bluuebunny/crossref_metadata_2025_split huggingface dataset:
In-depth proteomic analysis of Varroa destructor: Detection of DWV-complex, ABPV, VdMLV and honeybee proteins in the mite
Authors: Erban Tomas , Harant Karel , Hubalek Martin , Vitamvas Pavel , Kamler Martin , Poltronieri Palmiro , Tyl Jan , Markovic Martin , Titera Dalibor 
Published: September 2015

AbstractWe investigated pathogens in the parasitic honeybee mite Varroa destructor using nanoLC-MS/MS (TripleTOF) and 2D-E-MS/MS proteomics approaches supplemented with affinity-chromatography to concentrate trace target proteins. Peptides were detected from the currently uncharacterized Varroa destructor Macula-like virus (VdMLV), the deformed wing virus (DWV)-complex and the acute bee paralysis virus (ABPV). Peptide alignments revealed detection of complete structural DWV-complex block VP2-VP1-VP3, VDV-1 helicase and single-amino-acid substitution A/K/Q in VP1, the ABPV structural block VP1-VP4-VP2-VP3 including uncleaved VP4/VP2 and VdMLV coat protein. Isoforms of viral structural proteins of highest abundance were localized via 2D-E. The presence of all types of capsid/coat proteins of a particular virus suggested the presence of virions in Varroa. Also, matches between the MWs of viral structural proteins on 2D-E and their theoretical MWs indicated that viruses were not digested. The absence/scarce detection of non-structural proteins compared with high-abundance structural proteins suggest that the viruses did not replicate in the mite; hence, virions accumulate in the Varroa gut via hemolymph feeding. Hemolymph feeding also resulted in the detection of a variety of honeybee proteins. The advantages of MS-based proteomics for pathogen detection, false-positive pathogen detection, virus replication, posttranslational modifications and the presence of honeybee proteins in Varroa are discussed.
Updating stored memory requires adult hippocampal neurogenesis
Authors: Suárez-Pereira Irene , Carrión Ángel M 
Published: September 2015

AbstractAdult hippocampal neurogenesis appears to influence hippocampal functions, such as memory formation for example. While adult hippocampal neurogenesis is known to be involved in hippocampal-dependent learning and consolidation processes, the role of such immature neurons in memory reconsolidation, a process involved in the modification of stored memories, remains unclear. Here, using a novel fast X-ray ablation protocol to deplete neurogenic cells, we have found that adult hippocampal neurogenesis is required to update object recognition stored memory more than to reinforce it. Indeed, we show that immature neurons were selectively recruited to hippocampal circuits during the updating of stored information. Thus, our data demonstrate a new role for neurogenesis in cognitive processes, adult hippocampal neurogenesis being required for the updating of stored OR memories. These findings suggest that manipulating adult neurogenesis may have a therapeutic application in conditions associated with traumatic stored memory, for example.
Control of plasmonic nanoantennas by reversible metal-insulator transition
Authors: Abate Yohannes , Marvel Robert E. , Ziegler Jed I. , Gamage Sampath , Javani Mohammad H. , Stockman Mark I. , Haglund Richard F. 
Published: September 2015

AbstractWe demonstrate dynamic reversible switching of VO2 insulator-to-metal transition (IMT) locally on the scale of 15 nm or less and control of nanoantennas, observed for the first time in the near-field. Using polarization-selective near-field imaging techniques, we simultaneously monitor the IMT in VO2 and the change of plasmons on gold infrared nanoantennas. Structured nanodomains of the metallic VO2 locally and reversibly transform infrared plasmonic dipole nanoantennas to monopole nanoantennas. Fundamentally, the IMT in VO2 can be triggered on femtosecond timescale to allow ultrafast nanoscale control of optical phenomena. These unique features open up promising novel applications in active nanophotonics.
Magnetic Particle Imaging tracks the long-term fate of in vivo neural cell implants with high image contrast
Authors: Zheng Bo , Vazin Tandis , Goodwill Patrick W. , Conway Anthony , Verma Aradhana , Ulku Saritas Emine , Schaffer David , Conolly Steven M. 
Published: September 2015

