gebhart/patrepeval huggingface dataset:
Bovine UDP-N-acetylglucosamine:Lysosomal-enzyme N-Acetylglucosamine-1-phosphotransferase I (1996)

UDP-N-acetylglucosamine:lysosomal-enzyme N-acetylglucosamine-1-phosphotransferase (GlcNAc-phosphotransferase) catalyzes the initial step in the synthesis of the mannose 6-phosphate determinant required for efficient intracellular targeting of newly synthesized lysosomal hydrolases to the lysosome. The enzyme was partially purified approximately 30,000-fold by chromatography of solubilized membrane proteins from lactating bovine mammary glands on DEAE-Sepharose, reactive green 19-agarose, and Superose 6. The partially purified enzyme was used to generate a panel of murine monoclonal antibodies. The anti-GlcNAc-phosphotransferase monoclonal antibody PT18 was coupled to a solid support and used to immunopurify the enzyme approximately 480,000-fold to apparent homogeneity with an overall yield of 29%. The purified enzyme has a specific activity of 10-12 micromol of GlcNAc phosphate transferred per h/mg using 100 mM alpha-methylmannoside as acceptor. The subunit structure of the enzyme was determined using a combination of analytical gel filtration chromatography, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and amino-terminal sequencing. The data indicate that bovine GlcNAc-phosphotransferase is a 540,000-Da complex composed of disulfide-linked homodimers of 166,000- and 51,000-Da subunits and two identical, noncovalently associated 56,000-Da subunits.
Genetic Linkage Analysis (1999)

Genetic linkage analysis is a powerful tool to detect the chromosomal location of disease genes. It is based on the observation that genes that reside physically close on a chromosome remain linked during meiosis. For most neurologic diseases for which the underlying biochemical defect was not known, the identification of the chromosomal location of the disease gene was the first step in its eventual isolation. By now, genes that have been isolated in this way include examples from all types of neurologic diseases, from neurodegenerative diseases such as Alzheimer, Parkinson, or ataxias, to diseases of ion channels leading to periodic paralysis or hemiplegic migraine, to tumor syndromes such as neurofibromatosis types 1 and 2.
Implementation and Evaluation of On-Chip Network Architectures (2006)

Driven by the need for higher bandwidth and complexity reduction, off-chip interconnect has evolved from proprietary busses to networked architectures. A similar evolution is occurring in on-chip interconnect. This paper presents the design, implementation and evaluation of one such on-chip network, the TRIPS OCN. The OCN is a wormhole routed, 4x10, 2D mesh network with four virtual channels. It provides a high bandwidth, low latency interconnect between the TRIPS processors, L2 cache banks and I/O units. We discuss the tradeoffs made in the design of the OCN, in particular why area and complexity were traded off against latency. We then evaluate the OCN using synthetic as well as realistic loads. We found that synthetic benchmarks do not provide sufficient indication of the behavior of realistic loads on this network. Finally, we examine the effect of link bandwidth and router FIFO depth on overall performance.
Company Stock Prices Before and After Public Announcements Related to Oncology Drugs (2011)

Trends in company stock prices before the first public announcement differ for companies that report positive vs negative trials. This finding has important legal and ethical implications for investigators, drug companies, and the investment industry.
The primary structure of component 8c-1, a subunit protein of intermediate filaments in wool keratin. Relationships with proteins from other intermediate filaments (1986)

