gebhart/patrepeval huggingface dataset:
Inhibition of herpes simplex virus 1 gene expression and replication by RNase P-associated external guide sequences (2016)

An external guide sequence (EGS) is a RNA sequence which can interact with a target mRNA to form a tertiary structure like a pre-tRNA and recruit intracellular ribonuclease P (RNase P), a tRNA processing enzyme, to degrade target mRNA. Previously, an in vitro selection procedure has been used by us to engineer new EGSs that are more robust in inducing human RNase P to cleave their targeted mRNAs. In this study, we constructed EGSs from a variant to target the mRNA encoding herpes simplex virus 1 (HSV-1) major transcription regulator ICP4, which is essential for the expression of viral early and late genes and viral growth. The EGS variant induced human RNase P cleavage of ICP4 mRNA sequence 60 times better than the EGS generated from a natural pre-tRNA. A decrease of about 97% and 75% in the level of ICP4 gene expression and an inhibition of about 7,000- and 500-fold in viral growth were observed in HSV infected cells expressing the variant and the pre-tRNA-derived EGS, respectively. This study shows that engineered EGSs can inhibit HSV-1 gene expression and viral growth. Furthermore, these results demonstrate the potential for engineered EGS RNAs to be developed and used as anti-HSV therapeutics.
A New Tool for Dissecting Genetic Control of Type 1 Diabetes (2013)

The NOD mouse has been a critical tool in the quest to understand the genetic control of type 1 diabetes (T1D), and over 25 murine insulin-dependent diabetes ( Idd ) loci that modulate the natural history of T1D have been identified (1). Several of the candidate genes identified in NOD mice also play a role in human T1D, suggesting that dysregulated immune pathways in NOD may closely resemble those found in humans, and justifying continuing work on the genetic origin of T1D in NOD (2). The role of specific genes in T1D has been explored by constructing congenic mice (carrying disease-protective Idd loci), by creating transgenic mice, and by knocking out genes. In each case, however, these studies have had a significant potential drawback: the presence of “passenger DNA” that can potentially confound the interpretation of the results (Fig. 1 A , top panel ) (3). Knockout mice, for example, have previously been made almost exclusively using non-NOD embryonic stem (ES) cells; the resulting non-NOD mice were backcrossed to NOD mice. The backcrossing process ensures that non-NOD genetic material is bred along with the genetic region of interest (Fig. 1 A , top panel ). This is not merely a theoretical concern, as some published studies of transgenic or deleted genes showed an effect on T1D that was later proven to arise from non-NOD passenger DNA (3).



Figure 1 
A : Zinc-finger nuclease (ZFN) knockout technology eliminates passenger DNA. The top panel illustrates chromosomal DNA from a conventional knockout bred onto the NOD genetic …
A spatial light modulator for terahertz beams (2009)

We design and implement a multipixel spatial modulator for terahertz beams using active terahertz metamaterials. Our first-generation device consists of a 4×4 pixel array, where each pixel is an array of subwavelength-sized split-ring resonator elements fabricated on a semiconductor substrate, and is independently controlled by applying an external voltage. Through terahertz transmission experiments, we show that the spatial modulator has a uniform modulation depth of around 40% across all pixels, and negligible crosstalk, at the resonant frequency. This device can operate under small voltage levels, at room temperature, with low power consumption and reasonably high switching speed.
Enhanced flux pinning in a high- <i>T</i> <sub>C</sub> superconducting film by a ferromagnetic buffer layer (2001)

A YBa<sub>2</sub>Cu<sub>3</sub>O<sub>7</sub> (30 nm) superconductor layer and a YBa<sub>2</sub>Cu<sub>3</sub>O<sub>7</sub> (30 nm)/ Pr<sub>0.67</sub>Sr<sub>0.33</sub>MnO<sub>3</sub> (30 nm) superconducting/ferromagnetic bilayer were epitaxially grown on the single-crystal (100) SrTiO<sub>3</sub> substrates. Magnetic characterizations on both samples were very carefully performed over wide temperature and field ranges. The enhanced flux pinning by the ferromagnetic layer in the bilayer sample is clearly seen in the comparison of the temperature-dependent magnetization data obtained in the zero-field-cooled and field-cooled processes for both samples. The fact that the temperature-dependent remanent magnetization in the bilayer shows a sharper transition near the T<sub>C</sub> than that in the YBCO single layer is also consistent with the picture of the enhanced flux pinning. The above observations are confirmed by the enhanced critical current density, J<sub>c</sub> ∞ ΔM, where ΔM is the magnetic irreversibility in the hysteresis loops.
Condensation‐Induced Particle Formation during Vacuum Pump Down (1993)

