bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatic Construction of Predictive Neuron Models through Large Scale Assimilation of Electrophysiological Data
Authors: Nogaret Alain , Meliza C. Daniel , Margoliash Daniel , Abarbanel Henry D. I. 
Published: September 2016

AbstractWe report on the construction of neuron models by assimilating electrophysiological data with large-scale constrained nonlinear optimization. The method implements interior point line parameter search to determine parameters from the responses to intracellular current injections of zebra finch HVC neurons. We incorporated these parameters into a nine ionic channel conductance model to obtain completed models which we then use to predict the state of the neuron under arbitrary current stimulation. Each model was validated by successfully predicting the dynamics of the membrane potential induced by 20–50 different current protocols. The dispersion of parameters extracted from different assimilation windows was studied. Differences in constraints from current protocols, stochastic variability in neuron output, and noise behave as a residual temperature which broadens the global minimum of the objective function to an ellipsoid domain whose principal axes follow an exponentially decaying distribution. The maximum likelihood expectation of extracted parameters was found to provide an excellent approximation of the global minimum and yields highly consistent kinetics for both neurons studied. Large scale assimilation absorbs the intrinsic variability of electrophysiological data over wide assimilation windows. It builds models in an automatic manner treating all data as equal quantities and requiring minimal additional insight.
Multiple intrinsic factors act in concert with Lhx2 to direct retinal gliogenesis
Authors: de Melo Jimmy , Clark Brian S. , Blackshaw Seth 
Published: September 2016

AbstractMüller glia (MG) are the principal glial cell type in the vertebrate retina. Recent work has identified the LIM homeodomain factor encoding gene Lhx2 as necessary for both Notch signaling and MG differentiation in late-stage retinal progenitor cells (RPCs). However, the extent to which Lhx2 interacts with other intrinsic regulators of MG differentiation is unclear. We investigated this question by investigating the effects of overexpression of multiple transcriptional regulators that are either known or hypothesized to control MG formation, in both wildtype and Lhx2-deficient RPCs. We observe that constitutively elevated Notch signaling, induced by N1ICD electroporation, inhibited gliogenesis in wildtype animals, but rescued MG development in Lhx2-deficient retinas. Electroporation of Nfia promoted the formation of cells with MG-like radial morphology, but did not drive expression of MG molecular markers. Plagl1 and Sox9 did not induce gliogenesis in wildtype animals, but nonetheless activated expression of the Müller marker P27Kip1 in Lhx2-deficient cells. Finally, Sox2, Sox8, and Sox9 promoted amacrine cell formation in Lhx2-deficient cells, but not in wildtype retinas. These findings demonstrate that overexpression of individual gliogenic factors typically regulates only a subset of characteristic MG markers, and that these effects are differentially modulated by Lhx2.
Quantifying the pharmacology of antimalarial drug combination therapy
Authors: Hastings Ian M. , Hodel Eva Maria , Kay Katherine 
Published: September 2016

AbstractMost current antimalarial drugs are combinations of an artemisinin plus a ‘partner’ drug from another class, and are known as artemisinin-based combination therapies (ACTs). They are the frontline drugs in treating human malaria infections. They also have a public-health role as an essential component of recent, comprehensive scale-ups of malaria interventions and containment efforts conceived as part of longer term malaria elimination efforts. Recent reports that resistance has arisen to artemisinins has caused considerable concern. We investigate the likely impact of artemisinin resistance by quantifying the contribution artemisinins make to the overall therapeutic capacity of ACTs. We achieve this using a simple, easily understood, algebraic approach and by more sophisticated pharmacokinetic/pharmacodynamic analyses of drug action; the two approaches gave consistent results. Surprisingly, the artemisinin component typically makes a negligible contribution (≪0.0001%) to the therapeutic capacity of the most widely used ACTs and only starts to make a significant contribution to therapeutic outcome once resistance has started to evolve to the partner drugs. The main threat to antimalarial drug effectiveness and control comes from resistance evolving to the partner drugs. We therefore argue that public health policies be re-focussed to maximise the likely long-term effectiveness of the partner drugs.
Assessing morphology and function of the semicircular duct system: introducing new in-situ visualization and software toolbox
Authors: David R. , Stoessel A. , Berthoz A. , Spoor F. , Bennequin D. 
Published: September 2016

