gebhart/patrepeval huggingface dataset:
Dissecting the Role of the Extracellular Matrix in Heart Disease: Lessons from the Drosophila Genetic Model (2017)

The extracellular matrix (ECM) is a dynamic scaffold within organs and tissues that enables cell morphogenesis and provides structural support. Changes in the composition and organisation of the cardiac ECM are required for normal development. Congenital and age-related cardiac diseases can arise from mis-regulation of structural ECM proteins (Collagen, Laminin) or their receptors (Integrin). Key regulators of ECM turnover include matrix metalloproteinases (MMPs) and their inhibitors, tissue inhibitors of matrix metalloproteinases (TIMPs). MMP expression is increased in mice, pigs, and dogs with cardiomyopathy. The complexity and longevity of vertebrate animals makes a short-lived, genetically tractable model organism, such as <i>Drosophila melanogaster</i>, an attractive candidate for study. We survey ECM macromolecules and their role in heart development and growth, which are conserved between <i>Drosophila</i> and vertebrates, with focus upon the consequences of altered expression or distribution. The <i>Drosophila</i> heart resembles that of vertebrates during early development, and is amenable to in vivo analysis. Experimental manipulation of gene function in a tissue- or temporally-regulated manner can reveal the function of adhesion or ECM genes in the heart. Perturbation of the function of ECM proteins, or of the MMPs that facilitate ECM remodelling, induces cardiomyopathies in <i>Drosophila</i>, including cardiodilation, arrhythmia, and cardia bifida, that provide mechanistic insight into cardiac disease in mammals.
Application of laser scanning for the rapid and automated detection of bacteria in water samples (1999)

It is widely accepted that the heterotrophic plate count method may not support the growth of all viable bacteria which may be present within a water sample and that alternative procedures using 'viability markers' may yield additional information. In this study, ChemChrome B (CB), which is converted to a fluorescent product by esterase activity, was used to stain viable bacteria (captured by membrane filtration) from potable water samples. The labelled bacteria from each sample were subsequently enumerated using a novel laser scanning instrument (ChemScan). Analysis of 107 potable water samples using this procedure demonstrated the presence of a significantly greater number of bacteria than were detected by culture (z-test, P < 0.05). The mean number of bacteria isolated by culture on R2A agar incubated at 22 degrees C for 7 d was only 25.2% of the total number of viable bacteria detected using the CB/ChemScan viability assay. Further analysis of 81 water samples using a 5-cyano-2,3,4-tolyl-tetrazolium chloride (CTC) viability assay also demonstrated the presence of many viable bacteria which were not capable of growth under the culture conditions employed in this study. However, the results indicate that ChemChrome B has the ability to stain a significantly greater number of heterotrophs than CTC (z-test, P < 0.05). In contrast, six potable waters were identified in which the CTC viability assay resulted in counts greater than those obtained using CB. The ChemScan instrument was successfully used for rapid and accurate enumeration of labelled micro-organisms, allowing information on the total viable microbial load of a water sample to be determined within 1 h. Furthermore, the ChemScan system has the potential for use in detecting specific organisms labelled with fluorescently-labelled antibodies or nucleic acid probes.
Highly Efficient Ultracentrifugation-free Chromatographic Purification of Recombinant AAV Serotype 9 (2018)

Recombinant adeno-associated virus serotype 9 (rAAV9) can specifically transduce muscle and neuronal tissues; thus, rAAV9 can potentially be used in gene therapy. However, rAAV9 is the most challenging rAAV serotype to purify. Traditionally, rAAV9 has been purified by ultracentrifugation, which is not scalable. We recently described a chromatographic purification protocol for rAAV1; this protocol can achieve scalable purifications. In this study, we attempted to optimize this protocol for purifying rAAV9 preparations, and we developed a novel, effective method for high-yield purification of rAAV9 using quaternary ammonium anion exchangers and size-exclusion chromatography. The final purified rAAV9 contained mainly three capsid proteins, as observed by SDS-PAGE. Furthermore, negative-stain electron microscopy demonstrated that 96.1% ± 1.1% of rAAV9 particles carried the viral genome containing the EGFP transgene, indicating that impurities and empty capsids can be eliminated with our purification protocol. The final rAAV9 titer obtained by our protocol totaled 2.5 ± 0.4 × 10<sup>15</sup> viral genomes produced from ∼3.2 × 10<sup>9</sup> HEK293EB cells. We confirmed that our protocol can also be applied to purify other varied AAV genome constructs. Our protocol can scale up production of pure rAAV9, in compliance with current good manufacturing practice, for clinical applications in human gene therapy.
Highly Diastereoselective Synthesis of Homoallylic Alcohols Bearing Adjacent Quaternary Centers Using Substituted Allylic Zinc Reagents (2007)

