gebhart/patrepeval huggingface dataset:
Injury Leads to the Appearance of Cells with Characteristics of Both Microglia and Astrocytes in Mouse and Human Brain (2017)

Microglia and astrocytes have been considered until now as cells with very distinct identities. Here, we assessed the heterogeneity within microglia/monocyte cell population in mouse hippocampus and determined their response to injury, by using single-cell gene expression profiling of cells isolated from uninjured and deafferented hippocampus. We found that in individual cells, microglial markers Cx3cr1, Aif1, Itgam, and Cd68 were co-expressed. Interestingly, injury led to the co-expression of the astrocyte marker Gfap in a subpopulation of Cx3cr1-expressing cells from both the injured and contralesional hippocampus. Cells co-expressing astrocyte and microglia markers were also detected in the in vitro LPS activation/injury model and in sections from human brain affected by stroke, Alzheimer's disease, and Lewy body dementia. Our findings indicate that injury and chronic neurodegeneration lead to the appearance of cells that share molecular characteristics of both microglia and astrocytes, 2 cell types with distinct embryologic origin and function.
Plaque‐associated disruption of CSF and plasma amyloid‐β (Aβ) equilibrium in a mouse model of Alzheimer's disease (2002)

To better understand amyloid-beta (Abeta) metabolism in vivo, we assessed the concentration of Abeta in the CSF and plasma of APP(V717F) (PDAPP) transgenic mice, a model that develops age-dependent Alzheimer's disease (AD)-like pathology. In 3-month-old mice, prior to the development of Abeta deposition in the brain, there was a highly significant correlation between Abeta levels in CSF and plasma. In 9-month-old-mice, an age at which some but not all mice have developed Abeta deposition, there was also a significant correlation between CSF and plasma Abeta; however, the correlation was not as strong as that present in young mice. In further exploring CSF and plasma Abeta levels in 9-month-old mice, levels of CSF Abeta were found to correlate highly with Abeta burden. Analysis of the CSF: plasma Abeta ratio revealed a selective two-fold increase in plaque versus non-plaque bearing mice, strongly suggesting a plaque-mediated sequestration of soluble Abeta in brain. Interestingly, in 9-month-old mice, a significant correlation between CNS and plasma Abeta was limited to mice lacking Abeta deposition. These findings suggest that there is a dynamic equilibrium between CNS and plasma Abeta, and that plaques create a new equilibrium because soluble CNS Abeta not only enters the plasma but also deposits onto amyloid plaques in the CNS.
A Convenient One-Step, High-Yield Preparation of Methylphosphonyl Dichloride from Dimethyl Methylphosphonate (1974)

Abstract Based on a 1H and 31P nmr study of the interactions of alkyl-phosphonyl dichlorides, RP(O)Cl2, with dialkyl alkylphosphonates, RP(O)(OR)2, a method was developed for the preparation of CH3P(O)Cl2 (R [dbnd] CH3) in 98% yield. This method consists of the slow addition of the phosphonate to an excess of refluxing SOCl2, thus suppressing irreversible side reactions. For R [dbnd] C2H5, a yield of 72% was achieved; for R [dbnd] C4H9 and ClCH2CH2 pure product could not be isolated.
Cationic Polymer Nanoparticles and Nanogels: From Synthesis to Biotechnological Applications (2013)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTCationic Polymer Nanoparticles and Nanogels: From Synthesis to Biotechnological ApplicationsJose Ramos†, Jacqueline Forcada*†, and Roque Hidalgo-Alvarez*‡View Author Information† POLYMAT, Bionanoparticles Group, Departamento de Química Aplicada, UFI 11/56, Facultad de Ciencias Químicas, Universidad del País Vasco UPV/EHU, Apdo. 1072, 20080 Donostia-San Sebastián, Spain‡ Grupo de Física de Fluidos y Biocoloides, Departamento de Física Aplicada, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain*E-mail: [email protected]*E-mail: [email protected]Cite this: Chem. Rev. 2014, 114, 1, 367–428Publication Date (Web):September 5, 2013Publication History Received2 July 2012Published online5 September 2013Published inissue 8 January 2014https://pubs.acs.org/doi/10.1021/cr3002643https://doi.org/10.1021/cr3002643review-articleACS PublicationsCopyright © 2013 American Chemical SocietyRequest reuse permissionsArticle Views11313Altmetric-Citations155LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Colloidal particles,Nanogels,Nanoparticles,Polymer particles,Radical polymerization Get e-Alerts
Comprehensive MicroRNA Profiling Reveals a Unique Human Embryonic Stem Cell Signature Dominated by a Single Seed Sequence (2008)

