gebhart/patrepeval huggingface dataset:
Matrigel: A complex protein mixture required for optimal growth of cell culture (2010)

Numerous cell types require a surface for attachment to grow and proliferate. Certain cells, particularly primary and stem cells, necessitate the use of specialized growth matrices along with specific culture media conditions to maintain the cells in an undifferentiated state. A gelatinous protein mixture derived from mouse tumor cells and commercialized as Matrigel is commonly used as a basement membrane matrix for stem cells because it retains the stem cells in an undifferentiated state. However, Matrigel is not a well-defined matrix, and therefore can produce a source of variability in experimental results. In this study, we present an in-depth proteomic analysis of Matrigel using a dynamic iterative exclusion method coupled with fractionation protocols that involve ammonium sulfate precipitation, size exclusion chromatography, and one-dimensional SDS-PAGE. The ability to identify the low mass and abundance components of Matrigel illustrates the utility of this method for the analysis of the extracellular matrix, as well as the complexity of the matrix itself.
Mesenchymal stem cell intracellular labeling using silica-coated superparamagnetic iron oxide nanoparticles with amine functional peripheries (2008)

Two types of superparamagnetic iron oxide nanoparticles designed for mesenchymal stem cell labeling and magnetic resonance imaging in vivo tracking were constructed in our laboratories. Both types of nanoparticles have an iron oxide core and a thin layer of silica coating, one of them has additional surface modification with amine. The overall particle size was around 8 nanometers. The in vitro study results demonstrated that, without the application of a transfection agent, both nanoparticles could be incorporated into bone marrow derived mesenchymal stem cells and located in lysosomes. Surface modification with amine significantly increased mesenchymal stem cell labeling efficiency, leading to an increased magnetic resonance imaging detection sensitivity of 2-5 folds.
A Bayesian Hierarchical Model for Learning Natural Scene Categories (2005)

We propose a novel approach to learn and recognize natural scene categories. Unlike previous work, it does not require experts to annotate the training set. We represent the image of a scene by a collection of local regions, denoted as codewords obtained by unsupervised learning. Each region is represented as part of a "theme". In previous work, such themes were learnt from hand-annotations of experts, while our method learns the theme distributions as well as the codewords distribution over the themes without supervision. We report satisfactory categorization performances on a large set of 13 categories of complex scenes.
Isolation and physical mapping of nitrogen fixation genes from the cyanobacterium Anabaena 7120. (1982)

DNA restriction fragments containing nitrogen fixation (nifi genes of the cyanobacterium Anabaena 7120 were isolated as inserts in bacteriophage X, using plasmids containing Klebsiella pneumoniae nif genes as heterologous hybridization probes.Four contiguous E m RI fragments, comprising a 39-kilobase pair segment of the Anabaena chromosome, were physically mapped and those regions homologous to IL pneumoniae nif genes were identified by Southern hybridization and by electron microscope examination of heteroduplex DNA molecules.Regions of Anabaena DNA were found homologous to the following K. pneumoniae nif genes: nif H, the structural gene for nitrogenase reductase; nif D and nif K, the structural genes for the two subunits of nitrogenase; and either nif V or nif S, genes whose products are required for the maturation of nitrogenase.The four Anabaena nif genes so identified are transcribed in the same direction, as is the case in K. pneumoniae.However, the genes are rearranged with respect to the map of K. pneumoniae.In K. pneumoniae, nif H, nif D, and nif K are adjacent and cotranscribed.In Anabaena, nif H and nif D are adjacent but nif K is separated from nif D by 11 kilobase pairs of DNA.In K.pneumoniae, the nif V-nif S genes are to the left of the nif HDK cluster, while in Anabaena, the homologous region is to the right of the nif H gene. Hybridization of labeled subclones of Anabaena DNA to filter-bound RNA prepared from cells induced for nitrogenase indicated that most of the 11 kilobase pairs between nif K and nif D are not transcribed, while fragments containing the identified nif genes are transcribed abundantly.An additional fragment of Anabaena 7120 DNA was isolated, in recombinant X, which is apparently unlinked to the 39-kilobase pair region described above.This fragment contains a region homologous to K. pneumoniae nif H, but not to nif D. The restriction map of the nif H-homologous region of this Anabaena fragment is different from that of the nif H gene described above.
Plasmids of corynebacteria (1999)

