gebhart/patrepeval huggingface dataset:
Preparation of Pooled Human Platelet Lysate (pHPL) as an Efficient Supplement for Animal Serum-Free Human Stem Cell Cultures (2009)

Platelet derived growth factors have been shown to stimulate cell proliferation efficiently in vivo(1,2) and in vitro. This effect has been reported for mesenchymal stromal cells (MSCs), fibroblasts and endothelial colony-forming cells with platelets activated by thrombin(3-5) or lysed by freeze/thaw cycles(6-14) before the platelet releasate is added to the cell culture medium. The trophic effect of platelet derived growth factors has already been tested in several trials for tissue engineering and regenerative therapy.(1,15-17) Varying efficiency is considered to be at least in part due to individually divergent concentrations of growth factors(18,19) and a current lack of standardized protocols for platelet preparation.(15,16) This protocol presents a practicable procedure to generate a pool of human platelet lysate (pHPL) derived from routinely produced platelet rich plasma (PRP) of forty to fifty single blood donations. By several freeze/thaw cycles the platelet membranes are damaged and growth factors are efficiently released into the plasma. Finally, the platelet fragments are removed by centrifugation to avoid extensive aggregate formation and deplete potential antigens. The implementation of pHPL into standard culture protocols represents a promising tool for further development of cell therapeutics propagated in an animal protein-free system.
Design of Organic Semiconductors: Tuning the Electronic Properties of π‐Conjugated Oligothiophenes with the 3,4‐Ethylenedioxythiophene (EDOT) Building Block (2005)

Hybrid oligothiophenes based on a various combinations of thiophene and 3,4-ethylenedioxythiophene (EDOT) groups have been synthesized. UV/Vis absorption spectra show that the number and relative positions of the EDOT groups considerably affect the width of the HOMO-LUMO gap and the rigidity of the conjugated system. Analysis of the crystallographic structure of two hybrid quaterthiophenes confirms that insertion of two adjacent EDOT units in the middle of the molecule leads to a self-rigidification of the conjugated systems by intramolecular SO interactions. Cyclic voltammetry data shows that the first oxidation potential of the oligomers decreases with increasing chain length and increasing number of EDOT groups for a given chain length. Electrochemical studies and theoretical calculations show that the positions of the EDOT units in the conjugated chain control the potential difference (DeltaE(p)) between the first and second oxidation steps. Moving the EDOT groups from the outer to the inner positions of the conjugated system increases DeltaE(p). Theoretical calculations confirm that this phenomenon reflects an increase of the intramolecular coulombic repulsion between positive charges in the dication. A thin-film field-effect transistor was fabricated by vacuum sublimation of a pentamer with alternating thiophene-EDOT structure, and the hole mobility was determined.
Identification of a Staphylococcus aureus extracellular matrix-binding protein with broad specificity (1993)

A staphylococal surface protein capable of binding several extracellular matrix glycoproteins was purified as a result of our attempts to identify a receptor(s) for bone sialoprotein (BSP) on Staphylococcus aureus cells. Proteins from different staphylococcal strains were solubilized in sodium lauryl sulfate, separated by polyacrylamide gel electrophoresis, blotted onto Immobilon P membranes, and probed with 125I-BSP. Several bacterial proteins bound the radiolabeled ligand, and various strains expressed different repertoirs of BSP-binding proteins. Major BSP-binding proteins with apparent M(r)s of 72,000 or 60,000 were present on most strains, and these proteins were further studied. The 72- and 60-kDa proteins were preferentially expressed when bacteria were cultured in Luria broth compared with when they were cultured on tryptic soy broth, and the abundance of the proteins could be correlated to an increased 125I-BSP binding. Both the 72-kDa and the 60-kDa proteins were solubilized by extraction of cells with 1 M LiCl and were purified by cation-exchange chromatography. Amino acid composition analysis of the purified 72-kDa protein indicated a high content of lysine (11.9%) and hydrophobic amino acids (28.0% combined). In Western ligand blotting (immunoblotting) experiments, the 72-kDa protein bound not only BSP but also radiolabeled fibronectin, fibrinogen, vitronectin, thrombospondin, and, to some extent, collagen. Addition of the purified 60-kDa protein to S. aureus cells did not inhibit binding of the different ligands but in some cases resulted in an augmentation of the binding of 125I-ligand. Purified 60-kDa protein could hemagglutinate sheep erythrocytes at a concentration of 61 micrograms/ml. The agglutination reaction was inhibited by high concentrations of fucose, mannose, or melibiose. These data suggest that the purified proteins may serve as bacterial receptors with broad specificity for matrix glycoproteins and that the proteins may act as carbohydrate-binding proteins.
A promising retrieval algorithm for systems based on the conceptual graphs formalism (2002)