AbstractWe demonstrate that Magnetic Particle Imaging (MPI) enables monitoring of cellular grafts with high contrast, sensitivity and quantitativeness. MPI directly detects the intense magnetization of iron-oxide tracers using low-frequency magnetic fields. MPI is safe, noninvasive and offers superb sensitivity, with great promise for clinical translation and quantitative single-cell tracking. Here we report the first MPI cell tracking study, showing 200-cell detection in vitro and in vivo monitoring of human neural graft clearance over 87 days in rat brain.
Antimony porphyrins as red-light powered photocatalysts for solar fuel production from halide solutions in the presence of air
Authors: Ertl M. , Wöß E. , Knör G. 
Published: September 2015

Abstract
Halide ions (X−) as cheap and abundant electron donors are oxidized with simulated sunlight in a photocatalytic reaction based on robust antimony porphyrins acting as red-light harvesting multielectron transfer sensitizers. Besides halogen formation (X2/X3
−) this solar energy storing process under certain conditions also accumulates hydrogen peroxide (H2O2) as a second energy-rich compound.
Shape-designed frustration by local polymorphism in a near-equilibrium colloidal glass
Authors: Zhao Kun , Mason Thomas G. 
Published: September 2015

SignificanceThe origin of disorder in glasses is one of the most important unresolved questions in materials science. In many cases, for materials made of monodisperse components that are not attractive and have the capacity to crystallize, such as dispersions of colloidal hard spheres, the disorder is typically associated with rapid, out-of-equilibrium quenching of the density that causes components to jam into disordered configurations. By contrast, here we reveal that hard colloidal kite-shaped particles, which have the geometric capacity to crystallize, instead form a disordered glass when compressed very slowly and quasi-statically. We show that this glassy disorder results from a high diversity of different local configurations of kites, effectively masking the one global crystal phase.
Quantifying a Manual Triangulation Technique for Aquatic Ultrasonic Telemetry
Authors: Taylor Andrew D. , Litvak Matthew K. 
Published: September 2015

Abstract
Ultrasonic telemetry is widely used to determine the large-scale migrations and movements of aquatic animals, but it can also be used to monitor fine-scale movements and habitat occupancy. We tested the accuracy and precision of a method that manually triangulates transmitter locations from a series of bearings recorded at known observer locations. Bearing estimates were based on the direction of the strongest transmitter pulse received at each stationary position. With a minimum of three bearing estimates, transmitter locations and 95% confidence ellipses were calculated. Testing within a blind experimental design showed that triangulation improved accuracy and precision when additional bearings were used and that it was optimized when bearings were recorded from widespread locations. Using 3–7 bearing positions, 95% of all location estimates were within 34 m of the actual transmitter. Triangulation is best suited for monitoring animals during periods of quiescence, and it can be used effectively to describe the extent of home ranges, spawning areas, and overwintering habitat, among other factors. Understanding the fine-scale habitat occupancy of aquatic animals is critical to species management, and triangulation can provide substantial improvements to the traditional location estimates used in ultrasonic telemetry.
Received December 30, 2014; accepted June 2, 2015
High-performance liquid chromatographic method for profiling 2-oxo acids in urine and its application in evaluating vitamin status in rats
Authors: Shibata Katsumi , Nakata Chifumi , Fukuwatari Tsutomu 
Published: September 2015

Abstract
B-group vitamins are involved in the catabolism of 2-oxo acids. To identify the functional biomarkers of B-group vitamins, we developed a high-performance liquid chromatographic method for profiling 2-oxo acids in urine and applied this method to urine samples from rats deficient in vitamins B1 and B6 and pantothenic acid. 2-Oxo acids were reacted with 1,2-diamino-4,5-methylenebenzene to produce fluorescent derivatives, which were then separated using a TSKgel ODS-80Ts column with 30 mmol/L of KH2PO4 (pH 3.0):acetonitrile (7:3) at a flow rate of 1.0 mL/min. Vitamin B1 deficiency increased urinary levels of all 2-oxo acids, while vitamin B6 deficiency only increased levels of sum of 2-oxaloacetic acid and pyruvic acid, and pantothenic acid deficiency only increased levels of 2-oxoisovaleric acid. Profiles of 2-oxo acids in urine samples might be a non-invasive way of clarifying the functional biomarker of B-group vitamins.
Group and sparse group partial least square approaches applied in genomics context
Authors: Liquet Benoît , de Micheaux Pierre Lafaye , Hejblum Boris P. , Thiébaut Rodolphe 
Published: September 2015