Corynebacteria are pleomorphic, asporogenous, Gram-positive bacteria. Included in this group are nonpathogenic soil corynebacteria, which are widely used for the industrial production of amino acids and detergents, and in biotransformation of steroids. Other members of this group are plant and animal pathogens. This review summarizes the current information available about the plasmids of corynebacteria. The emphasis is mainly on the small plasmids, which have been used for construction of vectors for expression of genes in these bacteria. Moreover, considerable information is now available on their nucleotide sequence, gene organization and modes of replication, which would make it possible to further manipulate these plasmids. Other plasmid properties, such as incompatibility and host range, are also discussed. Finally, use of these plasmids as cloning vectors for the expression of heterologous proteins using corynebacteria as hosts is also summarized to highlight the potential of these bacteria as hosts for recombinant DNA.
ZnO and ε-Zn(OH)2 Composite Nanoparticles by Pulsed Laser Ablation on Zn in Water (2010)

Wurtzite-type (W)-ZnO and ε-Zn(OH)2 composite nanoparticles following a specific crystallographic relationship (0001)W//(010)ε; [112̅0]W//[100]ε were fabricated by pulsed laser ablation on a Zn target in water and then characterized by analytical electron microscopy. The composite nanoparticles are platy and equiaxed in shape when fabricated by a peak power density of 1.7 × 1011 W/cm2 (1064 nm excitation) and 8.3 × 1010 W/cm2 (532 nm excitation), respectively. The W-ZnO nanoplates showed well-developed (0001) terraces for mutual coalescence and {101̅0} and {112̅0} edges for lateral growth. The W-ZnO and ε-Zn(OH)2 composite nanocondensates have an internal compressive stress up to ca. 0.7 GPa and a minimum band gap of ∼3.1 eV for potential optoelectronic applications in water environment.
Mass Spectrometry of Large, Fragile, and Involatile Molecules (1982)

Desorption ionization makes it possible to obtain mass spectra of molecules whose vaporization by heating may lead to thermal degradation. Several methods are in use, but in general desorption is achieved by particle or photon bombardment of the sample and the mass spectra obtained by different methods are fundamentally similar. Desorption ionization techniques have been used to obtain mass spectra of biomolecules, including peptides, antibiotics, and oligosaccharides, for which normal mass spectral methods have been of limited power. Several examples are given of recent applications of these new techniques, and prospects for their further evolution are discussed.
Molecular Features of Hormone-Refractory Prostate Cancer Cells by Genome-Wide Gene Expression Profiles (2007)

One of the most critical issues in prostate cancer clinic is emerging hormone-refractory prostate cancers (HRPCs) and their management. Prostate cancer is usually androgen dependent and responds well to androgen ablation therapy. However, at a certain stage, they eventually acquire androgen-independent and more aggressive phenotype and show poor response to any anticancer therapies. To characterize the molecular features of clinical HRPCs, we analyzed gene expression profiles of 25 clinical HRPCs and 10 hormone-sensitive prostate cancers (HSPCs) by genome-wide cDNA microarrays combining with laser microbeam microdissection. An unsupervised hierarchical clustering analysis clearly distinguished expression patterns of HRPC cells from those of HSPC cells. In addition, primary and metastatic HRPCs from three patients were closely clustered regardless of metastatic organs. A supervised analysis and permutation test identified 36 up-regulated genes and 70 down-regulated genes in HRPCs compared with HSPCs (average fold difference > 1.5; P < 0.0001). We observed overexpression of AR, ANLN, and SNRPE and down-regulation of NR4A1, CYP27A1, and HLA-A antigen in HRPC progression. AR overexpression is likely to play a central role of hormone-refractory phenotype, and other genes we identified were considered to be related to more aggressive phenotype of clinical HRPCs, and in fact, knockdown of these overexpressing genes by small interfering RNA resulted in drastic attenuation of prostate cancer cell viability. Our microarray analysis of HRPC cells should provide useful information to understand the molecular mechanism of HRPC progression and to identify molecular targets for development of HRPC treatment.
Preparation of cell suspensions (2000)