Conceptual graphs can be used as a simple and expressive language for indexing and retrieving non-textual documents. In this knowledge representation formalism, the implementation of the matching function between a query and a document is obtained by the so-called projection operator between two conceptual graphs. A good implementation of the projection algorithm is therefore crucial for managing large bases of text and image documents. We present a new promising implementation. It has the important feature that it applies the projection to the whole document index database. We implemented the approach on top of the OO-DBMS O/sub 2/. As the matching function is reduced to a sequence of set operators, the time performance is improved as compared to previous implementations of the projection as an inference process. The experimental results prove the feasibility of the approach in terms of retrieval time performance.
Oligonucleotide-Mediated Gene Targeting in Human Hepatocytes: Implications of Mismatch Repair (2008)

Gene therapy using viral vectors for liver diseases, particularly congenital disorders, is besought with difficulties, particularly immunologic reactions to viral antigens. As a result, nonviral methods for gene transfer in hepatocytes have also been explored. Gene repair by small synthetic single-stranded oligodeoxynucleotides (ODNs) produces targeted alterations in the genome of mammalian cells and represents a great potential for nonviral gene therapy. To test the feasibility of ODN-mediated gene repair within chromosomal DNA in human hepatocytes, two new cell lines with stably integrated mutant reporter genes, namely neomycin and enhanced green fluorescent protein were established. Targeting theses cells with ODNs specifically designed for repair resulted in site-directed and permanent gene conversion of the single-point mutation of the reporter genes. Moreover, the frequency of gene alteration was highly dependent on the mitotic activity of the cells, indicating that the proliferative status is an important factor for successful targeting in human hepatocytes. cDNA array expression profiling of DNA repair genes under different cell culture conditions combined with RNA interference assay showed that mismatch repair (MMR) in actively growing hepatocytes imposes a strong barrier to efficient gene repair mediated by ODNs. Suppression of MSH2 activity in hepatocytes transduced with short hairpin RNAs (shRNAs) targeted to MSH2 mRNA resulted in 25- to 30-fold increase in gene repair rate, suggesting a negative effect of MMR on ODN-mediated gene repair. Taken together, these data suggest that under appropriate conditions nonviral chromosomal targeting may represent a feasible approach to gene therapy in liver disease.
Genome Sequence of the Polymyxin-Producing Plant-Probiotic Rhizobacterium Paenibacillus polymyxa E681 (2010)

Paenibacillus polymyxa E681, a spore-forming, low-G+C, Gram-positive bacterium isolated from the rhizosphere of winter barley grown in South Korea, has great potential for agricultural applications due to its ability to promote plant growth and suppress plant diseases. Here we present the complete genome sequence of P. polymyxa E681. Its 5.4-Mb genome encodes functions specialized to the plant-associated lifestyle and characteristics that are beneficial to plants, such as the production of a plant growth hormone, antibiotics, and hydrolytic enzymes.
Endoscopic system for simultaneous visual examination and electronic detection of fluorescence (1980)

A sensitive parallel system for visual examination of a target area with simultaneous detection and measurement of fluorescent emission from the same region is described. This device, originally designed and constructed for bronchial cancer detection, alternates visual illumination and narrow band excitation radiation in conjunction with a synchronously shuttered PMT at frequencies above the visual flicker fusion threshold to provide parallel operation. The signal from the PMT is synchronously amplified using a lock-in amplifier, the dc output of which is voltage-to-frequency converted and amplified to provide an audible tone whose frequency is proportional to the fluorescence sensed.
Physiological responses to protein aggregates: Fibrinolysis, coagulation and inflammation (new roles for old factors) (2009)

