gebhart/patrepeval huggingface dataset:
Circular dichroism spectra of short, fixed-nucleus alanine helices (2002)

Very short alanine peptide helices can be studied in a fixed-nucleus, helix-forming system [Siedlicka, M., Goch, G., Ejchart, A., Sticht, H. & Bierzynski, A. (1999) Proc. Natl. Acad. Sci. USA 96, 903-908]. In a 12-residue sequence taken from an EF-hand protein, the four C-terminal peptide units become helical when the peptide binds La(3+), and somewhat longer helices may be made by adding alanine residues at the C terminus. The helices studied here contain 4, 8, or 11 peptide units. Surprisingly, these short fixed-nucleus helices remain almost fully helical from 4 to 65 degrees C, according to circular dichroism results reported here, and in agreement with titration calorimetry results reported recently. These peptides are used here to define the circular dichroism properties of short helices, which are needed for accurate measurement of helix propensities. Two striking properties are: (i) the temperature coefficient of mean peptide ellipticity depends strongly on helix length; and (ii) the intensity of the signal decreases much less rapidly with helix length, for very short helices, than supposed in the past. The circular dichroism spectra of the short helices are compared with new theoretical calculations, based on the experimentally determined direction of the NV(1) transition moment.
The Grid 2: Blueprint for a New Computing Infrastructure (1998)

Preface Foreword 1. Grids in Context 2. Computational Grids I Applications 3 Distributed Supercomputing Applications 4 Real-Time Widely Distributed Instrumentation Systems 5 Data-Intensive Computing 6 Teleimmersion II Programming Tools 7 Application-Specific Tools 8 Compilers, Languages, and Libraries 9 Object-Based Approaches 10 High-Performance Commodity Computing III Services 11 The Globus Toolkit 12 High-Performance Schedulers 13 High-Throughput Resource Management 14 Instrumentation and Measurement 15 Performance Analysis and Visualization 16 Security, Accounting, and Assurance IV Infrastructure 17 Computing Platforms 18 Network Protocols 19 Network Quality of Service 20 Operating Systems and Network Interfaces 21 Network Infrastructure 22 Testbed Bridges from Research to Infrastructure Glossary Bibliography Contributor Biographies
Adenylate kinase enzyme activity in cases of brain infarction (1989)

The adenylate kinase (AK) enzyme activity in plasma and CSF of acute brain infarctions was examined. The normal values of enzyme activity in plasma reached from 1.7-5.6 U/l, and in CSF from 0.23-0.71 U/l. According to this present classification a significant CSF increase in AK activity was found with semi-severe and severe brain infarctions. With the CCT an increased enzyme activity was shown with infarction in or close to the cortex. In no case was an alteration of AK activity in the serum sample. CSF samples showing blood contamination or pleocytosis led to false pathological results with examination of AK activity.
Identification of distal regulatory regions in the human αIIb gene locus necessary for consistent, high-level megakaryocyte expression (2002)

The alphaIIb/beta3-integrin receptor is present at high levels only in megakaryocytes and platelets. Its presence on platelets is critical for hemostasis. The tissue-specific nature of this receptor's expression is secondary to the restricted expression of alphaIIb, and studies of the alphaIIb proximal promoter have served as a model of a megakaryocyte-specific promoter. We have examined the alphaIIb gene locus for distal regulatory elements. Sequence comparison between the human (h) and murine (m) alphaIIb loci revealed high levels of conservation at intergenic regions both 5' and 3' to the alphaIIb gene. Additionally, deoxyribonuclease (DNase) I sensitivity mapping defined tissue-specific hypersensitive (HS) sites that coincide, in part, with these conserved regions. Transgenic mice containing various lengths of the h(alpha)IIb gene locus, which included or excluded the various conserved/HS regions, demonstrated that the proximal promoter was sufficient for tissue specificity, but that a region 2.5 to 7.1 kb upstream of the h(alpha)IIb gene was necessary for consistent expression. Another region 2.2 to 7.4 kb downstream of the gene enhanced expression 1000-fold and led to levels of h(alpha)IIb mRNA that were about 30% of the native m(alpha)IIb mRNA level. These constructs also resulted in detectable h(alpha)IIb/m(beta)3 on the platelet surface. This work not only confirms the importance of the proximal promoter of the alphaIIb gene for tissue specificity, but also characterizes the distal organization of the alphaIIb gene locus and provides an initial localization of 2 important regulatory regions needed for the expression of the alphaIIb gene at high levels during megakaryopoiesis.
Aglycosylated immunoglobulin G1variants productively engage activating Fc receptors (2008)