Systematic experiments were performed to examine the inhibitory effects of oxygen on perchlorate reduction and to identify the components and branches in the electron transport chains involved in perchlorate reduction and aerobic respiration by Dechlorosoma sp. KJ (ATCC strain BAA-592). To investigate the effect of dissolved oxygen (DO) on perchlorate reduction, anaerobically grown cultures of Dechlorosoma sp. KJ were exposed to near-saturated concentration of DO for various periods of time. It was determined that cells exposed to oxygen for more than 12 hours were incapable of reducing perchlorate. It was determined that cells exposed to oxygen for more than 12 hours were incapable of reducing perchlorate. Cells exposed to oxygen for less than 12 hours, when re-introduced to anoxic conditions, quickly reduced the redox potential to highly negative values (-127 mV to -337 mV) and were able to reduce perchlorate or chlorite.
Interaction of the E1A Oncoprotein with Yak1p, a Novel Regulator of Yeast Pseudohyphal Differentiation, and Related Mammalian Kinases (2001)

The C-terminal portion of adenovirus E1A suppresses ras-induced metastasis and tumorigenicity in mammalian cells; however, little is known about the mechanisms by which this occurs. In the simple eukaryote Saccharomyces cerevisiae, Ras2p, the homolog of mammalian h-ras, regulates mitogen-activated protein kinase (MAPK) and cyclic AMP-dependent protein kinase A (cAMP/PKA) signaling pathways to control differentiation from the yeast form to the pseudohyphal form. When expressed in yeast, the C-terminal region of E1A induced pseudohyphal differentiation, and this was independent of both the MAPK and cAMP/PKA signaling pathways. Using the yeast two-hybrid system, we identified an interaction between the C-terminal region of E1A and Yak1p, a yeast dual-specificity serine/threonine protein kinase that functions as a negative regulator of growth. E1A also physically interacts with Dyrk1A and Dyrk1B, two mammalian homologs of Yak1p, and stimulates their kinase activity in vitro. We further demonstrate that Yak1p is required in yeast to mediate pseudohyphal differentiation induced by Ras2p-regulated signaling pathways. However, pseudohyphal differentiation induced by the C-terminal region of E1A is largely independent of Yak1p. These data suggest that mammalian Yak1p-related kinases may be targeted by the E1A oncogene to modulate cell growth.
Comparison between intermittent intravenous analgesia and intermittent paravertebral subpleural analgesia for pain relief after thoracotomy (2011)

The patients undergoing lung resection through a thoracotomy were observed with reduced postoperative pain and better surgical outcomes with respect to the length of hospital stay, postoperative forced expiratory volume in the first second, pulmonary complications, and need for bronchoscopic management, when paravertebral subpleural analgesia was induced by morphine.
Glucose-induced transcription of the insulin gene is mediated by factors required for beta-cell-type-specific expression. (1994)

The insulin gene is expressed exclusively in pancreatic islet beta cells. The principal regulator of insulin gene transcription in the islet is the concentration of circulating glucose. Previous studies have demonstrated that transcription is regulated by the binding of trans-acting factors to specific cis-acting sequences within the 5'-flanking region of the insulin gene. To identify the cis-acting control elements within the rat insulin II gene that are responsible for regulating glucose-stimulated expression in the beta cell, we analyzed the effect of glucose on the in vivo expression of a series of transfected 5'-flanking deletion mutant constructs. We demonstrate that glucose-induced transcription of the rat insulin II gene is mediated by sequences located between -126 and -91 bp relative to the transcription start site. This region contains two cis-acting elements that are essential for directing pancreatic beta-cell-type-specific expression of the rat insulin II gene, the insulin control element (ICE; -100 to -91 bp) and RIPE3b1 (-115 to -107 bp). The gel mobility shift assay was used to determine whether the formation of the ICE- and RIPE3b1-specific factor-DNA element complexes were affected in glucose-treated beta-cell extracts. We found that RIPE3b1 binding activity was selectively induced by about eightfold. In contrast, binding to other insulin cis-acting element sequences like the ICE and RIPE3a2 (-108 to -99 bp) were unaffected by these conditions. The RIPE3b1 binding complex was shown to be distinct from the glucose-inducible factor that binds to an element located between -227 to -206 bp of the human and rat insulin I genes (D. Melloul, Y. Ben-Neriah, and E. Cerasi, Proc. Natl. Acad. Sci. USA 90:3865-3869, 1993). We have also shown that mannose, a sugar that can be metabolized by the beta cell, mimics the effects of glucose in the in vivo transfection assays and the in vitro RIPE3b1 binding assays. These results suggested that the RIPE3b1 transcription factor is a primary regulator of glucose-mediated transcription of the insulin gene. However, we found that mutations in either the ICE or the RIPE3b1 element reduced glucose-responsive expression from transfected 5'-flanking rat insulin II gene constructs. We therefore conclude that glucose-regulated transcription of the insulin gene is mediated by cis-acting elements required for beta-cell-type-specific expression.
Molecular cloning and characterisation of a novel putative protein‐serine kinase related to the cAMP‐dependent and protein kinase C families (1991)