Component 8c-1, one of four highly homologous component-8 subunit proteins present in the microfibrils of wool, was isolated as its S-carboxymethyl derivative and its amino acid sequence was determined. Large peptides were isolated after cleaving the protein chemically or enzymically and the sequence of each was determined with an automatic Sequenator. The peptides were ordered by sequence overlaps and, in some instances, by homology with known sequences from other component-8 subunits. The C-terminal residues were identified by three procedures. Full details of the various procedures used have been deposited as Supplementary Publication SUP 50133 (4 pp.) at the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1986) 233, 5. The result showed that the protein comprises 412 residues and has an Mr, including the N-terminal acetyl group, of 48,300. The sequence of residues 98-200 of component 8c-1 was found to correspond to the partial or complete sequences of four homologous type I helical segments previously isolated from helical fragments recovered from chymotryptic digests of microfibrillar proteins of wool [Crewther & Dowling (1971) Appl. Polym. Symp. 18, 1-20; Crewther, Gough, Inglis & McKern (1978) Text. Res. J. 48, 160-162; Gough, Inglis & Crewther (1978) Biochem. J. 173, 385]. Considered in relation to amino acid sequences of other intermediate-filament proteins, the sequence is in accord with the view that keratin filament proteins are of two types [Hanukoglu & Fuchs (1983) Cell (Cambridge, Mass.) 33, 915-924]. Filament proteins from non-keratinous tissues, such as desmin, vimentin, neurofilament proteins and the glial fibrillary acidic protein, which form monocomponent filaments, constitute a third type. It is suggested that as a whole the proteins from intermediate filaments be classed as filamentins, the three types at present identified forming subgroups of this class. The significant homologies between types I, II and III occur almost exclusively in segments of the chain that have been identified as having a coiled-coil structure together with the relatively short sections connecting these segments. The non-coiled-coil segments at the C- and N-termini show no significant homology between types, nor is homology in these segments apparent in all members of one type. Component 8c-1 does not show homology in its terminal segments with the known sequence of any other filamentin.(ABSTRACT TRUNCATED AT 400 WORDS)
Molecular cloning of two west African human immunodeficiency virus type 2 isolates that replicate well in macrophages: a Gambian isolate, from a patient with neurologic acquired immunodeficiency syndrome, and a highly divergent Ghanian isolate. (1989)

Human immunodeficiency virus type 2 (HIV-2)-related viruses were isolated from a Gambian dying of exclusively neurological disease (HIV-2D194) and from an asymptomatic Ghanian (HIV-2D205). Both strains exhibited properties of HIV-1 biological subtype c: they grew slowly and induced few or no syncytia but eventually produced high levels of particle-associated reverse transcriptase in cultures of fresh peripheral blood lymphocytes, and they established stable infection of T-lymphoma (HUT-78) and monocytic (U937) cell lines. Each produced even higher levels of reverse transcriptase when fresh human monocytes/macrophages were used as target cells. The viruses were molecularly cloned after a single passage in culture, in order to minimize in vitro selection of subtypes present in vivo. Restriction-site analysis showed heterogeneity within each isolate. Nucleotide sequence analysis of a portion of the HIV-2D194 genome revealed that it is a member of the prototypic HIV-2 family, displaying 13% divergence versus HIV-2ROD and HIV-2NIHZ, as compared to 9% divergence between HIV-2ROD and HIV-2NIHZ. In contrast, HIV-2D205 is the most highly divergent HIV-2 strain yet described: it is equidistant in relation between the known HIV-2 strains and the simian immunodeficiency virus isolates from rhesus macaque monkeys (23-25% divergence).
A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart (2008)

From a large-scale screen using splicing microarrays and RT-PCR, we identified 63 alternative splicing (AS) events that are coordinated in 3 distinct temporal patterns during mouse heart development. More than half of these splicing transitions are evolutionarily conserved between mouse and chicken. Computational analysis of the introns flanking these splicing events identified enriched and conserved motifs including binding sites for CUGBP and ETR-3-like factors (CELF), muscleblind-like (MBNL) and Fox proteins. We show that CELF proteins are down-regulated >10-fold during heart development, and MBNL1 protein is concomitantly up-regulated nearly 4-fold. Using transgenic and knockout mice, we show that reproducing the embryonic expression patterns for CUGBP1 and MBNL1 in adult heart induces the embryonic splicing patterns for more than half of the developmentally regulated AS transitions. These findings indicate that CELF and MBNL proteins are determinative for a large subset of splicing transitions that occur during postnatal heart development.
Sequence saturation mutagenesis (SeSaM): a novel method for directed evolution (2004)

