bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel mutations in the COL2A1 gene in Japanese patients with Stickler syndrome
Authors: Kondo Hiroyuki , Matsushita Itsuka , Nagata Tatsuo , Hayashi Takaaki , Kakinoki Masashi , Uchio Eiichi , Kondo Mineo , Ohji Masahito , Kusaka Shunji 
Published: July 2016

AbstractStickler syndrome is an inherited connective tissue disorder that affects the eyes, cartilage and articular tissues. The phenotypes of Stickler syndrome include congenital high myopia, retinal detachment, premature joint degeneration, hearing impairment and craniofacial anomalies, such as cleft palate and midline facial hypoplasia. The disease is genetically heterogeneous, and the majority of the cases are caused by mutations in the COL2A1 gene. We examined 40 Japanese patients with Stickler syndrome from 23 families to determine whether they had mutations in the COL2A1 gene. This analysis was conducted by examining each patient’s genomic DNA by Sanger sequencing. Five nonsense, 4 splicing and 8 deletion mutations in the COL2A1 gene were identified, accounting for 21 of the 23 families. Different mutations of the COL2A1 gene were associated with similar phenotypes but with different degrees of expressivity.
aMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data
Authors: Niedworok Christian J. , Brown Alexander P. Y. , Jorge Cardoso M. , Osten Pavel , Ourselin Sebastien , Modat Marc , Margrie Troy W. 
Published: July 2016

AbstractThe validation of automated image registration and segmentation is crucial for accurate and reliable mapping of brain connectivity and function in three-dimensional (3D) data sets. While validation standards are necessarily high and routinely met in the clinical arena, they have to date been lacking for high-resolution microscopy data sets obtained from the rodent brain. Here we present a tool for optimized automated mouse atlas propagation (aMAP) based on clinical registration software (NiftyReg) for anatomical segmentation of high-resolution 3D fluorescence images of the adult mouse brain. We empirically evaluate aMAP as a method for registration and subsequent segmentation by validating it against the performance of expert human raters. This study therefore establishes a benchmark standard for mapping the molecular function and cellular connectivity of the rodent brain.
Thermodynamics of quantum systems with multiple conserved quantities
Authors: Guryanova Yelena , Popescu Sandu , Short Anthony J. , Silva Ralph , Skrzypczyk Paul 
Published: July 2016

AbstractRecently, there has been much progress in understanding the thermodynamics of quantum systems, even for small individual systems. Most of this work has focused on the standard case where energy is the only conserved quantity. Here we consider a generalization of this work to deal with multiple conserved quantities. Each conserved quantity, which, importantly, need not commute with the rest, can be extracted and stored in its own battery. Unlike the standard case, in which the amount of extractable energy is constrained, here there is no limit on how much of any individual conserved quantity can be extracted. However, other conserved quantities must be supplied, and the second law constrains the combination of extractable quantities and the trade-offs between them. We present explicit protocols that allow us to perform arbitrarily good trade-offs and extract arbitrarily good combinations of conserved quantities from individual quantum systems.
Microcanonical and resource-theoretic derivations of the thermal state of a quantum system with noncommuting charges
Authors: Yunger Halpern Nicole , Faist Philippe , Oppenheim Jonathan , Winter Andreas 
Published: July 2016

AbstractThe grand canonical ensemble lies at the core of quantum and classical statistical mechanics. A small system thermalizes to this ensemble while exchanging heat and particles with a bath. A quantum system may exchange quantities represented by operators that fail to commute. Whether such a system thermalizes and what form the thermal state has are questions about truly quantum thermodynamics. Here we investigate this thermal state from three perspectives. First, we introduce an approximate microcanonical ensemble. If this ensemble characterizes the system-and-bath composite, tracing out the bath yields the system’s thermal state. This state is expected to be the equilibrium point, we argue, of typical dynamics. Finally, we define a resource-theory model for thermodynamic exchanges of noncommuting observables. Complete passivity—the inability to extract work from equilibrium states—implies the thermal state’s form, too. Our work opens new avenues into equilibrium in the presence of quantum noncommutation.
White spot syndrome virus entry is dependent on multiple endocytic routes and strongly facilitated by Cq-GABARAP in a CME-dependent manner
Authors: Chen Rong-yuan , Shen Kai-li , Chen Zhen , Fan Wei-wei , Xie Xiao-lu , Meng Chuang , Chang Xue-jiao , Zheng Li-bing , Jeswin Joseph , Li Cheng-hua , Wang Ke-jian , Liu Hai-peng 
Published: July 2016

