35,678 research outputs found
Integrating Horizontal Gene Transfer and Common Descent to Depict Evolution and Contrast It with ââCommon Design
Horizontal gene transfer (HGT) and common descent interact in space and time. Because events of HGT co-occur with phylogenetic evolution, it is difficult to depict evolutionary patterns graphically. Tree-like representations of lifeâs diversification are useful, but they ignore the significance of HGT in evolutionary history, particularly of unicellular organisms, ancestors of multicellular life. Here we integrate the reticulated-tree model, ring of life, symbiogenesis whole-organism model, and eliminative pattern pluralism to represent evolution. Using Entamoeba histolytica alcohol dehydrogenase 2 (EhADH2), a bifunctional enzyme in the glycolytic pathway of amoeba, we illustrate how EhADH2 could be the product of both horizontally acquired features from ancestral prokaryotes (i.e. aldehyde dehydrogenase [ALDH] and alcohol dehydrogenase [ADH]), and subsequent functional integration of these enzymes into EhADH2, which is now inherited by amoeba via common descent. Natural selection has driven the evolution of EhADH2 active sites, which require specific amino acids (cysteine 252 in the ALDH domain; histidine 754 in the ADH domain), iron- and NAD1 as cofactors, and the substrates acetyl-CoA for ALDH and acetaldehyde for ADH. Alternative views invoking ââcommon designââ (i.e. the non-naturalistic emergence of major taxa independent from ancestry) to explain the interaction between horizontal and vertical evolution are unfounded
Deep learning in remote sensing: a review
Standing at the paradigm shift towards data-intensive science, machine
learning techniques are becoming increasingly important. In particular, as a
major breakthrough in the field, deep learning has proven as an extremely
powerful tool in many fields. Shall we embrace deep learning as the key to all?
Or, should we resist a 'black-box' solution? There are controversial opinions
in the remote sensing community. In this article, we analyze the challenges of
using deep learning for remote sensing data analysis, review the recent
advances, and provide resources to make deep learning in remote sensing
ridiculously simple to start with. More importantly, we advocate remote sensing
scientists to bring their expertise into deep learning, and use it as an
implicit general model to tackle unprecedented large-scale influential
challenges, such as climate change and urbanization.Comment: Accepted for publication IEEE Geoscience and Remote Sensing Magazin
Deep Adaptive Feature Embedding with Local Sample Distributions for Person Re-identification
Person re-identification (re-id) aims to match pedestrians observed by
disjoint camera views. It attracts increasing attention in computer vision due
to its importance to surveillance system. To combat the major challenge of
cross-view visual variations, deep embedding approaches are proposed by
learning a compact feature space from images such that the Euclidean distances
correspond to their cross-view similarity metric. However, the global Euclidean
distance cannot faithfully characterize the ideal similarity in a complex
visual feature space because features of pedestrian images exhibit unknown
distributions due to large variations in poses, illumination and occlusion.
