gebhart/patrepeval huggingface dataset:
Two Subunits of Glycosylphosphatidylinositol Transamidase, GPI8 and PIG-T, Form a Functionally Important Intermolecular Disulfide Bridge (2003)

Many eukaryotic proteins are tethered to the plasma membrane via glycosylphosphatidylinositol (GPI). GPI transamidase is localized in the endoplasmic reticulum and mediates post-translational transfer of preformed GPI to proteins bearing a carboxyl-terminal GPI attachment signal. Mammalian GPI transamidase is a multimeric complex consisting of at least five subunits. Here we report that two subunits of mammalian GPI transamidase, GPI8 and PIG-T, form a functionally important disulfide bond between conserved cysteine residues. GPI8 and PIG-T mutants in which relevant cysteines were replaced with serines were unable to fully restore the surface expression of GPI-anchored proteins upon transfection into their respective mutant cells. Microsomal membranes of these transfectants had markedly decreased activities in an in vitro transamidase assay. The formation of this disulfide bond is not essential but required for full transamidase activity. Antibodies against GPI8 and PIG-T revealed that endogenous as well as exogenous proteins formed a disulfide bond. Furthermore trypanosome GPI8 forms a similar intermolecular disulfide bond via its conserved cysteine residue, suggesting that the trypanosome GPI transamidase is also a multimeric complex likely containing the orthologue of PIG-T. We also demonstrate that an inactive human GPI transamidase complex that consists of non-functional GPI8 and four other components was co-purified with the proform of substrate proteins, indicating that these five components are sufficient to hold the substrate proteins.
A wireless neural/EMG telemetry system for freely moving insects (2010)

We have developed a miniature telemetry system that captures neural, EMG, and acceleration signals from a freely moving insect and transmits the data wirelessly to a remote digital receiver. The system is based on a custom low-power integrated circuit that amplifies and digitizes four biopotential signals as well as three acceleration signals from an off-chip MEMS accelerometer, and transmits this information over a wireless 920-MHz telemetry link. The unit weighs 0.79 g and runs for two hours on two small batteries. We have used this system to monitor neural and EMG signals in jumping and flying locusts.
A new multiparameter flow cytometer: Optical and electrical cell analysis in combination with video microscopy in flow (1999)

Test results indicate that our instrument can perform Coulter measurements in combination with flexible optical analysis. Moreover, integration of an adapted video microscope into a flow cytometer is an approach to overcome the gap between flow and image cytometry.
Purification and cloning of interferon-stimulated gene factor 2 (ISGF2): ISGF2 (IRF-1) can bind to the promoters of both beta interferon- and interferon-stimulated genes but is not a primary transcriptional activator of either. (1990)

Interferon-stimulated gene factor 2 (ISGF2) was purified from HeLa cells treated with alpha interferon. The factor, a single polypeptide of 56 kilodaltons (kDa), bound both to the central 9 base pairs of the 15-base-pair interferon-stimulated response element (ISRE) that is required for transcriptional activation of interferon-stimulated genes and to the PRD-I regulatory element of the beta interferon gene. ISGF2 was a phosphoprotein, and dephosphorylation in vitro reduced its DNA-binding activity. However, conditions that changed the amount of ISGF2 did not change the phosphorylated isoforms in vivo. ISGF2 in unstimulated cells existed in trace amounts and was induced by both alpha interferon and gamma interferon as well as by virus infection. Plasmid-bearing Escherichia coli clones encoding ISGF2 were selected with antibody against purified ISGF2. Sequence analysis revealed that the ISGF2 protein was the same as that encoded by the cDNA clone IRF-1, which has been claimed to activate transcription of interferon genes. We show that transcription of the ISGF2 gene was induced by alpha interferon, gamma interferon, and double-stranded RNA. However, ISGF2 was neither necessary nor sufficient for induced transcription of the beta interferon gene, while the factor NF kappa B was clearly involved.
Toward virtual data scientist with visual means (2017)

