bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using camouflage for conservation: colour change in juvenile European lobster
Authors: Mynott Sara , Daniels Carly , Widdicombe Stephen , Stevens Martin 
Published: October 2018

AbstractChanges in coloration enable animals to refine their camouflage to match different visual environments. Such plasticity provides ecological benefits and could potentially be exploited to support conservation or stock enhancement efforts. One application could be ensuring that hatchery-reared animals, reared to stock wild populations, are appropriately matched to their environment on release. European lobster (Homarus gammarus) hatcheries aim to restock or enhance local lobster populations by rearing juveniles through their most vulnerable stages, then releasing them into the wild. However, little consideration has been given to their camouflage and the implications of matching individuals to their release site. This study assesses to what extent juvenile lobsters can change coloration to match their background and whether hatchery practices could be altered to enhance lobster camouflage. We test this by switching individuals between black or white backgrounds in the laboratory and monitoring their coloration over time. Our work demonstrates the capacity of juvenile lobsters to change lightness in response to their surroundings. We show that juvenile lobsters are capable of small changes in luminance (perceived lightness) to better match their background over 2-3 weeks. These changes potentially correspond to improved camouflage, based on a model of predator (European pollack,Pollachius pollachius) vision. However, over a longer period (5 weeks), lobsters maintained on either background converged on the same darker coloration, suggesting that lobsters also experience changes in appearance associated with ontogeny. By refining the approaches used here, there is potential for hatcheries to rear lobsters on backgrounds that better match their release site. However, such manipulations should be considered in the context of ontogenetic changes and release timing (which varies between stocking programmes). This study highlights the potential to use colour change in stocking and aquaculture, as well as gaps that could be addressed through further research in this area.
An Orthographic Prediction Error as the basis for efficient Visual Word Recognition
Authors: Gagl Benjamin , Sassenhagen Jona , Haan Sophia , Gregorova Klara , Richlan Fabio , Fiebach Christian J. 
Published: October 2018

AbstractMost current models assume that the perceptual and cognitive processes of visual word recognition and reading operate upon neuronally coded domain-general low-level visual representations – typically oriented line representations. We here demonstrate, consistent with neurophysiological theories of Bayesian-like predictive neural computations, that prior visual knowledge of words may be utilized to ‘explain away’ redundant and highly expected parts of the visual percept. Subsequent processing stages, accordingly, operate upon an optimized representation of the visual input, the orthographic prediction error, highlighting only the visual information relevant for word identification. We show that this optimized representation is related to orthographic word characteristics, accounts for word recognition behavior, and is processed early in the visual processing stream, i.e., in V4 and before 200 ms after word-onset. Based on these findings, we propose that prior visual-orthographic knowledge is used to optimize the representation of visually presented words, which in turn allows for highly efficient reading processes.
There is no single functional atlas even for a single individual: Parcellation of the human brain is state dependent
Authors: Salehi Mehraveh , Greene Abigail S. , Karbasi Amin , Shen Xilin , Scheinost Dustin , Constable R.Todd 
Published: October 2018

AbstractThe goal of human brain mapping has long been to delineate the functional subunits in the brain and elucidate the functional role of each of these brain regions. Recent work has focused on whole-brain parcellation of functional Magnetic Resonance Imaging (fMRI) data to identify these subunits and create a functional atlas. Functional connectivity approaches to understand the brain at the network level require such an atlas to assess connections between parcels and extract network properties. While no single functional atlas has emerged as the dominant atlas to date, there remains an underlying assumption that such an atlas exists. Using fMRI data from a highly sampled subject as well as two independent replication data sets, we demonstrate that functional parcellations based on fMRI connectivity data reconfigure substantially and in a meaningful manner, according to brain state.
Hexameric helicase G40P unwinds DNA in single base pair steps
Authors: Schlierf Michael , Wang Ganggang , Chen Xiaojiang S. , Ha Taekjip 
Published: October 2018

AbstractMost replicative helicases are hexameric, ring-shaped motor proteins that translocate on and unwind DNA. Despite extensive biochemical and structural investigations, how their translocation activity is utilized chemo-mechanically in DNA unwinding is poorly understood. We examined DNA unwinding by G40P, a DnaB-family helicase, using a single-molecule fluorescence assay with a single base pair resolution. The high-resolution assay revealed that G40P by itself is a very weak helicase that stalls at barriers as small as a single GC base pair and unwinds DNA with the step size of a single base pair. Single ATPγS binding could stall unwinding, demonstrating highly coordinated ATP hydrolysis between the six identical subunits. We observed frequent slippage of the helicase, which is fully suppressed by the primase DnaG. We anticipate that these findings allow a better understanding on the fine balance of thermal fluctuation activation and energy derived from hydrolysis.
PUMILIO hyperactivity drives premature aging ofNorad-deficient mice
Authors: Kopp Florian , Yalvac Mehmet E. , Chen Beibei , Zhang He , Lee Sungyul , Gillett Frank A. , Elguindy Mahmoud M. , Sivakumar Sushama , Yu Hongtao , Xie Yang , Mishra Prashant , Sahenk Zarife , Mendell Joshua T. 
Published: October 2018