AbstractWhite spot syndrome virus (WSSV) is a lethal pathogen of shrimp and many other crustaceans, including crayfish. However, the molecular mechanism underlying its cellular entry remains elusive due to the lack of shrimp cell lines for viral propagation. Crayfish hematopoietic tissue (Hpt) cell culture was recently established as a good model for WSSV infection study. Here, we showed that multiple endocytic routes, including clathrin-mediated endocytosis (CME), macropinocytosis and caveolae-mediated endocytosis, were indispensably employed for the viral entry into Hpt cell of the crayfish Cherax quadricarinatus. Intriguingly, cellular autophagic activity was positively correlated with efficient viral entry, in which a key autophagy-related protein, γ-aminobutyric acid receptor-associated protein (Cq-GABARAP), that not only localized but also co-localized with WSSV on the Hpt cell membrane, strongly facilitated WSSV entry by binding to the viral envelope VP28 in a CME-dependent manner that was negatively regulated by Cq-Rac1. Furthermore, cytoskeletal components, including Cq-β-tubulin and Cq-β-actin, bound to both recombinant rCq-GABARAP and WSSV envelope proteins, which likely led to viral entry promotion via cooperation with rCq-GABARAP. Even under conditions that promoted viral entry, rCq-GABARAP significantly reduced viral replication at an early stage of infection, which was probably caused by the formation of WSSV aggregates in the cytoplasm.
Application of an in vitro-amplification assay as a novel pre-screening test for compounds inhibiting the aggregation of prion protein scrapie
Authors: Schmitz Matthias , Cramm Maria , Llorens Franc , Candelise Niccolò , Müller-Cramm Dominik , Varges Daniela , Schulz-Schaeffer Walter J. , Zafar Saima , Zerr Inga 
Published: July 2016

AbstractIn vitro amplification assays, such as real-time quaking-induced conversion (RT-QuIC) are used to detect aggregation activity of misfolded prion protein (PrP) in brain, cerebrospinal fluid (CSF) and urine samples from patients with a prion disease. We believe that the method also has a much broader application spectrum. In the present study, we applied RT-QuIC as a pre-screening test for substances that potentially inhibit the aggregation process of the cellular PrP (PrPC) to proteinase (PK)-resistant PrPres. We chose doxycycline as the test substance as it has been tested successfully in animal models and proposed in clinical studies as a therapeutic for prion diseases. The RT-QuIC-reaction was seeded with brain tissue or CSF from sCJD patients and doxycycline was then added in different concentrations as well as at different time points. In both experiments, we observed a dose- and time-dependent inhibition of the RT-QuIC seeding response and a decrease of PK resistant PrPres when doxycycline was added. In contrast, ampicillin or sucrose had no effect on the RT-QuIC seeding response. Our study is the first to apply RT-QuIC as a pre-screening assay for compounds inhibiting the PrP aggregation in vitro and confirms that doxycycline is an efficient inhibitor of the PrP aggregation process in RT-QuIC analysis.
Comparison of large networks with sub-sampling strategies
Authors: Ali Waqar , Wegner Anatol E. , Gaunt Robert E. , Deane Charlotte M. , Reinert Gesine 
Published: July 2016