The Big data challenge includes dealing with a big number of heterogeneous and multidimensional datasets of all possible sizes not only with data of big size. As a result a huge number of Machine Learning (ML) tasks, which must be solved dramatically exceeds the number of data scientists who can solve these tasks. Next many ML tasks require critical input from subject matter experts (SME) and end users/decision makers who are not ML experts. A set of tools that we call a “virtual data scientist” is needed to assist SMEs and end users to construct ML models for their tasks to meet this Big data challenge with a minimal contribution from data scientists. This paper describes our vision of such a “virtual data scientist” based on the visual approach with collocated and shifted paired coordinates. The approach is illustrated with real world data and ML tasks, as well as simulated data.
601. Structure of 3-alkyl-4-arylazoisoxazol-5-ones and related compounds (1965)

L. A. Summers, P. F. H. Freeman and D. J. Shields, J. Chem. Soc., 1965, 3312 DOI: 10.1039/JR9650003312
Membrane binding kinetics of factor VIII indicate a complex binding process. (1993)

Factor VIII functions as a component of the tenase enzyme complex upon phospholipid membranes. Factor VIII binds to phosphatidylserine-containing membranes and apparently provides high affinity binding sites for factor IXa upon these membranes. We have characterized the binding kinetics of human factor VIII with phosphatidylserine-containing membranes and directly compared the measured properties with those of factor V. The initial phase of association was evaluated in a stopped-flow apparatus by fluorescence energy transfer from aromatic residues in the protein to dansyl-labeled phosphatidylethanolamine in the vesicles. Association proceeded at an apparent second-order rate of 0.12 microM-1 s-1 for extruded phospholipid vesicles and 0.42 microM-1 s-1 for sonicated vesicles under pseudo-first-order conditions in which the phospholipid concentration determined the rate. Increased temperature resulted in more rapid association, and the effect decreased in the order extruded vesicles > sonicated vesicles > extruded vesicles of dioleoylphospholipids, indicating that the structure of the phospholipid membrane contributes to the activation energy of binding. The binding of fluorescein-labeled factor VIII to membranes supported on glass microspheres (lipospheres) was monitored by flow cytometry. Under conditions in which the factor VIII concentration determined the rate there was rapid initial association at 6.9 microM-1 s-1, accounting for half of the bound factor VIII, and a slower component of 0.87 microM-1 s-1, accounting for the other half. Likewise, the dissociation of factor VIII from liposphere membranes was biphasic with a faster component of 0.010 s-1 and a slower component of 0.0012 s-1. Rates of association and dissociation for factor V were similar to those for factor VIII and were biphasic. These results allow estimation of the size of the phospholipid sites that interact with factors VIII and V and suggest that both proteins bind to membranes via a multistep process in which rapid association is followed by a slower step yielding higher affinity binding.
Effect of phenylephrine vs. ephedrine on frontal lobe oxygenation during caesarean section with spinal anesthesia: an open label randomized controlled trial (2014)

Clinical trials NCT 01509521 and EudraCT 2001 006103 35.
ProteoWizard: open source software for rapid proteomics tools development (2008)

Cross-platform software that compiles using native compilers (i.e. GCC on Linux, MSVC on Windows and XCode on OSX) is available for download free of charge, at http://proteowizard.sourceforge.net. This website also provides code examples, and documentation. It is our hope the ProteoWizard project will become a standard platform for proteomics development; consequently, code use, contribution and further development are strongly encouraged.
Degradation of an alkaloid pheromone from the pale‐brown chafer, Phyllopertha diversa (Coleoptera: Scarabaeidae), by an insect olfactory cytochrome P450 (1999)

The pale-brown chafer, Phyllopertha diversa, utilizes an unusual alkaloid, 1,3-dimethyl-2,4-(1H,3H)-quinazolinedione, as its sex pheromone. This compound is rapidly degraded in vitro by the antennal protein extracts from this scarab beetle. Demethylation at the N-1 position and hydroxylation of the aromatic ring have been identified as the major catabolic pathways. The enzyme responsible for the pheromone degradation is membrane-bound, requires NAD(P)H for activity and is sensitive to cytochrome P450 inhibitors, such as proadifen and metyrapone. The ability to metabolize this unusual pheromone was not detected in 12 species tested, indicating that the P450 system, specific to male P. diversa antennae, has evolved as a mechanism for olfactory signal inactivation.
Intratumoral injection of dendritic cells in combination with local hyperthermia induces systemic antitumor effect in patients with advanced melanoma (2007)

