bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constraining the Age of Floodplain Levels Along the Lower Section of River Tisza, Hungary
Authors: Sipos György , Kiss Tímea , Tóth Orsolya 
Published: August 2016

Abstract
During the Late Pelistocene-Holocene transition the fluvial landscape of the Great Hungarian Plain changed considerably as a consequence of tectonic, climatic and geomorphological factors. Geochronology, and especially luminescence dating, is a very important tool in reconstructing these changes. The present study focuses on the Lower-Tisza region and addresses the timing of the development of different floodplain levels. In the meantime the luminescence characteristics of the investigated alluvial sediments were also assessed, with a special emphasis on the comparison of silty fine grain and sandy coarse grain results, as in the given medium and low energy environment fine grain sediments are more abundant, however, based on the literature, coarse grain samples are more reliable in terms of luminescence dating. Measurements were performed on 12 samples originating from the point bars of two large palaeo-meanders, representing different floodplain levels along the river. Results indicate the applicability of both grain size fractions for dating purposes, though fine grain subsamples overestimate in average by 1.5 ka the ages yielded by coarse grain subsamples. Consequently, fine grain samples can be used for outlining only general trends, and results need to be controlled by coarse grain measurements where possible. Based on the ages received, the upper floodplain was actively formed until 13-15 ka, when incision and the development of an intermediate floodplain level started. The meander on the intermediate flood plain level developed then very actively until 9 ka. As indicated by the received age information the intensity of meander formation could be highly affected by climatic and especially vegetation control. However, reconstruction can be refined later by further sampling and the application of the results of the present paper.
A density functional theory insight into the structure and reactivity of diphenyltin(IV) derivative of glycylphenylalanine
Authors: Pokharia Sandeep , Joshi Rachana , Pokharia Mamta , Yadav Swatantra Kumar , Mishra Hirdyesh 
Published: August 2016

Abstract
The quantum-chemical calculations based on density functional theory (DFT) have been performed on the diphenyltin(IV) derivative of glycyl-phenylalanine (H2L) at the B3LYP/6-31G(d,p)/LANL2DZ(Sn) level of theory without any symmetry constraint. The harmonic vibrational frequencies were computed at the same level of theory to find the true potential energy surface minima. The various geometrical and thermochemical parameters for the studied complex are obtained in the gas phase. The atomic charges at all the atoms were calculated using the Mulliken population analysis, the Hirshfeld population analysis, and the natural population analysis. The charge distribution within the studied complex is explained on the basis of molecular electrostatic potential maps, frontier molecular orbital analysis, and conceptual DFT-based reactivity (global and local) descriptors, using the finite difference approximation method. The nature of O-Sn, N-Sn, N→Sn, and C-Sn bonds is discussed in terms of the conceptual DFT-based reactivity descriptors. The structural analysis of the studied complex has been conducted in terms of the selected bond lengths and bond angles. The structural and the atomic charge analyses suggest a distorted trigonal bipyramidal arrangement consisting of negatively charged centers around the positively charged central Sn atom.
“Professional Amateurs”. Metal Detecting and Metal Detectorists in Denmark
Authors: Dobat Andres S. , Jensen Astrid T. 
Published: August 2016

AbstractFrom the beginning of metal-detector based archaeology practiced by members of the public, the
formal heritage sector in Denmark determined to pursue a liberal model based on cooperation and inclusion
rather than confrontation and criminalization. Based on the findings of the ‘2015 Danish detectorists survey’
it is argued that Danish metal-detector archaeology has challenged the classic division of roles in archaeology
and heritage management, and that at least a large proportion of Danish detectorists practice their hobby
adhering to the highest professional standards, which stand in sharp contrast to the often-cited stereotype of
the detectorists as mere ‘treasure hunter’.
CD44 expression trends of mesenchymal stem-derived cell, cancer cell and fibroblast spheroids on chitosan-coated surfaces
Authors: Tsai Ching-Wen , Young Tai-Horng 
Published: August 2016

