gebhart/patrepeval huggingface dataset:
The Structure of 3-Methylaspartase from Clostridium tetanomorphum Functions via the Common Enolase Chemical Step (2002)

Methylaspartate ammonia-lyase (3-methylaspartase, MAL; EC ) catalyzes the reversible anti elimination of ammonia from L-threo-(2S,3S)-3-methylaspartic acid to give mesaconic acid. This reaction lies on the main catabolic pathway for glutamate in Clostridium tetanomorphum. MAL requires monovalent and divalent cation cofactors for full catalytic activity. The enzyme has attracted interest because of its potential use as a biocatalyst. The structure of C. tetanomorphum MAL has been solved to 1.9-A resolution by the single-wavelength anomalous diffraction method. A divalent metal ion complex of the protein has also been determined. MAL is a homodimer with each monomer consisting of two domains. One is an alpha/beta-barrel, and the other smaller domain is mainly beta-strands. The smaller domain partially occludes the C terminus of the barrel and forms a large cleft. The structure identifies MAL as belonging to the enolase superfamily of enzymes. The metal ion site is located in a large cleft between the domains. Potential active site residues have been identified based on a combination of their proximity to a metal ion site, molecular modeling, and sequence homology. In common with all members of the enolase superfamily, the carboxylic acid of the substrate is co-ordinated by the metal ions, and a proton adjacent to a carboxylic acid group of the substrate is abstracted by a base. In MAL, it appears that Lys(331) removes the alpha-proton of methylaspartic acid. This motif is the defining mechanistic characteristic of the enolase superfamily of which all have a common fold. The degree of structural conservation is remarkable given only four residues are absolutely conserved.
Structure Analysis of Nanowires and Nanobelts by Transmission Electron Microscopy (2004)

One-dimensional (1D) nanostructures, such as nanowires, nanobelts, and nanorods, are attracting a great deal of research interest due to their unique properties and novel applications. Structure analysis of 1D nanostructures is an essential part of research because achieving structural control is the key step in controlling properties and device performances. Using ZnO, CdSe, and ZnS as examples, this work addresses the technical details of how to use transmission electron microscopy to correctly analyze the structure of nanowires and nanobelts, including growth direction, side/top surfaces, surface polar direction, surface reconstruction, point defects, dislocations, planar defects, and twin/bicrystal structures. The methodologies introduced can be applied to a wide range of 1D nanostructures.
Cell-type-specific expression of neural cell adhesion molecule (N-CAM) in Ito cells of rat liver. Up-regulation during in vitro activation and in hepatic tissue repair. (1996)

Ito cells (lipocytes, stellate cells) are regarded as the principle matrix-producing cell of the liver and have been shown recently to express glial fibrillary acidic protein, an intermediate filament typically found in glia cells of the nervous system. The present study examines 1) whether Ito cells of rat liver express central nervous system typical adhesion molecules, namely, neural cell adhesion molecule (N-CAM), in a cell-type-specific manner and 2) whether N-CAM expression is affected by activation of Ito cells in vitro and during rat liver injury in vivo. As assessed by reverse transcriptase polymerase chain reaction, Northern blotting, Western blotting, and immunocytochemistry of freshly isolated and cultivated hepatic cells, N-CAM expression was restricted to Ito cells and was absent in hepatocytes, Kupffer cells, and sinusoidal endothelial cells. Ito cells expressed predominantly N-CAM-coding transcripts of 6.1 and 4.8 kb in size and 140-kd isoforms of the N-CAM protein, which was localized on the cell surface membrane of Ito cells. In parallel to glial fibrillary acidic protein down-regulation and smooth muscle alpha-actin up-regulation, N-CAM expression was increased during in vitro transformation of Ito cells from resting to activated (myofibroblast-like) cells and by the fibrogenic mediator transforming growth factor-beta 1. By immunohistochemistry, N-CAM was detected in normal rat liver in the portal field as densely packed material and in a spot as well as fiber-like pattern probably representing nerve structures. However, after liver injury, N-CAM expression became detectable in mesenchymal cells within and around the necrotic area and within fibrotic septae. In serially cut tissue sections, N-CAM-positive cells were predominantly co-distributed with smooth muscle alpha-actin-positive cells rather than glial fibrillary acidic protein-positive cells, especially in fibrotic livers. The experimental results illustrate that N-CAM positivity in the liver cannot be solely ascribed to nerve endings as, among the different types of resident liver cells, Ito cells specifically express N-CAM in vitro and presumably in vivo. In addition to its role as potential cell-type-specific marker protein for activated Ito cells, the induction of N-CAM expression might illustrate a mechanism by which mesenchymal cell proliferation might be inhibited when tissue repair is concluded.
Protein Transduction Domain of HIV-1 Tat Protein Promotes Efficient Delivery of DNA into Mammalian Cells (2001)