Dendritic cells (DC) are potent antigen-presenting cells that can present tumor antigens chaperoned by heat shock proteins (HSPs), while local hyperthermia (LHT) can increase the expression of HSPs. In this study, we determine if intratumoral injection of immature DC after LHT (LHT+IT-DC) induces systemic antitumor immunity in patients with advanced melanoma, and investigate the potential immunological mechanisms involved in the treatments. Patients were randomly assigned to intratumoral administration of autologous immature DC triweekly, with (LHT+IT-DC, arm A, n = 9) or without (IT-DC, arm B, n = 9) LHT. Our results showed that there were no grade 3/4 toxicities. The time to progress (TTP) of arm A was 5 months, significantly longer than that in arm B (2 months, p < 0.05). However, the overall survival time had no statistical difference (13 months vs. 6 months, p > 0.05) between the 2 groups. Our ELISPOT assay showed a significantly increased melanoma-specific IFN-gamma production in arm A, suggesting that LHT+IT-DC was more effective in the induction of cytotoxic T lymphocytes (CTL) than IT-DC alone. Furthermore, we detected an increased HSPs expression 4 hr after the first LHT, an enhanced Th1/Th2 chemokines production 24 hr after the first LHT+IT-DC treatment, a promoted migration of DC to afferent lymph nodes, and a decreased infiltration of regulatory T cells (CD4(+)CD25(+)) and an increased infiltration of active CTL (CD8(+)CD28(+)) 48 hr after the third DC injection in arm A patients. Therefore, LHT+IT-DC can induce effective specific antitumor immunity and facilitate a Th1-polarized immune response in patients with advanced melanoma.
A Naive-Like Population of Human CD1d-Restricted T Cells Expressing Intermediate Levels of Promyelocytic Leukemia Zinc Finger (2011)

Rare CD1d-α-galactosylceramide-specific T cells that do not express the invariant Vα24 chain of human NKT cells were recently identified after expansion in vitro with the lipid Ag, but their phenotype and frequency in vivo and lineage relationship with NKT cells could not be elucidated. By using a CD1d tetramer-based method to enrich these cells from fresh peripheral blood, we demonstrated their naive-like CD62L(high)CD45RO(-)CD4(+) phenotype and relatively high frequency of ∼10(-5) in several healthy individuals. Notably, these cells expressed the NKT lineage-specific transcription promyelocytic leukemia zinc finger (PLZF), indicating a developmental relationship with NKT cells and ruling out the possibility that they were conventional MHC-restricted T cells cross-reacting against CD1d-α-galactosylceramide. Although PLZF is known to direct the effector program of NKT cells, we show in this study that the naive-like cells expressed it at a significantly lower amount than NKT cells. Further, we present mouse studies demonstrating a sharp PLZF expression threshold requirement for induction of the effector phenotype. These findings directly demonstrate in vivo the existence of naive-like CD1d-restricted human T cells marked by intermediate levels of PLZF.
A framework for dynamic data source identification and orchestration on the web (2010)

The current Web offers a very large number of solutions and services, ranging from social networking and content delivery services to business applications and management systems. However, in a general case the solutions provided are largely disintegrated, with each product operating in its own environment. Additionally, many of the products are unknown to the end user and finding the most suitable application is commonly a nontrivial task. The current project is an effort to provide an ubiquitous interface for Web application integration. The suggested approach allows for dynamic identification of the applications most suitable for a given task and access to their data using a unified interface in the REST architectural style. A novel algorithm for identification of the most appropriate data source is introduced within the study. Evaluation of the overall system and the obtained results is provided.
Cold-water marine natural products (2007)