Immunoglobulin G plays a vital role in adaptive immunity and antibody-based therapy through engagement of its Fc region by the Fc gamma receptors (Fc gammaRs) on immune cells. In addition to specific protein-protein contacts, N-linked glycosylation of the IgG Fc has been thought to be essential for the recognition of Fc by Fc gammaR. This requirement for the N-linked glycan has limited biomanufacture of therapeutic antibodies by restricting it to mammalian expression systems. We report here aglycosylated Fc domain variants that maintain engagement to Fc gammaRs, both in vitro and in vivo, demonstrating that Fc glycosylation is not strictly required for the activation of immune cells by IgG. These variants provide insight into how the N-linked glycan is used biologically in the recognition of Fc by Fc gammaRs, as well as represent a step toward the production in alternative expression systems of antibody-based therapeutics capable of eliciting immune effector functions.
What is the total number of protein molecules per cell volume? A call to rethink some published values (2013)

Novel methods such as mass-spectrometry enable a view of the proteomes of cells in unprecedented detail. Recently, these efforts have culminated in quantitative measurements of the number of copies per cell for most expressed proteins in organisms ranging from bacteria to mammalian cells. Here, we estimate the expected total number of proteins per unit of cell volume using known parameters related to the composition of cells such as the fraction of cell mass that is protein, and the average protein length. Using simple arguments, we estimate a range of 2-4 million proteins per cubic micron (i.e. 1 fL) in bacteria, yeast, and mammalian cells. Interestingly, we find that measured values that are reported for fission yeast and mammalian cells are often about 3-10 times lower. We discuss this apparent discrepancy and how to use the estimate as benchmark to recalibrate proteome-wide quantitative censuses or to revisit assumptions about cell composition.
Characterization of the lipolytic activity of endothelial lipase (2002)

Endothelial lipase (EL) is a new member of the triglyceride lipase gene family previously reported to have phospholipase activity. Using radiolabeled lipid substrates, we characterized the lipolytic activity of this enzyme in comparison to lipoprotein lipase (LPL) and hepatic lipase (HL) using conditioned medium from cells infected with recombinant adenoviruses encoding each of the enzymes. In the absence of serum, EL had clearly detectable triglyceride lipase activity. Both the triglyceride lipase and phospholipase activities of EL were inhibited in a dose-dependent fashion by the addition of serum. The ratio of triglyceride lipase to phospholipase activity of EL was 0.65, compared with ratios of 24.1 for HL and 139.9 for LPL, placing EL at the opposite end of the lipolytic spectrum from LPL. Neither lipase activity of EL was influenced by the addition of apolipoprotein C-II (apoC-II), indicating that EL, like HL, does not require apoC-II for activation. Like LPL but not HL, both lipase activities of EL were inhibited by 1 M NaCl. The relative ability of EL, versus HL and LPL, to hydrolyze lipids in isolated lipoprotein fractions was also examined using generation of FFAs as an end point. As expected, based on the relative triglyceride lipase activities of the three enzymes, the triglyceride-rich lipoproteins, chylomicrons, VLDL, and IDL, were efficiently hydrolyzed by LPL and HL. EL hydrolyzed HDL more efficiently than the other lipoprotein fractions, and LDL was a poor substrate for all of the enzymes.
M-CAT binding factor, a novel trans-acting factor governing muscle-specific transcription. (1990)

