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  • 1
    Publikationsdatum: 2015-09-11
    Beschreibung: Motivation: Model organisms play critical roles in biomedical research of human diseases and drug development. An imperative task is to translate information/knowledge acquired from model organisms to humans. In this study, we address a trans-species learning problem: predicting human cell responses to diverse stimuli, based on the responses of rat cells treated with the same stimuli. Results: We hypothesized that rat and human cells share a common signal-encoding mechanism but employ different proteins to transmit signals, and we developed a bimodal deep belief network and a semi-restricted bimodal deep belief network to represent the common encoding mechanism and perform trans-species learning. These ‘deep learning’ models include hierarchically organized latent variables capable of capturing the statistical structures in the observed proteomic data in a distributed fashion. The results show that the models significantly outperform two current state-of-the-art classification algorithms. Our study demonstrated the potential of using deep hierarchical models to simulate cellular signaling systems. Availability and implementation: The software is available at the following URL: http://pubreview.dbmi.pitt.edu/TransSpeciesDeepLearning/ . The data are available through SBV IMPROVER website, https://www.sbvimprover.com/challenge-2/overview , upon publication of the report by the organizers. Contact : xinghua@pitt.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Digitale ISSN: 1460-2059
    Thema: Biologie , Informatik , Medizin
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 2
    Publikationsdatum: 2016-07-30
    Beschreibung: A major assemblage of Mesolithic and Neolithic wooden artefacts has been recovered from the bed of the River Užava at Sise, in the coastal belt of western Latvia. New archaeological investigation has also produced wooden remains and other evidence of occupation on the riverbank. On the basis of multi-proxy environmental data and radiocarbon dating, this article offers a first attempt to place the human activity in a palaeolandscape context. The earliest evidence of human presence is provided by wooden artefacts dated to c . 10,500–9700 cal. BP, during the Ancylus Lake transgression. These remains are thought to reflect fishing activities in the shallows of the Ventspils Bay, which existed during the transgression. The regression that followed brought a return to river-valley conditions at the site, and the next recorded period of human activity, evidenced by 14 C-dated antler tool finds, is associated with the beginning of the Littorina Sea transgression, culminating c . 7500 cal. BP. With the formation of a new Ventspils Bay/Lagoon, the Sise site, at or near the river mouth, would have regained its status as an advantageous fishing location. Archaeological finds indicate continued human activity c . 6000–4000 cal. BP, even though the sea level was now lower and this was no longer a river-mouth location. Such a pattern of recurrent human occupation during the early to middle Holocene, associated with repeated shifts of the shoreline, appears to be characteristic of the central region of the Baltic Sea Basin.
    Print ISSN: 0959-6836
    Digitale ISSN: 1477-0911
    Thema: Geographie , Geologie und Paläontologie
    Publiziert von Sage
    Standort Signatur Erwartet Verfügbarkeit
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  • 3
    Publikationsdatum: 2015-02-04
    Beschreibung: We examine the relation between polycyclic aromatic hydrocarbon (PAH) emission at 8 μm and far-infrared emission from hot dust grains at 24 μm and from large dust grains at 160 and 250 μm in the nearby spiral galaxies NGC 2403 and M83 using data from the Spitzer Space Telescope and Herschel Space Observatory. We find that the PAH emission in NGC 2403 is better correlated with emission at 250 μm from dust heated by the diffuse interstellar radiation field (ISRF) and that the 8/250-μm surface brightness ratio is well correlated with the stellar surface brightness as measured at 3.6 μm. This implies that the PAHs in NGC 2403 are intermixed with cold large dust grains in the diffuse interstellar medium (ISM) and that the PAHs are excited by the diffuse ISRF. In M83, the PAH emission appears more strongly correlated with 160 μm emission originating from large dust grains heated by star-forming regions. However, the PAH emission in M83 is low where the 24-μm emission peaks within star-forming regions, and enhancements in the 8/160-μm surface brightness ratios appear offset relative to the dust and the star-forming regions within the spiral arms. This suggests that the PAHs observed in the 8 μm band are not excited locally within star-forming regions but either by light escaping non-axisymmetrically from star-forming regions or locally by young, non-photoionizing stars that have migrated downstream from the spiral density waves. The results from just these two galaxies show that PAHs may be excited by different stellar populations in different spiral galaxies.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 4
    Publikationsdatum: 2011-10-05
    Beschreibung: Neurogenesis requires mechanisms that coordinate early cell-fate decisions, migration, and terminal differentiation. Here, we show that the transcriptional repressor, repressor element 1 silencing transcription factor (REST), regulates radial migration and the timing of neural progenitor differentiation during neocortical development, and that the regulation is contingent upon differential REST levels. Specifically, a sustained presence of REST blocks migration and greatly delays—but does not prevent—neuronal differentiation, resulting in a subcortical band heterotopia-like phenotype, reminiscent of loss of doublecortin. We further show that doublecortin is a direct gene target of REST, and that its overexpression rescues, at least in part, the aberrant phenotype caused by persistent presence of REST. Our studies support the view that the targeted down-regulation of REST to low levels in neural progenitors, and its subsequent disappearance during neurogenesis, is critical for timing the spatiotemporal transition of neural progenitor cells to neurons.