AbstractThe semicircular duct system is part of the sensory organ of balance and essential for navigation and spatial awareness in vertebrates. Its function in detecting head rotations has been modelled with increasing sophistication, but the biomechanics of actual semicircular duct systems has rarely been analyzed, foremost because the fragile membranous structures in the inner ear are hard to visualize undistorted and in full. Here we present a new, easy-to-apply and non-invasive method for three-dimensionalin-situvisualization and quantification of the semicircular duct system, using X-ray micro tomography and tissue staining with phosphotungstic acid. Moreover, we introduce Ariadne, a software toolbox which provides comprehensive and improved morphological and functional analysis of any visualized duct system. We demonstrate the potential of these methods by presenting results for the duct system of humans, the squirrel monkey and the rhesus macaque, making comparisons with past results from neurophysiological, oculometric and biomechanical studies. Ariadne is freely available athttp://www.earbank.org.
Alterations of mitochondrial dynamics allow retrograde propagation of locally initiated axonal insults
Authors: Lassus Benjamin , Magnifico Sebastien , Pignon Sandra , Belenguer Pascale , Miquel Marie-Christine , Peyrin Jean-Michel 
Published: September 2016

AbstractIn chronic neurodegenerative syndromes, neurons progressively die through a generalized retraction pattern triggering retrograde axonal degeneration toward the cell bodies, which molecular mechanisms remain elusive. Recent observations suggest that direct activation of pro-apoptotic signaling in axons triggers local degenerative events associated with early alteration of axonal mitochondrial dynamics. This raises the question of the role of mitochondrial dynamics on both axonal vulnerability stress and their implication in the spreading of damages toward unchallenged parts of the neuron. Here, using microfluidic chambers, we assessed the consequences of interfering with OPA1 and DRP1 proteins on axonal degeneration induced by local application of rotenone. We found that pharmacological inhibition of mitochondrial fission prevented axonal damage induced by rotenone, in low glucose conditions. While alteration of mitochondrial dynamics per se did not lead to spontaneous axonal degeneration, it dramatically enhanced axonal vulnerability to rotenone, which had no effect in normal glucose conditions, and promoted retrograde spreading of axonal degeneration toward the cell body. Altogether, our results suggest a mitochondrial priming effect in axons as a key process of axonal degeneration. In the context of neurodegenerative diseases, like Parkinson’s and Alzheimer’s, mitochondria fragmentation could hasten neuronal death and initiate spatial dispersion of locally induced degenerative events.
Genome-wide Identification of TCP Family Transcription Factors from Populus euphratica and Their Involvement in Leaf Shape Regulation
Authors: Ma Xiaodong , Ma Jianchao , Fan Di , Li Chaofeng , Jiang Yuanzhong , Luo Keming 
Published: September 2016

AbstractHigher plants have been shown to experience a juvenile vegetative phase, an adult vegetative phase, and a reproductive phase during its postembryonic development and distinct lateral organ morphologies have been observed at the different development stages. Populus euphratica, commonly known as a desert poplar, has developed heteromorphic leaves during its development. The TCP family genes encode a group of plant-specific transcription factors involved in several aspects of plant development. In particular, TCPs have been shown to influence leaf size and shape in many herbaceous plants. However, whether these functions are conserved in woody plants remains unknown. In the present study, we carried out genome-wide identification of TCP genes in P. euphratica and P. trichocarpa, and 33 and 36 genes encoding putative TCP proteins were found, respectively. Phylogenetic analysis of the poplar TCPs together with Arabidopsis TCPs indicated a biased expansion of the TCP gene family via segmental duplications. In addition, our results have also shown a correlation between different expression patterns of several P. euphratica TCP genes and leaf shape variations, indicating their involvement in the regulation of leaf shape development.
Terrestrial biome distribution in the Late Neogene inferred from a black carbon record in the northeastern equatorial Pacific
Authors: Kim Donghyun , Lee Yong Il , Hyeong Kiseong , Yoo Chan Min 
Published: September 2016

