and pre-computations with an enhanced version of sign detection techniques. Considering 1024 bits architectures, the proposed design scored a maximum frequency of 181 MHz. It also has a better overall absolute time for a single operation.
Comparison of four different methods for detection of Cryptosporidium species (1995)

Newly available assays offer alternatives to conventional microscopic examination for Cryptosporidium spp. We compared two enzyme immunoassays, ProSpect Cryptosporidium microtiter assay (Alexon, Inc., Mountain View, Calif.) and Color Vue Cryptosporidium assay (Serady, Indianapolis, Ind.), and a direct immunofluorescent assay, Merifluor Cryptosporidium kit (Meridian Diagnostics, Cincinnati, Ohio), with acid-fast Kinyoun-staining for the detection of Cryptosporidium spp. Examinations were performed on 129 stool specimens received from patients during a recent waterborne outbreak. A specimen was considered positive when organisms could be identified visually by acid-fast and immunofluorescent stains or if organisms could be visualized by either acid-fast or immunofluorescent stain and detected by both enzyme immunoassays. The final number of positive specimens was 55. No single procedure detected all 55 positive specimens. Of these, ProSpect and Color Vue detected 52 (sensitivity, 94.5%), and the Kinyoun stain and Merifluor detected 53 (sensitivity, 96.4%). The final number of negative specimens was 74. One false-positive result was seen with both the Kinyoun stain and the ProSpect assay. The Color Vue and ProSpect assays required the most hands-on technologist time. The ProSpect assay and Merifluor kit were easiest to perform. The acid-fast stain was difficult to interpret. The Merifluor kit was easiest to read and was adaptable to both batch and single testing. Overall, the Kinyoun stain and the Merifluor test were preferable to both of the enzyme immunoassays because of the high reagent cost and hands-on time required for the enzyme immunoassays. The difficult interpretation of the Kinyoun stain smears made the Merifluor a more desirable test despite its higher cost. We conclude that all methods tested were equally sensitive and specific for the detection of Cryptosporidium spp. Ease of use, adaptability to batch testing, and cost are important criteria in determining the method of choice.
A commitment-based management strategy for the performance and reliability enhancement of flash-memory storage systems (2009)

Cost has been a major driving force in the development of the flash memory technology, but has also introduced serious challenges on reliability and performance for future products. In this work, we propose a commitment-based management strategy to resolve the reliability problem of many flash-memory products. A three-level address translation architecture with an adaptive block mapping mechanism is proposed to accelerate the address translation process with a limited amount of the RAM usage. Parallelism of operations over multiple chips is also explored with the considerations of the write constraints of multi-level-cell flash memory chips.
Wavelet-based lossless compression scheme with progressive transmission capability (1999)

Lossless image compression with progressive transmission capabilities plays a key role in measurement applications, requiring quantitative analysis and involving large sets of images. This work proposes a wavelet-based compression scheme that is able to operate in the lossless mode. The quantization module implements a new technique for the coding of the wavelet coefficients that is more effective than the classical zerotree coding. The experimental results obtained on a set of multimodal medical images show that the proposed algorithm outperforms the embedded zerotree coder combined with the integer wavelet transform by 0.28 bpp, the set-partitioning coder by 0.1 bpp, and the lossless JPEG coder by 0.6 bpp. The scheme produces a losslessly compressed embedded data stream; hence, it supports progressive refinement of the decompressed images. Therefore, it is a good candidate for telematics applications requiring fast user interaction with the image data, retaining the option of lossless transmission and archiving of the images. © 1999 John Wiley & Sons, Inc. Int J Imaging Syst Technol 10: 76–85, 1999
Erfolge gegen die sexuelle Vermarktung von Kindern. Erfahrungen von jugendschutz.net (2010)

Der JMS-Report informiert stets aktuell und ausführlich über Themen des Jugendmedienschutzes. Hauptbestandteil sind die Listen sämtlicher indizierter und beschlagnahmter/eingezogener Medien (Filme, Computer- und Videospiele, Printmedien und Tonträger).
Solving the riddle of codon usage preferences: a test for translational selection (2004)

Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of molecular evolution, yet, establishing the underlying causes for its idiosyncratic behaviour across living kingdoms has proven elusive to researchers over the past 20 years. In this study, a statistical model for measuring translational selection in any given genome is developed, and the test is applied to 126 fully sequenced genomes, ranging from archaea to eukaryotes. It is shown that tRNA gene redundancy and genome size are interacting forces that ultimately determine the action of translational selection, and that an optimal genome size exists for which this kind of selection is maximal. Accordingly, genome size also presents upper and lower boundaries beyond which selection on codon usage is not possible. We propose a model where the coevolution of genome size and tRNA genes explains the observed patterns in translational selection in all living organisms. This model finally unifies our understanding of codon usage across prokaryotes and eukaryotes. Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model.
Exon 13-skipped USH2A protein retains functional integrity in mice, suggesting an exo-skipping therapeutic approach to treat USH2A-associated disease (2020)

ABSTRACT Mutations in the USH2A gene are the most common cause of non-syndromic inherited retinal degeneration and Usher syndrome, which is characterized by congenital deafness and progressive vision loss. Development of a vector mediated therapy for USH2A -associated disease has been challenging due to its large size of coding sequence (~15.6kb). Therefore, there is an unmet need to develop alternative therapeutic strategies. The USH2A protein (Usherin) contains many repetitive domains, and it has been hypothesized that some domains may be dispensable with regard to protein function. Here, we show that skipping of exon 13 of the human USH2A gene or the equivalent exon 12 of the mouse Ush2a gene results in an in-frame transcript that produces functional Usherin protein. This nearly full length Usherin rescues the ciliogenesis in Ush2a null cells as well as the cochlear and retinal phenotypes in Ush2a null mice. Together, our results support the development of exon-skipping strategies to treat both visual and hearing loss in patients with USH2A -associated disease due to mutations in exon 13.
Arachidonic Acid-metabolizing Cytochrome P450 Enzymes Are Targets of ω-3 Fatty Acids* (2010)

Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) protect against cardiovascular disease by largely unknown mechanisms. We tested the hypothesis that EPA and DHA may compete with arachidonic acid (AA) for the conversion by cytochrome P450 (CYP) enzymes, resulting in the formation of alternative, physiologically active, metabolites. Renal and hepatic microsomes, as well as various CYP isoforms, displayed equal or elevated activities when metabolizing EPA or DHA instead of AA. CYP2C/2J isoforms converting AA to epoxyeicosatrienoic acids (EETs) preferentially epoxidized the ω-3 double bond and thereby produced 17,18-epoxyeicosatetraenoic (17,18-EEQ) and 19,20-epoxydocosapentaenoic acid (19,20-EDP) from EPA and DHA. We found that these ω-3 epoxides are highly active as antiarrhythmic agents, suppressing the Ca(2+)-induced increased rate of spontaneous beating of neonatal rat cardiomyocytes, at low nanomolar concentrations. CYP4A/4F isoforms ω-hydroxylating AA were less regioselective toward EPA and DHA, catalyzing predominantly ω- and ω minus 1 hydroxylation. Rats given dietary EPA/DHA supplementation exhibited substantial replacement of AA by EPA and DHA in membrane phospholipids in plasma, heart, kidney, liver, lung, and pancreas, with less pronounced changes in the brain. The changes in fatty acids were accompanied by concomitant changes in endogenous CYP metabolite profiles (e.g. altering the EET/EEQ/EDP ratio from 87:0:13 to 27:18:55 in the heart). These results demonstrate that CYP enzymes efficiently convert EPA and DHA to novel epoxy and hydroxy metabolites that could mediate some of the beneficial cardiovascular effects of dietary ω-3 fatty acids.
Integrated porous-silicon light-emitting diodes: A fabrication process using graded doping profiles (2001)

A fabrication process, compatible with an industrial bipolar+complementary metal–oxide–semiconductor (MOS)+diffusion MOS technology, has been developed for the fabrication of efficient porous-silicon-based light-emitting diodes. The electrical contact is fabricated with a double n+/p doping, achieving a high current injection efficiency and thus lower biasing voltages. The anodization is performed as the last step of the process, thus reducing potential incompatibilities with industrial processes. The fabricated devices show yellow-orange electroluminescence, visible with the naked eye in room lighting. A spectral characterization of light emission is presented and briefly discussed.
Activity and Expression of Murine Small Maf Family Protein MafK (1995)

