gebhart/patrepeval huggingface dataset:
Membrane Interactions of Cell-Penetrating Peptides Probed by Tryptophan Fluorescence and Dichroism Techniques:  Correlations of Structure to Cellular Uptake (2006)

This work reports on the binding and conformation of a series of CPPs in the bilayer membranes of large unilamellar vesicles and the effect of the presence of cholesterol. We show a negative correlation between alpha-helical structure and uptake efficiency for penetratin peptides where the two central arginine residues of penetratin are thought to be important for breaking the secondary structure. Penetratin alpha-helicity is also reduced upon incorporation of cholesterol into the membrane. Flow linear dichroism in the far-UV region shows that the penetratin peptides adopt a preferential orientation of the alpha-helix parallel to the bilayer, and the linear dichroism (LD) spectrum in the aromatic region indicates that the tryptophan residues are preferentially oriented parallel to the membrane. The Tat analogue TatP59W and the oligoarginine R7W, which are more efficient CPPs than penetratin, bind to membranes as random coils and do not show any orientation in LD, again indicating that alpha-helicity reduces uptake efficiency. Further, we observe large variations in tryptophan quantum yields for the five CPPs in this study and discuss this in terms of the ability to cause lipid rearrangement. Binding isotherms show that cholesterol increases the affinity of the peptide for the membrane, but tryptophan fluorescence lifetimes are essentially unaltered by incorporation of as much as 40 mol % cholesterol into the membrane, suggesting the absence of specific peptide-cholesterol interactions. Fluorescence emission maxima are insensitive to cholesterol and indicate that the peptide is positioned in the headgroup region. The results on peptide-membrane interactions are discussed in terms of possible uptake mechanisms.
Recovery of NV Knockout Infectious Hematopoietic Necrosis Virus Expressing Foreign Genes (2000)

Infectious hematopoietic necrosis virus (IHNV) is a Novirhabdovirus and is the causative agent of a devastating acute, lethal disease in wild and farmed rainbow trout. The virus is enzootic throughout western North America and has spread to Asia and Europe. A full-length cDNA of the IHNV antigenome (pIHNV-Pst) was assembled from subgenomic overlapping cDNA fragments and cloned in a transcription plasmid between the T7 RNA polymerase promoter and the autocatalytic hepatitis delta virus ribozyme. Recombinant IHNV (rIHNV) was recovered from fish cells at 14 degrees C, following infection with a recombinant vaccinia virus expressing the T7 RNA polymerase (vTF7-3) and cotransfection of pIHNV-Pst together with plasmids encoding the nucleoprotein N (pT7-N), the phosphoprotein P (pT7-P), the RNA polymerase L (pT7-L), and the nonvirion protein NV (pT7-NV). When pT7-N and pT7-NV were omitted, rIHNV was also recovered, although less efficiently. Incidental mutations introduced in pIHNV-Pst were all present in the rIHNV genome; however, a targeted mutation located in the L gene was eliminated from the recombinant genome by homologous recombination with the added pT7-L expression plasmid. To investigate the role of NV protein in virus replication, the pIHNV-Pst construct was engineered such that the entire NV open reading frame was deleted and replaced by the genes encoding green fluorescent protein or chloramphenicol acetyltransferase. The successful recovery of recombinant virus expressing foreign genes instead of the NV gene demonstrated that the NV protein was not absolutely required for viral replication in cell cultures, although its presence greatly improves virus growth. The ability to generate rIHNV from cDNA provides the basis to manipulate the genome in order to engineer new live viral vaccine strains.
뇌성마비 장애인의 자아존중감 증진 방안 (2009)