Abstract
CD44, a cell-surface glycoprotein, plays an important role in cell proliferation, adhesion, migration, and other biological functions, which are related with the physiological and pathologic activities of cells. Especially, CD44 is extensively expressed within adult bone marrow and has been considered as an important marker for some cancer stem cells (CSCs) in various types of tumors. Therefore, it is essential to understand the variations in CD44 expression of stem cells and cancer cells for further clinical applications. In this paper, CD44 expression was assessed on a human colon cancer cell line (SW620), a human mesenchymal stem-like cell line (3A6), and a human foreskin fibroblast line (Hs68). We used chitosan to establish a suspension culture model to develop multicellular spheroids to mimic a three-dimension (3D) in vivo environment. Obviously, CD44 expression on 3A6 and SW620 cells was dynamic and diverse when they were in the aggregated state suspended on chitosan, while Hs68 cells were relatively stable. Furthermore, we discuss how to regulate CD44 expression of 3A6 and SW620 cells by the interactions between cell and cell, cell and chitosan, as well as cell and microenvironment. Finally, the possible mechanism of chitosan to control CD44 expression of cells is proposed, which may lead to the careful use of chitosan for potential clinical applications.
Adaptive Aid on Targeted Robot Manipulator Movements in Tele-Assistance
Authors: Stoelen Martin F. , Tejada Virginia F. , Jardón Alberto , Bonsignorio Fabio , Balaguer Carlos 
Published: August 2016

AbstractThe teleoperation of robot manipulators over the internet suffers from variable delays in the communications. Here we address a tele-assistance scenario, where a remote operator assists a disabled or elderly user on daily life tasks. Our behavioral approach uses local environment information from robot sensing to help enable faster execution for a given movement tolerance. This is achieved through a controller that automatically slows the operator down before having collisions, using a set of distributed proximity sensors. The controller is made to gradually increase the assistance in situations similar to those where ollisions have occurred in the past, thus adapting to the given operator, robot and task-set. Two controlled virtual experiments for tele-assistance with a 5 DOF manipulator were performed, with 300 ms and 600 ms mean variable round-trip delays. The results showed significant improvements in the median times of 12.6% and 16.5%, respectively. Improvements in the subjective workload were also seen with the controller. A first implementation on a physical robot manipulator is described.
Preparation and characterization of carbon fiber/polylactic acid/thermoplastic polyurethane (CF/PLA/TPU) composites prepared by a vane mixer
Authors: Yin Xiaochun , Wang Liang , Li Sai , He Guangjian , Yang Zhitao , Feng Yanhong , Qu Jinping 
Published: August 2016

Abstract
Various quantities of carbon fibers (CFs) (from 5% to 20% in weight) were added to matrix by melt blending to produce polylactic acid (PLA)/thermoplastic polyurethane (TPU)/CF composites. Differential scanning calorimetry measurements revealed that the CF content and mixing time had little influence on the crystallization and melting behavior of PLA. Thermogravimetric analysis showed that the introduction of CFs tended to decrease the thermal stability of PLA/TPU/CF composites, and the increase of mixing time tended to increase the thermal stability of PLA/TPU/CF composites when the mixing time is <5 min. Rheological results showed that all the samples exhibited non-Newtonian and shear thinning characteristics. The storage modulus and complex viscosity both increased with the increase of the CF content. It also showed that the increase of mixing time tended to increase the storage modulus and complex viscosity of PLA/TPU/CF composites when the mixing time is <5 min. Scanning electron microscopy images showed that the TPU/PLA blends contain a continuous PLA phase with evenly distributed TPU particles in the size range of 0.25–3 μm, and the blends are immiscible at the micron scale. Mechanical properties showed that the addition of proper CF content could lead to an obvious increase (about 11.43%) in tensile strength.
L1 variation in object pronominalisation, and the import of pragmatics
Authors: Gavarró Anna 
Published: August 2016