Transcription factor NF-E2 is believed to be crucial for the regulation of erythroid-specific gene transcription. The three small Maf family proteins (MafF, MafG, and MafK), which are closely related to c-Maf proto-oncoprotein, constitute half of NF-E2 activity by virtue of forming heterodimers with the large, tissue-restricted subunit of NF-E2 (p45). We isolated cDNA clones encoding the murine small Maf family protein MafK and characterized the structure, activity, and expression profile of MafK mRNA. Functional analyses demonstrate that MafK binds to consensus NF-E2 sites in the absence of p45 in vitro and represses transcription of NF-E2 site-dependent reporter genes in transient transfection assays, while p45 introduced into cells alone does not effectively bind to DNA and does not affect transcription. In the presence of p45, MafK confers site-specific DNA binding activity to p45, and p45 in turn mediates transcriptional activation with its amino-terminal proline-rich domain. mRNA for MafK is expressed in fractions enriched for hematopoietic stem cells as well as erythroid cells, suggesting that MafK plays an important regulatory role in hematopoiesis.
Fibre optic confocal imaging (FOCI) for subsurface microscopy of the colon in vivo. (1994)

Fibre optic confocal imaging (FOCI) is a new type of microscopy which has been recently developed (Delaney et al. 1993). In contrast to conventional light microscopy, FOCI and other confocal techniques allow clear imaging of subsurface structures within translucent objects. However, unlike conventional confocal microscopes which are bulky (because of a need for accurate alignment of large components) FOCI allows the imaging end to be miniaturised and relatively mobile. FOCI is thus particularly suited for clear subsurface imaging of structures within living animals or subjects. The aim of the present study was to assess the suitability of using FOCI for imaging of subsurface structures within the colon, both in vitro (human and rat biopsies) and in vivo (in rats). Images were obtained in fluorescence mode (excitation 488 nm, detection above 515 nm) following topical application of fluorescein. By this technique the glandular structure of the colon was imaged. FOCI is thus suitable for subsurface imaging of the colon in vivo.
Circuits and design techniques for secure ICs resistant to side-channel attacks (2006)

Integrated circuits used for security applications, such as smart-cards, leak information. The key or other sensitive information can be guessed by monitoring the execution time, the power variation and/or the electromagnetic radiation of the integrated circuit. This class of so-called side-channel attacks doesn't need expensive equipment or intrusive monitoring to be effective. We have shown that we can obtain the secret key out of a regular standard CMOS implementation of the AES encryption algorithm by monitoring the power consumption of only 2000 encryptions. This is orders of magnitude lower than the mathematical security of 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">128</sup> possible encryption keys to break the algorithm. The root cause of this problem is that standard CMOS is power efficient and it will only consume dynamic power when nodes are switching. Mathematical solutions have been proposed that include randomization and masking techniques. Our original approach is that we address the problem at circuit level. Instead of a full custom layout, a few key modifications are incorporated in a regular synchronous CMOS standard cell design flow. We present the basis for side-channel attack resistance and adjust the library databases and constraint files of the synthesis and place & route procedures. We show the measurement results on two functionally identical co-processors which were fabricated using a TSMC 6M 0.18mum CMOS. We also discuss issues of side-channel resistance when implementing ICs in future technologies
Screening Pap Smears with Near-Infrared Spectroscopy (1995)

A rapid method for the analysis of Pap smears has been developed with the use of near-infrared spectroscopy. Spectra of Pap smears from 50 female patients including 30 with normal cells, 9 with atypical cells, and 11 with cervical cancer were measured in the near-IR region of 4000 to 10,000 cm −1 . Both the original spectra and the second-derivative spectra of Pap smears were subjected to data analysis. The malignant samples displayed abnormal spectra compared with the corresponding normal cervical samples; the atypical samples have spectral features characteristic of both normal and abnormal samples. With the use of principal component analysis (PCA) and discriminant analysis, the samples were grouped in patterns that were consistent with clinical analysis. Since obtaining near-infrared spectra of human tissues is a rapid and inexpensive process, the results suggest that the near-infrared spectra of human tissues may be of diagnostic value for cancer diagnosis.
Impulse response analysis of a real feeder for high impedance fault detection (2002)

A high impedance fault is an abnormal event that occurs in distribution feeders. Owing to its nature it cannot be detected by conventional protection. A technique for high impedance fault detection is presented in this work. The method consists in injecting an impulsive signal in the feeder followed by the monitoring of its response. High impedance faults are detected by comparisons between the feeder response operating in normal condition and that under fault condition. In the event of a high impedance fault the feeder response becomes different from that of normal switching operations. Although the difference in the feeder response for these cases can be very small, the presented technique recognizes them as different events. The validity of the method is supported by the results of tests performed on a 13.8 kV real feeder presented in the paper.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>