ABSTRACTAlthough numerous long noncoding RNAs (lncRNAs) have been identified, our understanding of their roles in mammalian physiology remains limited. Here we investigated the physiologic function of the conserved lncRNANorad in vivo.Deletion ofNoradin mice results in genomic instability and mitochondrial dysfunction, leading to a dramatic multi-system degenerative phenotype resembling premature aging. Loss of tissue homeostasis in Norad-deficient animals is attributable to augmented activity of PUMILIO proteins, which act as post-transcriptional repressors of target mRNAs to which they bind.Noradis the preferred RNA target of PUMILIO2 (PUM2) in mouse tissues and, upon loss ofNorad,PUM2 hyperactively represses key genes required for mitosis and mitochondrial function. Remarkably, enforcedPum2expression fully phenocopiesNoraddeletion, resulting in rapid-onset aging-associated phenotypes. These findings provide new insights and open new lines of investigation into the roles of noncoding RNAs and RNA binding proteins in normal physiology and aging.
Optogenetic control shows that kinetic proofreading regulates the activity of the T cell receptor
Authors: Yousefi O. Sascha , Günther Matthias , Hörner Maximilian , Chalupsky Julia , Wess Maximilian , Brandl Simon M. , Smith Robert W. , Fleck Christian , Kunkel Tim , Zurbriggen Matias D. , Höfer Thomas , Weber Wilfried , Schamel Wolfgang W.A. 
Published: October 2018

AbstractThe pivotal task of the immune system is to distinguish between self and foreign antigens. The kinetic proofreading model (KPR) proposes that T cells discriminate self from foreign ligands by the different ligand binding half-lives to the T cell receptor (TCR). It is challenging to test KPR as the available experimental systems fall short of only altering the binding half-lives and keeping other parameters of the ligand-TCR interaction unchanged. We engineered an optogenetic system using the plant photoreceptor phytochrome B to selectively control the dynamics of ligand binding to the TCR by light. Combining experiments with mathematical modeling we find that the ligand-TCR interaction half-life is the decisive factor for activating downstream TCR signaling, substantiating the KPR hypothesis.One Sentence SummaryThe half-life of the ligand-T cell receptor complex determines T cell activation.
Primary Cilium Disassembly in Mammalian Cells Occurs Predominantly by Whole-Cilium Shedding
Authors: Mirvis Mary , Siemers Kathleen , Nelson W. James , Stearns Tim 
Published: October 2018

AbstractThe primary cilium is a central signaling hub in cell proliferation and differentiation, and is built and disassembled every cell cycle in most animal cells. Disassembly is critically important: misregulation or delay of disassembly leads to cell cycle defects. The physical means by which cilia are disassembled are poorly understood, and thought to involve resorption of disassembled components into the cell body. To investigate cilium disassembly in mammalian cells, we used rapid live-cell imaging to comprehensively characterize individual disassembly events. The predominant mode of disassembly was rapid cilium loss via deciliation, in which the membrane and axoneme of the cilium was shed from the cell. Gradual resorption was also observed, as well as events in which a period of gradual resorption ended with rapid deciliation. Deciliation resulted in intact shed cilia that could be recovered from culture medium and contained both membrane and axoneme proteins. We modulated levels of katanin and intracellular calcium, two putative regulators of deciliation, and found that excess katanin promotes disassembly by deciliation, independently of calcium. Together, these results demonstrate that mammalian ciliary disassembly involves a tunable decision between deciliation and resorption.
Forensic STR profiling using Oxford Nanopore Technologies’ MinION sequencer
Authors: Cornelis Senne , Willems Sander , Van Neste Christophe , Tytgat Olivier , Weymaere Jana , Vander Plaetsen Ann-Sophie , Deforce Dieter , Van Nieuwerburgh Filip 
Published: October 2018

AbstractForensic STR profiling using massively parallel sequencing (MPS) has gained much attention as an alternative for the traditional capillary electrophoresis (CE) methods. Oxford Nanopore Technologies recently developed the ‘MinION’, a pocket-sized nanopore sequencer with promising features that could be useful in the field of forensic genetics. We applied this technology for forensic sequencing in a pilot study. Using standard STR primers, originally designed for multiplex PCR and CE, we developed a library preparation method suited for nanopore sequencing. Several analysis approaches were evaluated to explore the usefulness of the generated data: we developed and applied both a sequence-based and an amplicon length-based analysis on data originating from a 14-loci multiplex PCR on a single contributor DNA sample. Despite the high sequencing error rate, the analyses yielded partial forensic profiles with some useful evidential value.
Automatic local resolution-based sharpening of cryo-EM maps
Authors: Ramírez-Aportela Erney , Vilas Jose Luis , Melero Roberto , Conesa Pablo , Martínez Marta , Maluenda David , Mota Javier , Jiménez Amaya , Vargas Javier , Marabini Roberto , Carazo Jose Maria , Sorzano Carlos Oscar S. 
Published: October 2018