The cardiac troponin T (cTNT) promoter contains a highly muscle specific distal promoter element capable of conferring muscle-specific transcription from a heterologous TATA box-transcription initiation site. Three sequence motifs within this distal promoter element are conserved in the promoter and regulatory regions of many sarcomeric protein genes. Mutational analysis demonstrated that homologies to two of these conserved motifs (CArG/CBAR and MEF 1) were not required for activity of cTNT promoter-marker gene constructs in transfected embryonic skeletal muscle cells. In contrast, disruption of either or both copies of the conserved M-CAT motif (5'-CATTCCT-3') inactivated the cTNT promoter in these cells. Both M-CAT motifs were protected from DNase I cleavage in solution footprint assays by an M-CAT binding factor (MCBF) present in nuclear extracts from embryonic muscle tissue. M-CAT mutations that inactivated the cTNT promoter also disrupted MCBF binding, indicating that MCBF may be a key trans-acting factor required for muscle-specific expression of the cTNT promoter. MCBF also bound to the M-CAT motif in the distal promoter region of the skeletal alpha-actin gene, suggesting that it may play a role in the regulation of this and perhaps other muscle genes that contain M-CAT motifs.
Analysis of progressively overexpressed genes in tumorigenesis of colorectal cancers using cDNA microarray. (2005)

The identification of differentially expressed genes has important implications in understanding the biology of colorectal tumorigenesis and progression, as well as developing new diagnostic and therapeutic strategies. In this study, cDNA microarray technology was used to identify colorectal tumor-related functional genes, which are overexpressed continuously from colorectal adenoma to adenocarcinoma. A set of 23 genes with progressive overexpression in the development of colorectal cancer (CRC) was identified by cDNA microarray, then analyzed by sequencing and Northern blot analysis. Validation of our array results was simultaneously performed by exploring the SAGEmap database. Furthermore, the gradually over-expressed genes from adenoma to adenocarcinoma were validated by Northern blot analysis with additional samples from three patients with synchronous colorectal adenocarcinoma and adenoma and four patients with CRC. Of these 23 genes, one was a function-unknown gene, designated as Homo sapiens chromosome 21q22.1 anonymous mRNA sequence (Genbank accession no. AF003738), and 22 were function-known genes. Searching through the Gene Ontology Browser at the Cancer Genome Analysis Project website revealed that the biological roles of these 22 function-known genes are involved in cell motility, cell adhesion, chemokine activity, signal transduction, cytoskeleton organization, proteolysis, apoptosis, and cell proliferation. The genes identified in the present study offer valuable information on colorectal carcinogenesis and metastasis, and represent a potential source of novel targets for new strategies for CRC diagnosis and therapy.
Thermosensitive Pluronic&reg; hydrogel: prolonged injectable formulation for drug abuse (2010)

The results of the current in vitro study indicate that PF-127 gel formulations containing drug complexes with hydrophobic cyclodextrin could be useful for the preparation of a controlled delivery system of water-soluble drugs such as NTX, for a period of more than 140 hours.
Structural studies of tau protein and Alzheimer paired helical filaments show no evidence for beta-structure. (1994)

We have studied the conformation of tau protein and Alzheimer paired helical filaments (PHF) by several spectroscopic, scattering, and imaging methods revealing the overall shape and the conformation of the polypeptide backbone. Tau protein behaves in solution as if it were denatured; no evidence for compact folding was detected. The protein is highly extended, there is no defined radius of gyration, and the scattering is best described by that of a random ("Gaussian") polymer. CD and Fourier transform infrared spectroscopy show only a minimal content of ordered secondary structure (alpha-helix or beta-sheet). Similarly, PHFs from Alzheimer brain tissue show no detectable secondary structure by x-ray diffraction or spectroscopy. It is thus unlikely that the aggregation of tau into Alzheimer PHFs is based on interactions between strands of beta-sheets (a model currently favored for other disease-related polymers such as beta-amyloid fibers of Alzheimer's disease).
Visualisation of ontological inferences for user control of personal Web agents (2004)

We describe a visualisation tool, VlUM, designed to support users in scrutinising models of their interests, preferences and knowledge. We also describe MECUREO, a tool for building lightweight ontologies from online dictionaries. It enables a user to see a model describing both their interests and additional analogically inferred interests. We report a small qualitative evaluation of this combined system. This indicates that users were able to use the system to explore models of two hypothetical users, making use of varying levels of ontological inference.
Scalable Join Queries in Cloud Data Stores (2012)

