bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of external magnetic field on the microwave absorption properties of carbonyl iron and polychloroprene composites film
Authors: Wang Haiyan , Li Mingjie , Li Xueai
Published: December 2016

The carbonyl iron particles were dispersed in a polychloroprene rubber (CR) matrix under a magnetic field for a practical application as microwave absorption composites film. In comparison with the carbonyl iron particles (CIP)/CR composites film prepared by general route, such films made with external magnetic field exhibit excellent microwave absorption properties, strongly depending on the increment of anisotropy and rearrangement of magnetic particles. The film made under external magnetic field with a thickness of only 0.54 mm shows least reflection loss of -15.98 dB and the reflection loss value less than -10.0 dB over the frequency range of 11.4∼14.8 GHz. The results indicated the composite film made under external magnetic field have excellent microwave absorption properties, which suggest that the composites thin film could be used as a thinner and lighter microwave absorber.
Tiny adiabatic-demagnetization refrigerator for a commercial superconducting quantum interference device magnetometer
Authors: Sato Taku J. , Okuyama Daisuke , Kimura Hideo
Published: December 2016

A tiny adiabatic-demagnetization refrigerator (T-ADR) has been developed for a commercial superconducting quantum interference device magnetometer [Magnetic Property Measurement System (MPMS) from Quantum Design]. The whole T-ADR system is fit in a cylindrical space of diameter 8.5 mm and length 250 mm, and can be inserted into the narrow sample tube of MPMS. A sorption pump is self-contained in T-ADR, and hence no complex gas handling system is necessary. With the single crystalline Gd3Ga5O12 garnet (∼2 g) used as a magnetic refrigerant, the routinely achievable lowest temperature is ∼0.56 K. The lower detection limit for a magnetization anomaly is ∼1 × 10−7 emu, estimated from fluctuation of the measured magnetization. The background level is ∼5 × 10−5 emu below 2 K at H = 100 Oe, which is largely attributable to a contaminating paramagnetic signal from the magnetic refrigerant.
Deuterium incorporation and diffusivity in plasma-exposed bulk Ga2O3
Authors: Ahn Shihyun , Ren F. , Patrick Erin , Law Mark E. , Pearton S. J. , Kuramata Akito
Published: December 2016

Deuterium incorporation depths of ∼0.13–0.65 μm were obtained in bulk, single-crystal Ga2O3 during exposure to 2H plasmas for 0.5 h at 100–270 °C. The data were fit using the Florida Object Oriented Process Simulator simulation code. The estimated diffusivities were in the range of 2.3 × 10−14–6 × 10−13 cm2/V·s over this temperature range. The activation energy for diffusion was 0.30 ± 0.08 eV, suggesting that the diffusing deuterium migrates as an interstitial. The solubility of the deuterium exhibited an activation energy of 0.35 eV. Subsequent annealing at 500 °C removed ∼85% of the deuterium out of the Ga2O3, with an activation energy of 1.35 eV. This indicates that the outdiffusion is mediated through defects or molecule formation. The thermal stability of deuterium retention is lower (∼150 °C shift to lower temperatures) than when the deuterium is incorporated in the Ga2O3 by direct ion implantation, due to trapping at residual damage in the latter case. The incorporation depths of deuterium in the Ga2O3 are significantly less than in bulk ZnO under the same conditions, where we observed incorporation to ∼25 μm.
Theoretical and experimental investigation of surface acoustic wave propagation on a hollow spherical shell using laser ultrasound
Authors: Ma Xiaojun , Tang Xing , Wang Zongwei , Gao Dangzhong , Tang Yongjian
Published: December 2016

An analytical model of surface acoustic waves on the surface of a hollow spherical shell generated by a pulsed laser source is proposed using the Legendre polynomials expansion and contour integration method. The model predicts two interesting phenomena. The dispersive characteristic of thick spherical shells is mainly determined by the spherical Rayleigh waves, but the corresponding characteristic of thin spherical shells is dominated by zero-order anti-symmetric plate waves; The hollow spherical spheres with the same ratio of thickness to radius have the same dispersive characteristic. Using laser ultrasound technique, the proposed model is confirmed experimentally on a hollow polymer sphere of mm-sized diameter.
A PMT-like high gain avalanche photodiode based on GaN/AlN periodically stacked structure
Authors: Zheng Jiyuan , Wang Lai , Wu Xingzhao , Hao Zhibiao , Sun Changzheng , Xiong Bing , Luo Yi , Han Yanjun , Wang Jian , Li Hongtao , Brault Julien , Matta Samuel , Khalfioui Mohamed Al , Yan Jianchang , Wei Tongbo , Zhang Yun , Wang Junxi
Published: December 2016

