gebhart/patrepeval huggingface dataset:
Bacillus anthracis Sortase A (SrtA) Anchors LPXTG Motif-Containing Surface Proteins to the Cell Wall Envelope (2005)

Cell wall-anchored surface proteins of gram-positive pathogens play important roles during the establishment of many infectious diseases, but the contributions of surface proteins to the pathogenesis of anthrax have not yet been revealed. Cell wall anchoring in Staphylococcus aureus occurs by a transpeptidation mechanism requiring surface proteins with C-terminal sorting signals as well as sortase enzymes. The genome sequence of Bacillus anthracis encodes three sortase genes and eleven surface proteins with different types of cell wall sorting signals. Purified B. anthracis sortase A cleaved peptides encompassing LPXTG motif-type sorting signals between the threonine (T) and the glycine (G) residues in vitro. Sortase A activity could be inhibited by thiol-reactive reagents, similar to staphylococcal sortases. B. anthracis parent strain Sterne 34F(2), but not variants lacking the srtA gene, anchored the collagen-binding MSCRAMM (microbial surface components recognizing adhesive matrix molecules) BasC (BA5258/BAS4884) to the bacterial cell wall. These results suggest that B. anthracis SrtA anchors surface proteins bearing LPXTG motif sorting signals to the cell wall envelope of vegetative bacilli.
A unified hardware/software runtime environment for FPGA-based reconfigurable computers using BORPH (2008)

This paper explores the design and implementation of BORPH, an operating system designed for FPGA-based reconfigurable computers. Hardware designs execute as normal UNIX processes under BORPH, having access to standard OS services, such as file system support. Hardware and software components of user designs may, therefore, run as communicating processes within BORPH's runtime environment. The familiar language independent UNIX kernel interface facilitates easy design reuse and rapid application development. To develop hardware designs, a Simulink-based design flow that integrates with BORPH is employed. Performances of BORPH on two on-chip systems implemented on a BEE2 platform are compared.
Metaphase Chromosome Tethering Is Necessary for the DNA Synthesis and Maintenance of oriP Plasmids but Is Insufficient for Transcription Activation by Epstein-Barr Nuclear Antigen 1 (2003)

Epstein-Barr Virus (EBV) infects resting B cells, within which it establishes latency as a stable, circular episome with only two EBV components, the cis element oriP and the latently expressed protein EBNA1. It is believed that EBNA1's ability to tether oriP episomes to metaphase chromosomes is required for its stable replication. We created fusions between the DNA-binding domain (DBD) of EBNA1 and the cellular chromatin-binding proteins HMGA1a and HMG1 to determine the minimal requirements for stable maintenance of an oriP-based episome. These two proteins differ in that HMGA1a can associate with metaphase chromosomes but HMG1 cannot. Interestingly, coinciding with metaphase chromosome association, HMGA1a-DBD but not HMG1-DBD supported both the transient replication and stable maintenance of oriP plasmids, with efficiencies quantitatively similar to that of EBNA1. However, HMGA1a-DBD activated transcription from EBNA1-dependent episomal reporter to only 20% of the level of EBNA1. Furthermore, EBNA1 but not HMGA1a-DBD activated transcription from a chromosomally integrated EBNA1-dependent transcription reporter. This indicates that EBNA1 possesses functional domains that support transcription activation independent of its ability to tether episomal oriP plasmids to cellular chromosomes. We provide evidence that metaphase chromosome tethering is a fundamental requirement for maintenance of an oriP plasmid but is insufficient for EBNA1 to activate transcription.
Melatonin attenuates isoproterenol‐induced protein kinase A overactivation and tau hyperphosphorylation in rat brain (2004)