본 연구는 뇌성마비 장애인의 자아존중감 증진방안을 연구하였다. 뇌성마비인이 부정적 자아개념을 가졌다는 선행연구결과이다. 그러나 뇌성마비를 가졌지만 긍정적 자아개념을 형성하여 성공적인 삶을 살고 있는 사람들을 대상으로 심층면접을 통해 자아존중감 증진방안을 연구하였다. 그 결과 첫 번째 사회적 요인으로 주양육자인 어머니의 헌신적인 사랑과 계속적인 관심과 격려가 가장 중요한 자아존중감 증진방안이다. 그러나 과잉보호는 오히려 뇌성마비 장애인의 능력을 저하시키는 원인이 된다는 연구 결과이다. 두 번째 육체적 활동강화로 보행과 일상생활 능력을 키우기 위해 계속적인 치료와 운동 스포츠에 참여하여 하도록 하는 것이다. 세 번째 정신적 요인으로 학습을 통해서 성취감을 느끼게 해주고 종교생활을 통해서 영적으로 안녕한 상태로 개인적으로는 평화하도록 도와주고 위안감을 얻을 수 있도록 환경을 만들어 주어야 한다는 것이다. 세가지 요인 중에서 사회적 요인이 가장 중요하다. 이는 아동기 즉 학령기와 청소년기가 자아존중감 형성에 가장 많은 영향을 미치는 시기이기 때문이다. 이에 아동기와 학령기 청소년기에 가족과 교사가 뇌성마비 아동을 이해하고 이들을 관심과 사랑과 격려로 지지해 준다면 긍정적 자아존중감을 형성할 수 있다는 연구 결과이다.
Lower concentration of La protein required for internal ribosome entry on hepatitis C virus RNA than on poliovirus RNA (1999)

Translation initiation of poliovirus and hepatitis C virus (HCV) RNA occurs by entry of ribosomes to the internal RNA sequence, called the internal ribosomal entry site (IRES). Both IRES bind to the La protein and are thought to require the protein for their translation initiation activity, although they are greatly different in both the primary and predicted secondary structures. To compare the La protein requirement for these IRES, we took advantage of I-RNA from the yeast Saccharomyces cerevisiae, which has been reported to bind to La protein and block poliovirus IRES-mediated translation initiation. In a cell-free translation system prepared from HeLa cells, yeast I-RNA inhibited translation initiation on poliovirus RNA as expected, but did not significantly inhibit translation initiation on HCV RNA. However, the translation initiation directed by either IRES was apparently inhibited by I-RNA in rabbit reticulocyte lysates, in which La protein is limiting. I-RNA-mediated inhibition of HCV IRES-dependent translation in rabbit reticulocyte lysates was reversed by exogenous addition of purified recombinant La protein of smaller amounts than necessary to reverse poliovirus IRES-dependent translation. These results suggest that HCV IRES requires lower concentrations of La protein for its function than does poliovirus IRES. Immunofluorescence studies showed that HCV infection appeared not to affect the subcellular localization of La protein, which exists mainly in the nucleus, although La protein redistributed to the cytoplasm after poliovirus infection. The data are compatible with the low requirement of La protein for HCV IRES activity.
The Implantable Defibrillator in Ventricular Arrhythmias (1983)

The most common cause of sudden cardiac death appears to be electrical instability that culminates in ventricular fibrillation. The implantable defibrillator, a self-contained diagnostic-therapeutic system, provides automatic detection and correction of malignant ventricular tachyarrhythmias. Principles involved in its development are reviewed, as are initial clinical results.
Fermentation and enzyme technology (1979)

Outlines the fundamental microbiological, biochemical, genetic, and engineering aspects of fermentation, presenting advanced methods of fermentation and control. Covers the isolation of enzymes, especially those found in intracellular contents of microorganisms. Discusses enzyme immobilization and the factors influencing the use of enzymes in reactors.
An Attenuating Mutation in nsP1 of the Sindbis-Group Virus S.A.AR86 Accelerates Nonstructural Protein Processing and Up-Regulates Viral 26S RNA Synthesis (2002)