AbstractNetworks are routinely used to represent large data sets, making the comparison of networks a tantalizing research question in many areas. Techniques for such analysis vary from simply comparing network summary statistics to sophisticated but computationally expensive alignment-based approaches. Most existing methods either do not generalize well to different types of networks or do not provide a quantitative similarity score between networks. In contrast, alignment-free topology based network similarity scores empower us to analyse large sets of networks containing different types and sizes of data. Netdis is such a score that defines network similarity through the counts of small sub-graphs in the local neighbourhood of all nodes. Here, we introduce a sub-sampling procedure based on neighbourhoods which links naturally with the framework of network comparisons through local neighbourhood comparisons. Our theoretical arguments justify basing the Netdis statistic on a sample of similar-sized neighbourhoods. Our tests on empirical and synthetic datasets indicate that often only 10% of the neighbourhoods of a network suffice for optimal performance, leading to a drastic reduction in computational requirements. The sampling procedure is applicable even when only a small sample of the network is known and thus provides a novel tool for network comparison of very large and potentially incomplete datasets.
The focus on sample quality: Influence of colon tissue collection on reliability of qPCR data
Authors: Korenkova Vlasta , Slyskova Jana , Novosadova Vendula , Pizzamiglio Sara , Langerova Lucie , Bjorkman Jens , Vycital Ondrej , Liska Vaclav , Levy Miroslav , Veskrna Karel , Vodicka Pavel , Vodickova Ludmila , Kubista Mikael , Verderio Paolo 
Published: July 2016

AbstractSuccessful molecular analyses of human solid tissues require intact biological material with well-preserved nucleic acids, proteins, and other cell structures. Pre-analytical handling, comprising of the collection of material at the operating theatre, is among the first critical steps that influence sample quality. The aim of this study was to compare the experimental outcomes obtained from samples collected and stored by the conventional means of snap freezing and by PAXgene Tissue System (Qiagen). These approaches were evaluated by measuring rRNA and mRNA integrity of the samples (RNA Quality Indicator and Differential Amplification Method) and by gene expression profiling. The collection procedures of the biological material were implemented in two hospitals during colon cancer surgery in order to identify the impact of the collection method on the experimental outcome. Our study shows that the pre-analytical sample handling has a significant effect on the quality of RNA and on the variability of qPCR data. PAXgene collection mode proved to be more easily implemented in the operating room and moreover the quality of RNA obtained from human colon tissues by this method is superior to the one obtained by snap freezing.
Investigation of Localized States in GaAsSb Epilayers Grown by Molecular Beam Epitaxy
Authors: Gao Xian , Wei Zhipeng , Zhao Fenghuan , Yang Yahui , Chen Rui , Fang Xuan , Tang Jilong , Fang Dan , Wang Dengkui , Li Ruixue , Ge Xiaotian , Ma Xiaohui , Wang Xiaohua 
Published: July 2016

AbstractWe report the carrier dynamics in GaAsSb ternary alloy grown by molecular beam epitaxy through comprehensive spectroscopic characterization over a wide temperature range. A detailed analysis of the experimental data reveals a complex carrier relaxation process involving both localized and delocalized states. At low temperature, the localized degree shows linear relationship with the increase of Sb component. The existence of localized states is also confirmed by the temperature dependence of peak position and band width of the emission. At temperature higher than 60 K, emissions related to localized states are quenched while the band to band transition dominates the whole spectrum. This study indicates that the localized states are related to the Sb component in the GaAsSb alloy, while it leads to the poor crystal quality of the material, and the application of GaAsSb alloy would be limited by this deterioration.
Dielectrophoretic behaviours of microdroplet sandwiched between LN substrates
Authors: Chen Lipin , Li Shaobei , Fan Bolin , Yan Wenbo , Wang Donghui , Shi Lihong , Chen Hongjian , Ban Dechao , Sun Shihao 
Published: July 2016

AbstractWe demonstrate a sandwich configuration for microfluidic manipulation in LiNbO3 platform based on photovoltaic effect and the behaviours of dielectric microdroplet under this sandwich configuration are investigated. It is found that the microdroplet can generate in the form of liquid bridge inside the LiNbO3-based sandwich structure under the governing dielectrophoretic force and the dynamic process of microdroplet generation highly depends on the substrate combinations. Dynamic features found for different combinations are explained by the different electrostatic field distribution basing on the finite-element simulation results. Moreover, the electrostatic field required by the microdroplet generation is estimated through meniscus evolution and it is found in good agreement with the simulated electrostatic field inside the sandwich gap. Several kinds of microdroplet manipulations are attempted in this work. We suggest that the local dielectrophoretic force acting on the microdroplet depends on the distribution of the accumulated irradiation dosage. Without using any additional pumping or jetting actuator, the microdroplet can be step-moved, deformed or patterned by the inconsecutive dot-irradiation scheme, as well as elastically stretched out and back or smoothly guided in a designed pass by the consecutive line-irradiation scheme.
Tunable C2N Membrane for High Efficient Water Desalination
Authors: Yang Yanmei , Li Weifeng , Zhou Hongcai , Zhang Xiaoming , Zhao Mingwen 
Published: July 2016