Moreover, intra-personal training samples within a local range are robust to
guide deep embedding against uncontrolled variations, which however, cannot be
captured by a global Euclidean distance. In this paper, we study the problem of
person re-id by proposing a novel sampling to mine suitable \textit{positives}
(i.e. intra-class) within a local range to improve the deep embedding in the
context of large intra-class variations. Our method is capable of learning a
deep similarity metric adaptive to local sample structure by minimizing each
sample's local distances while propagating through the relationship between
samples to attain the whole intra-class minimization. To this end, a novel
objective function is proposed to jointly optimize similarity metric learning,
local positive mining and robust deep embedding. This yields local
discriminations by selecting local-ranged positive samples, and the learned
features are robust to dramatic intra-class variations. Experiments on
benchmarks show state-of-the-art results achieved by our method.Comment: Published on Pattern Recognitio
Multimodal Grounding for Language Processing
This survey discusses how recent developments in multimodal processing
facilitate conceptual grounding of language. We categorize the information flow
in multimodal processing with respect to cognitive models of human information
processing and analyze different methods for combining multimodal
representations. Based on this methodological inventory, we discuss the benefit
of multimodal grounding for a variety of language processing tasks and the
challenges that arise. We particularly focus on multimodal grounding of verbs
which play a crucial role for the compositional power of language.Comment: The paper has been published in the Proceedings of the 27 Conference
of Computational Linguistics. Please refer to this version for citations:
https://www.aclweb.org/anthology/papers/C/C18/C18-1197
A Comprehensive Survey of Deep Learning in Remote Sensing: Theories, Tools and Challenges for the Community
In recent years, deep learning (DL), a re-branding of neural networks (NNs),
has risen to the top in numerous areas, namely computer vision (CV), speech
recognition, natural language processing, etc. Whereas remote sensing (RS)
possesses a number of unique challenges, primarily related to sensors and
applications, inevitably RS draws from many of the same theories as CV; e.g.,
statistics, fusion, and machine learning, to name a few. This means that the RS
community should be aware of, if not at the leading edge of, of advancements
like DL. Herein, we provide the most comprehensive survey of state-of-the-art
RS DL research. We also review recent new developments in the DL field that can
be used in DL for RS. Namely, we focus on theories, tools and challenges for
the RS community. Specifically, we focus on unsolved challenges and
opportunities as it relates to (i) inadequate data sets, (ii)
human-understandable solutions for modelling physical phenomena, (iii) Big
Data, (iv) non-traditional heterogeneous data sources, (v) DL architectures and
learning algorithms for spectral, spatial and temporal data, (vi) transfer
learning, (vii) an improved theoretical understanding of DL systems, (viii)
high barriers to entry, and (ix) training and optimizing the DL.Comment: 64 pages, 411 references. To appear in Journal of Applied Remote
Sensin
Production and analysis of synthetic Cascade variants
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR assoziiert) ist ein
adaptives Immunsystem in Archaeen und Bakterien, das fremdes genetisches Material mit Hilfe von
Ribonukleoprotein-Komplexen erkennt und zerstört. Diese Komplexe bestehen aus einer CRISPR RNA
(crRNA) und Cas Proteinen. CRISPR-Cas Systeme sind in zwei Hauptklassen und mehrere Typen
unterteilt, abhÀngig von den beteiligten Cas Proteinen. In Typ I Systemen sucht ein Komplex namens
Cascade (CRISPR associated complex for antiviral defence) nach eingedrungener viraler DNA wÀhrend
einer Folgeinfektion und bindet die zu der eingebauten crRNA komplementĂ€re Sequenz. AnschlieĂend
wird die Nuklease/Helikase Cas3 rekrutiert, welche die virale DNA degradiert (Interferenz).
Das Typ I System wird in mehrere Subtypen unterteilt, die Unterschiede im Aufbau von Cascade
vorweisen. Im Fokus dieser Arbeit steht eine minimale Cascade-Variante aus Shewanella putrefaciens
CN-32. Im Vergleich zur gut untersuchten Typ I-E Cascade aus Escherichia coli fehlen in diesem Komplex
zwei Untereinheiten, die gewöhnlicher Weise fĂŒr die Zielerkennung benötigt werden. Dennoch ist der
Komplex aktiv. Rekombinante I-Fv Cascade wurde bereits aus E. coli aufgereinigt und es war möglich,
den Komplex zu modifizieren, indem das RĂŒckgrat entweder verlĂ€ngert oder verkĂŒrzt wurde. Dadurch
wurden synthetische Varianten mit verÀnderter Protein-Stöchiometrie erzeugt.
In der vorliegenden Arbeit wurde I-Fv Cascade weiter mit in vitro Methoden untersucht. So wurde die
Bindung von Ziel-DNA beobachtet und die 3D Struktur zeigt, dass strukturelle VerÀnderungen im
Komplex die fehlenden Untereinheiten ersetzen, möglicherweise um viralen Anti-CRISPR Proteinen zu
entgehen. Die Nuklease/Helikase dieses Systems, Cas2/3fv, ist eine Fusion des Cas3 Proteins mit dem
Interferenz-unabhÀngigen Protein Cas2. Ein unabhÀngiges Cas3fv ohne Cas2 Untereinheit wurde
aufgereinigt und in vitro Assays zeigten, dass dieses Protein sowohl freie ssDNA als auch Cascadegebundene Substrate degradiert. Das komplette Cas2/3fv Protein bildet einen Komplex mit dem Protein
Cas1 und zeigt eine reduzierte AktivitĂ€t gegenĂŒber freier ssDNA, möglicherweise als
Regulationsmechanismus zur Vermeidung von unspezifischer AktivitÀt.