Embryonic stem cells are unique among cultured cells in their ability to self-renew and differentiate into a wide diversity of cell types, suggesting that a specific molecular control network underlies these features. Human embryonic stem cells (hESCs) are known to have distinct mRNA expression, global DNA methylation, and chromatin profiles, but the involvement of high-level regulators, such as microRNAs (miRNA), in the hESC-specific molecular network is poorly understood. We report that global miRNA expression profiling of hESCs and a variety of stem cell and differentiated cell types using a novel microarray platform revealed a unique set of miRNAs differentially regulated in hESCs, including numerous miRNAs not previously linked to hESCs. These hESC-associated miRNAs were more likely to be located in large genomic clusters, and less likely to be located in introns of coding genes. hESCs had higher expression of oncogenic miRNAs and lower expression of tumor suppressor miRNAs than the other cell types. Many miRNAs upregulated in hESCs share a common consensus seed sequence, suggesting that there is cooperative regulation of a critical set of target miRNAs. We propose that miRNAs are coordinately controlled in hESCs, and are key regulators of pluripotence and differentiation. Disclosure of potential conflicts of interest is found at the end of this article.
Clinical applications of nucleic acid aptamers in cancer (2014)

Nucleic acid aptamers are small single-stranded DNA or RNA oligonucleotide segments, which bind to their targets with high affinity and specificity via unique three-dimensional structures. Aptamers are generated by an iterative <i>in vitro</i> selection process, termed as systematic evolution of ligands by exponential enrichment. Owing to their specificity, non-immunogenicity, non-toxicity, easily modified chemical structure and wide range of targets, aptamers appear to be ideal candidates for various clinical applications (diagnosis or treatment), such as cell detection, target diagnosis, molecular imaging and drug delivery. Several aptamers have entered the clinical pipeline for applications in diseases such as macular degeneration, coronary artery bypass graft surgery and various types of cancer. The aim of this review was to summarize and highlight the clinical applications of aptamers in cancer diagnosis and treatment.
Dependency channel modeling for a LDPC-based Wyner-Ziv video compression scheme (2006)

Research in distributed video coding for low complexity encoding has shown that without knowledge of the correlation between source and side information (i.e. the behavior of the dependency channel), the performance is substantially below that of well known state-of-the-art video coders. In a practical system the decoder needs to estimate the statistics in this dependency channel. In this paper we investigate the relation between the compression ratio and the sensitivity of the estimated channel model parameter at the decoder side. We observe that this is a hard task, but not unrealistic. We show that the tolerable parameter range is very dependent on the compression ratio and the (actual) statistics in the dependency channel.
Vaccinia Virus Induces Strong Immunoregulatory Cytokine Production in Healthy Human Epidermal Keratinocytes: a Novel Strategy for Immune Evasion (2005)

Iatrogenic cutaneous infection with vaccinia virus (VV) and naturally occurring systemic infection with variola virus both lead to the characteristic skin "pox" lesions. Despite significant medical experience with both viruses, surprisingly little is understood about the interactions between these poxviruses and healthy resident skin cells. In recent years, it has become clear that skin plays an essential role in modulating both innate and adaptive immune responses, in part by producing and responding to a variety of cytokines and chemokines upon stimulation. Antagonists of many of these compounds are encoded in poxvirus genomes. Infection of skin cells with poxvirus may lead to a unique pattern of cytokine and chemokine production that might alter the cutaneous immune surveillance function. In this study, we infected primary cultures of human skin cells with VV and monitored antigen expression, virus replication, and cytokine production from the infected cells. While T cells, Langerhans cells, and dermal dendritic cells were infected abortively, keratinocytes, dermal fibroblasts, and dermal microvascular endothelial cells (HMVEC-d) all supported the complete virus life cycle. In contrast to the robust viral replication in fibroblasts and HMVEC-d, only limited viral replication was observed in keratinocytes. Importantly, VV infection of keratinocytes led to up-regulation of immunoregulatory and Th2 cytokines, including transforming growth factor beta, interleukin-10 (IL-10), and IL-13. We propose that the rapid induction of keratinocyte Th2 and immunoregulatory cytokines represents a poxvirus strategy to evade immune surveillance, and the limited viral multiplication in keratinocytes may be a protective mechanism to help the immune system "win the race."
Downregulation of Th1 cytokine production accompanies induction of Th2 responses by a parasitic helminth, Schistosoma mansoni. (1991)