When a vacuum system containing particle‐free, cleanroom air is pumped down from atmospheric pressure to produce a vacuum, the gas in the chamber expands and cools to cause water vapor condensation and droplet formation. Experiments have been performed to show that a stable aerosol of submicrometer residue particles on the order of 0.2 μm are formed when the water droplets have re‐evaporated. The residue particles are spherical in shape and appear to contain mainly sulfuric acid. The theoretical and experimental studies conducted strongly suggest that the main steps involved in the residue particle formation process are: (i) simultaneous absorption of and in the ppb range from the air into the water droplets during pump down, (ii) concentration of and in the liquid when the droplets re‐evaporate, and (iii) oxidation of by in the concentrated liquid solution during the final period of evaporation to produce stable, residue particles of . The mathematical model developed gives results that are consistent with the experimental observations.
Sobre o conceito de prática pedagógica e o professor de matemática (2013)

Na elaboracao deste artigo, realizou-se uma revisao literaria com a intencao de oferecer subsidios para promover a analise da pratica pedagogica do professor de Matematica, inserindo-se em um contexto de universalizacao da educacao no pais. Para isso, na introducao propoe-se um estudo sobre a definicao de pratica pedagogica numa perspectiva dialetica. No desenvolvimento, apresenta-se breve historico da educacao brasileira nas ultimas decadas, bem como a descricao do cenario atual da escola publica em nosso pais. Sao analisadas, ainda, as condicoes e caracteristicas do trabalho docente e discutido o ensino de Matematica tendo como desafio a inclusao social. As principais consideracoes se baseiam na necessidade de formacoes inicial e continuada para o professor, qualificando-o para exercer conscientemente seu papel de agente social.
σ-Acceptor, Z-type ligands for transition metals (2010)

The ability of Lewis acids to coordinate to transition metals as σ-acceptor ligands was recognized as early as in the 1970's, but so-called Z-type ligands remained curiosities until the early 2000's. Over the last decade, significant progress has been made in this area, especially via the incorporation of Lewis acid moieties into multidentate, ambiphilic ligands. Our understanding of the nature and influence of TM → Z interactions has considerably improved and the scope of Lewis acids susceptible to behave as σ-acceptor ligands has been significantly extended. This feature article summarizes these recent achievements.
Efficient methodology for implementation of Encrypted File System in User Space (2009)

The Encrypted File System (EFS) pushes encryption services into the file system itself. EFS supports secure storage at the system level through a standard UNIX file system interface to encrypted files. User can associate a cryptographic key with the directories they wish to protect. Files in these directories (as well as their pathname components) are transparently encrypted and decrypted with the specified key without further user intervention; clear text is never stored on a disk or sent to a remote file server. EFS can use any available file system for its underlying storage without modifications, including remote file servers such as NFS. System management functions, such as file backup, work in a normal manner and without knowledge of the key. Performance is an important factor to users since encryption can be time consuming. This paper describes the design and implementation of EFS in user space using faster cryptographic algorithms on UNIX Operating system. Implementing EFS in user space makes it portable and flexible; Kernel size will also not increase resulting in more reliable & efficient Operating System. Encryption techniques for file system level encryption are described, and general issues of cryptographic system interfaces to support routine secure computing are discussed.
Liquid-Crystalline Polymethacrylates by Atom-Transfer Radical Polymerization at Ambient Temperature (2002)