Avalanche photodiode (APD) has been intensively investigated as a promising candidate to replace the bulky and fragile photomultiplier tube (PMT) for weak light detection. However, the performance of most available APDs is barely satisfactory compared to that of the PMTs because of inter-valley scattering. Here, we demonstrate a PMT-like APD based on GaN/AlN periodically stacked-structure (PSS), in which the electrons encounter a much less inter-valley scattering during transport than holes. Uni-directional avalanche takes place with a high efficiency. According to our simulations based on a PSS with GaN (10 nm)/AlN (10 nm) in each period, the probability for electrons to trigger ionization in each cycle can reach as high as 80%, while that for holes is only 4%. A record high and stable gain (104) with a low ionization coefficient ratio of 0.05 is demonstrated under a constant bias in a prototype device.
High temperature gradient micro-sensor for wall shear stress and flow direction measurements
Authors: Ghouila-Houri C. , Claudel J. , Gerbedoen J.-C. , Gallas Q. , Garnier E. , Merlen A. , Viard R. , Talbi A. , Pernod P.
Published: December 2016

We present an efficient and high-sensitive thermal micro-sensor for near wall flow parameters measurements. By combining substrate-free wire structure and mechanical support using silicon oxide micro-bridges, the sensor achieves a high temperature gradient, with wires reaching 1 mm long for only 3 μm wide over a 20 μm deep cavity. Elaborated to reach a compromise solution between conventional hot-films and hot-wire sensors, the sensor presents a high sensitivity to the wall shear stress and to the flow direction. The sensor can be mounted flush to the wall for research studies such as turbulence and near wall shear flow analysis, and for technical applications, such as flow control and separation detection. The fabrication process is CMOS-compatible and allows on-chip integration. The present letter describes the sensor elaboration, design, and micro-fabrication, then the electrical and thermal characterizations, and finally the calibration experiments in a turbulent boundary layer wind tunnel.
Microstructure investigation of semi-polar (11-22) GaN overgrown on differently designed micro-rod array templates
Authors: Zhang Y. , Bai J. , Hou Y. , Yu X. , Gong Y. , Smith R. M. , Wang T.
Published: December 2016

In order to realize semi-polar (11-22) GaN based laser diodes grown on sapphire, it is necessary to further improve the crystal quality of the (11-22) GaN obtained by using our overgrowth approach developed on regularly arrayed micro-rod templates [T. Wang, Semicond. Sci. Technol. 31, 093003 (2016)]. This can be achieved by carefully designing micro-rod templates. Based on transmission electron microscopy and photoluminescence measurements, it has been found that the micro-rod diameter plays a vital role in effectively reducing both the dislocation density and the basal staking fault (BSF) density of the overgrown (11-22) GaN, but in different manners. The BSF density reduces monotonically with increasing the micro-rod diameter from 2 to 5 μm, and then starts to be saturated when the micro-rod diameter further increases. In contrast, the dislocation density reduces significantly when the micro-rod diameter increases from 2 to 4 μm, and then starts to increase when the diameter further increases to 5 μm. Furthermore, employing shorter micro-rods is useful for removing additional BSFs, leading to further improvement in crystal quality. The results presented provide a very promising approach to eventually achieving (11-22) semi-polar III-nitride laser diodes.
Supramolecular Assemblies of Cucurbit[10]uril Based on Outer Surface Interactions
Authors: Yao Yu-Qing , Liu Qing , Huang Ying , Zhu Qian-Jiang , Zhang Yun-Qian , Xiao Xin , Tao Zhu , Wei Gang
Published: December 2016

Using an established method, we isolated a large quantity of cucurbit[10]uril (Q[10]) and prepared Q[10]-based supramolecular assemblies via different approaches. For example, the structure-directing agent [CdCl4]2– was used or the Q[10] molecule itself acted as a self-structure-directing agent to form different Q[10]-based supramolecular assemblies through the outer surface interaction of Q[10]. Generally, the Q[10]-based supramolecular assemblies possess porous features that suggest that Q[n]-based compounds could be used to manufacture molecular sieves and sensors and applied in absorption and separation technologies.
Two-pore cation (TPC) channel: not a shorthanded one
Authors: Pottosin Igor , Dobrovinskaya Oxana
Published: December 2016

Two-pore cation (TPC) channels form functional dimers in membranes, delineating acidic intracellular compartments such as vacuoles in plants and lysosomes in animals. TPC1 is ubiquitously expressed in thousands of copies per vacuole in terrestrial plants, where it is known as slow vacuolar (SV) channel. An SV channel possesses high permeability for Na+, K+, Mg2+, and Ca2+, but requires high (tens of μM) cytosolic Ca2+ and non-physiological positive voltages for its full activation. Its voltage dependent activation is negatively modulated by physiological concentrations of vacuolar Ca2+, Mg2+and H+. Double control of the SV channel activity from cytosolic and vacuolar sides keeps its open probability at a minimum and precludes a potentially harmful global Ca2+ release. But this raises the question of what such’ inactive’ channel could be good for? One possibility is that it is involved in ultra-local Ca2+ signalling by generating ‘hotspots’ – microdomains of extremely high cytosolic Ca2+. Unexpectedly, recent studies have demonstrated the essential role of the TPC1 in the systemic Ca2+ signalling, and the crystal structure of plant TPC1, which became available this year, unravels molecular mechanisms underlying voltage and Ca2+ gating. This review emphasises the significance of these ice-breaking findings and sets a new perspective for the TPC1-based Ca2+ signalling.
GIS-modelling of land-use trends: impact of drought in the Naghamish Basin (North Western Egypt)
Authors: Saïdi S. , Gintzburger G. , Bonnet P. , Daoud I. , Alary V.
Published: December 2016