The plasma membrane of mammalian cells is one of the tight barriers against gene transfer by synthetic delivery systems. Various agents have been used to facilitate gene transfer by destabilizing the endosomal membrane under acidic conditions, but their utility is limited, especially for gene transfer in vivo. In this article, we report that the protein transduction domain of human immunodeficiency virus type 1 Tat protein (Tat peptide) greatly facilitates gene transfer via membrane destabilization. We constructed recombinant lambda phage particles displaying Tat peptide on their surfaces and carrying mammalian marker genes as part of their genomes (Tat-phage). We demonstrate that, when animal cells are briefly exposed to Tat-phage, significant expression of phage marker genes is induced with no harmful effects to the cells. In contrast, recombinant phage displaying other functional peptides, such as the integrin-binding domain or a nuclear localization signal, could not induce detectable marker gene expression. The expression of marker genes induced by Tat-phage is not affected by endosomotropic agents but is partially impaired by inhibitors of caveolae formation. These data suggest that Tat peptide will become a useful component of synthetic delivery vehicles that promote gene transfer independently of the classical endocytic pathway.
Crystalline Two‐Dimensional DNA‐Origami Arrays (2010)

DNA origami gets large: A double-layer DNA-origami tile with two orthogonal domains underwent self-assembly into well-ordered two-dimensional DNA arrays with edge dimensions of 2–3 μm (see schematic representation and AFM image). This size is likely to be large enough to connect bottom-up methods of patterning with top-down approaches. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Stop-Flow Programmable Selectivity with a Dual-Column Ensemble of Microfabricated Etched Silicon Columns and Air as Carrier Gas (2005)

A series-coupled ensemble of microfabricated GC columns made by dry reactive ion etching of silicon substrates is evaluated for use with pneumatic selectivity enhancement techniques for targeted pairs of volatile organic compounds. Each column is 3.0 m long with a 150 miceom wide by 240 microm deep cross section. Dynamic coating was used to prepare a nonpolar column with a dimethyl polysiloxane stationary phase and a moderately polar column with a trifluoropropylmethyl polysiloxane stationary phase. Each column generates 5000-6000 theoretical plates. The columns are operated in series with the nonpolar column connected to a split inlet, the polar column connected to a flame ionization detector, and a valve connected between the column junction point and the inlet to the first column. When the valve is closed, the effluent from the first column passes directly into the second column. When the valve is open, both ends of the first column are at the inlet pressure, and flow stops in this column while increased flow is obtained in the second column. For analyte pairs that are separated by the first column but coelute from the column ensemble, the valve is opened for a few seconds after the first component of the pair has passed into the second column but the second component is still in the first column. The result is enhanced separation of the pair in the ensemble chromatogram. Relatively thick cross-linked stationary-phase films are used to increase retention for volatile compounds. The combination of air carrier gas and stationary-phase film thickness in the range 1-2 microm requires the use of relatively low average carrier gas velocities (typically less than 10 cm/s) for adequate resolving power of the column ensemble. Selectivity enhancement under isothermal conditions for a 14-component mixture of volatile organic compounds is demonstrated where neither of the columns alone nor the column ensemble without selectivity enhancement could obtain a complete separation.
RBPjκ-dependent Notch function regulatesGata2and is essential for the formation of intra-embryonic hematopoietic cells (2005)