Marine natural products isolated from organisms collected from cold-water habitats are described. Emphasis is on bioactive compounds from tunicates, sponges, microbes, bryozoans, corals, algae, molluscs and echinoderms. Synthetic studies of several important classes of cold-water compounds are highlighted.
O-glycosylation delays the clearance of human IGF-binding protein-6 from the circulation (2000)

O-glycosylation delays the clearance of IGFBP-6 from the circulation and may therefore contribute to its role as a circulating inhibitor of IGF-II actions.
[Anti-neuronal antibodies and central nervous system diseases: contribution to diagnosis and pathophysiology]. (2000)

Antibodies against antigens found in the central nervous system have been evidenced in several neurological diseases. The most well-known are associated with paraneoplastic neurological diseases (Anti-Hu, Yo, Ri amphiphysin, Tr, CV2 and Ta antibodies). Some of these antibodies are specific for certain types of cancer or neurological syndromes and are highly useful diagnostic tools for the clinician. They have contributed to the hypothesis that these paraneoplastic neurological syndromes involve autoimmune cross reactions between tumoral and nervous system antigens. They are however most unlikely pathogenic on their own. Anti voltage-dependent calcium channel antibodies associated with Lambert-Eaton syndrome which is paraneoplastic in only 60 p. 100 of the cases are also observed in cases of paraneoplastic cerebellar atrophy. Anti-GAD antibodies are seen in non-paraneoplastic stiff man syndrome and in certain progressive cerebellar atrophies. Antibodies reacting with different glutamate receptors are detected in different neurological diseases including Rasmussen's encephalitis. Finally, antibodies are described in diverse conditions such as amyotrophic lateral sclerosis, Sydeham chorea or Gilles de la Tourette syndrome. The significance of the antibodies observed outside the context of paraneoplastic syndromes is not well understood, but the anti-GAD antibodies associated with progressive cerebellar disorders and autoimmune polyendocrinopathies could be an expression of the autoimmune nature of certain neurological degenerative processes affecting the central nervous system.
Dual role of Mpl receptor during the establishment of definitive hematopoiesis (2007)

Cytokine signaling pathways are important in promoting hematopoietic stem cell (HSC) self-renewal, proliferation and differentiation. Mpl receptor and its ligand, TPO, have been shown to play an essential role in the early steps of adult hematopoiesis. We previously demonstrated that the cytoplasmic domain of Mpl promotes hematopoietic commitment of embryonic stem cells in vitro, and postulated that Mpl could be important in the establishment of definitive hematopoiesis. To answer this question, we investigated the temporal expression of Mpl during mouse development by in situ hybridization. We found Mpl expression in the HSCs clusters emerging in the AGM region, and in the fetal liver (FL) as early as E10.5. Using Mpl(-/-) mice, the functional relevance of Mpl expression was tested by comparing the hematopoietic progenitor (HP) content, long-term hematopoietic reconstitution (LTR) abilities and HSC content of control and Mpl(-/-) embryos at different times of development. In the AGM, we observed delayed production of HSCs endowed with normal LTR but presenting a self-renewal defect. During FL development, we detected a decrease in HP and HSC potential associated with a defect in amplification and self-renewal/survival of the lin(-) AA4.1(+) Sca1(+) population of HSCs. These results underline the dual role of Mpl in the generation and expansion of HSCs during establishment of definitive hematopoiesis.
Multiple Sialyl Lewisx N‐Glycopeptides: Effective Ligands for E‐Selectin (1996)

Threefold condensation of the sialyl Lewisx amine derivative 1 with cyclopeptides leads to multivalent glycopeptides with repetitive saccharide units. A trivalent sialyl Lewisx N-glycopeptide proved to be a potent antagonist of E-selectin.
Effects of moisture on Fowler–Nordheim characterization of thin silicon-oxide films (1999)

A conducting-tip atomic force microscope was used as a Fowler–Nordheim characterization tool of thin silicon oxides. The system was operated under a controlled environment using novel cantilevers fabricated from platinum/iridium wire and nickel foil. With this tool, humidity-dependent field-induced oxidation of the samples and variations in the tunneling current due to uneven water layer coverage were investigated. It is shown that baking the samples and characterizing them under a dry environment alleviates problems arising from the humid environment.
Comparative evaluation of consumer grade cameras and mobile phone cameras for close range photogrammetry (2009)