The basic features of the Naghamish Basin and agro-ecosystem in the North West Coastal Zone of Egypt (climate, soils and vegetation cover) are mapped to analyse the wear and tear of physical components of the environment of three tribes’ territories between 2006 and 2011 when a dry spell struck. Our land use mapping and results using RS and GIS indicate considerable and quick changes in the agricultural and biotic components in spite of an inter-annual long-term rainfall variability appearing standard for this low-rainfall desert region. After good rainy years (1985–1995), the impact of the following drought (1996–2011) perceived by the farmer and Bedouin communities is real and confirmed by our land cover mapping changes of the Nagamish watershed. The communities are correct in their perception of the drought and are deeply affected in their economy and social life.
Intertextual relations in web localization
Authors: Sharifi Hamid
Published: December 2016

In this research, we studied localized commercial texts of globalized companies in the context of intertextuality on three levels: lexical, thematic, and cultural. Amongst many products of the three companies under study (Samsung, LG, and Sony), four smartphone models of each were selected (total: 12). Their introductory web pages both in Persian and English were the sources of the data. Furthermore, we used an online analyzer tool (online-utility.org/text/analyzer.jsp) so as to analyze the data; the results were also corroborated with other pieces of software packages and applications. In the scene of booming globalization, a better understanding of cross-cultural vocative communication proves to be helpful. One of the most active areas is to study flagship brands where rivals are trying their best at localizing their devices to the liking of potential customers. Descriptive and explanatory methods were brought into play in order to compare English and Persian commercial texts. The research revealed the critical role intertextuality plays in the process of glocalization. Developing companies should note that they, too, could utilize this great potentiality in the context of web localization. Therefore, the findings would be of benefit to Chief Executive Officers (CEOs), product developers and scholars interested in the subject.
Building stories onThe Brick People
Authors: Lanslots Inge , Van Hecke An
Published: December 2016

The focus of this study is an analysis of the novelThe Brick Peoplepublished by the Chicano author Alejandro Morales in 1988 and its homonymous documentary film from 2012. Both narratives are based on the same story, namely the lives of Mexican immigrants, who worked as employees inSimons Brickyardin Los Angeles, California, a city originally founded by Mexicans. In the official historiography, this part of Mexican migration in California has been ignored. This study will reveal how the novel and the documentary deal with this gap or interstice in North-American history and how they reflect the cultural divide in Southern California. We are particularly interested in how both the novelist and the documentary makers present the topics of integration, of preservation or construction of the Mexican cultural identity and of cross-cultural dialogue to an English speaking audience. Both the documentary and the novel narrate “value[s] that reflect […] the language, local conventions and culture of [the] geographic region” (ISO/TS 11669:2012(en), 2.1.10) of Los Angeles. The depiction of this target locale presents itself as a borderland that clusters a rich mix of cultural, historical, and (non) urban landscapes (Gersdorf 2009, 309). This ancient collective memory appears serendipitously as sudden sites or potential links of human action collected in one or more of the previous structures of consciousness and inspire individuals to perform and produce in unique and extraordinary ways (Morales 2012, 111).
Owners vs. non-owners?
Authors: Igwebuike Ebuka Elias
Published: December 2016

This study investigated lexical labelling of people and their actions in terms of ownership and non-ownership of territories by the Nigerian and Cameroonian newspaper reports on the Bakassi Peninsula border conflict, with a view to uncovering ideologies underlying the representations. Van Dijk’s socio-cognitive model of Critical Discourse Analysis which relates discursive practices to social and psychological dimensions was used to analyse instances of labelling in three Nigerian and three Cameroonian English-medium national newspapers. The analyses revealed that the newspapers generally labelled Nigerians in Bakassi as both owners (natives and indigenes) and non-owners (inhabitants and residents). Specifically, the Cameroonian news reports deployed more labels of non-ownership to project Nigerians in Bakassi as mere tenants and occupants of the region while the Nigerian news reports employed more labels of ownership to depict Nigerians as aboriginals and owners of the peninsula. The ideologies of economic interests and ancestral roots motivated the labelling of territorial ownership and non-ownership in both nations’ newspapers.
Stages and new conceptual tools for legitimizing military intervention
Authors: Küçükali Can
Published: December 2016

This paper delves into the problem of aggression in Turkish foreign-policy discourse on Syria which tries to legitimize a military operation. In order to understand how the policymaking preferences of a military operation are legitimized and promoted in governmental discourse, 166 governmental texts, from 2011 to 2013, are investigated in terms of the implementation of strategies proposed by several scholars (van Leeuwen and Wodak 1999; Reisigl and Wodak 2001, 2009; van Leeuwen 2007, 2008; Reyes 2011). The results show that the increasing willingness of the Turkish government to take military action in Syria is systematically operationalized in several stages within each type of legitimation strategy (van Leeuwen and Wodak 1999) to overcome international reluctance and provide support for a prospective conflict. At the end of the paper, the results are evaluated in light of recent political developments for a comprehensive understanding of the meaning and limits of the strategies implemented.
Meta-megastudies
Authors: Myers James
Published: December 2016