Misfolding is an inherent and potentially problematic propensity of proteins. Misfolded proteins tend to aggregate and the deposition of aggregated proteins is associated with a variety of highly debilitating diseases known as amyloidoses. Protein misfolding and aggregation is also increasingly recognized as the underlying cause of other health problems, including atherosclerosis and immunogenicity of biopharmaceuticals. This raises the question how nature deals with the removal of obsolete proteins in order to avoid their accumulation and disease. In recent years two proteases, tPA and factor XII, have been identified that specifically recognize aggregates of misfolded proteins. We here review these discoveries that have uncovered new roles for the fibrinolytic system and the contact activation system beyond haemostasis.
A minor fraction of basic fibroblast growth factor mRNA is deaminated in Xenopus stage VI and matured oocytes (1999)

Adenosine deaminases that act on RNA (ADARs) convert adenosine to inosine in double-stranded regions of RNA. ADAR activity is in the nucleus in Xenopus laevis stage VI oocytes, and released into the cytoplasm at oocyte maturation. We previously demonstrated that a cytoplasmic double-stranded RNA (dsRNA) binding factor(s), cyto-dsRBP, protects microinjected dsRNA from the ADAR released at maturation. Here we describe experiments to determine whether an endogenous dsRNA, the duplex formed between sense and antisense transcripts of basic fibroblast growth factor (bFGF), is protected in a similar manner. Consistent with the presence of cyto-dsRBP, we observed that the majority of bFGF RNA was not deaminated, before or after maturation. However, a minor fraction of the bFGF RNA was deaminated whether the RNA was isolated from stage VI oocytes or matured oocytes. Since ADAR activity is in the nucleus in stage VI oocytes, our results suggest that a fraction of the bFGF RNAs are hybridized in the nucleus and are ADAR substrates. Adenosine deaminations result in A-to-G changes in cDNAs, so we quantified the fraction of modified molecules using restriction-enzyme assays of RT-PCR products. Caveats due to recombination during RT-PCR are discussed.
Structural and Functional Analyses of the Major Outer Membrane Protein ofChlamydia trachomatis (2007)

Chlamydia trachomatis is a major pathogen throughout the world, and preventive measures have focused on the production of a vaccine using the major outer membrane protein (MOMP). Here, in elementary bodies and in preparations of the outer membrane, we identified native trimers of the MOMP. The trimers were stable under reducing conditions, although disulfide bonds appear to be present between the monomers of a trimer and between trimers. Cross-linking of the outer membrane complex demonstrated that the MOMP is most likely not in a close spatial relationship with the 60- and 12-kDa cysteine-rich proteins. Extraction of the MOMP from Chlamydia isolates under nondenaturing conditions yielded the trimeric conformation of this protein as shown by cross-linking and analysis by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis with different concentrations of acrylamide. Using circular dichroism spectroscopy, we determined that the trimers were formed mainly of beta-pleated sheet structures in detergent micelles. Using a liposomal swelling assay, the MOMP was found to have porin activity, and the size of the pore was estimated to be approximately 2 nm in diameter. The trimers were found to be stable in SDS at temperatures ranging from 4 to 37 degrees C and over a pH range of 5.0 to 8.0. In addition, the trimers of MOMP were found to be resistant to digestion with trypsin. In conclusion, these results show that the native conformation of the MOMP of C. trachomatis is a trimer with predominantly a beta-sheet structure and porin function.
Increased Ion Transport in Cultured Nasal Polyp Epithelial Cells (1994)

Polyp epithelia have increased Na+ absorption and Cl- permeability relative to turbinate epithelia. These results are consistent with the hypothesis that increased epithelial fluid absorption contributes to the development of nasal polyps.
Feature extraction of musical content for automatic music transcription (2006)