Sequence saturation mutagenesis (SeSaM) is a conceptually novel and practically simple method that truly randomizes a target sequence at every single nucleotide position. A SeSaM experiment can be accomplished within 2-3 days and comprises four steps: generating a pool of DNA fragments with random length, 'tailing' the DNA fragments with universal base using terminal transferase at 3'-termini, elongating DNA fragments in a PCR to the full-length genes using a single-stranded template and replacing the universal bases by standard nucleotides. Random mutations are created at universal sites due to the promiscuous base-pairing property of universal bases. Using enhanced green fluorescence protein as the model system and deoxyinosine as the universal base, we proved by sequencing 100 genes the concept of the SeSaM method and achieved a random distribution of mutations with the mutational bias expected for deoxyinosine.
The origin of efferent pathways from the primary visual cortex, area 17, of the macaque monkey as shown by retrograde transport of horseradish peroxidase (1975)

The retrograde transport of horseradish peroxidase has been used to identify efferent cells in area 17 of the macaque. Cells projecting to the lateral geniculate nucleus are small to medium sized pyramidal neurons with somata in lamina 6 and the adjacent white matter. The projection to the parvocellular division arises preferentially from the upper half of lamina 6, while that to the magnocellular division arises preferentially from the lower part of the lamina. The projection to both superior colliculus and inferior pulvinar arises from all sizes of pyramidal neurons lying in lamina 58 (Lund and Boothe, '75); at least pyramidal neurons of lamina 5B send collateral axon branches to both destinations. Injections with extensive spread of horseradish peroxidase show that many cells of lamina 4B and the large pyramidal neurons of upper lamina 6 also project extrinsically but their terminal sites have not been identified. Other studies have indicated that cells of laminae 2 and 3 project to areas 18 and 19. Therefore every lamina of the visual cortex, with the exception of those receiving a direct thalamic input, contains cells projecting extrinsically. Further, each lamina projects to a different destination and from Golgi studies can be shown to contain cells with specific patterns of dendritic branching which relate to the distribution of thalamic afferents and to the patterns of intracortical connections. These findings emphasise the significance of the horizontal organisation of the cortex with relation to the flow of information through it and contrast with the current concept of columnar organisation shown in physiological studies.
Human Leukocyte Antigen-A2–Restricted CTL Responses to Mutated BRAF Peptides in Melanoma Patients (2006)

Mutated BRAF (BRAF(V600E)) is a potential immunotherapeutic target for melanoma because of its tumor specificity and expression in the majority of these lesions derived from different patients. BRAF(V600E) is expressed intracellularly and not on the cell surface, therefore providing a target for T cells but not B cells. Demonstration of patients' T cell responses to BRAF(V600E) would suggest the feasibility of active specific immunotherapy targeting the mutation in these patients. In the present study, BRAF(V600E) peptides with putative binding sites for human leukocyte antigen (HLA)-A2 were used to stimulate T lymphocytes of HLA-A2-positive melanoma patients. Four of five patients with BRAF(V600E)-positive lesions showed lymphoproliferative responses to BRAF(V600E) peptide stimulation. These responses were specific for the mutated epitope and HLA-A2 was restricted in three patients. Lymphocytes from these three patients were cytotoxic against HLA-A2-matched BRAF(V600E)-positive melanoma cells. None of the four patients with BRAF(V600E)-negative lesions and none of five healthy donors had lymphoproliferative responses specific for the mutated epitope. The high prevalence (approximately 50%) of HLA-A2 among melanoma patients renders HLA-A2-restricted BRAF(V600E) peptides attractive candidate vaccines for these patients.
Protocol to Isolate a Large Amount of Functional Oligodendrocyte Precursor Cells from the Cerebral Cortex of Adult Mice and Humans (2013)