    Print ISSN: 0027-8424
    Digitale ISSN: 1091-6490
    Thema: Biologie , Medizin , Allgemeine Naturwissenschaft
    Standort Signatur Erwartet Verfügbarkeit
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  • 5
    Publikationsdatum: 2015-12-19
    Beschreibung: Author(s): O. D. Skoromnik, I. D. Feranchuk, D. V. Lu, and C. H. Keitel When a nonrelativistic particle interacts with a scalar quantum field, the standard perturbation theory leads to a dependence of the energy of its ground state on an undefined parameter—“momentum cutoff”—due to the ultraviolet divergence. We show that the use of nonasymptotic states of the system re… [Phys. Rev. D 92, 125019] Published Fri Dec 18, 2015
    Schlagwort(e): Field Theory, Formal Particle Theory
    Print ISSN: 0556-2821
    Digitale ISSN: 1089-4918
    Thema: Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 6
    Publikationsdatum: 2012-07-18
    Beschreibung: Reactive oxygen and nitrogen species (ROS and RNS) produced by macrophages are essential for protecting a human body against bacteria and viruses. Micrometer-sized electrodes coated with Pt black have previously been used for selective and sensitive detection of ROS and RNS in biological systems. To determine ROS and RNS inside macrophages, one needs smaller (i.e., nanometer-sized) sensors. In this article, the methodologies have been extended to the fabrication and characterization of Pt/Pt black nanoelectrodes. Electrodes with the metal surface flush with glass insulator, most suitable for quantitative voltammetric experiments, were fabricated by electrodeposition of Pt black inside an etched nanocavity under the atomic force microscope control. Despite a nanometer-scale radius, the true surface area of Pt electrodes was sufficiently large to yield stable and reproducible responses to ROS and RNS in vitro. The prepared nanoprobes were used to penetrate cells and detect ROS and RNS inside macrophages. Weak and very short leaks of ROS/RNS from the vacuoles into the cytoplasm were detected, which a macrophage is equipped to clean within a couple of seconds, while higher intensity oxidative bursts due to the emptying of vacuoles outside persist on the time scale of tens of seconds.
    Schlagwort(e): Electrochemistry Special Feature
    Print ISSN: 0027-8424
    Digitale ISSN: 1091-6490
    Thema: Biologie , Medizin , Allgemeine Naturwissenschaft
    Standort Signatur Erwartet Verfügbarkeit
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  • 7
    Publikationsdatum: 2011-02-02
    Beschreibung: Imaging systems that exploit arrays of photodetectors in curvilinear layouts are attractive due to their ability to match the strongly nonplanar image surfaces (i.e., Petzval surfaces) that form with simple lenses, thereby creating new design options. Recent work has yielded significant progress in the realization of such “eyeball” cameras, including examples of fully functional silicon devices capable of collecting realistic images. Although these systems provide advantages compared to those with conventional, planar designs, their fixed detector curvature renders them incompatible with changes in the Petzval surface that accompany variable zoom achieved with simple lenses. This paper describes a class of digital imaging device that overcomes this limitation, through the use of photodetector arrays on thin elastomeric membranes, capable of reversible deformation into hemispherical shapes with radii of curvature that can be adjusted dynamically, via hydraulics. Combining this type of detector with a similarly tunable, fluidic plano-convex lens yields a hemispherical camera with variable zoom and excellent imaging characteristics. Systematic experimental and theoretical studies of the mechanics and optics reveal all underlying principles of operation. This type of technology could be useful for night-vision surveillance, endoscopic imaging, and other areas that require compact cameras with simple zoom optics and wide-angle fields of view.