In the mouse, infection with Schistosoma mansoni results in an egg-producing infection and associated disease, whereas vaccination with attenuated larval stages produces a substantial and specific immunity in the absence of egg-induced pathology. Preliminary data showing enhanced interleukin-5 (IL-5) production by T cells from infected mice and interferon gamma (IFN-gamma) synthesis by cells from vaccinated animals (7), suggested differential CD4+ subset stimulation by the different parasite stimuli. To confirm this hypothesis, lymphocytes from vaccinated or infected animals were compared for their ability to produce IFN-gamma and IL-2 (secreted by Th1 cells) as compared with IL-4 and IL-5 (characteristic Th2 cytokines). After stimulation with specific antigen or mitogen, T cells from vaccinated mice or prepatently infected animals responded primarily with Th1 lymphokines, whereas lymphocytes from patently infected mice instead produced Th2 cytokines. The Th2 response in infected animals was shown to be induced by schistosome eggs and directed largely against egg antigens, whereas the Th1 reactivity in vaccinated mice was triggered primarily by larval antigens. Interestingly, Th1 responses in mice carrying egg-producing infections were found to be profoundly downregulated. Moreover, the injection of eggs into vaccinated mice resulted in a reduction of antigen and mitogen-stimulated Th1 function accompanied by a coincident expression of Th2 responses. Together, the data suggest that coincident with the induction of Th2 responses, murine schistosome infection results in an inhibition of potentially protective Th1 function. This previously unrecognized downregulation of Th1 cytokine production may be an important immunological consequence of helminth infection related to host adaptation.
Heterobimetallic Activation of Dioxygen:  Characterization and Reactivity of Novel Cu(I)−Ge(II) Complexes (2006)

Reaction of the known germylene Ge[N(SiMe3)2]2 and a new heterocyclic variant Ge[(NMes)2(CH)2] with [L(Me2)Cu]2 (L(Me2) = the beta-diketiminate derived from 2-(2,6-dimethylphenyl)amino-4-(2,6-dimethylphenyl)imino-2-pentene) yielded novel Cu(I)-Ge(II) complexes L(Me2)Cu-Ge[(NMes)2(CH)2] (1a) and L(Me2)Cu-Ge[N(SiMe3)2]2 (1b), which were characterized by spectroscopy and X-ray crystallography. The lability of the Cu(I)-Ge(II) bond in 1a and b was probed by studies of their reactivity with benzil, PPh3, and a N-heterocyclic carbene (NHC). Notably, both complexes are cleaved rapidly by PPh3 and the NHC to yield stable Cu(I) adducts (characterized by X-ray diffraction) and the free germylene. In addition, the complexes are highly reactive with O2 and exhibit chemistry which depends on the bound germylene. Thus, oxygenation of 1a results in scission and formation of thermally unstable L(Me2)CuO2, which subsequently decays to [(L(Me2)Cu)2(mu-O)2], while 1b yields L(Me2)Cu(mu-O)2Ge[N(SiMe3)2]2, a novel heterobimetallic intermediate having a [Cu(III)(mu-O)2Ge(IV)]3+ core. The isolation of the latter species by direct oxygenation of a Cu(I)-Ge(II) precursor represents a new route to heterobimetallic oxidants comprising copper.
Conformational Regulation of α4β1-Integrin Affinity by Reducing Agents (2004)