AbstractRecent technological advances and computational developments, have allowed the reconstruction of cryo-EM maps at near-atomic resolution structures. Cryo-EM maps benefit significantly of a “postprocessing” step, normally referred to as “sharpening”, that tends to increase signal at medium/high resolution. Here, we propose a new method for local sharpening of volumes generated by cryo-EM. The algorithm (LocalDeblur) is based on a local resolution-guided Wiener restoration approach, does not need any prior atomic model and it avoids artificial structure 1 factor corrections. LocalDeblur is fully automatic and parameter free. We show that the new method significantly and quantitatively improving map quality and interpretability, especially in cases of broad local resolution changes (as is often the case of membrane proteins).
Revealing the Complexities of Metabarcoding with a Diverse Arthropod Mock Community
Authors: Braukmann Thomas W. A. , Ivanova Natalia V. , Prosser Sean W. J. , Elbrecht Vasco , Steinke Dirk , Ratnasingham Sujeevan , deWaard Jeremy R. , Sones Jayme E. , Zakharov Evgeny V. , Hebert Paul D. N. 
Published: October 2018

AbstractDNA metabarcoding is an attractive approach for monitoring biodiversity. However, it is subject to biases that often impede detection of all species in a sample. In particular, the proportion of sequences recovered from each species depends on its biomass, mitome copy number, and primer set employed for PCR. To examine these variables, we constructed a mock community of terrestrial arthropods comprised of 374 BINs, a species proxy. We used this community to examine how species recovery was impacted when amplicon pools were constructed in four ways. The first two protocols involved the construction of bulk DNA extracts from different body partitions (Bulk Abdomen, Bulk Leg). The other protocols involved the production of DNA extracts from single legs which were then merged prior to PCR (Composite Leg) or PCR-amplified separately (Single Leg) and then pooled. The amplicon generated by these four treatments were then sequenced on three platforms (Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5). The choice of sequencing platform did not substantially influence species recovery, other variables did. As expected, the best recovery was obtained from the Single Leg treatment, but the Bulk Abdomen produced a more uniform read abundance than the Bulk Leg or Composite Leg samples. Primer choice also influenced species recovery. Our results reveal how variation in protocols can have substantive impacts on perceived diversity unless sequencing coverage is sufficient to reach an asymptote. Although metabarcoding is a powerful approach, further optimization of analytical protocols is crucial to obtain reproducible results and increase its cost-effectiveness.
GREB1 amplifies androgen receptor output in prostate cancer and contributes to antiandrogen resistance
Authors: Lee Eugine , Wongvipat John , Choi Danielle , Wang Ping , Zheng Deyou , Watson Philip A. , Gopalan Anuradha , Sawyers Charles L. 
Published: October 2018

AbstractGenomic amplification of the androgen receptor (AR) is an established mechanism of antiandrogen resistance in prostate cancer. Here we show that the magnitude of AR signaling output, independent of AR genomic alteration or expression level, also contributes to antiandrogen resistance, through upregulation of the coactivator GREB1. We demonstrate 100-fold heterogeneity in AR output within cell lines and show that cells with high AR output have reduced sensitivity to enzalutamide. Through transcriptomic and shRNA knockdown studies, together with analysis of clinical datasets, we identify GREB1 as a gene responsible for high AR output. We show that GREB1 is an AR target gene that amplifies AR output by enhancing AR DNA binding and promoting p300 recruitment. GREB1 knockdown in high AR output cells restores enzalutamide sensitivity in vivo. Thus, GREB1 is a candidate driver of enzalutamide resistance through a novel feed forward mechanism.
The X-ray structure of human calbindin-D28K: an improved model
Authors: Noble James W. , Almalki Rehab , Roe S. Mark , Wagner Armin , Duman Ramona , Atack John R. 
Published: October 2018