Abstract
Motivation: The association between two blocks of ‘omics’ data brings challenging issues in computational biology due to their size and complexity. Here, we focus on a class of multivariate statistical methods called partial least square (PLS). Sparse version of PLS (sPLS) operates integration of two datasets while simultaneously selecting the contributing variables. However, these methods do not take into account the important structural or group effects due to the relationship between markers among biological pathways. Hence, considering the predefined groups of markers (e.g. genesets), this could improve the relevance and the efficacy of the PLS approach.
Results: We propose two PLS extensions called group PLS (gPLS) and sparse gPLS (sgPLS). Our algorithm enables to study the relationship between two different types of omics data (e.g. SNP and gene expression) or between an omics dataset and multivariate phenotypes (e.g. cytokine secretion). We demonstrate the good performance of gPLS and sgPLS compared with the sPLS in the context of grouped data. Then, these methods are compared through an HIV therapeutic vaccine trial. Our approaches provide parsimonious models to reveal the relationship between gene abundance and the immunological response to the vaccine.
Availability and implementation: The approach is implemented in a comprehensive R package called sgPLS available on the CRAN.
Contact: b.liquet@uq.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
Natural vs. fishing disturbance: drivers of community composition on traditional king scallop,
Pecten maximus,
fishing grounds
Authors: Szostek Claire L. , Murray Lee G. , Bell Ewen , Rayner Gemma , Kaiser Michel J. 
Published: September 2015

Abstract
Scallop dredging is considered to be one of the most damaging forms of fishing to benthic habitats, although these effects vary among different habitats. The present study characterizes the biological communities that occur within the spatial limits of the English Channel king scallop dredge fishery in relation to key environmental drivers [mean seabed temperature; seabed temperature range; interannual temperature variation; bed shear stress (BSS); substrate characteristics; and depth] and across a gradient of scallop dredging intensity derived from vessel monitoring system data. Dredge fishing intensity was not correlated with species richness, species diversity, or species composition. However, increasing tidal BSS had a significant negative correlation with species richness and diversity. This outcome indicates that it is not possible to demonstrate that there is an effect of scallop fishing within the current spatial limits of the king scallop dredge fishery. This may be because historical dredge fishing could have already altered the benthic communities within the area of the scallop fishery to those that are resilient to scallop dredging, or that fishing disturbance has no impact over and above natural physical disturbance within the fishery. An analysis of biological and life history traits revealed that there was no relationship between recent fishing intensity, or BSS, and the functional composition of the communities present. However, even the lowest BSS values in the present study could be considered relatively high compared with areas outside the spatial boundaries of the fishery. Two distinct habitat groups were identified, based on the environmental drivers. These two groups were largely characterized by depth: deep (western) and shallow (eastern) sites. Species with traits that increase resilience to physical disturbance were abundant across all sample sites. Management concerning the environmental impacts of the fishery is discussed in terms of the spatial footprint of the fishery and predicted recovery time-scales for the associated benthic communities.
Growth and Maturation of Children and Adolescents
Authors: Rogol Alan D. 
Published: September 2015

Abstract
Normal growth of a child or adolescent likely indicates his or her good general health and well-being. However, there is great variability in the heights and weights that are within the range of normal. Abnormally slow growth may indicate a pathological process or disruption of the environment. Height is a genetically determined parameter, but, at least in the human, it is affected by the interactions of hundreds of genes. In otherwise well children, perhaps 80% of the variance is inherited. Pubertal maturation follows a “fixed” sequence in boys and girls, but its timing and tempo are both determined by the interactions of multiple genes. Environmental effects may play a role in the early initiation of puberty in the obese and the delayed initiation in those with caloric deprivation. Subjects with pathologic growth trajectories deserve medical evaluation because those processes may be abrogated with proper treatment.
Victimization Surveys
Authors: Bradford Ben , MacQueen Sarah 
Published: September 2015