Staring from readily available polysubstituted allylic chlorides, a range of polysubstituted allylic zinc chlorides were obtained using a LiCl-mediated zinc dust insertion in 55−84% yield. A highly diastereoselective synthesis of homoallylic alcohols bearing up to two adjacent quaternary centers was achieved using these polysubstituted allylic zinc reagents.
Role of phosphatidylinositol 3-kinase and Rab5 effectors in phagosomal biogenesis and mycobacterial phagosome maturation arrest (2001)

Phagosomal biogenesis is a fundamental biological process of particular significance for the function of phagocytic and antigen-presenting cells. The precise mechanisms governing maturation of phagosomes into phagolysosomes are not completely understood. Here, we applied the property of pathogenic mycobacteria to cause phagosome maturation arrest in infected macrophages as a tool to dissect critical steps in phagosomal biogenesis. We report the requirement for 3-phosphoinositides and acquisition of Rab5 effector early endosome autoantigen (EEA1) as essential molecular events necessary for phagosomal maturation. Unlike the model phagosomes containing latex beads, which transiently recruited EEA1, mycobacterial phagosomes excluded this regulator of vesicular trafficking that controls membrane tethering and fusion processes within the endosomal pathway and is recruited to endosomal membranes via binding to phosphatidylinositol 3-phosphate (PtdIns[3]P). Inhibitors of phosphatidylinositol 3'(OH)-kinase (PI-3K) activity diminished EEA1 recruitment to newly formed latex bead phagosomes and blocked phagosomal acquisition of late endocytic properties, indicating that generation of PtdIns(3)P plays a role in phagosomal maturation. Microinjection into macrophages of antibodies against EEA1 and the PI-3K hVPS34 reduced acquisition of late endocytic markers by latex bead phagosomes, demonstrating an essential role of these Rab5 effectors in phagosomal biogenesis. The mechanism of EEA1 exclusion from mycobacterial phagosomes was investigated using mycobacterial products. Coating of latex beads with the major mycobacterial cell envelope glycosylated phosphatidylinositol lipoarabinomannan isolated from the virulent Mycobacterium tuberculosis H37Rv, inhibited recruitment of EEA1 to latex bead phagosomes, and diminished their maturation. These findings define the generation of phosphatidylinositol 3-phosphate and EEA1 recruitment as: (a) important regulatory events in phagosomal maturation and (b) critical molecular targets affected by M. tuberculosis. This study also identifies mycobacterial phosphoinositides as products with specialized toxic properties, interfering with discrete trafficking stages in phagosomal maturation.
Carvedilol for Prevention of Restenosis After Directional Coronary Atherectomy (2000)

The maximum recommended daily dose of the antioxidant and beta-blocker carvedilol failed to reduce restenosis after successful atherectomy. These findings are in contrast to those of the Multivitamins and Probucol Trial, which raises doubts regarding the validity of the interpretation that restenosis reduction by probucol was via antioxidant effects. The relationship between antioxidant agents and restenosis remains to be elucidated.
ENZYMATIC DESTRUCTION of the ELASTIC LAMELLA AT the MOUTH of CEREBRAL BERRY ANEURYSM? (1976)