The Sindbis-group alphavirus S.A.AR86 encodes a threonine at nonstructural protein 1 (nsP1) 538 that is associated with neurovirulence in adult mice. Mutation of the nsP1 538 Thr to the consensus Ile found in nonneurovirulent Sindbis-group alphaviruses attenuates S.A.AR86 for adult mouse neurovirulence, while introduction of Thr at position 538 in a nonneurovirulent Sindbis virus background confers increased neurovirulence (M. T. Heise et al., J. Virol. 74:4207-4213, 2000). Since changes in the viral nonstructural region are likely to affect viral replication, studies were performed to evaluate the effect of Thr or Ile at nsP1 538 on viral growth, nonstructural protein processing, and RNA synthesis. Multistep growth curves in Neuro2A and BHK-21 cells revealed that the attenuated s51 (nsP1 538 Ile) virus had a slight, but reproducible growth advantage over the wild-type s55 (nsP1 538 Thr) virus. nsP1 538 lies within the cleavage recognition domain between nsP1 and nsP2, and the presence of the attenuating Ile at nsP1 538 accelerated the processing of S.A.AR86 nonstructural proteins both in vitro and in infected cells. Since nonstructural protein processing is known to regulate alphavirus RNA synthesis, experiments were performed to evaluate the effect of Ile or Thr at nsP1 538 on viral RNA synthesis. A combination of S.A.AR86-derived reporter assays and RNase protection assays determined that the presence of Ile at nsP1 538 led to earlier expression from the viral 26S promoter without affecting viral minus- or plus-strand synthesis. These results suggest that slower nonstructural protein processing and delayed 26S RNA synthesis in wild-type S.A.AR86 infections may contribute to the adult mouse neurovirulence phenotype of S.A.AR86.
Floral homeotic mutations produced by transposon-mutagenesis in Antirrhinum majus. (1990)

To isolate and study genes controlling floral development, we have carried out a large-scale transposon-mutagenesis experiment in Antirrhinum majus. Ten independent floral homeotic mutations were obtained that could be divided into three classes, depending on whether they affect (1) the identity of organs within the same whorl; (2) the identity and sometimes also the number of whorls; and (3) the fate of the axillary meristem that normally gives rise to the flower. The classes of floral phenotypes suggest a model for the genetic control of primordium fate in which class 2 genes are proposed to act in overlapping pairs of adjacent whorls so that their combinations at different positions along the radius of the flower can specify the fate and number of whorls. These could interact with class 1 genes, which vary in their action along the vertical axis of the flower to generate bilateral symmetry. Both of these classes may be ultimately regulated by class 3 genes required for flower initiation. The similarity between some of the homeotic phenotypes with those of other species suggests that the mechanisms controlling whorl identity and number have been highly conserved in plant evolution. Many of the mutations obtained show somatic and germinal instability characteristic of transposon insertions, allowing the cell-autonomy of floral homeotic genes to be tested for the first time. In addition, we show that the deficiens (def) gene (class 2) acts throughout organ development, but its action may be different at various developmental stages, accounting for the intermediate phenotypes conferred by certain def alleles. Expression of def early in development is not necessary for its later expression, indicating that other genes act throughout the development of specific organs to maintain def expression. Direct evidence that the mutations obtained were caused by transposons came from molecular analysis of leaf or flower pigmentation mutants, indicating that isolation of the homeotic genes should now be possible.
Adsorption of ordered zirconium phosphonate multilayer films on silicon and gold surfaces (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAdsorption of ordered zirconium phosphonate multilayer films on silicon and gold surfacesHaiwon Lee, Larry J. Kepley, Hun Gi Hong, Sohail Akhter, and Thomas E. MalloukCite this: J. Phys. Chem. 1988, 92, 9, 2597–2601Publication Date (Print):May 1, 1988Publication History Published online1 May 2002Published inissue 1 May 1988https://pubs.acs.org/doi/10.1021/j100320a040https://doi.org/10.1021/j100320a040research-articleACS PublicationsRequest reuse permissionsArticle Views1090Altmetric-Citations263LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Autoimmune Response to Acetylcholine Receptor (1973)