Weiterhin wurde ein Prozess namens âRNA wrappingâ etabliert. Synthetische Cascade-Komplexe
wurden erzeugt, in denen die grundlegende RNA-Bindung des charakteristischen Cas7fv RĂŒckgratProteins auf eine ausgewĂ€hlte RNA gelenkt wird. Diese spezifische Komplexbildung kann in vivo durch
eine Repeat-Sequenz der crRNA stromaufwÀrts der Zielsequenz und durch Bindung des Cas5fv Proteins
initiiert werden. Die erzeugten Komplexe beinhalten die ersten 100 nt der markierten RNA, die
anschlieĂend isoliert werden kann. Innerhalb der Komplexe ist die RNA stabilisiert und geschĂŒtzt vor
Degradation durch RNasen. Komplexbildung kann auĂerdem genutzt werden, um ReportergenTranskripte stillzulegen. ZusĂ€tzlich wurden erste Hinweise geliefert, dass das RĂŒckgrat der synthetischen
Komplexe durch Fusion mit weiteren Reporterproteinen modifiziert werden kann.CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR associated) is an
adaptive immune system of Archaea and Bacteria. It is able to target and destroy foreign genetic
material with ribonucleoprotein complexes consisting of CRISPR RNAs (crRNAs) and certain Cas proteins.
CRISPR-Cas systems are classified in two major classes and multiple types, according to the involved Cas
proteins. In type I systems, a ribonucleoprotein complex called Cascade (CRISPR associated complex for
antiviral defence) scans for invading viral DNA during a recurring infection and binds the sequence
complementary to the incorporated crRNA. After target recognition, the nuclease/helicase Cas3 is
recruited and subsequently destroys the viral DNA in a step termed interfere nce.
Multiple subtypes of type I exist that show differences in the Cascade composition. This work focuses on
a minimal Cascade variant found in Shewanella putrefaciens CN-32. In comparison to the well-studied
type I-E Cascade from Escherichia coli, this complex is missing two proteins usually required for target
recognition, yet it is still able to provide immunity. Recombinant I-Fv Cascade was previously purified
from E. coli and it was possible to modulate the complex by extending or shortening the backbone,
resulting in synthetic variants with altered protein stoichiometry.
In the present study, I-Fv Cascade was further analyzed by in vitro methods. Target binding was
observed and the 3D structure revealed structural variations that replace the missing subunits,
potentially to evade viral anti-CRISPR proteins. The nuclease/helicase of this system, Cas2/3fv, is a fusion
of the Cas3 protein with the interference-unrelated protein Cas2. A standalone Cas3fv was purified
without the Cas2 domain and in vitro cleavage assays showed that Cas3fv degrades both free ssDNA as
well as Cascade-bound substrates. The complete Cas2/3fv protein forms a complex with the protein
Cas1 and was shown to reduce cleave of free ssDNA, potentially as a regulatory mechanism against
unspecific cleavage.
Furthermore, we established a process termed âRNA wrappingâ. Synthetic Cascade assemblies can be
created by directing the general RNA-binding ability of the characteristic Cas7fv backbone protein on an
RNA of choice such as reporter gene transcripts. Specific complex formation can be initiated in vivo by
including a repeat sequence from the crRNA upstream a given target sequence and binding of the
Cas5fv protein. The created complexes contain the initial 100 nt of the tagged RNA which can be
isolated afterwards. While incorporated in complexes, RNA is stabilized and protected from degradation
by RNases. Complex formation can be used to silence reporter gene transcripts. Furthermore, we
provided initial indications that the backbone of synthetic complexes can be modified by addition of
reporter proteins
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