Cross-linguistic data have always been of interest to mental lexicon researchers, but only now are technological developments beginning to make it possible to treat language as a random variable, in an approach we dub meta-megastudies. A meta-megastudy uses regression techniques to tease apart not just factors that are partially confounded across items within languages, as in traditional megastudies, but also factors partially confounded across languages. While large-scale meta-megastudies will be logistically challenging, they promise great theoretical benefits and are becoming ever more feasible via Web-based coordination between independent research groups.
Functionalism in the lexicon
Authors: Richie Russell
Published: December 2016

Why do languages have the words they have, and not some other set of words? While certainly there is some arbitrariness in the lexicon (English ‘frog’ vs. Spanish ‘rana’), there is just as surely some systematicity or functionality in it as well. What exactly might the nature of this systematicity or functionality be? For example, might the lexicon be efficiently adapted for communication, learning, memory storage, retrieval, or other cognitive functions? This paper critically reviews evidence that natural language lexicons efficiently carve up semantic fields (e.g., color, space, kinship) and have phonological forms that are similarly efficient when the aggregate lexicon is considered. The paper also suggests additional ways functionalism in lexicons might be assessed, and speculates on how functional lexicons may have arisen.
El uso de los aproximativosmás o menosyaproximadamenteen el continuo variacional
Authors: Cardona Ana Llopis
Published: December 2016

Este artículo examina los aproximativosaproximadamenteymás o menos,considerados en la bibliografía como expresiones sinonímicas. Se indaga su uso a partir del análisis de un macrocorpus formado por cuatro géneros discursivos que abarcan el continuo variacional que va desde el registro informal hasta el formal. El análisis efectuado revela notorias diferencias entre ambos adverbios focales:aproximadamentees más propio del medio escrito, está vinculado a la cuantificación y adquiere otros valores pragmáticos en pocas ocasiones;más o menos,por el contrario, es más frecuente en el medio oral, predica una modificación de la extensión de lo designado y sirve como mecanismo para comunicar otros efectos pragmáticos, entre ellos, la atenuación.
La comprobación de los canales al inicio de encuentros por videoconferencia
Authors: Santos Muñoz Arantxa
Published: December 2016

Partiendo de la metodología del Análisis Conversacional, el presente estudio examina una práctica habitual durante el inicio de encuentros por videoconferencia: la comprobación de los canales de audio y vídeo. Se muestra que dicha práctica con frecuencia se lleva a cabo a través de elementos comoholaacompañados de marcas prosódicas concretas en función de las cuales los participantes pueden realizar diferentes acciones: solicitar una confirmación, confirmar el correcto funcionamiento de los canales o marcar la posible existencia de problemas técnicos. Se argumenta que aunque con dichos elementos también se contribuye al establecimiento de la orientación mutua y la disponibilidad recíproca de los participantes, la función principal de la primera secuencia de la interacción audiovisual es el chequeo del funcionamiento de los canales, por lo que se concluye que en videoconferencia la secuencia inicial de comprobación podría constituir la secuencia típica con la que se inicia la interacción oral.
Effective animal health programming requires consideration of and communication with those at the human-animal interface.
Authors: Bagnol B. , Naysmith S. , Bruyn J. de , Wong J. , Alders R.
Published: December 2016

Since the advent of agricultural support services, animal health programming has most often appeared as a linear and top-down activity with information and resources flowing from educated, official senders or communicators (the 'haves') to ignorant, passive recipients (the 'have nots') who work and live with animals. The lack of consideration for the experience and perception of those at the animal-human interface can negatively impact the efficacy of animal health programming. In development practice generally, and more recently in the veterinary field, the importance of open communication and participation with programme participants has been identified as integral to success. This paper reviews recent and extensive programming for rinderpest and highly pathogenic avian influenza to identify how participatory tools and approaches have been used and adapted for disease surveillance and response. In emphasizing the role that communication and local peoples' knowledge and experiences can play in shaping animal health programming, this paper contends that participatory methods can help promote both animal and human health. The success of future programming however will require greater interdisciplinary collaboration and communication, along with the integration and validation of multiple sources of evidence and knowledge. This can contribute to the development of adequate strategies for risk reduction and efficient incentives for the adoption of risk reduction guidelines.
Accuracy of plant specimen disease severity estimates: concepts, history, methods, ramifications and challenges for the future.
Authors: Bock C. H. , Chiang KuoSzu Chiang KuoSzu , Del Ponte E. M.
Published: December 2016