Injection of rabbits with acetylcholine receptor highly purified from the electric organ of Electrophorus electricus emulsified in complete Freund's adjuvant resulted in the production of precipitating antibody to acetylcholine receptor. After the second injection of antigen, the animals developed the flaccid paralysis and abnormal electromyographs characteristic of neuromuscular blockade. Treatment with the anticholinesterases edrophonium or neostigmine dramatically alleviated the paralysis and the fatigue seen in electromyography.
THE PREPARATION AND PROPERTIES OF ReF71 (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTHE PREPARATION AND PROPERTIES OF ReF71John G. Malm, Henry Selig, and Sherman FriedCite this: J. Am. Chem. Soc. 1960, 82, 6, 1510Publication Date (Print):March 1, 1960Publication History Published online1 May 2002Published inissue 1 March 1960https://doi.org/10.1021/ja01491a065Request reuse permissionsArticle Views86Altmetric-Citations23LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (150 KB) Get e-Alertsclose Get e-Alerts
Conformational constraints: Nonpeptide β‐turn mimics (1990)

The beta-turn, which has also been referred to as the beta-bend, beta-loop or reverse turn, has been implicated as an important site for molecular recognition in many biologically active peptides and in globular proteins. This small secondary structure therefore makes an attractive target for mimicry by a conformational constraint, because a peptide which is constrained in a biologically active conformation can display a number of advantages over the parent substrate. The less peptide-like such a constraint is, the more potential there is to maximize these advantages. A decade has passed since the first (and highly successful) attempt to mimic the beta-turn with a nonpeptide conformational constraint was disclosed by Freidinger et al. (1980). Since this report, rapidly growing interest in the field of nonpeptide beta-turn mimics has seen a variety of experimental approaches and a mixed bag of results. It is attempted in this review, not only to summarize and critically analyse these approaches, but also to touch on the complexities associated with the conformational mimicry of such a diverse structure as the beta-turn.
Bioelectrocatalytic System Coupled with Enzyme-Based Biocomputing Ensembles Performing Boolean Logic Operations: Approaching “Smart” Physiologically Controlled Biointerfaces (2008)

The modified electrode for electrocatalytic oxidation of NADH was developed using a pH-switchable redox interface. The operation of the modified electrode was controlled by logic operations performed by enzyme systems processing biochemical input signals. The electrocatalytic oxidation of NADH was activated upon appropriate combinations of the signals processed by the AND/OR logic operations performed by the enzymes. The modified interface was reset in a mute nonactive state by another enzyme reaction. The coupling between the enzyme logic systems and the bioelectrocatalytic interface was achieved by pH changes produced in situ by the enzyme reactions, resulting in different protonation states of the polymeric matrix associated with the electrode surface. The bioelectrocatalytic system integrated with biochemical computing systems opens the way to novel "smart" interfaces for multisignal biosensors and signal-controlled biofuel cells. In a long perspective, this approach will allow physiological control of implantable bioelectronic devices.
Manipulating secondary metabolism in cultured plant cells (1996)

This review attempts to present an overall strategy for the production of useful secondary metabolites by cultured plant cells. After consideration of the nature and utility of secondary metabolites and the possible role of these substances to the plant, the review focuses attention on the properties of the plant cells in culture and how the cell populations and their physical and chemical environment can be manipulated to encourage the synthesis and accumulation of secondary products. Finally, consideration is given to the involvement of genetic engineering in the production of cells to perform particular metabolic tasks and how these techniques might contribute to the development of a new strategy to enable the production of useful secondary metabolites on a commercial scale. CONTENTS Summary 553 I. Introduction 553 II. Development of a strategy 555 III. Concluding remarks 565 Acknowledgements 565 References 565.
PEPOP: Computational design of immunogenic peptides (2008)

PEPOP has the potential to guide experimentalists that want to localize an epitope or design immunogenic peptides for raising antibodies which target proteins at specific sites. More successful predictions of immunogenic peptides were obtained when a peptide was continuous as compared with peptides corresponding to discontinuous epitopes. PEPOP is available for use at http://diagtools.sysdiag.cnrs.fr/PEPOP/.
Pathogenesis of rotavirus infection in mice (1982)