Abstract
Much work on referential expressions in monolingual and bilingual acquisition rests on the assumption that early grammars licence null objects even when they are not possible in the corresponding target grammar, in virtue of discourse-pragmatic licencing. This proposal has been made mainly with reference to third person object pronominalisation. Less attention has been given to other pronouns. Here, I show how the pragmatic account of third person object pronouns (along the lines of Serratrice et al. [2004, Crosslinguistic influence in the syntax-pragmatics interface: Subjects and objects in English-Italian bilingual and monolingual acquisition. Bilingualism: Language and Cognition 7(3). 182–205], in the spirit of Hulk and Müller [2000, Bilingual first language acquisition at the interface between syntax and pragmatics. Bilingualism: Language and Cognition 3(3). 227–244], Müller and Hulk [2001, Crosslinguistic influence in bilingual language acquisition: Italian and French as recipient languages. Bilingualism: Language and Cognition 4(1). 1–21]) does not extend to clitics instantiating other person specifications or other grammatical functions. I present an alternative analysis, in terms of the Unique Checking Constraint (Wexler [1998, Very early parameter setting and the unique checking constraint: A new explanation for the optional infinitive stage. Lingua 106. 23–79]) that offers a generalisation over other clitics, in particular indirect object clitics and first person object clitics, which are generally preserved in child grammar – as witnessed by two experiments run on Catalan L1 reported here.
Simulating Cortical Feedback Modulation as Changes in Excitation and Inhibition in a Cortical Circuit Model
Authors: Zagha Edward , Murray John D. , McCormick David A. 
Published: August 2016

AbstractCortical feedback pathways are hypothesized to distribute context-dependent signals during flexible behavior. Recent experimental work has attempted to understand the mechanisms by which cortical feedback inputs modulate their target regions. Within the mouse whisker sensorimotor system, cortical feedback stimulation modulates spontaneous activity and sensory responsiveness, leading to enhanced sensory representations. However, the cellular mechanisms underlying these effects are currently unknown. In this study we use a simplified neural circuit model, which includes two recurrent excitatory populations and global inhibition, to simulate cortical modulation. First, we demonstrate how changes in the strengths of excitation and inhibition alter the input–output processing responses of our model. Second, we compare these responses with experimental findings from cortical feedback stimulation. Our analyses predict that enhanced inhibition underlies the changes in spontaneous and sensory evoked activity observed experimentally. More generally, these analyses provide a framework for relating cellular and synaptic properties to emergent circuit function and dynamic modulation.
IGFBP1 increases β‐cell regeneration by promoting α‐ to β‐cell transdifferentiation
Authors: Lu Jing , Liu Ka‐Cheuk , Schulz Nadja , Karampelias Christos , Charbord Jérémie , Hilding Agneta , Rautio Linn , Bertolino Philippe , Östenson Claes‐Göran , Brismar Kerstin , Andersson Olov 
Published: August 2016

AbstractThere is great interest in therapeutically harnessing endogenous regenerative mechanisms to increase the number of β cells in people with diabetes. By performing whole‐genome expression profiling of zebrafish islets, we identified 11 secreted proteins that are upregulated during β‐cell regeneration. We then tested the proteins' ability to potentiate β‐cell regeneration in zebrafish at supraphysiological levels. One protein, insulin‐like growth factor (Igf) binding‐protein 1 (Igfbp1), potently promoted β‐cell regeneration by potentiating α‐ to β‐cell transdifferentiation. Using various inhibitors and activators of the Igf pathway, we show that Igfbp1 exerts its regenerative effect, at least partly, by inhibiting Igf signaling. Igfbp1's effect on transdifferentiation appears conserved across species: Treating mouse and human islets with recombinant IGFBP1 in vitro increased the number of cells co‐expressing insulin and glucagon threefold. Moreover, a prospective human study showed that having high IGFBP1 levels reduces the risk of developing type‐2 diabetes by more than 85%. Thus, we identify IGFBP1 as an endogenous promoter of β‐cell regeneration and highlight its clinical importance in diabetes.
A Genome-Wide Screen for Dendritically Localized RNAs Identifies Genes Required for Dendrite Morphogenesis
Authors: Misra Mala , Edmund Hendia , Ennis Darragh , Schlueter Marissa A , Marot Jessica E , Tambasco Janet , Barlow Ida , Sigurbjornsdottir Sara , Mathew Renjith , Vallés Ana Maria , Wojciech Waldemar , Roth Siegfried , Davis Ilan , Leptin Maria , Gavis Elizabeth R 
Published: August 2016