Hyperphosphorylation of microtubule-associated protein tau at specific sites is a recognized pathological process in Alzheimer's disease (AD), and protein kinase A (PKA) is a crucial kinase in AD-like tau hyperphosphorylation. In the present study, isoproterenol (ISO) was injected bilaterally into hippocampus of rat brain; ISO is a specific PKA activator and it induces tau hyperphosphorylation. With this system, melatonin (MT) was shown to protect against ISO-induced tau hyperphosphorylation. We found that hippocampal injection of ISO (0.02 microm) induced PKA overactivation and tau hyperphosphorylation at both paired helical filament (PHF)-1 and tau-1 sites. ISO injection also resulted in activation of superoxide dismutase (SOD) and elevation of malondialdehyde (MDA), parameters suggesting elevated oxidative stress. Preinfusion of MT intraperitoneally partially reversed ISO-induced tau hyperphosphorylation at the PHF-1 epitope (1 and 10 mg/kg continuously for 4 wk or 10 mg/kg for 1, 2 or 3 wk) and tau-1 epitope (10 mg/kg for 2 wk). Furthermore, MT (10 mg/kg for 2 wk) obviously antagonized ISO-induced PKA overactivation, as well as enhanced SOD activity and decreased the level of MDA. It is suggested from these data that ISO may induce abnormal hyperphosphorylation of tau through not only the activation of PKA but also because of the fact that it increases oxidative stress; MT may protect against ISO-induced tau hyperphosphorylation through suppression of both PKA overactivation and oxidative stress.
CDS Annotation in Full-Length cDNA Sequence (2003)

The identification of coding sequences (CDS) is an important step in the functional annotation of genes. CDS prediction for mammalian genes from genomic sequence is complicated by the vast abundance of intergenic sequence in the genome, and provides little information about how different parts of potential CDS regions are expressed. In contrast, mammalian gene CDS prediction from cDNA sequence offers obvious advantages, yet encounters a different set of complexities when performed on high-throughput cDNA (HTC) sequences, such as the set of 60,770 cDNAs isolated from full-length enriched libraries of the FANTOM2 project. We developed a CDS annotation strategy that uses a variety of different CDS prediction programs to annotate the CDS regions of FANTOM2 cDNAs. These include rsCDS, which uses sequence similarity to known proteins; ProCrest; Longest-ORF and Truncated-ORF, which are ab initio based predictors; and finally, DECODER and NCBI CDS predictor, which use a combination of both principles. Aided by graphical displays of these CDS prediction results in the context of other sequence similarity results for each cDNA, FANTOM2 CDS inspection by curators and follow-up quality control procedures resulted in high quality CDS predictions for a total of 14,345 FANTOM2 clones.
Exosomes in the nose induce immune cell trafficking and harbour an altered protein cargo in chronic airway inflammation (2016)

Exosomes are nano-sized extracellular vesicles participating in cell-to-cell communication both in health and disease. However, the knowledge about the functions and molecular composition of exosomes in the upper airways is limited. The aim of the current study was therefore to determine whether nasal exosomes can influence inflammatory cells and to establish the proteome of nasal lavage fluid-derived exosomes in healthy subjects, as well as its alterations in individuals with chronic airway inflammatory diseases [asthma and chronic rhinosinusitis (CRS)]. Nasal lavage fluid was collected from 14 healthy subjects, 15 subjects with asthma and 13 subjects with asthma/CRS. Exosomes were isolated with differential centrifugation and the proteome was analysed by LC–MS/MS with the application of two exclusion lists as well as using quantitative proteomics. Ingenuity Pathways Analysis and GO Term finder was used to predict the functions associated with the exosomal proteome and a migration assay was used to analyse the effect on immune cells by nasal exosomes. Firstly, we demonstrate that nasal exosomes can induce migration of several immune cells, such as monocytes, neutrophils and NK cells in vitro. Secondly, a mass spectrometry approach, with the application of exclusion lists, was utilised to generate a comprehensive protein inventory of the exosomes from healthy subjects. The use of exclusion lists resulted in the identification of ~15 % additional proteins, and increased the confidence in ~20 % of identified proteins. In total, 604 proteins were identified in nasal exosomes and the nasal exosomal proteome showed strong associations with immune-related functions, such as immune cell trafficking. Thirdly, a quantitative proteomics approach was used to determine alterations in the exosome proteome as a result of airway inflammatory disease. Serum-associated proteins and mucins were more abundant in the exosomes from subjects with respiratory diseases compared to healthy controls while proteins with antimicrobial functions and barrier-related proteins had decreased expression. Nasal exosomes were shown to induce the migration of innate immune cells, which may be important as the airway epithelium is the first line of defence against pathogens and allergens. The decreased expression in barrier and antimicrobial exosomal proteins in subjects with airway diseases, could possibly contribute to an increased susceptibility to infections, which have important clinical implications in disease progression.
A new class of electrically small antennas (1965)