The purpose of this thesis is to develop new methods for automatic transcription of melody and harmonic parts of real-life music signal. Music transcription is here defined as an act of analyzing a piece of music signal and writing down the parameter representations, which indicate the pitch, onset time and duration of each pitch, loudness and instrument applied in the analyzed music signal. The proposed algorithms and methods aim at resolving two key sub-problems in automatic music transcription: music onset detection and polyphonic pitch estimation. There are three original contributions in this thesis. The first is an original frequency-dependent time-frequency analysis tool called the Resonator Time-Frequency Image (RTFI). By simply defining a parameterized function mapping frequency to the exponent decay factor of the complex resonator filter bank, the RTFI can easily and flexibly implement the time-frequency analysis with different time-frequency resolutions such as ear-like (similar to human ear frequency analyzer), constant-Q or uniform (evenly-spaced) time-frequency resolutions. The corresponding multi-resolution fast implementation of RTFI has also been developed. The second original contribution consists of two new music onset detection algorithms: Energy-based detection algorithm and Pitch-based detection algorithm. The Energy-based detection algorithm performs well on the detection of hard onsets. The Pitch-based detection algorithm is the first one, which successfully exploits the pitch change clue for the onset detection in real polyphonic music, and achieves a much better performance than the other existing detection algorithms for the detection of soft onsets. The third contribution is the development of two new polyphonic pitch estimation methods. They are based on the RTFI analysis. The first proposed estimation method mainly makes best of the harmonic relation and spectral smoothing principle, consequently achieves an excellent performance on the real polyphonic music signals. The second proposed polyphonic pitch estimation method is based on the combination of signal processing and machine learning. The basic idea behind this method is to transform the polyphonic pitch estimation as a pattern recognition problem. The proposed estimation method is mainly composed by a signal processing block followed by a learning machine. Multi-resolution fast RTFI analysis is used as a signal processing component, and support vector machine (SVM) is selected as learning machine. The experimental result of the first approach show clear improvement versus the other state of the art methods.
Clinical evaluation of a novel microfluidic device for epitope-independent enrichment of circulating tumour cells in patients with small cell lung cancer (2015)

Circulating tumour cells (CTCs) have potential utility as minimally-invasive biomarkers to aid cancer treatment decision making. However, many current CTC technologies enrich CTCs using specific surface epitopes that do not necessarily reflect CTC heterogeneity. Here we evaluated the epitope-independent Parsortix system which enriches CTCs based on size and rigidity using both healthy normal volunteer blood samples spiked with tumour cells and blood samples from patients with small cell lung cancer (SCLC). Blood samples were maintained unfractionated at room temperature for up to 4 days followed by plasma removal for circulating free DNA (cfDNA) isolation and direct application of the remaining cell component to the Parsortix system. For tumour cells expressing the EpCAM cell surface marker the numbers of spiked cells retained using the Parsortix system and by EpCAM-positive selection using CellSearch® were not significantly different, whereas only the Parsortix system showed strong enrichment of cells with undetectable EpCAM expression. In a pilot clinical study we banked both enriched CTCs as well as plasma from SCLC patient blood samples. Upon retrieval of the banked Parsortix cellular samples we could detect cytokeratin positive CTCs in all 12 SCLC patients tested. Interestingly, processing parallel samples from the same patients by EpCAM enrichment using CellSearch® revealed only 83% (10/12) with cytokeratin positive CTCs indicating the Parsortix system is enriching for EpCAM negative SCLC CTCs. Our combined results indicate the Parsortix system is a valuable tool for combined cfDNA isolation and CTC enrichment that enables CTC analysis to be extended beyond dependence on surface epitopes.
Divergent fates of von Willebrand factor and its propolypeptide (von Willebrand antigen II) after secretion from endothelial cells. (1987)