Definitive hematopoiesis in the mouse embryo originates from the aortic floor in the P-Sp/AGM region in close association with endothelial cells. An important role for Notch1 in the control of hematopoietic ontogeny has been recently established, although its mechanism of action is poorly understood. Here, we show detailed analysis of Notch family gene expression in the aorta endothelium between embryonic day (E) 9.5 and E10.5. Since Notch requires binding to RBPjkappa transcription factor to activate transcription, we analyzed the aorta of the para-aortic splanchnopleura/AGM in RBPjkappa mutant embryos. We found specific patterns of expression of Notch receptors, ligands and Hes genes that were lost in RBPjkappa mutants. Analysis of these mutants revealed the absence of hematopoietic progenitors, accompanied by the lack of expression of the hematopoietic transcription factors Aml1/Runx1, Gata2 and Scl/Tal1. We show that in wild-type embryos, a few cells lining the aorta endothelium at E9.5 simultaneously expressed Notch1 and Gata2, and demonstrate by chromatin immunoprecipitation that Notch1 specifically associated with the Gata2 promoter in E9.5 wild-type embryos and 32D myeloid cells, an interaction lost in RBPjkappamutants. Consistent with a role for Notch1 in regulating Gata2, we observe increased expression of this gene in 32D cells expressing activated Notch1. Taken together, these data strongly suggest that activation of Gata2 expression by Notch1/RBPjkappa is a crucial event for the onset of definitive hematopoiesis in the embryo.
Binding of Iron to the 5th Component of Human Complement Directs Oxygen Radical-Mediated Conversion to Specific Sites and Causes Nonenzymic Activation (1991)

It was earlier found that hydroxyl radicals (OH.) generated in a fluid phase system, convert human C5 to an activated, C5b-like form without cleavage. For the conversion catalytic amounts of divalent iron were necessary; upon their oxidation OH. are generated. In view of the extraordinary reactivity of OH. their specific effect on C5 was surprising. It has now turned out that C5 binds iron, about 13-15 Fe ions per molecule C5. C5 was fully bound to iron-loaded Chelating Sepharose and in this way removed form the medium. Only at the sites where iron is bound, is OH. generation possible. The half-life of OH. is extremely short and hence the radicals can act on C5 only in the immediate environment of the binding sites for iron. In this way the oxidative change of C5, induced by the radicals, is restricted to some sites on the molecule determined by the iron binding. The hydroxyl radical scavenger, dimethylsulfoxide (DMSO), is unable to interfere with the conversion of C5 by OH. generated on iron-Sepharose, it does not reach the site of reaction in that system. In fluid phase systems DMSO does inhibit the conversion of C5 to C5b-like C5.
Enumeration encoding and decoding algorithms for pyramid cubic lattice and trellis codes (1995)

A pyramid source code is a code that assigns equal-length binary strings to all reproduction codevectors of equal (weighted) /spl epsiv//sub 1/ norm. A pyramid source encoding is partitioned into two concatenated mappings; the first from source word to reproduction codeword within a codebook; the second from the reproduction codevector to a binary string. The first mapping allows distortion and is accomplished using lattice quantization or trellis-coded quantization. The second mapping is noiseless and is denoted as enumeration. Efficient pyramid enumeration encoding and decoding algorithms are presented, for use with fixed-rate or variable-rate pyramid lattice and trellis codes.
Nanocrystal technology, drug delivery and clinical applications (2008)