This paper describes a new class of electrically small antennas, of which the principal advantages are the resistive input impedance, the radiation resistance transformation which may be obtained within the structure, and the variety of shapes which the antennas may take. The antennas incorporate resonant half-wave windings, and a simple transmission line theory is presented by which antenna efficiency and bandwidth may be calculated. Experimental methods and results are described for antennas in the order of 0.01 wavelength in height and 0.05 wavelength in diameter.
Transplanted Neural Precursors Enhance Host Brain-Derived Myelin Regeneration (2009)

In multiple sclerosis lesions resident oligodendrocyte progenitor cells (OPCs) are present, but fail to remyelinate. In the current study we examined whether neural precursor cell (NPC) transplantation can facilitate host brain-derived remyelination. We used the chronic cuprizone-induced demyelination model in aged mice, in which slow remyelination follows cuprizone removal. NPCs were transplanted to the lateral ventricles (intracerebroventricular) of cuprizone-induced demyelinated brains. In this experimental setup, transplanted cells remained mostly in the periventricular area in an undifferentiated state. The extent of demyelination, remyelination, and proliferation of host brain regenerative cell population were examined at 1 week posttransplantation in the splenium of the corpus callosum, which was devoid of any transplanted cells. Transplantation of NPCs, but not of control, human embryonic kidney cells, significantly enhanced remyelination compared with sham-operated mice. Remyelination was performed exclusively by host brain OPCs. The proregenerative effect of transplanted NPCs was related to an increase in the proliferation of host brain OPCs. To examine the mechanism that underlies the proregenerative effect of NPCs in vitro, we used an NPC-OPC coculture system. These experiments indicated that NPCs induced the proliferation of OPCs and facilitated their differentiation into mature oligodendrocytes. The mitogenic effect of NPCs was mediated by platelet-derived growth factor-AA and fibroblast growth factor-2. In conclusion, NPC transplantation enhances host-derived myelin regeneration following chronic demyelination. This trophic effect may stimulate resident OPCs to overcome the remyelination failure in multiple sclerosis.
On the cyclization to the elusive amino‐4H‐pyran ring some new facts (1990)

Abstract The reaction of 2‐indolinone ( 1 ) with arylidenemalononitriles ( 2 ) or benzylidenecyanoacetamide ( 9 ) yields the Michael adducts 3 , 10 and the spiro compound 4a . No cyclization to a 4 H ‐pyran ring is achieved. Similar results are obtained from the unsaturated lactone 11 and the carbonyl compound 13 . In contrast, 1,3‐cyclohexanedione ( 15 ) leads to the fused 2‐amino‐4 H ‐pyran 16 upon reaction with benzylidenemalononitrile ( 2 ).
Histone H1 variant-specific lysine methylation by G9a/KMT1C and Glp1/KMT1D (2010)

We have characterised a novel methylation site in the C-terminus of H1 that is the target of G9a/Glp1 both in vitro and in vivo. To our knowledge, this is the first demonstration of variant-specific histone methylation by the same methyltransferases, but with differing downstream readers, thereby supporting the hypothesis of H1 variants having specific functions.
The Minimum Papr Code For Ofdm Systems (2008)

In this paper, a block code to minimize the peak-toaverage power ratio (PAPR) of orthogonal frequency division multiplexing (OFDM) signals is proposed. It is shown that cyclic shift and codeword inversion cause not change to peak envelope power. The encoding rule for the proposed code comprises of searching for a seed codeword, shifting the register elements, and determining codeword inversion, eliminating the look-up table for one-to-one correspondence between the source and the coded data. Simulation results show that OFDM systems with the proposed code always have the minimum PAPR.
Two Constituents of the Initiation Complex of the Mannan-Binding Lectin Activation Pathway of Complement Are Encoded by a Single Structural Gene (1999)

Mannan-binding lectin (MBL) forms a multimolecular complex with at least two MBL-associated serine proteases, MASP-1 and MASP-2. This complex initiates the MBL pathway of complement activation by binding to carbohydrate structures present on bacteria, yeast, and viruses. MASP-1 and MASP-2 are composed of modular structural motifs similar to those of the C1q-associated serine proteases C1r and C1s. Another protein of 19 kDa with the same N-terminal sequence as the 76-kDa MASP-2 protein is consistently detected as part of the MBL/MASP complex. In this study, we present the primary structure of this novel MBL-associated plasma protein of 19 kDa, MAp19, and demonstrate that MAp19 and MASP-2 are encoded by two different mRNA species generated by alternative splicing/polyadenylation from one structural gene.
Deregulated expression of TCL1 causes T cell leukemia in mice (1998)