Knowledge of the extent of the symptoms of a plant disease, generally referred to as severity, is a key to both fundamental and applied aspects of plant pathology. Most commonly, severity is obtained visually and the accuracy of each estimate (closeness to the actual value) by individual raters is paramount as it directly affects inferences and decisions based on average data. Thus, the more accurate the visual estimate of severity made by a rater for each specimen, the lower the magnitude of errors in the analysis, and thus the lower the risk of incorrect decisions. Errors in estimates of severity on diseased specimens are becoming better understood and ways to minimize them have been developed during the last 25 years. The development of various tools to aid raters prior to, or during the assessments provides a basis for greater accuracy. Severity is often based on the continuous percentage scale to represent the proportion of area diseased. However, some tools, such as those based on category scales have been shown to harm accuracy of some estimates under specific conditions, potentially leading to Type II errors. On the other hand, ensuring raters are familiar with symptom identity, assessment training and the use of standard area diagrams (a series of pictorial representations of examples of actual severity), can lead to improved accuracy of each (or at least most) estimate(s) by raters, particularly those who are innately less accurate. In this review, the need for accuracy of visual estimates of disease severity on plant specimens is emphasized in relation to the sample mean and variance, and the history of accuracy in disease estimation is described, the advantages of tools to aid accuracy are presented and future research needs are outlined.
Sudden death syndrome - a growing threat of losses in soybeans.
Authors: Navi S. S. , Yang X. B.
Published: December 2016

Sudden death syndrome (SDS) caused by
Fusarium virguliforme
is one of the major yield-limiting soil borne diseases of soybean (
Glycine max
). The SDS has been reported from 21 US states and is known to occur in Africa, North America and South America. In the USA the losses due to SDS was estimated at US$3.06 billion for a period from 1988 to 2010. Since 1983, several management approaches have been investigated to reduce SDS and yet, continued efforts are necessary to develop long-term disease management programs and to sustain disease below economic threshold levels. Integrating available control measures is an option, but adaptability and real-world assessments are equally important. Support of several funding agencies to better understand the disease in identifying suitable control measures to reduce yield losses in commercial cultivations has been indispensable in accomplishing these goals. In spite of sustained efforts, SDS continued to spread within the USA and reported in seven other countries since its first report in 1971. In this review, updated information on geographic distribution and economic significance of SDS, epidemiology, factors affecting SDS and management options for SDS including screening techniques have been compiled. Also, discussed significant gaps in use of plant, fungi and bacteria-based biocontrol agents in addressing management of SDS.
Generalized R-squared for detecting dependence
Authors: Wang X. , Jiang B. , Liu J. S.
Published: December 2016

Detecting dependence between two random variables is a fundamental problem. Although the Pearson correlation coefficient is effective for capturing linear dependence, it can be entirely powerless for detecting nonlinear and/or heteroscedastic patterns. We introduce a new measure, G-squared, to test whether two univariate random variables are independent and to measure the strength of their relationship. The G-squared statistic is almost identical to the square of the Pearson correlation coefficient, R-squared, for linear relationships with constant error variance, and has the intuitive meaning of the piecewise R-squared between the variables. It is particularly effective in handling nonlinearity and heteroscedastic errors. We propose two estimators of G-squared and show their consistency. Simulations demonstrate that G-squared estimators are among the most powerful test statistics compared with several state-of-the-art methods.
Single-cell studies of IFN-β promoter activation by wild-type and NS1-defective influenza A viruses
Authors: Killip M. J , Jackson D , Pérez-Cidoncha M , Fodor E , Randall R. E
Published: December 2016

Deletion or truncation of NS1, the principal IFN antagonist of influenza viruses, leads to increased IFN induction during influenza virus infection. We have studied activation of the IFN induction cascade by both wild-type and NS1-defective viruses at the single-cell level using a cell line expressing GFP under the control of the IFN-β promoter and by examining MxA expression. The IFN-β promoter was not activated in all infected cells even during NS1-defective virus infections. Loss of NS1 expression is therefore insufficient per se to induce IFN in an infected cell, and factors besides NS1 expression status must dictate whether the IFN response is activated. The IFN response was efficiently stimulated in these cells following infection with other viruses; the differential IFN response we observe with influenza viruses is therefore not cell specific but is likely due to differences in the nature of the infecting virus particles and their subsequent replication.
Perturbed human sub-networks byFusobacterium nucleatumcandidate virulence proteins
Authors: Zanzoni Andreas , Spinelli Lionel , Braham Shérazade , Brun Christine
Published: December 2016

F. nucleatumis a gram-negative anaerobic species residing in the oral cavity and implicated in several inflammatory processes in the human body. AlthoughF. nucleatumabundance is increased in inflammatory bowel disease subjects and is prevalent in colorectal cancer patients, the causal role of the bacterium in gastrointestinal disorders and the mechanistic details of host cell functions subversion are not fully understood.

We devised a computational strategy to identify putative secretedF. nucleatumproteins (FusoSecretome) and to infer their interactions with human proteins based on the presence of host molecular mimicry elements.FusoSecretome proteins share similar features with known bacterial virulence factors thereby highlighting their pathogenic potential. We show that they interact with human proteins that participate in infection-related cellular processes and localize in established cellular districts of the host-pathogen interface. Our network-based analysis identified 31 functional modules in the human interactome preferentially targeted by 138FusoSecretome proteins, among which we selected 26 as main candidate virulence proteins, representing both putative and known virulence proteins. Finally, 6 of the preferentially targeted functional modules are implicated in the onset and progression of inflammatory bowel diseases and colorectal cancer.