Nanotechnology will affect our lives tremendously over the next decade in very different fields, including medicine and pharmacy. Transfer of materials into the nanodimension changes their physical properties which were used in pharmaceutics to develop a new innovative formulation principle for poorly soluble drugs: the drug nanocrystals. The drug nanocrystals do not belong to the future; the first products are already on the market. The industrially relevant production technologies, pearl milling and high pressure homogenization, are reviewed. The physics behind the drug nanocrystals and changes of their physical properties are discussed. The marketed products are presented and the special physical effects ofnanocrystals explained which are utilized in each market product. Examples of products in the development pipelines (clinical phases) are presented and the benefits for in vivo administration of drug nanocrystals are summarized in an overview.
An Ultra Low Voltage SOI CMOS Pass-Gate Logic (1997)

Between September 1972 and March 1979, 169 patients suffering from Ph1-positive chronic granulocytic leukaemia (CGL) were entered into a randomized trial designed to discover whether early elective splenectomy would defer the onset of transformation and so prolong survival and whether the quality of life following transformation was improved. In contrast with the findings in the non-randomized comparison which led to this trial, no benefit of splenectomy was found in either respect. Four features recorded at presentation were found to be strongly related to prognosis; namely, spleen size, haemoglobin concentration, leucocyte count, and clinical grade. As a result of the high degree of correlation between these features, however, information on more than one allowed a prediction of prognosis that was only marginally better than that achieved by just one. Comparison with another large series illustrates the difficulty of discovering generally applicable 'staging' systems. Furthermore the prognostic features which have emerged in several large series have not been entirely consistent. On balance, for the majority of patients with no specially extreme other features, spleen size is probably as reliable an indicator of prognosis as any other feature or combination of features.
AAA protocols: authentication, authorization, and accounting for the Internet (1999)

Internet service providers (ISPs) offering dial-up access and purveyors of enterprise networks supporting telecommuters face some difficult challenges. Ever-increasing residential dialup subscribers demand available modem (or ISDN) ports, or threaten to take their business elsewhere. To meet this demand, ISPs (dial providers) are deploying a large number of-complex, port-dense network access servers (NAS) to handle thousands of individual dial-up connections. At the same time, the miniaturization of stationary office essentials, such as the laptop computer and cellular telephone, has coupled with the need for maximum customer face time to create a workforce in perpetual motion. These "road warriors" require secure and reliable access to email and Web resources from hotels, airports, and virtual offices around the world. But dial providers must do more than simply offer an available modem port at the other end of a telephone call. They must protect against theft-of-service attacks by unscrupulous individuals with excess free time; they must verify subscribers' levels of access authorization; and for cost recovery, billing, and resource planning purposes, they may need to meter the connection time to the network. Furthermore, to provide maximum coverage to a growing roaming and mobile subscriber base, they may choose to pool their NAS resources while retaining control over their subscribers' access, usage, and billing information. All these services require coordination between the various administrative systems supported by the dial providers in partnership with each other.
Studies of Alkane/Water Interfaces by Total Internal Reflection Second Harmonic Generation. (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies of Alkane/Water Interfaces by Total Internal Reflection Second Harmonic Generation.J Conboy, J Daschbach, and G RichmondCite this: J. Phys. Chem. 1994, 98, 39, 9688–9692Publication Date (Print):September 1, 1994Publication History Published online19 February 2003Published inissue 1 September 1994https://pubs.acs.org/doi/10.1021/j100090a600https://doi.org/10.1021/j100090a600research-articleACS PublicationsRequest reuse permissionsArticle Views432Altmetric-Citations91LEARN 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
Clostridium coccoides, a New Species from the Feces of Mice (1976)

Clostridium coccoides sp. nov. is described on the basis of 12 strains isolated from a number of fecal specimens from mice fed a high-lactose diet. The isolates are obligately anaerobic, gram-positive, sporeforming, nonmotile, coccobacillary to rod-shaped cells which occur singly, in pairs, and sometimes in chains. They differ from other clostridia principally in morphology; the nearly spherical form of the cells, particularly on agar media, is rather distinctive. The guanine plus cytosine (G+C) contents of the deoxyribonucleic acids of the new strains are 43 to 45 mol%, values similar to those of clostridia with high G+C contents, such as Clostridium sphenoides, C. oroticum, C. indolis, C. innocuum, C. barkeri, and C. nexile; however, C. coccoides can be clearly differentiated from these organisms by numerous biochemical characteristics and/or fermentation products. The type strain ofC. coccoides is CLC-1 (— ATCC 29236 = NCTC 11035).
ANTHELMINTIC POTENTIAL OF CRUDE EXTRACT OF CAMELLIA SINENSIS (GREEN TEA) (2013)