The alpha(4)beta(1)-integrin (very late antigen-4 (VLA-4), CD49d/CD29) is an adhesion receptor involved in the interaction of lymphocytes, dendritic cells, and stem cells with the extracellular matrix and endothelial cells. This and other integrins have the ability to regulate their affinity for ligands through a process termed "inside-out" signaling that affects cell adhesion avidity. Several mechanisms are known to regulate integrin affinity and conformation: conformational changes induced by separation of the C-terminal tails, divalent ions, and reducing agents. Recently, we described a fluorescent LDV-containing small molecule that was used to monitor VLA-4 affinity changes in live cells (Chigaev, A., Blenc, A. M., Braaten, J. V., Kumaraswamy, N., Kepley, C. L., Andrews, R. P., Oliver, J. M., Edwards, B. S., Prossnitz, E. R., Larson, R. S., and Sklar, L. A. (2001) J. Biol. Chem. 276, 48670-48678). Using the same molecule, we also developed a fluorescence resonance energy transfer-based assay to probe the "switchblade-like" opening of VLA-4 upon activation. Here, we investigated the effect of reducing agents on the affinity and conformational state of the VLA-4 integrin simultaneously with cell activation initiated by inside-out signaling through G protein-coupled receptors or Mn(2+) in live cells in real time. We found that reducing agents (dithiothreitol and 2,3-dimercapto-1-propanesulfonic acid) induced multiple states of high affinity of VLA-4, where the affinity change was accompanied by an extension of the integrin molecule. Bacitracin, an inhibitor of the reductive function of the plasma membrane, diminished the effect of dithiothreitol, but had no effect on inside-out signaling. Based on this result and differences in the kinetics of integrin activation, we conclude that conformational activation of VLA-4 by inside-out signaling is independent of and additive to reduction-regulated integrin activation.
HiRLoc: high-resolution robust localization for wireless sensor networks (2006)

In this paper, we address the problem of robustly estimating the position of randomly deployed nodes of a wireless sensor network (WSN), in the presence of security threats. We propose a range-independent localization algorithm called high-resolution range-independent localization (HiRLoc), that allows sensors to passively determine their location with high resolution, without increasing the number of reference points, or the complexity of the hardware of each reference point. In HiRLoc, sensors determine their location based on the intersection of the areas covered by the beacons transmitted by multiple reference points. By combining the communication range constraints imposed by the physical medium with computationally efficient cryptographic primitives that secure the beacon transmissions, we show that HiRLoc is robust against known attacks on WSN, such as the wormhole attack, the Sybil attack, and compromise of network entities. Finally, our performance evaluation shows that HiRLoc leads to a significant improvement in localization accuracy compared with state-of-the-art range-independent localization schemes, while requiring fewer reference points.
An Efficient Gradient-Based Algorithm for On-Line Training of Recurrent Network Trajectories (1990)

A novel variant of the familiar backpropagation-through-time approach to training recurrent networks is described. This algorithm is intended to be used on arbitrary recurrent networks that run continually without ever being reset to an initial state, and it is specifically designed for computationally efficient computer implementation. This algorithm can be viewed as a cross between epochwise backpropagation through time, which is not appropriate for continually running networks, and the widely used on-line gradient approximation technique of truncated backpropagation through time.
Electronic structure and optical properties of silicon crystallites: Application to porous silicon (1992)

We have calculated the electronic structure of spherical silicon crystallites containing up to 2058 Si atoms. We predict a variation of the optical band gap with respect to the size of the crystallites in very good agreement with available experimental results. We also calculate the electron-hole recombination time which is of the order of 10−4–10−6 s for crystallites with diameters of 2.0–3.0 nm. We conclude that small silicon crystallites can have interesting optical properties in the visible range. These results are applied to porous silicon for which we confirm that a possible origin of the luminescence is the quantum confinement.
The First Direct Synthesis of Corroles from Pyrrole (1999)

The solvent-free, catalyst-free condensation of pyrrole and aldehydes provides an extremely facile synthetic pathway to novel corroles [Eq. (1); Ar=C<sub>6</sub> F<sub>5</sub> , 2,6-F<sub>2</sub> C<sub>6</sub> H<sub>3</sub> , 2,6-Cl<sub>2</sub> C<sub>6</sub> H<sub>3</sub> ]. The product containing pentafluorophenyl groups is an excellent precursor of other derivatives, including an ionic, water-soluble corrole.
Characterization and Functional Analysis of the Promoter of RAGE, the Receptor for Advanced Glycation End Products (1997)