AbstractThe appearance and expansion of C4plants in the Late Cenozoic was a dramatic example of terrestrial ecological change. The fire hypothesis, which suggests fire as a major cause of C4grassland is gaining support, yet a more detailed relationship between fire and vegetation-type change remains unresolved. We report the content and stable carbon isotope record of black carbon (BC) in a sediment core retrieved from the northeastern equatorial Pacific that covers the past 14.3 million years. The content record of BC suggests the development process of a flammable ecosystem. The stable carbon isotope record of BC reveals the existence of the Late Miocene C4expansion, the ‘C4maximum period of burned biomass’ during the Pliocene to Early Pleistocene, and the collapse of the C4in the Late Pleistocene. Records showing the initial expansion of C4plants after large fire support the role of fire as a destructive agent of C3-dominated forest, yet the weak relationships between fire and vegetation after initial expansion suggest that environmental advantages for C4plants were necessary to maintain the development of C4plants during the late Neogene. Among the various environmental factors, aridity is likely most influential in C4expansion.
Site-specific fluorescent labeling to visualize membrane translocation of a myristoyl switch protein
Authors: Yang Sung-Tae , Lim Sung In , Kiessling Volker , Kwon Inchan , Tamm Lukas K. 
Published: September 2016

AbstractFluorescence approaches have been widely used for elucidating the dynamics of protein-membrane interactions in cells and model systems. However, non-specific multi-site fluorescent labeling often results in a loss of native structure and function, and single cysteine labeling is not feasible when native cysteines are required to support a protein’s folding or catalytic activity. Here, we develop a method using genetic incorporation of non-natural amino acids and bio-orthogonal chemistry to site-specifically label with a single fluorescent small molecule or protein the myristoyl-switch protein recoverin, which is involved in rhodopsin-mediated signaling in mammalian visual sensory neurons. We demonstrate reversible Ca2+-responsive translocation of labeled recoverin to membranes and show that recoverin favors membranes with negative curvature and high lipid fluidity in complex heterogeneous membranes, which confers spatio-temporal control over down-stream signaling events. The site-specific orthogonal labeling technique is promising for structural, dynamical, and functional studies of many lipid-anchored membrane protein switches.
Evaluating the time trends in prevalence of exomphalos in 14 cities of Liaoning province, 2006 to 2015
Authors: Gong Ting-Ting , Wu Qi-Jun , Chen Yan-Ling , Jiang Cheng-Zhi , Li Jing , Li Li-Li , Liu Cai-Xia , Li Da , Zhou Chen , Huang Yan-Hong 
Published: September 2016

AbstractTo evaluate time trends of exomphalos prevalence using a large population-based study with cases identified by the Liaoning Birth Defects Registry including 14 cities over the course of a 10-year period. Exomphalos prevalence, percent change, annual percent change (APC), and contribution rates of each city were calculated. Additionally, epidemiological characteristics of this malformation were described. We observed 516 cases of exomphalos among 3,248,954 live births. Birth prevalence of exomphalos was 1.59 per 10,000 live births with non-significant change during the observational period (APC = −1.19%, P = 0.48). However, significantly decreasing trends were noticed in three cities: Fushun (APC = −9.15%, P = 0.03), Benxi (APC = −11.49%, P = 0.05), and Yingkou (APC = −16.47%, P = 0.04), contributing 62.77% of the decreasing trend of overall prevalence. The mean maternal age, gestational age, and birth weight was 28.4 years (standard deviation [SD], 6.1 years), 25.6 weeks (SD, 8.6 weeks), and 1236.2 gram (SD, 1164.4 gram). For time of diagnosis, 79.8% (n = 412) cases were diagnosed during pregnancy. In summary, the prevalence of exomphalos in Liaoning province did not change remarkably during 2006 to 2015. Future studies are warranted to investigate the risk factors and create prevention strategies for this disease.
Detecting Thermal Cloaks via Transient Effects
Authors: Sklan Sophia R. , Bai Xue , Li Baowen , Zhang Xiang 
Published: September 2016