AbstractThis chapter considers the history, development, and uses of crime victimization surveys. Offering a wide view of the topic at hand, discussion ranges from the historical development and political economy of crime surveys to consideration of the many methodological challenges they face. A key thread running through the chapter, however, is that although they face many intractable problems, crime surveys are indispensible in terms of generating insight into temporal change in levels of crime and investigating the distribution of various forms of victimization across the population. Despite growing budgetary constraints, victimization surveys look set to continue as part of academic and policy attempts to “know” crime.
White Matter Associations With Performance Validity Testing in Veterans With Mild Traumatic Brain Injury: The Utility of Biomarkers in Complicated Assessment
Authors: Clark Alexandra L. , Sorg Scott F. , Schiehser Dawn M. , Bigler Erin D. , Bondi Mark W. , Jacobson Mark W. , Jak Amy J. , Delano-Wood Lisa 
Published: September 2015

Objective:
Failure on performance validity tests (PVTs) is common in Veterans with histories of mild traumatic brain injury (mTBI), leading to questionable validity of clinical presentations.

Participants:
Using diffusion tensor imaging, we investigated white matter (WM) integrity and cognition in 79 Veterans with history of mTBI who passed PVTs (n = 43; traumatic brain injury [TBI]-passed), history of mTBI who failed at least 1 PVT (n = 13; TBI-failed), and military controls (n = 23; MCs) with no history of TBI.

Results:
The TBI-failed group demonstrated significantly lower cognitive scores relative to MCs and the TBI-passed group; however, no such differences were observed between MCs and the TBI-passed group. On a global measure of WM integrity (ie, WM burden), the TBI-failed group showed more overall WM abnormalities than the other groups. However, no differences were observed between the MCs and TBI-passed group on WM burden. Interestingly, regional WM analyses revealed abnormalities in the anterior internal capsule and cingulum of both TBI subgroups relative to MCs. Moreover, compared with the TBI-passed group, the TBI-failed group demonstrated significantly decreased WM integrity in the corpus callosum.

Conclusions:
Findings revealed that, within our sample, WM abnormalities are evident in those who fail PVTs. This study adds to the burgeoning PVT literature by suggesting that poor PVT performance does not negate the possibility of underlying WM abnormalities in military personnel with history of mTBI.
Long-Term Motor Recovery After Severe Traumatic Brain Injury: Beyond Established Limits
Authors: D'Arcy Ryan C. N. , Lindsay D. Stephen , Song Xiaowei , Gawryluk Jodie R. , Greene Debbie , Mayo Chantel , Ghosh Hajra Sujoy , Mandziuk Lila , Mathieson John , Greene Trevor 
Published: September 2015

Objective:
To report neural plasticity changes after severe traumatic brain injury.

Setting:
Case-control study.

Participants:
Canadian soldier, Captain Trevor Greene survived a severe open-traumatic brain injury during a 2006 combat tour in Afghanistan.

Design:
Longitudinal follow-up for more than 6 years.

Main Measures:
Twelve longitudinal functional magnetic imaging (fMRI) examinations were conducted to investigate lower limb activation changes in association with clinical examination. Trevor Greene's lower limb fMRI activation was compared with control fMRI activation of (1) mental imagery of similar movement and (2) matched control subject data.

Results:
Trevor Greene's motor recovery and corresponding fMRI activation increased significantly over time (F = 32.54, P < .001). Clinical measures of functional recovery correlated strongly with fMRI motor activation changes (r = 0.81, P = .001). By comparison, while Trevor Greene's mental imagery activated similar motor regions, there was no evidence of fMRI activation change over time. While comparable, control motor activation did not change over time and there was no significant mental imagery activation.