Overall, our computational analysis identified candidate virulence proteins potentially involved in theF. nucleatum– human cross-talk in the context of gastrointestinal diseases.
Rigid geometry solves “curse of dimensionality” effects in clustering methods: An application to omics data
Authors: Adachi Shun
Published: December 2016

The quality of samples preserved long term at ultralow temperatures has not been adequately studied. To improve our understanding, we need a strategy to analyze protein degradation and metabolism at subfreezing temperatures. To do this, we obtained liquid chromatography-mass spectrometry (LC/MS) data of calculated protein signal intensities in HEK-293 cells. Our first attempt at directly clustering the values failed, most likely due to the so-called “curse of dimensionality”. The clusters were not reproducible, and the outputs differed with different methods. By utilizing rigid geometry with a prime idealI-adic (p-adic) metric, however, we rearranged the sample clusters into a meaningful and reproducible order, and the results were the same with each of the different clustering methods tested. Furthermore, we have also succeeded in application of this method to expression array data in similar situations. Thus, we eliminated the “curse of dimensionality” from the data set, at least in clustering methods. It is possible that our approach determines a characteristic value of systems that follow a Boltzmann distribution.
Cell cycle dynamics of chromosomal organisation at single-cell resolution
Authors: Nagano Takashi , Lubling Yaniv , Varnai Csilla , Dudley Carmel , Leung Wing , Baran Yael , Mandelson-Cohen Netta , Wingett Steven , Fraser Peter , Tanay Amos
Published: December 2016

Chromosomes in proliferating metazoan cells undergo dramatic structural metamorphoses every cell cycle, alternating between a highly condensed mitotic structure facilitating chromosome segregation, and a decondensed interphase structure accommodating transcription, gene silencing and DNA replication. These cyclical structural transformations have been evident under the microscope for over a century, but their molecular-level analysis is still lacking. Here we use single-cell Hi-C to study chromosome conformations in thousands of individual cells, and discover a continuum ofcis-interaction profiles that finely position individual cells along the cell cycle. We show that chromosomal compartments, topological domains (TADs), contact insulation and long-range loops, all defined by ensemble Hi-C maps, are governed by distinct cell cycle dynamics. In particular, DNA replication correlates with build-up of compartments and reduction in TAD insulation, while loops are generally stable from G1 through S and G2. Analysing whole genome 3D structural models using haploid cell data, we discover a radial architecture of chromosomal compartments with distinct epigenomic signatures. Our single-cell data creates an essential new paradigm for the re-interpretation of chromosome conformation maps through the prism of the cell cycle.
A computational method for detection of structural variants using Deviant Reads and read pair Orientation: DevRO
Authors: Sayyab Shumaila , Rafati Nima , Carneiro Miguel , Garreau Hervé , Andersson Göran , Andersson Leif , Johan Rubin Carl
Published: December 2016

Background

Next generation sequencing (NGS) technology has made it possible to perform high-resolution screens for structural variants. Computational methods for detection of structural variants utilize paired-end mapping information, depth of coverage, split reads, or some combination of such data. The available methods are particularly designed to detect structural variants in single genomes or multiple genomes in a pairwise manner. The aim of this study was to develop a bioinformatics pipeline for detection of large structural variants using multiple pooled populations.

Results

Here we describe the method “DevRO”, developed to enable identification of structural variants using short insert paired-ends and long-range mate-pairs. DevRO uses paired-end mapping information from both types of libraries for identification of inversions, deletions and duplications followed by read depth information to screen for copy number variants. DevRO can detect structural variants in multiple populations without the need for pairwise comparisons. It uses a combined approach based on (i) paired-end mapping and (ii) depth of coverage that gives power to the study as compared to traditional methods that are based on either of these. DevRO is also designed to detect deletions in the reference assembly, which is an added functionality as compared to available methods.

Conclusion

We report a bioinformatics pipeline “DevRO” for detection of structural variants using paired-end mapping and depth of coverage methods tested on sequencing reads from multiple pooled rabbit populations. This method is useful when large numbers of populations have been re-sequenced as compared to traditional methods that can detect structural variants in a pairwise manner.
Single-channel in-Ear-EEG detects the focus of auditory attention to concurrent tone streams and mixed speech
Authors: Fiedler Lorenz , Wöstmann Malte , Graversen Carina , Brandmeyer Alex , Lunner Thomas , Obleser Jonas
Published: December 2016

Objective

Conventional, multi-channel scalp electroencephalography (EEG) allows the identification of the attended speaker in concurrent-listening (“cocktail party”) scenarios. This implies that EEG might provide valuable information to complement hearing aids with some form of EEG and to install a level of neuro-feedback.

Approach

To investigate whether a listener’s attentional focus can be detected from single-channel hearing-aid-compatible EEG configurations, we recorded EEG from three electrodes inside the ear canal (“in-Ear-EEG”) and additionally from 64 electrodes on the scalp. In two different, concurrent listening tasks, participants (n = 7) were fitted with individualized in-Ear-EEG pieces and were either asked to attend to one of two dichotically-presented, concurrent tone streams or to one of two diotically-presented, concurrent audiobooks. A forward encoding model was trained to predict the EEG response at single EEG channels.