Three parameters of rotavirus infection, i.e., clinical disease, viral antigen in infected intestines, and infectious virus in feces, were assessed in infant mice nursed by mothers with or without preexisting rotavirus antibody. Diarrhea was the only consistent sign of clinical disease, and its course followed that of infection by about 1 day. Infected intestinal epithelial cells, except crypt cells, were observed by immunofluorescence microscopy in the duodenum, jejunum, ileum, and colon. Infection progressed in a proximal-to-distal direction with time. Viral antigen appeared in intestinal tissue later, was present in lower amounts, and disappeared sooner from infants nursed by mothers with preexisting rotavirus antibody, indicating that protection was passively transferred to these infants although the course of clinical disease was not changed.
Directed evolution of an esterase for the stereoselective resolution of a key intermediate in the synthesis of epothilones (1998)

The directed evolution of an esterase from Pseudomonas fluorescens using the mutator strain Epicurian coli XL1-Red was investigated. Mutants were assayed for their ability to hydrolyze a sterically hindered 3-hydroxy ester, which can serve as a building block in the synthesis of epothilones. Screening was performed by plating esterase producing colonies derived from mutation cycles onto minimal media agar plates containing indicator substances (neutral red and crystal violet). Esterase-catalyzed hydrolysis of the 3-hydroxy ester (ethyl or glycerol ester) was detected by the formation of a red color due to a pH decrease caused by the released acid. Esterases isolated from positive clones were used in preparative biotransformations of the ethyl ester. One variant containing two mutations (A209D and L181V) stereoselectively hydrolyzed the ethyl ester resulting in 25% ee for the remaining ester.
Expression of a retinoic acid response element-hsplacZ transgene defines specific domains of transcriptional activity during mouse embryogenesis. (1991)

Treatment with retinoic acid (RA) is known to produce complex teratogenic effects in vertebrates, and its presence in the developing embryo as an endogenous substance has led to the suggestion that RA might be a natural morphogenetic agent. Although our understanding of the molecular mechanism of RA action has improved considerably with the identification of nuclear receptors for RA (RARs) and RA-responsive genes, the exact relationship between the proposed morphogenetic activity of RA and its teratogenic effects remains to be characterized. Here, we show that a RA response element (RARE) present in the RAR beta gene can direct specific spatial and temporal expression of an hsplacZ transgene during mouse embryogenesis. In the early embryo, the transgene is expressed in a specific anterior-posterior domain that is completely obliterated by treatment of pregnant mice with teratogenic doses of RA. The expression of the transgene becomes more restricted as organogenesis progresses and mimics closely the reported expression of the RAR beta gene. These results suggest that, in vivo, some of the morphogenetic effects of RA could be mediated through localized transcriptional activity controlled by the various RARs. The specific pattern of expression of the RAREhsplacZ transgene does not correlate with the proposed sites of action of RA as defined by its teratogenic effects but does support a role for RA in early anterior-posterior patterning along the body axis.
Burn Out or Fade Away? (2010)

A protein whose expression is turned on by stress delays the onset of age-related pathologies.
<title>Optical-tiled AMLCD for very large display applications</title> (1992)

We present a new method of tiling flat panel displays to a continuous large display. The method was tested for color Active Matrix Liquid Crystal Display (AMLCD) with backlight. Diverging glass fiber-optic faceplates configuration were used to show the principle however the method is applicable and was verified also with plastic faceplates and micro-channels (hollow pipes). The manufacturing of the displays and the faceplates are done separately and then assembled together. The method presented shows very little loss of resolution and very wide viewing angles. There are no limitations to the number of tiled displays in both horizontal and vertical directions.
Adaptive Distributed Load Balancing Algorithm Based on Live Migration of Virtual Machines in Cloud (2009)

EUCALYPTUS, an open source cloud-computing framework, is still lack of load balancing. In the paper, we provide a kind of implementation by adaptive live migration of virtual machines. We design and implement a simple model which decreases the migration time of virtual machines by shared storage and fulfills the zero-downtime relocation of virtual machines by transforming them as Red Hat cluster services. During the migration process, we also keep the inclusion relationship between VLAN and virtual machines. We propose a distributed load balancing algorithm COMPARE_AND_BALANCE based on sampling to reach an equilibrium solution. The experimental results show that it converges quickly.