Conclusion:
Motor function recovery can occur beyond 6 years after severe traumatic brain injury, both in neural plasticity and clinical outcome. This demonstrates that continued benefits in physical function due to rehabilitative efforts can be achieved for many years following injury. The finding challenges current practices and assumptions in rehabilitation following traumatic brain injury.
Crucial Roles of the Arp2/3 Complex during Mammalian Corticogenesis
Authors: Wang Pei-Shan , Chou Fu-Sheng , Guo Fengli , Suraneni Praveen , Xia Sheng , Ramachandran Sree , Li Rong 
Published: September 2015

HIGHLIGHTSDisruption of the Arp2/3 complex impairs cortical development The Arp2/3 complex promotes RGC basal process extension and apical adhesion Loss of Arp2/3 complex leads to altered RGC polarity and cell fate The Arp2/3 complex has non-cell-autonomous and cell-autonomous roles in neuronal migration The Arp2/3 complex enables neuronal cells to migrate on soft or less adhesive substratesSUMMARYThe polarity and organization of radial glial cells (RGCs), which serve as both stem cells and scaffolds for neuronal migration, are crucial for cortical development. However, the cytoskeletal mechanisms that drive radial glial outgrowth and maintain RGC polarity remain poorly understood. Here, we show that the Arp2/3 complex, the unique actin nucleator that produces branched actin networks, plays essential roles in RGC polarity and morphogenesis. Disruption of the Arp2/3 complex in RGCs retards process outgrowth toward the basal surface and impairs apical polarity and adherens junctions. Whereas the former is correlated with abnormal actin-based leading edge, the latter is consistent with blockage in membrane trafficking. These defects result in altered cell fate, disrupted cortical lamination and abnormal angiogenesis. In addition, we present evidence that the Arp2/3 complex is a cell-autonomous regulator of neuronal migration. Our data suggest that Arp2/3-mediated actin assembly may be particularly important for neuronal cell motility in soft or poorly adhesive matrix environment.
Prediction of Hfq in actinobacteria
Authors: Bora Nagamani , Ward Alan C , Kim Wonyong 
Published: September 2015

AbstractHfq is the bacterial orthologue of the eukaryotic (L)Sm family of proteins found across all domains of life and potentially an ancient protein, but it has not been found in all phyletic lines. A careful search successfully identified a distant hfq orthologue in the cyanobacteria leaving the actinobacteria as the major phylum with no known hfq orthologue. A search for hfq in actinobacteria, using domain enhanced searching (DELTA-BLAST) with cyanobacterial hfq, identified a conserved actinobacterial specific protein as remotely homologous. Structural homology modelling using profile matching to fold libraries andab initio3D structure determination supports this prediction and suggests module shuffling in the evolution of the actinobacterial hfq. Our results provide the basis to explore this prediction, and exploit it, across diverse taxa with potentially important post-transcriptional regulatory effects in virulence, antibiotic production and interactions in human microbiomes. However, the role of hfq in gram positive bacteria has remained elusive and experimental verification will be challenging.
Decomposing variability in protein levels from noisy expression, genome duplication and partitioning errors during cell-divisions
Authors: Soltani M. , Vargas-Garcia C. A. , Antunes D. , Singh A. 
Published: September 2015

AbstractInside individual cells, expression of genes is inherently stochastic and manifests as cell-to-cell variability or noise in protein copy numbers. Since proteins half-lives can be comparable to the cell-cycle length, randomness in cell-division times generates additional intercellular variability in protein levels. Moreover, as many mRNA/protein species are expressed at low-copy numbers, errors incurred in partitioning of molecules between the mother and daughter cells are significant. We derive analytical formulas for the total noise in protein levels for a general class of cell-division time and partitioning error distributions. Using a novel hybrid approach the total noise is decomposed into components arising from i) stochastic expression; ii) partitioning errors at the time of cell-division and iii) random cell-division events. These formulas reveal that random cell-division times not only generate additional extrinsic noise but also critically affect the mean protein copy numbers and intrinsic noise components. Counter intuitively, in some parameter regimes noise in protein levels can decrease as cell-division times become more stochastic. Computations are extended to consider genome duplication, where the gene dosage is increased by two-fold at a random point in the cell-cycle. We systematically investigate how the timing of genome duplication influences different protein noise components. Intriguingly, results show that noise contribution from stochastic expression is minimized at an optimal genome duplication time. Our theoretical results motivate new experimental methods for decomposing protein noise levels from single-cell expression data. Characterizing the contributions of individual noise mechanisms will lead to precise estimates of gene expression parameters and techniques for altering stochasticity to change phenotype of individual cells.