Side-on and side-end liquid-crystalline (LC) polymethacrylates were synthesized by atom-transfer radical polymerization at 20°C using monofunctional and difunctional initiators. The polymers have narrow molecular-weight distributions (M̄w /M̄n = 1.15–1.45). The polymerization kinetics were determined for a side-on LC methacrylate, and appear to be first-order, whatever the initiator used. However, the measured molecular weight is much larger than expected, probably because the initiation step is slow. The thermotropic properties of the LC polymers were studied by thermal optical polarizing microscopy, differential scanning calorimetry, and X-ray diffraction. For a side-end LC polymethacrylate, two LC phases were detected although only one has been reported in the literature. The phase sequence was shown to be Cr–SmA–N–Iso.
THE PROGRESS OF HIMAC AND PARTICLE THERAPY FACILITIES IN JAPAN (2001)

More than 1,000 patients have been treated with carbon ions accelerated by a medical synchrotron HIMAC at National Institute of Radiological Sciences, NIRS. Treated patients have tumors on sites of head and neck, lungs, livers, prostates, uteruses, bones and soft tissues, etc. The results of the phase I/II clinical studies, the purposes of which are to confirm the effectiveness of the carbon therapy keeping side effects at extremely low levels, seem excellent, and a part of the clinical studies have advanced in phase II where the optimum way of treatment are studied. Total of six particle therapy facilities are now in operation or under construction in Japan. Only one of these facilities, NIRS, is designed for carbon or heavier ions. Another one, Hyogo can provides both carbons and protons for the cancer treatments whereas the other four facilities, Kashiwa, Wakasa, Tsukuba and Shizuoka use only protons for the treatment. Brief status of these five facilities is also presented.
Molecular Analysis of an Auxin Binding Protein Gene Located on Chromosome 4 of Arabidopsis (1992)

Klaus Palme, Thomas Hesse, Narciso Campos, Christine Garbers, Martin F. Yanofsky, Jeff Schell, Molecular Analysis of an Auxin Binding Protein Gene Located on Chromosome 4 of Arabidopsis, The Plant Cell, Vol. 4, No. 2 (Feb., 1992), pp. 193-201
Design of On-Chip Debug Module Based on MCU (2007)

A design method of embedded OCD (On-Chip Debugging) based on Intel 8051 MCU architecture is proposed. The OCD module named E-OCD-SFRB (Enhanced OCD module with SFR (Special Function Register) Breakpoint Function) is integrated into an existing MCU core, implementing several debugging function. The method we proposed is able to switch from running mode and debugging mode conveniently by controlling the debugging enable port and also enables controlling the MCU core in debugging mode by additional SFR. The function of SFR breakpoint is added, so we could trace the particular SFR, this is the reinforcement to the exiting OCD methods. The principles of E-OCD-SFR_B and detailed implemental method and simulation solution based on EDA platform are presented and validated. The simulation result indicates the completely observing and controlling to the core is achieved without any effect to original functions of the system.
Comparison of conventional tube test with diamed gel microcolumn assay for anti-D titration (2003)

Anti-D titration is the first step in the evaluation of the RhD-sensitized patient. Traditionally, anti-D titration has been performed by tube agglutination. Gel microcolumn assay is a method that has gained widespread usage throughout the world, mainly for ABO/Rh typing, unexpected antibody screening and direct antiglobulin tests. As gel assay has become widely used as a routine method to detect red blood cell alloantibodies, a critical anti-D titer needs to be established. Seventy-nine known blood samples with anti-D (titers 1-32) were titrated simultaneously by the conventional tube test and the gel microcolumn assay. Red blood cells (R0r phenotype) were used, with a final concentration of 3% for tube and 0.8% for gel. Serial twofold dilutions (2-2.048) were prepared for each technique, followed by reading in antiglobulin phase. Anti-D titration in the gel microcolumn assay showed significantly higher titers (mean 3.4-fold) than the conventional tube test in all samples studied. Based on these data, it was not possible to determine a critical titer for anti-D titration by the gel microcolumn assay.
Violation of Bell's Inequality under Strict Einstein Locality Conditions (1998)

We observe strong violation of Bell's inequality in an Einstein-Podolsky-Rosen-type experiment with independent observers. Our experiment definitely implements the ideas behind the well-known work by Aspect et al. We for the first time fully enforce the condition of locality, a central assumption in the derivation of Bell's theorem. The necessary spacelike separation of the observations is achieved by sufficient physical distance between the measurement stations, by ultrafast and random setting of the analyzers, and by completely independent data registration.
Assessment Of Gastric Emptying In The Mouse Using The [<sup>13</sup>C]‐Octanoic Acid Breath Test (2000)