Destruction of the elastic tissue is probably an acquired lesion and is decisive for the appearance of cerebral arterial aneurysms at the sites of congenital media defects. the elastic component in the mouths of aneurysms has therefore been studied by electron microsocpy, using two new staining methods, i.e. ruthenium-red staining and prolonged osmium-tetroxide treatment. the hypertrophic, duplicated, elastic lamellae showed a disintegration of their luminal portions not earlier described. In close connection with the disintegrated portions, extracellular lysosome-like granules were observed. It is hypothesized that discharged leucocyte granules containing elastase help to destroy the elastic lamellae.
Adaptive Time Segment Analysis for Steady-State Visual Evoked Potential Based Brain–Computer Interfaces (2020)

The research in non-invasive Brain-Computer Interface (BCI) has led to significant improvements in the recent years for potential end users. However, the user experience and the BCI illiteracy problem remains challenging areas to address for obtaining robust and resilient clinical applications. In this study, we address the choice of the time segment for the detection of steady state visual evoked potential (SSVEP) detection. This problem has been widely addressed for the detection of event-related potentials compared to SSVEP based BCIs. The choice of this parameter is typically fixed and has a direct influence on both the detection accuracy and the information transfer rate. We propose to shift the problem of the time segment to the choice of the threshold for determining if a response has been properly detected. We consider two open-datasets for benchmarking the rationale of the approach. The results support the conclusion that an adaptive time segment for each trial, based on the selection of a threshold, can lead to a substantial higher ITR (86.92 bits/min), compared to the time segment chosen at the user (79.56 bits/min) or group level (73.78 bits/min). Finally, the results suggest that the threshold could be determined automatically in relation to the number of classes. Such an approach can leverage the literacy of SSVEP based BCI.
Local probing of thermal properties at submicron depths with megahertz photothermal vibrations (2003)

We demonstrate the imaging of buried features in a microstructure—a tiny hole in an aluminum thin film covered by a chromium layer—with nanometer lateral resolution using a transient temperature distribution restricted to within ∼0.5 μm of the sample surface. This is achieved by mapping photothermally induced megahertz surface vibrations in an atomic force microscope. Local thermal probing with megahertz-frequency thermal waves is thus shown to be a viable method for imaging subsurface thermal features at submicron depths.
Scalable Realization of Surface Code Quantum Memory by Applying Multi-Qubit Parity Detector Gates (2018)

We analytically designed the control bias pulses to realize new multi-qubit parity detector gates for 2-Dimensional (2D) array of superconducting flux qubits with non-tunable couplings. We designed two 5-qubit gates such that the middle qubit is the target qubit and all four coupled neighbors are the control qubits. These new gates detect the parity between two vertically/horizontally coupled neighbor qubits while cancelling out the coupling effect of horizontally/vertically coupled neighbor qubits. For a 3 by 3 array of 9 qubits with non-tunable couplings, we simulated the effect of our new 5-qubit horizontal and vertical parity detector gates. We achieved the intrinsic fidelity of 99.9% for horizontal and vertical parity detector gates. In this paper we realize Surface Code memories based on the multi-qubit parity detector gates for nearest neighbor superconducting flux qubits with and without tunable couplings. However, our scheme is applicable to other superconducting qubits as well. In our proposed memory realization, error correction cycles can be performed in parallel on several logical qubits or even on the entire 2D array of qubits, this makes it a desirable candidate for large scale and longtime quantum computation. In addition to extensive reduction of the number of control parameters in our method, the error correction cycle time is reduced and does not grow by increasing the number of qubits in the logical qubit layout. Another advantage of this approach is that there will not be any dephasing from idle qubits since all the qubits are used in the error correction cycles.
A new edge detection algorithm in image processing based on LIP-ratio approach (2009)

In this paper, we propose a new edge detection method that combines the concepts of Logarithmic Image Processing (LIP) and gray level ratio operations. The presented method provides a new approach in edge detection where edges are detected at different ratios of gray levels independently. The proposed method detects edge details based on the band of gray levels ratio of interest that these details lie within, while current edge detection algorithms control such edge details by threshold variations. In the proposed algorithm, variations of some introduced constant value introduce different edge details and not necessarily more or less details. Extensive simulations demonstrate that this method produces competitive results by suppressing impulsive noise, the ability to trace the development of certain object structures, and segmenting objects that belong to a certain area of interest.
Microxine, a New cdc2 Kinase Inhibitor from the Australian Marine Sponge <i>Microxina</i> Species (2001)