AbstractWater scarcity represents one of the most serious global problems of our time and challenges the advancements in desalination techniques. Although water-filtering architectures based on graphene have greatly advanced the approach to high performance desalination membranes, the controlled-generation of nanopores with particular diameter is tricky and has stunted its wide applications. Here, through molecular dynamic simulations and first-principles calculations, we propose that the recently reported graphene-like carbon nitride (g-C2N) monolayer can serve as high efficient filters for water desalination. Taking the advantages of the intrisic nanoporous structure and excellent mechanical properties of g-C2N, high water transparency and strong salt filtering capability have been demonstrated in our simulations. More importantly, the “open” and “closed” states of the g-C2N filter can be precisely regulated by tensile strain. It is found that the water permeability of g-C2N is significantly higher than that reported for graphene filters by almost one order of magnitude. In the light of the abundant family of graphene-like carbon nitride monolayered materials, our results thus offer a promising approach to the design of high efficient filteration architectures.
Sonar beam dynamics in leaf-nosed bats
Authors: Linnenschmidt Meike , Wiegrebe Lutz 
Published: July 2016

AbstractUltrasonic emissions of bats are directional and delimit the echo-acoustic space. Directionality is quantified by the aperture of the sonar beam. Recent work has shown that bats often widen their sonar beam when approaching movable prey or sharpen their sonar beam when navigating through cluttered habitats. Here we report how nose-emitting bats, Phyllostomus discolor, adjust their sonar beam to object distance. First, we show that the height and width of the bats sonar beam, as imprinted on a parabolic 45 channel microphone array, varies even within each animal and this variation is unrelated to changes in call level or spectral content. Second, we show that these animals are able to systematically decrease height and width of their sonar beam while focusing on the approaching object. Thus it appears that sonar beam sharpening is a further, facultative means of reducing search volume, likely to be employed by stationary animals when the object position is close and unambiguous. As only half of our individuals sharpened their beam onto the approaching object we suggest that this strategy is facultative, under voluntary control and that beam formation is likely mediated by muscular control of the acoustic aperture of the bats’ nose leaf.
Phenotypic flexibility of gape anatomy fine-tunes the aquatic prey-capture system of newts
Authors: Van Wassenbergh Sam , Heiss Egon 
Published: July 2016

AbstractA unique example of phenotypic flexibility of the oral apparatus is present in newts (Salamandridae) that seasonally change between an aquatic and a terrestrial habitat. Newts grow flaps of skin between their upper and lower jaws, the labial lobes, to partly close the corners of the mouth when they adopt an aquatic lifestyle during their breeding season. Using hydrodynamic simulations based on μCT-scans and cranial kinematics during prey-capture in the smooth newt (Lissotriton vulgaris), we showed that this phenotypic flexibility is an adaptive solution to improve aquatic feeding performance: both suction distance and suction force increase by approximately 15% due to the labial lobes. As the subsequent freeing of the corners of the mouth by resorption of the labial lobes is assumed beneficial for the terrestrial capture of prey by the tongue, this flexibility of the mouth fine-tunes the process of capturing prey throughout the seasonal switching between water and land.
Optic-null space medium for cover-up cloaking without any negative refraction index materials
Authors: Sun Fei , He Sailing 
Published: July 2016

AbstractWith the help of optic-null medium, we propose a new way to achieve invisibility by covering up the scattering without using any negative refraction index materials. Compared with previous methods to achieve invisibility, the function of our cloak is to cover up the scattering of the objects to be concealed by a background object of strong scattering. The concealed object can receive information from the outside world without being detected. Numerical simulations verify the performance of our cloak. The proposed method will be a great addition to existing invisibility technology.
Bisphenol A affects early bovine embryo development and metabolism that is negated by an oestrogen receptor inhibitor
Authors: Choi Bom-Ie , Harvey Alexandra J. , Green Mark P. 
Published: July 2016