The purpose of the undertaken study was the evaluation of anthelmintic activity of Camellia sinensis (green tea) aqueous extract in experimental adult earthworm's Pheritima posthuma. The aqueous extract as well as control and standard drug for different concentration of 25 mg/ml, 50 mg/ml, 100 mg/ml were tested which included determination of paralysis time and death time in minutes. The extract showed the anthelminthic activity in dose dependent manner .Piperazine citrate was used as standard.
Purification and Properties of Ribonuclease III from Escherichia coli (1968)

Abstract A nuclease with specificity for double-stranded RNA (RNase III) has been found in extracts of Escherichia coli. It remains within osmotically shocked cells attached to the ribosomes. It sediments with the ribosomes in less than 0.20 m NH4Cl, but is detached at higher concentrations. A purification is described which utilizes this property. The free enzyme, after diethylaminoethyl Sephadex and carboxymethyl Sephadex chromatography, shows an absolute specificity for polymers containing double helical polyribonucleotide regions—other polymers (single- and double-stranded DNAs, single-stranded RNAs) are not digested, nor do they inhibit the digestion of double-stranded RNAs when present in excess. RNase III shows an absolute requirement for divalent cations, including Mg++ and Mn++, and for monovalent cations, including NH4+, K+, and Na+. The optimal pH range for the reaction is from pH 7.6 to pH 9.75. RNase III is inactivated by exposure to many substances at monovalent cation concentrations below 0.2 m. The enzyme is not a factor required for protein synthesis in vitro. Its mode of action appears to be endonucleolytic.
MultiNet: Real-time Joint Semantic Reasoning for Autonomous Driving (2018)

While most approaches to semantic reasoning have focused on improving performance, in this paper we argue that computational times are very important in order to enable real time applications such as autonomous driving. Towards this goal, we present an approach to joint classification, detection and semantic segmentation using a unified architecture where the encoder is shared amongst the three tasks. Our approach is very simple, can be trained end-to-end and performs extremely well in the challenging KITTI dataset. Our approach is also very efficient, allowing us to perform inference at more then 23 frames per second. Training scripts and trained weights to reproduce our results can be found here: https://github.com/MarvinTeichmann/MultiNet
Recombinant Vaccine Vector‐Induced Protection of Athymic, Nude Mice from Influenza A Virus Infection. Analysis of Protective Mechanisms (1992)

Athymic, nude mice, which normally succumb to virus infection, can resolve infection with recombinant vaccinia virus (rVV) engineered to express IL-2. We have demonstrated that interferon-gamma (IFN-gamma) produced by natural killer (NK) cells and other immunocytes in response to the virus-encoded interleukin-2 (IL-2) is crucial to recovery. Here, we extend this work to show that nude mice, when primed intravenously with rVV co-expressing both IL-2 and an influenza virus haemagglutinin (HA) gene, are also protected following challenge with a lethal dose of homologous influenza virus. A substantial increase in the number of influenza virus-reactive antibody-secreting cells producing antibody of the IgM isotype, but not of the IgG or IgA isotypes, was found in spleens and lungs of the protected mice. Treatment with monoclonal antibodies to IFN-gamma or to the NK marker, as GM1, at challenge and thereafter, led to their death however, though the specific IgM antibody response was unaffected. These data suggest that both specific antibody and non-specific antiviral reactivity are important elements of the protective response and show that this immunization strategy may be used to protect severely immunocompromised individuals.