The receptor for advanced glycation end products, RAGE, is a member of the immunoglobulin superfamily of cell surface molecules differentially expressed on a range of cell types. Ligation of RAGE perturbs homeostatic mechanisms and, potentially, provides a basis for cellular dysfunction in pathologic situations in which its ligands accumulate. To understand factors underlying RAGE expression, we cloned the 5'-flanking region of the RAGE gene and characterized putative regulatory motifs. Analysis of the putative promoter region revealed the presence of three potential NF-kappaB-like and two SP1 binding sites. Transient transfection of vascular endothelial and smooth muscle cells using chimeric 5'-deletion constructs linked to luciferase reporter revealed that the region -1543/-587 contributed importantly to both basal and stimulated expression of the RAGE gene. This region of the RAGE gene contained three putative NF-kappaB-like binding sites and was responsible for increased luciferase activity observed when endothelial or smooth muscle cells were stimulated with lipopolysaccharide. DNase I footprinting assays and electrophoretic mobility shift assay revealed that two of the three NF-kappaB-like binding sites (1 and 2) were likely functional and responsive to stimuli. Upon simultaneous mutation of NF-kappaB-like sites 1 and 2, both basal promoter expression and response to stimulation with LPS, as measured by relative luciferase activity, were significantly diminished. These results point to NF-kappaB-dependent mechanisms regulating cellular expression of RAGE and suggest a means of linking RAGE to the inflammatory response.
Silver Nanoparticles as Pigments for Water-Based Ink-Jet Inks (2003)

Stabilized concentrated citrate-reduced silver nanocolloids for use as pigments in ink-jet inks were prepared. Carboxymethyl cellulose was used as a polymeric stabilizer providing both electrostatic and steric stabilization. X-ray diffraction pattern, optical properties (UV−visible spectroscopy), size (TEM and dynamic light scattering), and zeta potentials of the nanoparticles were studied. It was shown that the product is silver with cubic symmetry. Absorption spectra are characterized, as a rule, by asymmetric absorption bands with maxima at 417−440 nm and shoulders at 350−352 and 380−382 nm. TEM images of unstabilized and stabilized colloids indicate the formation of nanoparticles of different shapes (spheres, hexagons, cubes, and rods) with rather wide size distribution in the range from several nanometers (spheres) up to several hundreds of nanometers (rods). CMC was found to be an effective stabilizer of silver nanoparticles, and the average particle size at CMC concentrations from 0.025 to 0.2 wt % does not exceed 50 nm. Both unstabilized and stabilized silver nanoparticles display negative zeta potentials in the pH range from 2 to 9; the maximal negative values are observed at pH 6−8 (−27 ± 5 mV for unstabilized and −33 ± 5 mV for CMC-stabilized colloids, respectively). Concentrated dispersions of silver nanoparticles (1.1 wt % of silver), which were stable for at least 7 months, were prepared by exhausted lyophilization of the freshly prepared colloids followed by redispersion. These nanoparticles in the presence of proper wetting agent, such as Disperbyk, can be used as pigments in ink-jet ink formulations for printing on various substrates (paper, glass, and transparencies). The stabilizing agent, carboxymethyl cellulose, also acts as a binder, providing good adhesion of ink to the substrates.
Self-Assembled Monolayers of Thiol-End-Labeled DNA at Mercury Electrodes (2006)

We show for the first time that thiol-end-labeled oligodeoxynucleotides form self-assembled monolayer (SAM) at Hg electrodes. Changes in voltammetric signals due to cytosine and Hg-S bond reduction indicated changes in positioning of the HS-(TTC)(7) molecules at the electrode with increasing HS-(TTC)7 concentration from lying flat with respect to SAMs, forming upright-standing molecules. This SAM behaved as an insulator not allowing electron transfer between [Ru(NH3)6]3+ and the electrode. Different adsorption modes of thiolated and thiol-free DNAs were observed.