The TCL1 oncogene on human chromosome 14q32.1 is involved in the development of T cell leukemia in humans. These leukemias are classified either as T prolymphocytic leukemias, which occur very late in life, or as T chronic lymphocytic leukemias, which often arise in patients with ataxia telangiectasia (AT) at a young age. The TCL1 oncogene is activated in these leukemias by juxtaposition to the alpha or beta locus of the T cell receptor, caused by chromosomal translocations t(14:14)(q11:q32), t(7:14)(q35:q32), or by inversions inv(14)(q11:q32). To show that transcriptional alteration of TCL1 is causally involved in the generation of T cell neoplasia we have generated transgenic mice that carry the TCL1 gene under the transcriptional control of the p56(lck) promoter element. The lck-TCL1 transgenic mice developed mature T cell leukemias after a long latency period. Younger mice presented preleukemic T cell expansions expressing TCL1, and leukemias developed only at an older age. The phenotype of the murine leukemias is CD4-CD8+, in contrast to human leukemias, which are predominantly CD4+CD8-. These studies demonstrate that transcriptional activation of the TCL1 protooncogene can cause malignant transformation of T lymphocytes, indicating the role of TCL1 in the initiation of malignant transformation in T prolymphocytic leukemias and T chronic lymphocytic leukemias.
Escape from the Dominant HLA-B27-Restricted Cytotoxic T-Lymphocyte Response in Gag Is Associated with a Dramatic Reduction in Human Immunodeficiency Virus Type 1 Replication (2007)

Human leukocyte antigen (HLA)-B27-positive subjects are uncommon in their ability to control infection with human immunodeficiency virus type 1 (HIV-1). However, late viral escape from a narrowly directed immunodominant Gag-specific CD8(+) T-lymphocyte (CTL) response has been linked to AIDS progression in these individuals. Identifying the mechanism of the immune-mediated control may provide critical insights into HIV-1 vaccine development. Here, we illustrate that the CTL escape mutation R(264)K in the HLA-B27-restricted KK10 epitope in the capsid resulted in a significant defect in viral replication in vitro. The R(264)K variant was impaired in generating late reverse transcription products, indicating that replication was blocked at a postentry step. Notably, the R(264)K mutation was associated in vivo with the development of a rare secondary mutation, S(173)A, which restored viral replication in vitro. Furthermore, infectivity of the R(264)K variant was rescued by the addition of cyclosporine A or infection of a cyclophilin A-deficient cell line. These data demonstrate a severe functional defect imposed by the R(264)K mutation during an early step in viral replication that is likely due to the inability of this variant to replicate efficiently in the presence of normal levels of cyclophilin A. We conclude that the impact of the R(264)K substitution on capsid structure constrains viral escape and enables long-term maintenance of the dominant CTL response against B27-KK10, providing an explanation for the protective effect of HLA-B27 during HIV infection.
On the sequencing of the human genome (2002)

Two recent papers using different approaches reported draft sequences of the human genome. The international Human Genome Project (HGP) used the hierarchical shotgun approach, whereas Celera Genomics adopted the whole-genome shotgun (WGS) approach. Here, we analyze whether the latter paper provides a meaningful test of the WGS approach on a mammalian genome. In the Celera paper, the authors did not analyze their own WGS data. Instead, they decomposed the HGP's assembled sequence into a "perfect tiling path", combined it with their WGS data, and assembled the merged data set. To study the implications of this approach, we perform computational analysis and find that a perfect tiling path with 2-fold coverage is sufficient to recover virtually the entirety of a genome assembly. We also examine the manner in which the assembly was anchored to the human genome and conclude that the process primarily depended on the HGP's sequence-tagged site maps, BAC maps, and clone-based sequences. Our analysis indicates that the Celera paper provides neither a meaningful test of the WGS approach nor an independent sequence of the human genome. Our analysis does not imply that a WGS approach could not be successfully applied to assemble a draft sequence of a large mammalian genome, but merely that the Celera paper does not provide such evidence.
Bi-doped Fiber Lasers: New Type of High-Power Radiation Sources (2007)