The authors have been concentrating on developing convenient 3D measurement methods using consumer grade digital cameras, and it was concluded that consumer grade digital cameras are expected to become a useful photogrammetric device for the various close range application fields. On the other hand, mobile phone cameras which have 10 mega pixels were appeared on the market in Japan. In these circumstances, we are faced with alternative epoch-making problem whether mobile phone cameras are able to take the place of consumer grade digital cameras in close range photogrammetric applications. In order to evaluate potentials of mobile phone cameras in close range photogrammetry, comparative evaluation between mobile phone cameras and consumer grade digital cameras are investigated in this paper with respect to lens distortion, reliability, stability and robustness. The calibration tests for 16 mobile phone cameras and 50 consumer grade digital cameras were conducted indoors using test target. Furthermore, practability of mobile phone camera for close range photogrammetry was evaluated outdoors. This paper presents that mobile phone cameras have ability to take the place of consumer grade digital cameras, and develop the market in digital photogrammetric fields.
Mechanisms of spontaneous resolution of rat liver fibrosis. Hepatic stellate cell apoptosis and reduced hepatic expression of metalloproteinase inhibitors. (1998)

Liver fibrosis results from the excessive secretion of matrix proteins by hepatic stellate cells (HSC), which proliferate during fibrotic liver injury. We have studied a model of spontaneous recovery from liver fibrosis to determine the biological mechanisms mediating resolution.
Gene amplification in Rhynchosciara salivary gland chromosomes. (1982)

Late in the fourth larval instar, several regions of the Rhynchosciara americana salivary gland chromosomes undergo "DNA puffing." We have constructed a library of cloned cDNAs synthesized from poly(A)+RNA isolated from salivary glands during the period of development when the DNA puffs are active. From this library we have studied clones representative of three genes active during this period but not active at earlier developmental periods of the gland. One of these genes is not amplified during the developmental process and encodes a 0.6-kilobase RNA molecule. The other two genes are located within the DNA-puff sites C3 and C8 and encode 1.25-kilobase and 1.95-kilobase RNA molecules, respectively. We estimate from the quantitation of transfer hybridization experiments that each of these genes undergoes 16-fold amplification during DNA puffing.
Simultaneous source separation: A prediction‐subtraction approach (2008)

The acquisition of n‐shots, more or less simultaneously, increases acquisition efficiency and collects a wider range of information for imaging and reservoir characterisation. Its success relies critically on the ability to separate n‐shots from one recording. Stefani et al (2007) showed that while some datasets may be easily separated, others are more difficult. Using the more difficult data example from Stefani et al (loc.cit.), we show that a PEF‐based adaptive subtraction (Spitz, 2007) of the estimated wavefield due to a secondary source provides an effective separation of the sources.
Structural Mass Spectrometry: Rapid Methods for Separation and Analysis of Peptide Natural Products (2012)

A significant challenge in natural product discovery is the initial discrimination of discrete secondary metabolites alongside functionally similar primary metabolic cellular components within complex biological samples. A property that has yet to be fully exploited for natural product identification and characterization is the gas-phase collision cross section, or, more generally, the mobility-mass correlation. Peptide natural products possess many of the properties that distinguish natural products, as they are frequently characterized by a high degree of intramolecular bonding and possess extended and compact conformations among other structural modifications. This report describes a rapid structural mass spectrometry technique based on ion mobility-mass spectrometry for the comparison of peptide natural products to their primary metabolic congeners using mobility-mass correlation. This property is empirically determined using ion mobility-mass spectrometry, applied to the analysis of linear versus modified peptides, and used to discriminate peptide natural products in a crude microbial extract. Complementary computational approaches are utilized to understand the structural basis for the separation of primary metabolism derived linear peptides from secondary metabolite cyclic and modified cyclic species. These findings provide a platform for enhancing the identification of secondary metabolic peptides with distinct mobility-mass ratios within complex biological samples.