AbstractLocalizing messenger RNAs at specific subcellular sites is a conserved mechanism for targeting the synthesis of cytoplasmic proteins to distinct subcellular domains, thereby generating the asymmetric protein distributions necessary for cellular and developmental polarity. However, the full range of transcripts that are asymmetrically distributed in specialized cell types, and the significance of their localization, especially in the nervous system, are not known. We used the EP-MS2 method, which combines EP transposon insertion with the MS2/MCP in vivo fluorescent labeling system, to screen for novel localized transcripts in polarized cells, focusing on the highly branched Drosophila class IV dendritic arborization neurons. Of a total of 541 lines screened, we identified 55 EP-MS2 insertions producing transcripts that were enriched in neuronal processes, particularly in dendrites. The 47 genes identified by these insertions encode molecularly diverse proteins, and are enriched for genes that function in neuronal development and physiology. RNAi-mediated knockdown confirmed roles for many of the candidate genes in dendrite morphogenesis. We propose that the transport of mRNAs encoded by these genes into the dendrites allows their expression to be regulated on a local scale during the dynamic developmental processes of dendrite outgrowth, branching, and/or remodeling.
A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize
Authors: Jia Shangang , Li Aixia , Morton Kyla , Avoles-Kianian Penny , Kianian Shahryar F , Zhang Chi , Holding David 
Published: August 2016

Abstract
To better understand maize endosperm filling and maturation, we used γ-irradiation of the B73 maize reference line to generate mutants with opaque endosperm and reduced kernel fill phenotypes, and created a population of 1788 lines including 39 Mo17 × F2s showing stable, segregating, and viable kernel phenotypes. For molecular characterization of the mutants, we developed a novel functional genomics platform that combined bulked segregant RNA and exome sequencing (BSREx-seq) to map causative mutations and identify candidate genes within mapping intervals. To exemplify the utility of the mutants and provide proof-of-concept for the bioinformatics platform, we present detailed characterization of line 937, an opaque mutant harboring a 6203 bp in-frame deletion covering six exons within the Opaque-1 gene. In addition, we describe mutant line 146 which contains a 4.8 kb intragene deletion within the Sugary-1 gene and line 916 in which an 8.6 kb deletion knocks out a Cyclin A2 gene. The publically available algorithm developed in this work improves the identification of causative deletions and its corresponding gaps within mapping peaks. This study demonstrates the utility of γ-irradiation for forward genetics in large nondense genomes such as maize since deletions often affect single genes. Furthermore, we show how this classical mutagenesis method becomes applicable for functional genomics when combined with state-of-the-art genomics tools.
A Genome-Wide Association Study for Regulators of Micronucleus Formation in Mice
Authors: McIntyre Rebecca E , Nicod Jérôme , Robles-Espinoza Carla Daniela , Maciejowski John , Cai Na , Hill Jennifer , Verstraten Ruth , Iyer Vivek , Rust Alistair G , Balmus Gabriel , Mott Richard , Flint Jonathan , Adams David J 
Published: August 2016

Abstract
In mammals the regulation of genomic instability plays a key role in tumor suppression and also controls genome plasticity, which is important for recombination during the processes of immunity and meiosis. Most studies to identify regulators of genomic instability have been performed in cells in culture or in systems that report on gross rearrangements of the genome, yet subtle differences in the level of genomic instability can contribute to whole organism phenotypes such as tumor predisposition. Here we performed a genome-wide association study in a population of 1379 outbred Crl:CFW(SW)-US_P08 mice to dissect the genetic landscape of micronucleus formation, a biomarker of chromosomal breaks, whole chromosome loss, and extranuclear DNA. Variation in micronucleus levels is a complex trait with a genome-wide heritability of 53.1%. We identify seven loci influencing micronucleus formation (false discovery rate &lt;5%), and define candidate genes at each locus. Intriguingly at several loci we find evidence for sexual dimorphism in micronucleus formation, with a locus on chromosome 11 being specific to males.
Mutations inDnaaf1andLrrc48Cause Hydrocephalus, Laterality Defects, and Sinusitis in Mice
Authors: Ha Seungshin , Lindsay Anna M , Timms Andrew E , Beier David R 
Published: August 2016