Main results

Each individual participants’ attentional focus could be detected from single-channel EEG response recorded from short-distance configurations consisting only of a single in-Ear-EEG electrode and an adjacent scalp-EEG electrode. The differences in neural responses to attended and ignored stimuli were consistent in morphology (i.e., polarity and latency of components) across subjects.

Significance

In sum, our findings show that the EEG response from a single-channel, hearing-aid-compatible configuration provides valuable information to identify a listener’s focus of attention.
Dynamically controlled light delivery over large brain volumes through tapered optical fibers
Authors: Pisanello Ferruccio , Mandelbaum Gil , Pisanello Marco , Oldenburg Ian A. , Sileo Leonardo , Markowitz Jeffrey E. , Peterson Ralph E. , Della Patria Andrea , Haynes Trevor M. , Emara Mohamed S. , Spagnolo Barbara , Datta Sandeep R. , Sabatini Bernardo L. , De Vittorio Massimo
Published: December 2016

Optogenetics promises spatiotemporal precise control of neural processes using light. However, the spatial extent of illumination within the brain is difficult to control and cannot be adjusted using standard fiber optics. We demonstrate that optical fibers with tapered tips can be used to illuminate either large brain volumes or dynamically selectable subregions. Remotely adjusting the light input angle to the fiber varies the light-emitting portion of the taper over several millimeters without movement of the implant. We use this mode to activate dorsal versus ventral striatum of individual mice and reveal different effects of each manipulation on motor behavior. Conversely injecting light over the full numerical aperture of the fiber results in light emission from the entire taper surface, achieving broader and more efficient optogenetic activation of neurons when compared to the standard flat-faced fiber stimulation. Thus, tapered fibers permit focal or broad illumination that can be precisely and dynamically matched to experimental needs.
Model-based branching point detection in single-cell data by K-Branches clustering
Authors: Chlis Nikolaos K. , Wolf F. Alexander , Theis Fabian J.
Published: December 2016

Motivation

The identification of heterogeneities in cell populations by utilizing single-cell technologies such as single-cell RNA-Seq, enables inference of cellular development and lineage trees. Several methods have been proposed for such inference from high-dimensional single-cell data. They typically assign each cell to a branch in a differentiation trajectory. However, they commonly assume specific geometries such as tree-like developmental hierarchies and lack statistically sound methods to decide on the number of branching events.

Results

We present K-Branches, a solution to the above problem by locally fitting half-lines to single-cell data, introducing a clustering algorithm similar to K-Means. These halflines are proxies for branches in the differentiation trajectory of cells. We propose a modified version of the GAP statistic for model selection, in order to decide on the number of lines that best describe the data locally. In this manner, we identify the location and number of subgroups of cells that are associated with branching events and full differentiation, respectively. We evaluate the performance of our method on single-cell RNA-Seq data describing the differentiation of myeloid progenitors during hematopoiesis, single-cell qPCR data of mouse blastocyst development and artificial data.

Availability

An R implementation of K-Branches is freely available athttps://github.com/theislab/kbranches

Contact

fabian.theis@helmholtz-muenchen.de
Development of Narrow Spectrum ATP-competitive Kinase Inhibitors as Probes for BIKE and AAK1
Authors: Couñago Rafael M. , Axtman Alison D. , Capuzzi Stephen J. , Azevedo Hátylas , Drewry David H. , Elkins Jonathan M. , Gileadi Opher , Guimarães Cristiano R. W. , Mascarello Alessandra , Serafim Ricardo A. M. , Wells Carrow I. , Willson Timothy M. , Zuercher William J.
Published: December 2016

Understanding the structural determinants of inhibitor selectivity would facilitate the design and preparation of kinase probes. We describe a pair of matched compounds differing only by one degree of saturation but showing dramatic differential activities at select kinases. We utilized x-ray crystallography and computational analysis to rationalize the basis of the differential activity.
Circadian and feeding cues integrate to drive rhythms of physiology in Drosophila insulin-producing cells
Authors: Barber Annika F. , Erion Renske , Holmes Todd C. , Sehgal Amita
Published: December 2016

Circadian clocks regulate much of behavior and physiology, but the mechanisms by which they do so remain poorly understood. While cyclic gene expression is thought to underlie metabolic rhythms, little is known about cycles in cellular physiology. We found that Drosophila insulin-producing cells (IPCs), which are located in the pars intercerebralis and lack an autonomous circadian clock, are functionally connected to the central circadian clock circuit via DN1 neurons. Insulin mediates circadian output by regulating the rhythmic expression of a metabolic gene (sxe2) in the fat body. Patch clamp electrophysiology reveals that IPCs display circadian clock-regulated daily rhythms in firing event frequency and bursting proportion under light:dark conditions. The activity of IPCs and the rhythmic expression of sxe2 are additionally regulated by feeding, as demonstrated by night feeding-induced changes in IPC firing characteristics and sxe2 levels in the fat body. These findings indicate circuit-level regulation of metabolism by clock cells in Drosophila and support a role for the pars intercerebralis in integrating circadian control of behavior and physiology.
Reward retroactively enhances memory consolidation for related items
Authors: Patil Anuya , Murty Vishnu P. , Dunsmoor Joseph E. , Phelps Elizabeth A. , Davachi Lila
Published: December 2016