    Print ISSN: 0027-8424
    Digitale ISSN: 1091-6490
    Thema: Biologie , Medizin , Allgemeine Naturwissenschaft
    Standort Signatur Erwartet Verfügbarkeit
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  • 8
    Publikationsdatum: 2011-07-20
    Beschreibung: Evidence for cooperation between actin nucleators is growing. The WH2-containing nucleator Spire and the formin Cappuccino interact directly, and both are essential for assembly of an actin mesh during Drosophila oogenesis. Their interaction requires the kinase noncatalytic C-lobe domain (KIND) domain of Spire and the C-terminal tail of the formin. Here we describe the crystal structure of the KIND domain of human Spir1 alone and in complex with the tail of Fmn2, a mammalian ortholog of Cappuccino. The KIND domain is structurally similar to the C-lobe of protein kinases. The Fmn2 tail is coordinated in an acidic cleft at the base of the domain that appears to have evolved via deletion of a helix from the canonical kinase fold. Our functional analysis of Cappuccino reveals an unexpected requirement for its tail in actin assembly. In addition, we find that the KIND/tail interaction blocks nucleation by Cappuccino and promotes its displacement from filament barbed ends providing insight into possible modes of cooperation between Spire and Cappuccino.
    Print ISSN: 0027-8424
    Digitale ISSN: 1091-6490
    Thema: Biologie , Medizin , Allgemeine Naturwissenschaft
    Standort Signatur Erwartet Verfügbarkeit
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  • 9
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2019
    Beschreibung: 〈p〉Plasma shocks are the primary means of accelerating electrons in planetary and astrophysical settings throughout the universe. Which category of shocks, quasi-perpendicular or quasi-parallel, accelerates electrons more efficiently is debated. Although quasi-perpendicular shocks are thought to be more efficient electron accelerators, relativistic electron energies recently observed at quasi-parallel shocks exceed theoretical expectations. Using in situ observations at Earth’s bow shock, we show that such relativistic electrons are generated by the interaction between the quasi-parallel shock and a related nonlinear structure, a foreshock transient, through two betatron accelerations. Our observations show that foreshock transients, overlooked previously, can increase electron acceleration efficiency at a quasi-parallel shock by an order of magnitude. Thus, quasi-parallel shocks could be more important in generating relativistic electrons, such as cosmic ray electrons, than previously thought.〈/p〉
    Digitale ISSN: 2375-2548
    Thema: Allgemeine Naturwissenschaft
    Standort Signatur Erwartet Verfügbarkeit
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  • 10
    Publikationsdatum: 2015-03-20
    Beschreibung: Cardiac left ventricular outflow tract (LVOT) defects represent a common but heterogeneous subset of congenital heart disease for which gene identification has been difficult. We describe a 46,XY,t(1;5)(p36.11;q31.2)dn translocation carrier with pervasive developmental delay who also exhibited LVOT defects, including bicuspid aortic valve (BAV), coarctation of the aorta (CoA) and patent ductus arteriosus (PDA). The 1p breakpoint disrupts the 5' UTR of AHDC1 , which encodes AT-hook DNA-binding motif containing-1 protein, and AHDC1 -truncating mutations have recently been described in a syndrome that includes developmental delay, but not congenital heart disease [Xia, F., Bainbridge, M.N., Tan, T.Y., Wangler, M.F., Scheuerle, A.E., Zackai, E.H., Harr, M.H., Sutton, V.R., Nalam, R.L., Zhu, W. et al . (2014) De Novo truncating mutations in AHDC1 in individuals with syndromic expressive language delay, hypotonia, and sleep apnea. Am. J. Hum. Genet ., 94, 784–789]. On the other hand, the 5q translocation breakpoint disrupts the 3' UTR of MATR3 , which encodes the nuclear matrix protein Matrin 3, and mouse Matr3 is strongly expressed in neural crest, developing heart and great vessels, whereas Ahdc1 is not. To further establish MATR3 3' UTR disruption as the cause of the proband's LVOT defects, we prepared a mouse Matr3 Gt-ex13 gene trap allele that disrupted the 3' portion of the gene. Matr3 Gt-ex13 homozygotes are early embryo lethal, but Matr3 Gt-ex13 heterozygotes exhibit incompletely penetrant BAV, CoA and PDA phenotypes similar to those in the human proband, as well as ventricular septal defect (VSD) and double-outlet right ventricle (DORV). Both the human MATR3 translocation breakpoint and the mouse Matr3 Gt-ex13 gene trap insertion disturb the polyadenylation of MATR3 transcripts and alter Matrin 3 protein expression, quantitatively or qualitatively. Thus, subtle perturbations in Matrin 3 expression appear to cause similar LVOT defects in human and mouse.
    Print ISSN: 0964-6906
    Digitale ISSN: 1460-2083
    Thema: Biologie , Medizin
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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