Calbindin-D28K is a widely expressed calcium-buffering cytoplasmic protein that is involved in many physiological processes. It has been shown to interact with other proteins, suggesting a role as a calcium sensor. Many of the targets of calbindin-D28K are of therapeutic interest: for example, inositol monophosphatase, the putative target of lithium therapy in bipolar disorder. Presented here is the first crystal structure of human calbindin-D28K. There are significant deviations in the tertiary structure when compared with the NMR structure of rat calbindin-D28K (PDB entry 2g9b), despite 98% sequence identity. Small-angle X-ray scattering (SAXS) indicates that the crystal structure better predicts the properties of calbindin-D28K in solution compared with the NMR structure. Here, the first direct visualization of the calcium-binding properties of calbindin-D28K is presented. Four of the six EF-hands that make up the secondary structure of the protein contain a calcium-binding site. Two distinct conformations of the N-terminal EF-hand calcium-binding site were identified using long-wavelength calcium single-wavelength anomalous dispersion (SAD). This flexible region has previously been recognized as a protein–protein interaction interface. SAXS data collected in both the presence and absence of calcium indicate that there are no large structural differences in the globular structure of calbindin-D28K between the calcium-loaded and unloaded proteins.
Robot nonlinear control for Unmanned Aerial Vehicles’ multitasking
Authors: Andaluz Víctor H. , Gallardo Cristian M. , Chicaiza Fernando A. , Carvajal Christian P. , Morales José , Cuzco Giovanny , Morales Vicente , Vaca Byron E. , Samaniego Nicolay 
Published: October 2018

Purpose
This paper aims to present a unified motion control scheme for quadcopters which not only solves the point stabilization and trajectory tracking problems but also the path following problem.

Design/methodology/approach
The control problem is solved based on the kinematic model of the unmanned aerial vehicles (UAV). Next, a dynamic compensation controller is considered through of a quadcopter-inner-loop system to independently track four velocity commands: forward, lateral, up/downward and heading rate. Stability and robustness of the whole control system are proved through the Lyapunov’s method. To evaluate the controller’s performance, a multi-user application which allows bilateral communication between a ground station and the Phantom 3 PRO quadrotor is developed.

Findings
The performance of the proposed unified controller is shown through real experiments for the different motion control objectives: point stabilization, trajectory tracking and path following. The experiments confirm the capability of the unified controller to solve different motion problems by an adequate selection of the control references.

Originality/value
This work proposes the design of three types of motion controllers, which can be switched to comply a task in outdoor. Based on the software development kit provided by the company DJI, an application to get and send data to the UAV is developed. By means of this application, the three tasks are tested and the robustness of the controllers is proved.
Analysing the accounting measurement of financial sustainability in local governments through political factors
Authors: Rodríguez Bolívar Manuel Pedro , Navarro Galera Andrés , López Subirés María Deseada , Alcaide Muñoz Laura 
Published: October 2018

Purpose
The purpose of this paper is to obtain new knowledge about the accounting measurement of financial sustainability in local governments, by studying the influence of political factors on the evolution of income statements.

Design/methodology/approach
This paper analyses income statements of Spanish municipalities from 2006 to 2014, together with mayor profiles and political-institutional factors, using the generalised method of moments system.

Findings
The income statement represents a useful measure to assess financial sustainability, showing the effect of political factors on three dimensions proposed by IFAC (i.e. service, revenue and debt), such as ideological coincidence, political competition, political ideology, and absolute majority or political fragmentation.

Practical implications
The findings can be useful for policymakers and accountants responsible for accountability, supervisory bodies, fiscal authorities, voters, users of public services and other stakeholders interested in governmental income statements.

Social implications
In the Eurozone, the crisis of government finance has made the citizens and the policymakers question the size and volume of public services. Likewise, in countries such as Spain, politicians remain one of the main problems for citizens. These circumstances make it very interesting and timely to study the accounting measurement of financial sustainability and its political explanations.

Originality/value
The findings provide new empirical evidence about the accounting measurement of financial sustainability in local governments, and they identify political factors that influence the evolution of income statements.
Tensile strength of GFRP and hybrid composites under various environmental conditions
Authors: Chelladhurai Praveen Shaju 
Published: October 2018

Purpose
The purpose of this paper is to study the mechanical behavior of glass fiber reinforced polymer (GFRP) and hybrid composites under various adverse environmental conditions. This mainly helps the researchers to overcome the obstacles that have been met when they use the materials individually and also to know the impacts of environment on them.

Design/methodology/approach
The GFRP and hybrid specimens are made according to the American Society for Testing and Materials standard. The specimens are then immersed in aviation turbine fuel, hydraulic fluid and concentrated sulfuric acid. The tensile strength of the specimens is then determined using the universal testing machine.

Findings
The tensile strengths of the normal specimens and the specimens subjected to various environmental conditions are determined. The results obtained for GFRP and hybrid specimens are then compared.

Research limitations/implications
The researchers can extend the time intervals further for a better understanding of the strength of the composites.

Practical implications
Once better combinations are found out with the highest strength to weight ratio and its resistance to various adverse environmental conditions, it can be used in real-time applications.

Social implications
The best hybrid combinations can be used in place of metals in future.

Originality/value
This is an original research and is clearly based on the experimental results, so it adds very much value to the aviation industry because strength to weight ratio is one of the major issues to be taken into consideration.