The intracellular site of cleavage of pro-von Willebrand factor subunit and the subsequent fate of the propolypeptide (von Willebrand antigen II) and of the mature von Willebrand factor (vWf) were investigated. Both the propolypeptide, which was found to be a homodimer of noncovalently linked subunits, and mature vWf were released from Weibel-Palade bodies of endothelial cells following stimulation with secretagogues. The stoichiometry of the two released proteins was essentially equimolar. This indicates that vWf and the propolypeptide were packaged into the Weibel-Palade bodies as one unit, pro-vWf, and that the proteolytic cleavage of pro-vWf is likely to be a post-Golgi event. The association of prosequences into dimers supports their hypothetical role in the multimerization process. After secretion, the two proteins were distributed differently, as based on the following observations. The propolypeptide did not associate with vWf in the culture medium, did not codistribute with vWf in the extracellular "patches of release" on stimulated endothelial cells, and was not detected in the endothelial cell extracellular matrix, which did contain vWf. Additionally, in contrast to vWf, the propolypeptide did not bind to the matrix of human foreskin fibroblasts. Since the propolypeptide does not associate with vWf and does not interact with extracellular matrices in vitro, it is highly unlikely that it would promote platelet adhesion to subendothelium in vivo.
Non‐viral vector‐mediated uptake, distribution, and stability of chimeraplasts in human airway epithelial cells (2002)

Both Cytofectin and PEI are efficient for chimeraplast nuclear uptake into airway epithelial cells. However, despite the distinct structures and trafficking pathways of the corresponding complexes, none of them could prevent nuclease-mediated metabolism of the chimeric oligonucleotides. These findings should be taken into account for future investigations of chimeraplast-mediated gene repair in airway epithelial cells.
More marked stimulation by lithium than insulin of the glycogenic pathway in rat skeletal muscle. (1997)

Lithium's impact on glucose metabolism was compared with that of insulin in isolated rat soleus muscle. Lithium chloride (20 mmol/l) induced a 4.8-fold more pronounced increment over basal glycogen synthase activity than insulin (10 nmol/l) (nmol UDP-glucose into glycogen in synthase activity assay.g-1.min-1: lithium, +22.1 +/- 1.8 vs. insulin, +4.6 +/- 3.9; P < 0.01). In parallel, lithium was less efficient than insulin in stimulating glucose transport (counts per minute 2-deoxy-D-[3H]glucose.mg-1.h-1: lithium, +211 +/- 19 vs. insulin, +311 +/- 57; P < 0.05) and lactate release (mumol.g-1.h-1: lithium, +1.0 +/- 0.5 vs. insulin, +3.9 +/- 0.5; P < 0.01), and similar increments were induced in glycogen synthesis (mumol glucose into glycogen.g-1.h-1: lithium, +3.32 +/- 0.43 vs. insulin, +3.46 +/- 0.47; not significant). Full additivity of glycogenic effects and divergent dependency on phosphatidylinositol 3-kinase activation provided further evidence for different mechanisms of action. In muscle from insulin-resistant obese Zucker rats (fa/fa), failure of lithium to reverse deficits in glucose metabolism suggested a primary deficit in muscle glucose uptake rather than glycogen synthesis. Hence lithium distinctly stimulates glycogen synthase activity in skeletal muscle and may therefore be regarded as a candidate for the treatment of disorders associated with primary deficits in the glycogenic pathway.
Mesenchymal Stem Cell Graft Improves Recovery after Spinal Cord Injury in Adult Rats through Neurotrophic and Pro-Angiogenic Actions (2012)

Numerous strategies have been managed to improve functional recovery after spinal cord injury (SCI) but an optimal strategy doesn't exist yet. Actually, it is the complexity of the injured spinal cord pathophysiology that begets the multifactorial approaches assessed to favour tissue protection, axonal regrowth and functional recovery. In this context, it appears that mesenchymal stem cells (MSCs) could take an interesting part. The aim of this study is to graft MSCs after a spinal cord compression injury in adult rat to assess their effect on functional recovery and to highlight their mechanisms of action. We found that in intravenously grafted animals, MSCs induce, as early as 1 week after the graft, an improvement of their open field and grid navigation scores compared to control animals. At the histological analysis of their dissected spinal cord, no MSCs were found within the host despite their BrdU labelling performed before the graft, whatever the delay observed: 7, 14 or 21 days. However, a cytokine array performed on spinal cord extracts 3 days after MSC graft reveals a significant increase of NGF expression in the injured tissue. Also, a significant tissue sparing effect of MSC graft was observed. Finally, we also show that MSCs promote vascularisation, as the density of blood vessels within the lesioned area was higher in grafted rats. In conclusion, we bring here some new evidences that MSCs most likely act throughout their secretions and not via their own integration/differentiation within the host tissue.