AbstractIncreasing evidence supports an association between exposure to endocrine disruptors, such as the xenoestrogen bisphenol A (BPA), a commonly used plasticiser and the developmental programming of offspring health. To date however animal studies to investigate a direct causal have mainly focussed on supra-environmental BPA concentrations, without investigating the effect on the early embryo. In this study we investigated the effect of acute BPA exposure (days 3.5 to 7.5 post-fertilisation) at environmentally relevant concentrations (1 and 10 ng/mL) on in vitro bovine embryo development, quality and metabolism. We then examined whether culturing embryos in the presence of the oestrogen receptor inhibitor fulvestrant could negate effects of BPA and 17β-oestradiol (E2). Exposure to BPA or E2 (10 ng/mL) decreased blastocyst rate and the percentage of transferrable quality embryos, without affecting cell number, lineage allocation or metabolic gene expression compared to untreated embryos. Notably, blastocysts exposed to BPA and E2 (10 ng/mL) displayed an increase in glucose consumption. The presence of fulvestrant however negated the adverse developmental and metabolic effects, suggesting BPA elicits its effects via oestrogen-mediated pathways. This study demonstrates that even acute exposure to an environmentally relevant BPA concentration can affect early embryo development and metabolism. These may have long-term health consequences on an individual.
Sexual complementarity between host humoral toxicity and soldier caste in a polyembryonic wasp
Authors: Uka Daisuke , Sakamoto Takuma , Yoshimura Jin , Iwabuchi Kikuo 
Published: July 2016

AbstractDefense against enemies is a type of natural selection considered fundamentally equivalent between the sexes. In reality, however, whether males and females differ in defense strategy is unknown. Multiparasitism necessarily leads to the problem of defense for a parasite (parasitoid). The polyembryonic parasitic wasp Copidosoma floridanum is famous for its larval soldiers’ ability to kill other parasites. This wasp also exhibits sexual differences not only with regard to the competitive ability of the soldier caste but also with regard to host immune enhancement. Female soldiers are more aggressive than male soldiers and their numbers increase upon invasion of the host by other parasites. In this report, in vivo and in vitro competition assays were used to test whether females have a toxic humoral factor; if so, then its strength was compared with that of males. We found that females have a toxic factor that is much weaker than that of males. Our results imply sexual complementarity between host humoral toxicity and larval soldiers. We discuss how this sexual complementarity guarantees adaptive advantages for both males and females despite the one-sided killing of male reproductives by larval female soldiers in a mixed-sex brood.
Immunophenotyping of rheumatoid arthritis reveals a linkage between HLA-DRB1 genotype, CXCR4 expression on memory CD4+ T cells and disease activity
Authors: Nagafuchi Yasuo , Shoda Hirofumi , Sumitomo Shuji , Nakachi Shinichiro , Kato Rika , Tsuchida Yumi , Tsuchiya Haruka , Sakurai Keiichi , Hanata Norio , Tateishi Shoko , Kanda Hiroko , Ishigaki Kazuyoshi , Okada Yukinori , Suzuki Akari , Kochi Yuta , Fujio Keishi , Yamamoto Kazuhiko 
Published: July 2016

AbstractRheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease that leads to destructive arthritis. Although the HLA class II locus is the strongest genetic risk factor for rheumatoid arthritis, the relationship between HLA class II alleles and lymphocyte activation remains unclear. We performed immunophenotyping of peripheral blood mononuclear cells on 91 HLA-DRB1-genotyped RA patients and 110 healthy donors. The frequency of memory CXCR4+CD4+T cells and not Th1 and Th17 cells, was significantly associated with disease severity by multiple linear regression analysis. RA patients with one or more susceptible HLA-DR haplotypes (shared epitope: SE) displayed a significantly higher frequency of memory CXCR4+CD4+T cells. Moreover, the frequency of memory CXCR4+CD4+T cells significantly correlated with the expression level of HLA-DR on B cells, which was elevated in RA patients with SE.In vitroanalysis and transcriptomic pathway analysis suggested that the interaction between HLA-DR and T cell receptors is an important regulator of memory CXCR4+CD4+T cells. Clinically, a higher frequency of memory CXCR4+CD4+T cells predicted a better response to CTLA4-Ig. Memory CXCR4+CD4+T cells may serve as a powerful biomarker for unraveling the linkage between HLA-DRB1 genotype and disease activity in RA.