AbstractRecent research on the development of a thermal cloak has concentrated on engineering an inhomogeneous thermal conductivity and an approximate, homogeneous volumetric heat capacity. While the perfect cloak of inhomogeneous κ and inhomogeneous ρcp is known to be exact (no signals scattering and only mean values penetrating to the cloak’s interior), the sensitivity of diffusive cloaks to defects and approximations has not been analyzed. We analytically demonstrate that these approximate cloaks are detectable. Although they work as perfect cloaks in the steady-state, their transient (time-dependent) response is imperfect and a small amount of heat is scattered. This is sufficient to determine the presence of a cloak and any heat source it contains, but the material composition hidden within the cloak is not detectable in practice. To demonstrate the feasibility of this technique, we constructed a cloak with similar approximation and directly detected its presence using these transient temperature deviations outside the cloak. Due to limitations in the range of experimentally accessible volumetric specific heats, our detection scheme should allow us to find any realizable cloak, assuming a sufficiently large temperature difference.
Influence of single and binary doping of strontium and lithium on in vivo biological properties of bioactive glass scaffolds
Authors: Khan Pintu Kumar , Mahato Arnab , Kundu Biswanath , Nandi Samit K. , Mukherjee Prasenjit , Datta Someswar , Sarkar Soumya , Mukherjee Jayanta , Nath Shalini , Balla Vamsi K. , Mandal Chitra 
Published: September 2016

AbstractEffects of strontium and lithium ion doping on the biological properties of bioactive glass (BAG) porous scaffolds have been checked in vitro and in vivo. BAG scaffolds were prepared by conventional glass melting route and subsequently, scaffolds were produced by evaporation of fugitive pore formers. After thorough physico-chemical and in vitro cell characterization, scaffolds were used for pre-clinical study. Soft and hard tissue formation in a rabbit femoral defect model after 2 and 4 months, were assessed using different tools. Histological observations showed excellent osseous tissue formation in Sr and Li + Sr scaffolds and moderate bone regeneration in Li scaffolds. Fluorochrome labeling studies showed wide regions of new bone formation in Sr and Li + Sr doped samples as compared to Li doped samples. SEM revealed abundant collagenous network and minimal or no interfacial gap between bone and implant in Sr and Li + Sr doped samples compared to Li doped samples. Micro CT of Li + Sr samples showed highest degree of peripheral cancellous tissue formation on periphery and cortical tissues inside implanted samples and vascularity among four compositions. Our findings suggest that addition of Sr and/or Li alters physico-chemical properties of BAG and promotes early stage in vivo osseointegration and bone remodeling that may offer new insight in bone tissue engineering.
3D Holographic Observatory for Long-term Monitoring of Complex Behaviors in Drosophila
Authors: Kumar S. Santosh , Sun Yaning , Zou Sige , Hong Jiarong 
Published: September 2016

AbstractDrosophila is an excellent model organism towards understanding the cognitive function, aging and neurodegeneration in humans. The effects of aging and other long-term dynamics on the behavior serve as important biomarkers in identifying such changes to the brain. In this regard, we are presenting a new imaging technique for lifetime monitoring of Drosophila in 3D at spatial and temporal resolutions capable of resolving the motion of limbs and wings using holographic principles. The developed system is capable of monitoring and extracting various behavioral parameters, such as ethograms and spatial distributions, from a group of flies simultaneously. This technique can image complicated leg and wing motions of flies at a resolution, which allows capturing specific landing responses from the same data set. Overall, this system provides a unique opportunity for high throughput screenings of behavioral changes in 3D over a long term in Drosophila.
Structural insights into Parkin substrate lysine targeting from minimal Miro substrates
Authors: Klosowiak Julian L. , Park Sungjin , Smith Kyle P. , French Michael E. , Focia Pamela J. , Freymann Douglas M. , Rice Sarah E. 
Published: September 2016