AbstractWe have previously described a forward genetic screen in mice for abnormalities of brain development. Characterization of two hydrocephalus mutants by whole-exome sequencing after whole-genome SNP mapping revealed novel recessive mutations in Dnaaf1 and Lrrc48. Mouse mutants of these two genes have not been previously reported. The Dnaaf1 mutant carries a mutation at the splice donor site of exon 4, which results in abnormal transcripts. The Lrrc48 mutation is a missense mutation at a highly conserved leucine residue, which is also associated with a decrease in Lrrc48 transcription. Both Dnaaf1 and Lrrc48 belong to a leucine-rich repeat-containing protein family and are components of the ciliary axoneme. Their Chlamydomonas orthologs are known to be required for normal ciliary beat frequency or flagellar waveform, respectively. Some Dnaaf1 or Lrrc48 homozygote mutants displayed laterality defects, suggesting a motile cilia defect in the embryonic node. Mucus accumulation and neutrophil infiltration in the maxillary sinuses suggested sinusitis. Dnaaf1 mutants showed postnatal lethality, and none survived to weaning age. Lrrc48 mutants survive to adulthood, but had male infertility. ARL13B immunostaining showed the presence of motile cilia in the mutants, and the distal distribution of DNAH9 in the axoneme of upper airway motile cilia appeared normal. The phenotypic abnormalities suggest that mutations in Dnaaf1 and Lrrc48 cause defects in motile cilia function.
flyDIVaS: A Comparative Genomics Resource for Drosophila Divergence and Selection
Authors: Stanley Craig E , Kulathinal Rob J 
Published: August 2016

AbstractWith arguably the best finished and expertly annotated genome assembly, Drosophila melanogaster is a formidable genetics model to study all aspects of biology. Nearly a decade ago, the 12 Drosophila genomes project expanded D. melanogaster’s breadth as a comparative model through the community-development of an unprecedented genus- and genome-wide comparative resource. However, since its inception, these datasets for evolutionary inference and biological discovery have become increasingly outdated, outmoded, and inaccessible. Here, we provide an updated and upgradable comparative genomics resource of Drosophila divergence and selection, flyDIVaS, based on the latest genomic assemblies, curated FlyBase annotations, and recent OrthoDB orthology calls. flyDIVaS is an online database containing D. melanogaster-centric orthologous gene sets, CDS and protein alignments, divergence statistics (% gaps, dN, dS, dN/dS), and codon-based tests of positive Darwinian selection. Out of 13,920 protein-coding D. melanogaster genes, ∼80% have one aligned ortholog in the closely related species, D. simulans, and ∼50% have 1–1 12-way alignments in the original 12 sequenced species that span over 80 million yr of divergence. Genes and their orthologs can be chosen from four different taxonomic datasets differing in phylogenetic depth and coverage density, and visualized via interactive alignments and phylogenetic trees. Users can also batch download entire comparative datasets. A functional survey finds conserved mitotic and neural genes, highly diverged immune and reproduction-related genes, more conspicuous signals of divergence across tissue-specific genes, and an enrichment of positive selection among highly diverged genes. flyDIVaS will be regularly updated and can be freely accessed at www.flydivas.info. We encourage researchers to regularly use this resource as a tool for biological inference and discovery, and in their classrooms to help train the next generation of biologists to creatively use such genomic big data resources in an integrative manner.
Interallelic Transcriptional Enhancement as an in Vivo Measure of Transvection in Drosophila melanogaster
Authors: Noble Geoffrey P , Dolph Patrick J , Supattapone Surachai 
Published: August 2016

Abstract
Transvection—pairing-dependent interallelic regulation resulting from enhancer action in trans—occurs throughout the Drosophila melanogaster genome, likely as a result of the extensive somatic homolog pairing seen in Dipteran species. Recent studies of transvection in Drosophila have demonstrated important qualitative differences between enhancer action in cisvs.in trans, as well as a modest synergistic effect of cis- and trans-acting enhancers on total tissue transcript levels at a given locus. In the present study, we identify a system in which cis- and trans-acting GAL4-UAS enhancer synergism has an unexpectedly large quantitative influence on gene expression, boosting total tissue transcript levels at least fourfold relative to those seen in the absence of transvection. We exploit this strong quantitative effect by using publicly available UAS-shRNA constructs from the TRiP library to assay candidate genes for transvection activity in vivo. The results of the present study, which demonstrate that in trans activation by simple UAS enhancers can have large quantitative effects on gene expression in Drosophila, have important new implications for experimental design utilizing the GAL4-UAS system.