During development, oligodendrocytes are generated from oligodendrocyte precursor cells (OPCs), a cell type that is a significant proportion of the total cells (3-8%) in the adult central nervous system (CNS) of both rodents and humans. Adult OPCs are responsible for the spontaneous remyelination that occurs in demyelinating diseases like Multiple Sclerosis (MS) and they constitute an interesting source of cells for regenerative therapy in such conditions. However, there is little data regarding the neurobiology of adult OPCs isolated from mice since an efficient method to isolate them has yet to be established. We have designed a protocol to obtain viable adult OPCs from the cerebral cortex of different mouse strains and we have compared its efficiency with other well-known methods. In addition, we show that this protocol is also useful to isolate functional OPCs from human brain biopsies. Using this method we can isolate primary cortical OPCs in sufficient quantities so as to be able to study their survival, maturation and function, and to facilitate an evaluation of their utility in myelin repair.
Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus (1993)

Several nuclear activities and components are concentrated in discrete nuclear compartments. To understand the functional significance of nuclear compartmentalization, knowledge on the spatial distribution of transcriptionally active chromatin is essential. We have examined the distribution of sites of transcription by RNA polymerase II (RPII) by labeling nascent RNA with 5-bromouridine 5'-triphosphate, in vitro and in vivo. Nascent RPII transcripts were found in over 100 defined areas, scattered throughout the nucleoplasm. No preferential localization was observed in either the nuclear interior or the periphery. Each transcription site may represent the activity of a single gene or, considering the number of active pre-mRNA genes in a cell, of a cluster of active genes. The relation between the distribution of nascent RPII transcripts and that of the essential splicing factor SC-35 was investigated in double labeling experiments. Antibodies against SC-35 recognize a number of well-defined, intensely labeled nuclear domains, in addition to labeling of more diffuse areas between these domains (Spector, D. L., X. -D. Fu, and T. Maniatis. 1991. EMBO (Eur. Mol. Biol. Organ.) J. 10:3467-3481). We observe no correlation between intensely labeled SC-35 domains and sites of pre-mRNA synthesis. However, many sites of RPII synthesis colocalize with weakly stained areas. This implies that contranscriptional splicing takes place in these weakly stained areas. These areas may also be sites where splicing is completed posttranscriptionally. Intensely labeled SC-35 domains may function as sites for assembly, storage, or regeneration of splicing components, or as compartments for degradation of introns.
Image gathering and processing for enhanced resolution (1984)

Traditional approaches to optical resolution enhancement have involved either the design of appropriate image-formation systems or some type of postprocessing of an image that has already been formed. Results presented in this paper suggest that improved images can be obtained if the image-gathering system is designed specifically to enhance the performance of the image-restoration algorithm to be used. We consider a class of problems in which the total available spatial bandwidth is fixed but the location of this bandwidth along the spatial-frequency axis is to some extent under our control. For example, we might consider either a low-pass system or a bandpass system of the same total bandwidth. We show that system performance can be substantially improved by proper allocation of the available bandwidth in the spatial-frequency domain. The optimum allocation is shown to be a function of the signal-to-noise ratio. We also describe coherent and incoherent optical image-gathering systems that can achieve the desired spatial-frequency passbands.
Rapid Detection of S‐Adenosyl Homocysteine Using Self‐Assembled Optical Diffraction Gratings (2007)

I saw the SAH: Clinically relevant concentrations of S-adenosyl homocysteine (SAH) can be rapidly detected using self-assembled diffraction gratings. SAH bound to antibody-conjugated (Ab) microbeads (see picture) and then incubated with a gold chip functionalized with SAH-specific aptamer in alternating line patterns produces gratings that are detected by optical diffraction intensity measurements (detection limit: 64 pmol L−1). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2008/z703222_s.pdf or from the author. 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.
The influence of the nature of the asparagine 289-linked oligosaccharide on the activation by urokinase and lysine binding properties of natural and recombinant human plasminogens. (1993)