Highly degenerate oligonucleotide primers designed from regions conserved between protein-serine kinases have been used specifically to amplify human epithelial (HeLa) cDNA by the polymerase chain reaction (PCR). Of several novel cDNA fragments encoding putative kinases thus isolated, one was further characterised. Screening of human fibroblast and bovine brain cDNA libraries with the PCR fragment yielded several clones with an open reading frame of 479 amino acids containing all of the conserved sequence motifs of protein-serine kinases. The predicted protein was most similar to the protein kinase C (PKC)/cAMP-dependent protein kinase (PKA) families and its gene has thus been termed pkb. Expression of the pkb gene is general but highest in brain, heart and lung. Translation of pkb RNA in vitro generated a 57-kDa protein (PKB) recognised by antisera raised to a bacterially expressed PKB/TrpE fusion protein. Transfection of COS cells with the kinase cDNA resulted in the synthesis of a 60-kDa protein which was partially purified by Mono Q anion-exchange chromatography. Column fractions containing PKB-immunoreactive protein exhibited elevated histone H1 kinase activity compared with similar fractions from control cells, demonstrating the enzymatic activity of this protein kinase.
Active Control of Wall Acoustic Impedance (1999)

A novel kind of acoustic liner with controllable impedance is proposed. A set of active control systems has been designed for this kind of liner to control the sound absorption coefficient or the impedance of the liner. The control is achieved by adjusting the liner cavity depth and bias flow rate through the perforated plate of the liner. The theory needed to assess the details of this idea is described. Results also are provided of control experiments in which the sound absorption coefficient of the liner is controlled to remain optimal for any external sound source condition or the impedance is controlled to satisfy a specific impedance condition. When compared with existing methods for the active control of sound propagation with loudspeakers as the actuators, active control of acoustic impedance might lead to a new concept for the control of sound propagation and unsteady flow in turbomachinery. The present experiments show the possibility of using this kind of liner to realize these objectives.
Study of Transmembrane Potentials of Inner and Outer Membranes Induced by Pulsed-Electric-Field Model and Simulation (2007)

A more proper and realistic multilayer dielectric model of spherical biological cell, in which nuclear was taken into consideration, was proposed based on the classic dielectric model in this paper. The general analytical method was also deduced and analyzed in detail in calculating the time courses of transmembrane potentials of both inner and outer membranes induced by constant and time-varying electric field. The time course of transmembrane potential of the outer membrane for multilayer dielectric model was compared to that of the classical model. It is shown that the latter is larger than the former, particularly for a cell with larger nuclear. The time courses of transmembrane potentials of both inner and outer membranes induced by pulsed electric fields (PEFs) with different durations were also studied based on the multilayer dielectric model. Long PEF targets outer membrane mainly, and there is little influence to cell nucleus, mitochondrion, and other organelles; thus, it causes electroporation to the outer membrane. As the pulse duration decreases, the electroporation effect changes gradually from the outer membrane to intracellular organelle membrane. Ultrashort PEF (tens of nanoseconds) induces larger voltage across the inner membrane and acts mostly on intracellular substructures. However, submicrosecond PEF (several hundreds of nanoseconds) can induce significant voltages across both the inner and outer membranes, therefore, causing damage to both the inner and outer membranes. This property of submicrosecond PEF has much practical value for tumor treatment.
Promoting neurite outgrowth from spiral ganglion neuron explants using polypyrrole/BDNF‐coated electrodes (2008)