1. Gastric emptying studies in small laboratory animals are hampered by the deficiency of a technique that is non-invasive and repeatable. The aim of the present study was to adapt the non-invasive [13C]-octanoic acid breath test, which has been validated in humans, to assess both liquid and solid gastric emptying in the mouse. 2. Gastric emptying rates were investigated for a liquid meal (Intralipid; Kabi Pharmacia AB, Stockholm, Sweden; n = 7) and two solid meals (egg yolk and mouse chow; n = 7) incorporating [13C]-octanoic acid. All meals were analysed for natural enrichment of [13C]. Mathematical analysis of the 13CO2 excretion rate allowed the determination of gastric emptying parameters. 3. Gastric emptying of Intralipid was more rapid than egg yolk (P < 0.0001). Gastric emptying of mouse chow could not be assessed due to intragastric separation of [13C]-octanoic acid and natural [13C] enrichment of the pellet. 4. The [13C]-octanoic acid breath test can reproducibly assess both liquid and solid gastric emptying non-invasively in the mouse. This method can now be used to assess gastric emptying in drug studies and disease studies for which there are established mouse models.
Deep-level transient spectroscopy studies of electron and hole traps in n-type GaN homoepitaxial layers grown by quartz-free hydride-vapor-phase epitaxy (2019)

We studied deep levels in quartz-free hydride-vapor-phase epitaxy (QF-HVPE)-grown homoepitaxial n-type GaN layers within which three electron and eight hole traps were detected. The dominant electron and hole traps observed in the QF-HVPE-grown GaN layers were E3 (EC − 0.60 eV) and H1 (EV + 0.87 eV), respectively. We found that the E3 trap density of QF-HVPE-grown GaN (∼1014 cm−3) was comparable with that of MOVPE-grown GaN layers, whereas the H1 trap density of QF-HVPE-grown GaN (∼1014 cm−3) was much smaller than that of an MOVPE-grown GaN layer with a low-residual-carbon growth condition. A detailed analysis of the QF-HVPE-grown GaN layers revealed that the H1 trap density is almost equal to the carbon impurity concentration and other impurities that compensate the Si donors besides the carbon impurity were hardly detected in the QF-HVPE-grown GaN layers.
Calculation of risk and statistical indices associated with available transfer capability (2003)

A complete evaluation of available transfer capability (ATC) involves the determination of total transfer capability (TTC), transmission reliability margin (TRM) and capacity benefit margin (CBM). Due to the stochastic nature of power system behaviour, which is considered by TRM, it is important to assess ATC from a statistical and risk analysis point of view. Based on a combination of repeated AC power flow and Monte Carlo methods, risk assessment of the ATC value is described and a set of statistical indices and plots is presented, which provides important information for transmission customers, system operators and power marketers. In addition, two methods of incorporating CBM into ATC are presented and compared. Case studies with the IEEE Reliability Test System (RTS) demonstrate the effectiveness of the proposed methods, indices and plots. The impact of uncertainty, CBM and methods of incorporating CBM on ATC are also investigated.
Attempts to target antitumor drugs toward opioid receptor-rich mouse tumor cells with enkephalin-ellipticinium conjugates. (1989)