Reward motivation has been shown to modulate episodic memory processes in order to support future adaptive behavior. However, for a memory system to be truly adaptive, it should enhance memory for rewarded events as well as for neutral events that may seem inconsequential at the time of encoding but can gain importance later. Here, we investigated the influence of reward motivation on retroactive memory enhancement selectively for conceptually related information. We found behavioral evidence that reward retroactively enhances memory at a 24-h memory test, but not at an immediate memory test, suggesting a role for post-encoding mechanisms of consolidation.
Respective role of the dorsal hippocampus and the entorhinal cortex during the recombination of previously learned olfactory–tactile associations in the rat
Authors: Boisselier Lise , Ferry Barbara , Gervais Rémi
Published: December 2016

The hippocampal formation has been extensively described as a key component for object recognition in conjunction with place and context. The present study aimed at describing neural mechanisms in the hippocampal formation that support olfactory–tactile (OT) object discrimination in a task where space and context were not taken into account. The task consisted in discriminating one baited cup among three, each of them presenting overlapping olfactory or tactile elements. The experiment tested the involvement of the entorhinal cortex (EC) and the dorsal hippocampus (DH) in the acquisition of this cross-modal task, either with new items or with familiar but recombined items. The main results showed that DH inactivation or cholinergic muscarinic blockade in the DH selectively and drastically disrupted performance in the recombination task. EC inactivation impaired OT acquisition of any OT combinations while cholinergic blockade only delayed it. Control experiments showed that neither DH nor EC inactivation impaired unimodal olfactory or tactile tasks. As a whole, these data suggest that DH–EC interactions are of importance for flexibility of cross-modal representations with overlapping elements.
Vagus nerve stimulation reduces cocaine seeking and alters plasticity in the extinction network
Authors: Childs Jessica E. , DeLeon Jaime , Nickel Emily , Kroener Sven
Published: December 2016

Drugs of abuse cause changes in the prefrontal cortex (PFC) and associated regions that impair inhibitory control over drug-seeking. Breaking the contingencies between drug-associated cues and the delivery of the reward during extinction learning reduces rates of relapse. Here we used vagus nerve stimulation (VNS) to induce targeted synaptic plasticity to facilitate extinction of appetitive behaviors and to reduce relapse. Rats self-administered cocaine and were given VNS during extinction. Relapse to drug-seeking was assessed in a cued reinstatement session. We used immunohistochemistry to measure changes in the expression of the phosphorylated transcription factor cAMP response-element binding protein (pCREB) in the PFC and the basolateral amygdala (BLA), which regulate cue learning and extinction. In vivo recordings of evoked field potentials measured drug- and VNS-induced changes in metaplasticity in the pathway from the PFC to the BLA. VNS-treated rats showed improved rates of extinction and reduced reinstatement. Following reinstatement, pCREB levels were reduced in the IL and BLA of VNS-treated rats. Evoked responses in the BLA were greatly reduced in VNS-treated rats, and these rats were also resistant to the induction of LTD. Taken together, these results show that VNS facilitates extinction and reduces reinstatement. Changes in the pathway between the PFC and the amygdala may contribute to these beneficial effects.
A PKM generated by calpain cleavage of a classical PKC is required for activity-dependent intermediate-term facilitation in the presynaptic sensory neuron of Aplysia
Authors: Farah Carole A. , Hastings Margaret H. , Dunn Tyler W. , Gong Katrina , Baker-Andresen Danay , Sossin Wayne S.
Published: December 2016

Atypical PKM, a persistently active form of atypical PKC, is proposed to be a molecular memory trace, but there have been few examinations of the role of PKMs generated from other PKCs. We demonstrate that inhibitors used to inhibit PKMs generated from atypical PKCs are also effective inhibitors of other PKMs. In contrast, we demonstrate that dominant-negative PKMs show isoform-specificity. A dominant-negative PKM from the classical PKC Apl I blocks activity-dependent intermediate-term facilitation (a-ITF) when expressed in the sensory neuron, while a dominant-negative PKM from the atypical PKC Apl III does not. Consistent with a specific role for PKM Apl I in activity-dependent facilitation, live imaging FRET-based cleavage assays reveal that activity leads to cleavage of the classical PKC Apl I, but not the atypical PKC Apl III in the sensory neuron varicosities of Aplysia. In contrast, massed intermediate facilitation (m-ITF) induced by 10 min of 5HT is sufficient for cleavage of the atypical PKC Apl III in the motor neuron. Interestingly, both cleavage of PKC Apl I in the sensory neuron during a-ITF and cleavage of PKC Apl III in the motor neuron during m-ITF are inhibited by a dominant-negative form of a penta-EF hand containing classical calpain cloned from Aplysia. Consistent with a role for PKMs in plasticity, this dominant-negative calpain also blocks both a-ITF when expressed in the sensory neuron and m-ITF when expressed in the motor neuron. This study broadens the role of PKMs in synaptic plasticity in two significant ways: (i) PKMs generated from multiple isoforms of PKC, including classical isoforms, maintain memory traces; (ii) PKMs play roles in the presynaptic neuron.