A new purine derivative microxine (1) was isolated from the Australian marine sponge Microxina sp. The compound was isolated via reversed-phase chromatography and its structure determined spectroscopically. Microxine was found to weakly inhibit cdc2 kinase activity with an IC(50) of 13 microM.
Study of the dominant luminescence mechanism in InGaN∕GaN multiple quantum wells comprised of ultrasmall InGaN quasiquantum dots (2005)

High quality green (508nm) and blue (424nm) light emitting diodes (LEDs) from InGaN∕GaN multiple quantum wells with stable ultrasmall indium-rich clusters of 2nm and 3nm from two different nominal indium contents have been grown by metalorganic chemical vapor deposition. Comprehensive calculations including polarization, piezoelectric field, and size effect help derive an indium composition of 59% and 31% for the In-rich clusters of 2nm and 3nm, which agrees amazingly well with the asymmetric phase diagram for phase separation. From this model, we can further demonstrate that the dominant emitting mechanism for green LED is the polarization field, however, for blue LED, both the size effect and polarization effect are equally important.
Characterization of two cDNAs (ERD11 and ERD13) for dehydration‐inducible genes that encode putative glutathione <i>S</i>‐transferases in <i>Arabidopsis thaliana</i> L (1993)

Two cDNA clones, designated ERD11 and ERD13, isolated from a cDNA library from Arabidopsis thaliana L. plants dehydrated for 1 h were sequenced and characterized. These clones encoded polypeptides that were homologous to glutathione S-transferases of tobacco and maize. Genomic Southern hybridization suggested that there are a few additional genes showing high similarity to the ERD11 gene in the Arabidopsis genome. The expression of the genes for ERD11 and ERD13 was induced by dehydration, but was not affected by the application of four plant growth regulators, 2,4-dichlorophenoxyacetic acid 6-benzylaminopurine, abscisic acid, or gibberellic acid.
Footprints of the sun: memory of UV and light stress in plants (2014)

Sunlight provides the necessary energy for plant growth via photosynthesis but high light and particular its integral ultraviolet (UV) part causes stress potentially leading to serious damage to DNA, proteins, and other cellular components. Plants show adaptation to environmental stresses, sometimes referred to as "plant memory." There is growing evidence that plants memorize exposure to biotic or abiotic stresses through epigenetic mechanisms at the cellular level. UV target genes such as CHALCONE SYNTHASE (CHS) respond immediately to UV treatment and studies of the recently identified UV-B receptor UV RESISTANCE LOCUS 8 (UVR8) confirm the expedite nature of UV signaling. Considering these findings, an UV memory seems redundant. However, several lines of evidence suggest that plants may develop an epigenetic memory of UV and light stress, but in comparison to other abiotic stresses there has been relatively little investigation. Here we summarize the state of knowledge about acclimation and adaptation of plants to UV light and discuss the possibility of chromatin based epigenetic memory.
Promoter Specificity and Biological Activity of Tethered AP-1 Dimers (2002)

Activator protein 1 (AP-1) is a group of dimeric transcription factors composed of Jun, Fos, and ATF family proteins. Both gain- and loss-of-function studies have revealed specific roles for individual AP-1 components in cell proliferation, differentiation, apoptosis, and other biological processes. However, little is known about the functions of specific AP-1 dimers. To test the importance of AP-1 composition in transcriptional activation, AP-1 monomers were joined via a flexible polypeptide tether to force specific pairing. The resultant single-chain AP-1 molecules showed DNA binding specificity and transcriptional activation potentials similar to those of untethered dimers, even in the presence of dominant-negative AP-1 monomers. c-Jun-containing dimers showed distinct promoter specificity in transient-transfection experiments, depending on the Fos, Fra, or ATF partner. When stably expressed in NIH 3T3 cells, c-Jun tethered dimer Fra2, but not c-Jun tethered dimer Fra1 and c-Jun tethered dimer cFos (the tilde indicates a tethered dimer), inhibited G(0) arrest at confluency and under low-serum conditions and specifically activated cyclin A expression. These data suggest that the choice of dimerization partner defines the role of c-Jun in gene activation and cell cycle regulation and that single-chain AP-1 molecules provide a powerful tool for assessing the role of specific AP-1 dimers.
Poly (acetyl, arginyl) glucosamine disrupts Pseudomonas aeruginosa biofilms and enhances bacterial clearance in a rat lung infection model (2022)