Cloud data stores provide scalability and high availability properties for Web applications, but do not support complex queries such as joins. Web application developers must therefore design their programs according to the peculiarities of No SQL data stores rather than established software engineering practice. This results in complex and error-prone code, especially with respect to subtle issues such as data consistency under concurrent read/write queries. We present join query support in Cloud TPS, a middleware layer which stands between a Web application and its data store. The system enforces strong data consistency and scales linearly under a demanding workload composed of join queries and read-write transactions. In large-scale deployments, Cloud TPS outperforms replicated Postgre SQL up to three times.
An Interactive Graphics System for the Design of Integrated Circuits (1978)

IGS (Interactive Graphics System) is a computer design aid specifically developed for the layout of integrated circuits. User specification of process information makes the system process-independent while retaining the features which make it a useful layout tool. The ability to place interconnect on a coarse grid greatly diminishes the chances of misalignment. Automatic, incremental checking of cell-to-cell, cell-to-component, and component-to-component spacing reduces the number of design rule violations. Rudimentary forms of topology verification are provided in the ability to trace electrical connectivity.
Intranasal Administration of CNS Therapeutics to Awake Mice (2013)

Intranasal administration is a method of delivering therapeutic agents to the central nervous system (CNS). It is non-invasive and allows large molecules that do not cross the blood-brain barrier access to the CNS. Drugs are directly targeted to the CNS with intranasal delivery, reducing systemic exposure and thus unwanted systemic side effects. Delivery from the nose to the CNS occurs within minutes along both the olfactory and trigeminal neural pathways via an extracellular route and does not require drug to bind to any receptor or axonal transport. Intranasal delivery is a widely publicized method and is currently being used in human clinical trials. Intranasal delivery of drugs in animal models allows for initial evaluation of pharmacokinetic distribution and efficacy. With mice, it is possible to administer drugs to awake (non-anesthetized) animals on a regular basis using a specialized intranasal grip. Awake delivery is beneficial because it allows for long-term chronic dosing without anesthesia, it takes less time than with anesthesia, and can be learned and done by many people so that teams of technicians can dose large numbers of mice in short periods. Efficacy of therapeutics administered intranasally in this way to mice has been demonstrated in a number of studies including insulin in diabetic mouse models and deferoxamine in Alzheimer's mouse models. The intranasal grip for mice can be learned, but is not easy and requires practice, skill, and a precise grip to effectively deliver drug to the brain and avoid drainage to the lung and stomach. Mice are restrained by hand using a modified scruff in the non-dominant hand with the neck held parallel to the floor, while drug is delivered with a pipettor using the dominant hand. It usually takes 3-4 weeks of acclimating to handling before mice can be held with this grip without a stress response. We have prepared this JoVE video to make this intranasal delivery technique more accessible.
Chebyshev rational spectral and pseudospectral methods on a semi‐infinite interval (2001)

Abstract A weighted orthogonal system on the half‐line based on the Chebyshev rational functions is introduced. Basic results on Chebyshev rational approximations of several orthogonal projections and interpolations are established. To illustrate the potential of the Chebyshev rational spectral method, a model problem is considered both theoretically and numerically: error estimates for the Chebyshev rational spectral and pseudospectral methods are established; preliminary numerical results agree well with the theoretical estimates and demonstrate the effectiveness of this approach. Copyright © 2001 John Wiley &amp; Sons, Ltd.
Nanophotonic Spectrometer for Optical Coherence Tomography (2013)

We introduce OCTANE, the first product line of chip-based spectrometers using silicon photonics for spectral domain optical coherence tomography (SD-OCT). It is well suited for low-cost, high-volume applications in both the medical and industrial fields.
Characterization of a cardiac-selective and developmentally upregulated promoter in transgenic mice. (1994)