CW lasing of a new type of lasers-Bi-doped fiber lasers- in a wavelength range of 1150-1215 nm at high output power level (15 W) and efficiency of 22% has been obtained for the first time.
Epidemiologic aspects of necrotic enteritis in broiler chickens – disease occurrence and production performance (2016)

Since future conventional broiler production can no longer rely upon in-feed antimicrobials (anticoccidials and antibiotic growth promoters), understanding the most important non-antimicrobial factors influencing occurrence of necrotic enteritis (NE) in poultry will become urgent. Solid population-based data on NE occurrence are scarce. Additionally, data on cholangiohepatitis (CPH) at slaughter is a useful indirect measurement of NE occurrence. Existing data suggest that coccidiosis and nutritional factors are among the most important determinants of NE occurrence. Dietary cereal contents and dietary level of animal proteins can both influence NE occurrence, but cereal composition may be more important because cereals constitute a larger portion of the diet. Losses associated with NE vary depending on the severity of the disease, but data indicate that the farmers' profit may be reduced on average with as much as one third during an epidemic of clinical disease.
Molecular Machines Based on Metal Ion Translocation (2001)

Transition metal ions can be moved reversibly between the two coordinatively unequivalent compartments A and B of a ditopic ligand, using as an input the variation of a bulk solution parameter, either pH or redox potential. In a redox-driven translocation, the metal moves reversibly from A to B on cycling between two consecutive oxidation states (e.g., Cu(II)/Cu(I); Fe(III)/Fe(II)) by means of auxiliary oxidation and reduction reactions. In a pH-driven process, one compartment displays also acid-base properties (AH(n)() left arrow over right arrow A(n)(-) + nH(+)), and the M(n)(+) ion is translocated between B and A(n)(-) through consecutive addition of base and acid.
Real-time fluorescence genotyping of factor V Leiden during rapid-cycle PCR (1997)

A single-step method for factor V Leiden genotyping is presented that uses rapid-cycle PCR and simultaneous fluorescence analysis with resonance energy transfer probes. A fragment of the factor V gene containing the mutation is amplified asymmetrically through use of a primer labeled with Cy5 in the presence of a 3'-fluorescein-labeled probe that covers the mutation site. When the fluorescein probe is annealed to the extension product of the Cy5-labeled primer, the fluorophores are brought into close enough contact for resonance energy transfer to occur. As the temperature increases, the probe melts from its target, decreasing the resonance energy transfer. When the probe is complementary to the product strand, it melts at 65 degrees C; if the single-base mutation is present, the probe melts at 57 degrees C. Concurrent amplification and analysis from genomic DNA takes 20-45 min and requires no sample manipulation after the fluorescence thermal cycler is loaded.
Involvement of tryptase‐related cellular protease(s) in human immunodeficiency virus type 1 infection (1989)

Trypstatin, a new cellular Kunitz-type protease inhibitor purified from rat mast cells, inhibited syncytium formation in human immunodeficiency virus type 1 (HIV-1)-infected CCRF-CEM and uninfected Molt-4 clone 8 at a concentration of 1 microM. Anti-rat tongue mast cell tryptase antibodies reacted with Molt-4 clone 8 cells, as determined by Western blot and by immunofluorescence. In addition, the antibody inhibited syncytium formation. These findings along with homologous sequences with trypstatin and a neutralizing epitope of gp120 of HIV-1 suggest that a tryptase-like cellular enzyme(s) is involved in HIV-1 infection.
Interacting Mobile Robots on the Web (1999)

The internet has become the most important network for communication and the biggest data storage. However, real interaction through this fast growing network is only possible through robots connected to it. This paper discusses the approach and preliminary results of interdisciplinary projects in Internetrobotics. After a discussion of the basic issues, our modular framework for mobile robots on the Web is described. Running and future applications at EPFL, ranging from mini-robots up to experimental robot connected to the Web, are presented. 1 Introduction The Internet connects millions of computers all over the world, giving access to communication, data, pictures, videos and even real images of distant environments. However, only a few examples of real physical interaction with distant places is available at the moment. The goal of the described projects at EPFL is to add a new dimension to the Internet by combining network technology with the capabilities of mobile robots. Thi...
Proinflammatory Role of Trypsin and Protease-activated Receptor-2 in a Rat Model of Acute Pancreatitis (2005)

These results suggest that trypsin and its specific receptor, PAR-2, play an important role in cytokine production and the resultant development of distant organ injury during rat acute pancreatitis.