Release of neurotrophin-3 (NT3) and brain-derived neurotrophic factor (BDNF) from hair cells in the cochlea is essential for the survival of spiral ganglion neurons (SGNs). Loss of hair cells associated with a sensorineural hearing loss therefore results in degeneration of SGNs, potentially reducing the performance of a cochlear implant. Exogenous replacement of either or both neurotrophins protects SGNs from degeneration after deafness. We previously incorporated NT3 into the conducting polymer polypyrrole (Ppy) synthesized with para-toluene sulfonate (pTS) to investigate whether Ppy/pTS/NT3-coated cochlear implant electrodes could provide both neurotrophic support and electrical stimulation for SGNs. Enhanced and controlled release of NT3 was achieved when Ppy/pTS/NT3-coated electrodes were subjected to electrical stimulation. Here we describe the release dynamics and biological properties of Ppy/pTS with incorporated BDNF. Release studies demonstrated slow passive diffusion of BDNF from Ppy/pTS/BDNF, with electrical stimulation significantly enhancing BDNF release over 7 days. A 3-day SGN explant assay found that neurite outgrowth from explants was 12.3-fold greater when polymers contained BDNF (p < 0.001), although electrical stimulation did not increase neurite outgrowth further. The versatility of Ppy to store and release neurotrophins, conduct electrical charge, and act as a substrate for nerve-electrode interactions is discussed for specialized applications such as cochlear implants.
Modulated wideband converter with non-ideal lowpass filters (2010)

We investigate the impact of using non-ideal lowpass filters in the modulated wideband (MWC) converter, which is a recent sub-Nyquist sampling system for sparse wideband analog signals. We begin by deriving a perfect reconstruction condition for general lowpass filters, which coincides with the well-known Nyquist inter-symbol interference (ISI) criterion in communication theory. Then, we propose to compensate for the non-ideal lowpass filters using a digital FIR correction scheme. The proposed solution is validated by experimental results.
Mineral Dissolution and Precipitation Kinetics:: Macroscopic, Microscopic and Nanoscopic Techniques (2011)

espanolVision general sobre el conocimiento de la cinetica de disolucion y precipitacion de minerales adquirido en los ultimos veinte anos a partir de estudios en los que el autor ha participado EnglishIn this communication I comment on the studies in which I participated in the last two decades, covering the science of mineral dissolution/precipitation kinetics. The objective is to give a brief overview of the acquired knowledge about kinetics of complex processes, emphasizing on the various experimental approaches and methodologies utilized for this investigation.
Mouse Models of Multiple Sclerosis: Experimental Autoimmune Encephalomyelitis and Theiler’s Virus-Induced Demyelinating Disease (2012)

Experimental autoimmune encephalomyelitis (EAE) and Theiler's Murine Encephalitis Virus-Induced Demyelinating Disease (TMEV-IDD) are two clinically relevant murine models of multiple sclerosis (MS). Like MS, both are characterized by mononuclear cell infiltration into the CNS and demyelination. EAE is induced by either the administration of myelin protein or peptide in adjuvant or by the adoptive transfer of encephalitogenic T cell blasts into naïve recipients. The relative merits of each of these protocols are compared. Depending on the type of question being asked, different mouse strains and peptides are used. Different disease courses are observed with different strains and different peptides in active EAE. These variations are also addressed. Additionally, issues relevant to clinical grading of EAE in mice are discussed. In addition to EAE induction, useful references for other disease indicators such as DTH, in vitro proliferation, and immunohistochemistry are provided. TMEV-IDD is a useful model for understanding the possible viral etiology of MS. This section provides detailed information on the preparation of viral stocks and subsequent intracerebral infection of mice. Additionally, virus plaque assay and clinical disease assessment are discussed. Recently, recombinant TMEV strains have been created for the study of molecular mimicry which incorporate various 30 amino acid myelin epitopes within the leader region of TMEV.