<i>Pseudomonas aeruginosa</i> is a common opportunistic pathogen that can cause chronic infections in multiple disease states, including respiratory infections in patients with cystic fibrosis (CF) and non-CF bronchiectasis. Like many opportunists, <i>P. aeruginosa</i> forms multicellular biofilm communities that are widely thought to be an important determinant of bacterial persistence and resistance to antimicrobials and host immune effectors during chronic/recurrent infections. Poly (acetyl, arginyl) glucosamine (PAAG) is a glycopolymer that has antimicrobial activity against a broad range of bacterial species, and also has mucolytic activity, which can normalize the rheological properties of cystic fibrosis mucus. In this study, we sought to evaluate the effect of PAAG on <i>P. aeruginosa</i> bacteria within biofilms <i>in vitro</i>, and in the context of experimental pulmonary infection in a rodent infection model. PAAG treatment caused significant bactericidal activity against <i>P. aeruginosa</i> biofilms, and a reduction in the total biomass of preformed <i>P. aeruginosa</i> biofilms on abiotic surfaces, as well as on the surface of immortalized cystic fibrosis human bronchial epithelial cells. Studies of membrane integrity indicated that PAAG causes changes to <i>P. aeruginosa</i> cell morphology and dysregulates membrane polarity. PAAG treatment reduced infection and consequent tissue inflammation in experimental <i>P. aeruginosa</i> rat infections. Based on these findings we conclude that PAAG represents a novel means to combat <i>P. aeruginosa</i> infection, and may warrant further evaluation as a therapeutic.
Incorporation of Disulfide Containing Protein Modules into Multivalent Antigenic Conjugates: Generation of Antibodies against the Thrombin-Sensitive Region of Murine Protein S (2012)

Antigenic peptide conjugates can be used as vaccines and for the production of antibodies for clinical and research use. A method is presented here for the construction of conjugates incorporating oxidatively folded protein domains in their native conformation. This method was used to prepare multiple antigenic peptide constructs of the thrombin-sensitive loop region of murine anticoagulant protein S.
TEST AND ANALYSIS ON THE MECHANICAL PROPERTIES OF CASSAVA STALKS (2015)

The mechanical properties of the cassava stalk play an important role in the design of cassava harvesting and cassava stalk recycling machines. Axial and radial compression tests with different loading rates were conducted on 3 groups of cassava stalks with 5 moisture contents in 3 stalk levels at the harvest time. Slidin g cutting tests as well as cutting tests with different loading rates and cutting angles were conducted on 5 groups of root samples of cassava stalks having 5 moisture contents at harvest time. The overall failure loads and the strengths of the cassava sta lks were analyzed with respect to the different factors under investigation in this study using SAS software. The following results were obtained: in the axial compression of the stalks, the average values of the failure load and compressive strength were respectively for different levels 2187.28N and 10.65MPa (the upper), 3867.63N and 11.97MPa (the middle) and 5892.03N and 12.81MPa (the lower); in the radial compression of the stalks, the average values of the failure load and compressive strength were respectively for different levels 345.40N and 1.24MPa (the upper), 542.90N and 1.19MPa (the middle) as well as 662.97N and 1.09MPa (the lower). For the sliding cutting, the range of the failure load was between 241.22~1150.32 N with an average value of 662.30 N and the range of the strength was between 1.55~7.51MPa with an average value of 4.20MPa. For the cutting, the range of failure load was between 261.84~1235.64 N with an average value of 649.24N and the range of the strength was between 1.12~4.99MPa with an average value of 2.17MPa. The ANOVA results showed that the impacts of the moisture content and the stalk levels on the axial compressive strength were significant (P 0.05). The sliding cutting angle and loading rates respectively had a significant and a highly significant impact on the sliding cutting strength (P<0.05), as well as the moisture content, cutting angle and loading rate were significant to the cutting strength (P<0.05).