Transcriptional regulatory mechanisms which mediate cardiac-specific gene expression have not yet been completely understood. Potential cardiac-specific promoter sequences, sharing similar protein binding motives, show either coexpression in skeletal muscle, local restriction to the atrium or late onset of expression during fetogenesis. Based on in situ hybridization studies that indicated the expression of the cardiac myosin-light-chain-2 (MLC-2) gene in ventricular myocardium and in the lower outflow tract, a model system for selective targeting of foreign genes to the heart of transgenic mice has been developed. The regulatory promoter element was derived from the rat cardiac MLC-2 gene. 2100 bp of the 5' regulatory MLC-2 sequences were found to drive constitutive cardiac expression of a firefly luciferase reporter gene from early tubular heart formation. During ventricular loop and septum formation luciferase activity was 10-fold upregulated in comparison to steady-state levels observed 10 days after birth. No luciferase activity was detectable in any other muscle or non-muscle tissue of transgenic mice. These data suggest that the 2.1 kb DNA sequences of the 5' flanking region of the cardiac MLC-2 gene contain sufficient regulatory elements for a selective gene expression in cardiac myocytes from embryogenesis. The transgenic model should aid in determining the influences of pathogenic gene products on developing and mature heart muscle to elucidate the etiology of myocardial diseases such as cardiomyopathies.
Apolipoprotein A1-derived amyloid in human aortic atherosclerotic plaques. (1995)

Amyloid deposits in the aortic intima are very common in association with atherosclerosis and aging. In the present study, a major fibril protein purified from amyloid present in human atherosclerotic plaques was shown to be a 69-amino acid N-terminal fragment of apolipoprotein AI. Although senile form of localized apolipoprotein AI-derived amyloidosis has recently been documented in pulmonary vessels of dogs, this is the first example of a localized human amyloid derived from this apolipoprotein.
On OWL/SWRL mapping to UML/OCL (2010)

Nowadays, there is a great interest on OWL/SWRL (the Semantic Web Rule Language), language for integrity and derivation rules in onlologies and ontology-based systems, its application and its transformation to UML/OCL (Object Constraint Language). Though, it is suggested some approaches on transforming OWL/SWRL to UML/OCL, in this paper we are aiming to review existing situation and to formulate future works.
Clostridium difficile Testing: after 20 Years, Still Challenging (2003)

More than 20 years ago, as Clostridium difficile was being established as the cause of pseudomembranous colitis and antibiotic-associated diarrhea (AAD), many clinical laboratories were using or beginning to use cycloserine-cefoxitin-fructose agar, a selective medium developed by Lance George and
Saccharomyces cerevisiae PKC1 encodes a protein kinase C (PKC) homolog with a substrate specificity similar to that of mammalian PKC (1994)

The PKC1 gene of the budding yeast Saccharomyces cerevisiae encodes a homolog of the alpha, beta, and gamma isoforms of mammalian protein kinase C (PKC) that is essential for cell growth. Loss of PKC1 function results in a cell lysis defect that is due to a deficiency in cell wall construction. In this study, Pkc1p was modified at its COOH terminus with the influenza virus hemagglutinin epitope and was detected by SDS-polyacrylamide gel electrophoresis as a 145- and 150-kDa doublet when overproduced in yeast cells. Pkc1p displayed intrinsic Ser/Thr protein kinase activity in vitro, possessing a substrate specificity similar to that described for mammalian PKC. Specifically, preferred substrates possess an arginine at position -3 and a basic residue at position +2 relative to the target site. A catalytically inactive missense mutant of Pkc1p failed to complement a pkc1 delta mutant, suggesting that protein kinase activity is required for the biological function of Pkc1p. Both wild-type Pkc1p and the inactive form were isolated as phosphoproteins, indicating that Pkc1p is phosphorylated in vivo by another protein kinase. In vitro protein kinase activity of Pkc1p was not dependent on activating cofactors normally required for stimulation of mammalian PKC. However, mutational incapacitation of the pseudosubstrate site of Pkc1p resulted in constitutive activation of the enzyme, both in vivo and in vitro, suggesting that Pkc1p is normally regulated by a mechanism similar to that of its mammalian counterparts. The apparent molecular mass and substrate specificity of Pkc1p, together with its failure to respond to activating cofactors, suggest that this enzyme is distinct from an enzyme purified previously from budding yeast that has enzymatic properties similar to those of mammalian PKC.
Human Inhibitory Receptor Immunoglobulin-Like Transcript 2 Amplifies CD11b+Gr1+ Myeloid-Derived Suppressor Cells That Promote Long-Term Survival of Allografts (2008)

Our results suggest that induction of MDSCs using ILT2 inhibitory receptor/HLA-G ligand may be an attractive strategy for preventing rejection of immunogenic organs or tissues in clinical transplantation.