Human colorectal and pulmonary carcinomas have been shown to contain high levels of opioid peptides and their corresponding membrane-bound receptors. Therefore possible targeted drugs, consisting of modified enkephalins linked to cytotoxic drugs, were designed. Such conjugates were expected to be specifically internalized within opioid receptor-bearing cells. As a model to this approach, we have synthesized enkephalin-ellipticinium conjugates in which the D-Ala2-D-Leu5-enkephalin (DADLE) was coupled to the 2-nitrogen of either ellipticine or 9-hydroxyellipticine, two drugs acting through different mechanisms of cytotoxicity. These conjugates, DADLE-ellipticinium (NME) and DA-DLE-9-hydroxyellipticinium (NMHE), respectively, were previously shown to retain in vitro both opioid receptors and DNA affinities close to those of the parent compounds. In this paper, we first show that each individual moiety in the complexes remains capable of recognizing its cellular targets. Thus, pretreatment of NG108-15 cells containing delta-opioid receptors by the DADLE-ellipticinium conjugates induced a loss of opioid receptor (down-regulation), while the smaller peptide conjugates, tyrosinyl-D-alanylglycine-ellipticinium, prepared as control, do not. On the other hand, peptide-NMHE conjugates were able to induce DNA topoisomerase II-associated DNA strand breaks suggesting that they have a mode of action similar to that of their parent molecule, NMHE. We then examined whether or not these molecules could exert a specific toxicity on opioid receptor-bearing cells. However, when tested on NG108-15 tumor cells and L-fibroblasts as control, the enkephalin-ellipticinium conjugates (DADLE-NME and DADLE-NMHE) proved to be similarly more cytotoxic on both cell lines than their ellipticinium (NME and NMHE) precursors. In order to understand this apparent lack of specificity we examined the cellular accumulation and distribution of DADLE-NME by fluorescence techniques. These experiments revealed that an important intracellular overconcentration caused by a nonspecific process is probably masking the specific targeted effect of the conjugates. Hence, the project of linking DADLE to highly cytotoxic molecules which cannot cross the plasma membrane without site-directed targeting is discussed.
Segment Routing in Software Defined Networks: A Survey (2018)

Segment routing (SR) has emerged as a promising source-routing methodology to overcome the challenges in the current routing schemes. It has received noticeable attention both in industry and academia, due to its flexibility, scalability, and applicability, especially in software defined networks. The emerging cloud services require strict service level agreements such as packet loss, delay, and jitter. Studies have shown that traditional network architectures lack the essential flexibility and scalability to offer these services. To combat this, a more flexible and agile routing paradigm of SR enables a source node to steer an incoming packet along a performance engineered path represented as an ordered list of instructions called segment list. This is encoded as a multiprotocol label switching label stack or an IPv6 address list in the packet header. This paper provides a comprehensive review of the novel SR technology by describing its architecture, operations, and key applications to date. SR paradigm can be effectively applied to a wide range of network applications, such as traffic engineering, network resiliency, network monitoring, and service function chaining, to achieve efficient network solutions. Furthermore, this paper identifies an interesting set of future research directions and open issues that can help realize the full potential of the emergent SR paradigm.
Protein Antigens Secreted by <i>Mycobacterium paratuberculosis</i> (1992)

Proteins secreted by Mycobacterium paratuberculosis (M.ptb) during short-term cultivations were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western(Immuno) blotting. Cultivation in a defined medium containing 35S methionine allowed autoradiographic detection of proteins which had been secreted or passively released by actively metabolizing M.ptb organisms. After the first 3 days of cultivation, 4 proteins with molecular weights of approximately 38, 50, 65 and 110 kilodaltons (kd) were detected on SDS gels. Longer incubation up to 12 days resulted in an increased concentration of these proteins as well as in appearance of additional proteins ranging from 14 to over 90 kd. In long-term (8-10 weeks) culture filtrates only two prominent proteins with molecular weights of 30 and 65 kd proteins could be detected. Immunoblot analysis showed that some of the proteins secreted during short-term cultivations were recognized by sera from M.ptb-infected sheep and more significantly by sera from animals which had been immunized with a M.ptb live vaccine strain. The study indicates that during short incubation times M.ptb may secrete immunoreactive proteins which are not dominant in long-term cultures.
USE OF PERMANENTLY PRESSURE‐SENSITIVE CHEMICAL ADHESIVES IN ROBOT GRIPPING DEVICES (1991)

Recent advances in both robotic technology and polymer chemistry have yielded techniques and materials capable of handling textile fabrics without excessive engineering complexity or fear of damage to the fabric. Chemical adhesives have often been used in the past for fabric manipulation but due to some serious constraints inherent in most adhesives the technology has been largely relegated to the use of consumable adhesive tapes. Many of the problems previously encountered have now been overcome by the use of polymer gum materials which have extremely long tack lifetimes. This has led to the development of a number of gum unit end effectors (GUE) for the purposes of fabric handling, manipulation and ply separation.