AbstractHereditary Parkinson’s disease is commonly caused by mutations in the protein kinase PINK1 or the E3 ubiquitin ligase Parkin, which function together to eliminate damaged mitochondria. PINK1 phosphorylates both Parkin and ubiquitin to stimulate ubiquitination of dozens of proteins on the surface of the outer mitochondrial membrane. However, the mechanisms by which Parkin recognizes specific proteins for modification remain largely unexplored. Here, we show that the C-terminal GTPase (cGTPase) of the Parkin primary substrate human Miro is necessary and sufficient for efficient ubiquitination. We present several new X-ray crystal structures of both human Miro1 and Miro2 that reveal substrate recognition and ubiquitin transfer to be specific to particular protein domains and lysine residues. We also provide evidence that Parkin substrate recognition is functionally separate from substrate modification. Finally, we show that prioritization for modification of a specific lysine sidechain of the cGTPase (K572) within human Miro1 is dependent on both its location and chemical microenvironment. Activation of Parkin by phosphorylation or by binding of pUb is required for prioritization of K572 for modification, suggesting that Parkin activation and acquisition of substrate specificity are coupled.
A Non-catalytic Deep Desulphurization Process using Hydrodynamic Cavitation
Authors: Suryawanshi Nalinee B. , Bhandari Vinay M. , Sorokhaibam Laxmi Gayatri , Ranade Vivek V. 
Published: September 2016

AbstractA novel approach is developed for desulphurization of fuels or organics without use of catalyst. In this process, organic and aqueous phases are mixed in a predefined manner under ambient conditions and passed through a cavitating device. Vapor cavities formed in the cavitating device are then collapsed which generate (in-situ) oxidizing species which react with the sulphur moiety resulting in the removal of sulphur from the organic phase. In this work, vortex diode was used as a cavitating device. Three organic solvents (n-octane, toluene and n-octanol) containing known amount of a model sulphur compound (thiophene) up to initial concentrations of 500 ppm were used to verify the proposed method. A very high removal of sulphur content to the extent of 100% was demonstrated. The nature of organic phase and the ratio of aqueous to organic phase were found to be the most important process parameters. The results were also verified and substantiated using commercial diesel as a solvent. The developed process has great potential for deep of various organics, in general, and for transportation fuels, in particular.
Molecular archeological evidence in support of the repeated loss of a papillomavirus gene
Authors: Van Doorslaer Koenraad , McBride Alison A. 
Published: September 2016

AbstractIt is becoming clear that, in addition to gene gain, the loss of genes may be an important evolutionary mechanism for many organisms. However, gene loss is often associated with an increased mutation rate, thus quickly erasing evidence from the genome. The analysis of evolutionarily related sequences can provide empirical evidence for gene loss events. This paper analyzes the sequences of over 300 genetically distinct papillomaviruses and provides evidence for a role of gene loss during the evolution of certain papillomavirus genomes. Phylogenetic analysis suggests that the viral E6 gene was lost at least twice. Despite belonging to distant papillomaviral genera, these viruses lacking a canonical E6 protein may potentially encode a highly hydrophobic protein from an overlapping open reading frame, which we designate E10. Evolutionary pressure working on this alternative frame, may explain why, despite having lost the E6 open reading frame between 20 and 60 million years ago, evidence of an E6-like protein is conserved.
Diversity of bacterial dimethylsulfoniopropionate degradation genes in surface seawater of Arctic Kongsfjorden
Authors: Zeng Yin-Xin , Qiao Zong-Yun , Yu Yong , Li Hui-Rong , Luo Wei 
Published: September 2016

AbstractDimethylsulfoniopropionate (DMSP), which is the major source of organic sulfur in the world’s oceans, plays a significant role in the global sulfur cycle. This compound is rapidly degraded by marine bacteria either by cleavage to dimethylsulfide (DMS) or demethylation to 3-methylmercaptopropionate (MMPA). The diversity of genes encoding bacterial demethylation (dmdA) and DMS production (dddL and dddP) were measured in Arctic Kongsfjorden. Both dmdA and dddL genes were detected in all stations along a transect from the outer to the inner fjord, while dddP gene was only found in the outer and middle parts of the fjord. The dmdA gene was completely confined to the Roseobacter clade, while the dddL gene was confined to the genus Sulfitobacter. Although the dddP gene pool was also dominated by homologs from the Roseobacter clade, there were a few dddP genes showing close relationships to both Alphaproteobacter and Gammaproteobacter. The results of this study suggest that the Roseobacter clade may play an important role in DMSP catabolism via both demethylation and cleavage pathways in surface waters of Kongsfjorden during summer.