Several strategies have been used to obtain recombinant (r) human plasminogens (HPg) containing different oligosaccharide side chains on its sole N-linked glycosylation site, present at Asn289. The approaches included expression of the cDNA for HPg in insect cell lines under various conditions, addition of glycosidase inhibitors during expression, and purification of specific glycoforms of HPg using affinity chromatography on an insolubilized lectin column. The activation kinetics for urokinase (UK) of each of the purified HPgs, as well as their relative abilities to bind to the ligand, epsilon-aminocaproic acid (EACA), were then determined. Removal of both N- and O-linked oligosaccharide from HPg resulted in a slight increase in the Kcat/Km for its activation, while a glycoform containing tetrasialyl-tetra-antennary complex oligosaccharide on Asn289 was a slightly poorer substrate for UK than plasma HPg, which contains bisialyl-biantennary complex carbohydrate on Asn289. The most dramatic differences were observed for HPgs with high mannose-type glycans on Asn289. (Man9GlcNAc2)-HPg possessed only approximately 6% of the kcat/Km of plasma HPg, whereas (Glc3Man9GlcNAc2)-HPg did not undergo activation at a significant rate by UK. Differences were also found in the relative abilities of the HPg glycoforms to interact with EACA. The most effective interactions were observed with HPgs containing complex-type glycans, and the least effective binding was found for HPgs with high mannose-type oligosaccharides. The full range of the binding effects is represented by a fourfold difference between HPg containing tetrasialyl-tetra-antennary glycan and HPg with (Glc3Man9GlcNAc2) assembled on Asn289. These results clearly demonstrate that the nature of the N-linked glycan assembled on HPg dramatically influences its ability to be activated by UK and to bind to omega-amino acid effector molecules.
Knowledge-based Configuration for Configuring Combined Hardware/Software Systems . (2002)

Abstract. In this paper, we present a survey on research topics we consider with in the EU project ConIPF (Configuration of Industrial Product Families). The application domain which is considered in this project contains combined hardware/software systems. Those systems share a lot of commonalities and are configured in a rich variety of outcoming products. Besides others, we discuss issues concerning features and evolution. Feature trees describing the functionality in terms of customer requirements are used to efficiently select, combine and configure components from the product catalogue. Mappings between these feature models and the product descriptions have to be developed and modeled sufficiently for the configuration task. A further problem area arises in this application domain with evolution in both the products themselves and the models describing the product catalogue.
Thermal Conductivity and Thermal Expansion Properties of AlN/EP Composite (2012)

AlN/epoxy (AlN/EP) composites were fabricated by casting method. The effects of the AlN content on microstructure, thermal conductivity and thermal expansion properties of composites were investigated. The results indicate that with the AlN content increasing, the thermal conductivity increase, while the coefficient of thermal expansion (CTE) decreases. When the volume fraction of AlN is 25%, the thermal conductivity is 0.507 W/m•K, which is about 2.5 times higher than that of the epoxy matrix, while the coefficient of thermal expansion is 53.7 ppm/°C. The thermal conductivity results obtained were also analyzed using the Maxwell-Eucken model to explain the effect of AlN fillers on the formation of thermal conductive networks.
Demonstration of a scalable, multiplexed ion trap for quantum information processing (2009)

A scalable, multiplexed ion trap for quantum information processing is fabricated and tested. The trap design and fabrication process are optimized for scalability to small trap size and large numbers of interconnected traps, and for integration of control electronics and optics. Multiple traps with similar designs are tested with 111Cd+, 25Mg+, and 88Sr+ ions at room temperature and with 88Sr+ at 6 K, with respective ion lifetimes of 90 s, 300 ± 30 s, 56 ± 6 s, and 4.5 ± 1.1 hours. The motional heating rate for 25Mg+ at room temperature and a trap frequency of 1.6 MHz is measured to be 7 ± 3 quanta per millisecond. For 88Sr+ at 6 K and 540 kHz the heating rate is measured to be 220 ± 30 quanta per second.