bluuebunny/crossref_metadata_2025_split huggingface dataset:
The draft genome of the lichen-forming fungusLasallia hispanica(Frey) Sancho & A. Crespo
Authors: DAL GRANDE Francesco , MEISER Anjuli , GRESHAKE TZOVARAS Bastian , OTTE Jürgen , EBERSBERGER Ingo , SCHMITT Imke 
Published: May 2018

AbstractLasallia hispanica (Frey) Sancho & A. Crespo is one of threeLasalliaspecies occurring in central-western Europe. It is an orophytic, photophilous Mediterranean endemic which is sympatric with the closely related, widely distributed, highly clonal sister taxonL. pustulatain the supra- and oro-Mediterranean belts. We sequenced the genome ofL. hispanicafrom a multispore isolate. The total genome length is 41·2 Mb, including 8488 gene models. We present the annotation of a variety of genes that are involved in protein secretion, mating processes and secondary metabolism, and we report transposable elements. Additionally, we compared the genome ofL. hispanicato the closely related, yet ecologically distant,L. pustulataand found high synteny in gene content and order. The newly assembled and annotatedL. hispanicagenome represents a useful resource for future investigations into niche differentiation, speciation and microevolution inL. hispanicaand other members of the genus.
Assessing phylogeny and historical biogeography of the largest genus of lichen-forming fungi, Xanthoparmelia (Parmeliaceae, Ascomycota)
Authors: LEAVITT Steven D. , KIRIKA Paul M. , AMO DE PAZ Guillermo , HUANG Jen-Pan , HUR Jae-Seoun , ELIX John A. , GREWE Felix , DIVAKAR Pradeep K. , LUMBSCH H. Thorsten 
Published: May 2018

AbstractSpecies richness is not evenly distributed across the tree of life and a limited number of lineages comprise an extraordinarily large number of species. In lichen-forming fungi, only two genera are known to be ‘ultradiverse’ (>500 species), with the most diverse genus, Xanthoparmelia, consisting of c. 820 species. While Australia and South Africa are known as current centres of diversity for Xanthoparmelia, it is not well known when and where this massive diversity arose. To better understand the geographical and temporal context of diversification in this diverse genus, we sampled 191 Xanthoparmelia specimens representing c. 124 species/species-level lineages from populations worldwide. From these specimens, we generated a multi-locus sequence data set using Sanger and high-throughput sequencing to reconstruct evolutionary relationships in Xanthoparmelia, estimate divergence times and reconstruct biogeographical histories in a maximum likelihood and Bayesian framework. This study corroborated the phylogenetic placement of several morphologically or chemically diverse taxa within Xanthoparmelia, such as Almbornia, Chondropsis, Karoowia, Namakwa, Neofuscelia, Omphalodiella, Paraparmelia, Placoparmelia and Xanthomaculina, in addition to improved phylogenetic resolution and reconstruction of previously unsampled lineages within Xanthoparmelia. Our data indicate that Xanthoparmelia most likely originated in Africa during the early Miocene, coinciding with global aridification and development of open habitats. Reconstructed biogeographical histories of Xanthoparmelia reveal diversification restricted to continents with infrequent intercontinental exchange by long-distance dispersal. While likely mechanisms by which Xanthoparmelia obtained strikingly high levels of species richness in Australia and South Africa remain uncertain, this study provides a framework for ongoing research into diverse lineages of lichen-forming fungi. Finally, our study highlights a novel approach for generating locus-specific molecular sequence data sets from high throughput metagenomic reads.
Disrupted rich club organization and structural brain connectome in unmedicated bipolar disorder
Authors: Wang Ying , Deng Feng , Jia Yanbin , Wang Junjing , Zhong Shuming , Huang Huiyuan , Chen Lixiang , Chen Guanmao , Hu Huiqing , Huang Li , Huang Ruiwang 
Published: May 2018

AbstractBackgroundBipolar disorder (BD) has been associated with altered brain structural and functional connectivity. However, little is known regarding alterations of the structural brain connectome in BD. The present study aimed to use diffusion-tensor imaging (DTI) and graph theory approaches to investigate the rich club organization and white matter structural connectome in BD.MethodsForty-two patients with unmedicated BD depression and 59 age-, sex- and handedness-matched healthy control participants underwent DTI. The whole-brain structural connectome was constructed by a deterministic fiber tracking approach. Graph theory analysis was used to examine the group-specific global and nodal topological properties, and rich club organizations, and then nonparametric permutation tests were used for group comparisons of network parameters.ResultsCompared with healthy control participants, the patients with BD showed abnormal global properties, including increased characteristic path length, and decreased global efficiency and local efficiency. Locally, the patients with BD showed abnormal nodal parameters (nodal strength, nodal efficiency, and nodal betweenness) predominantly in the parietal, orbitofrontal, occipital, and cerebellar regions. Moreover, the patients with BD showed decreased rich club and feeder connectivity density.ConclusionsOur results may reflect the disrupted white matter topological organization in the whole-brain, and abnormal regional connectivity supporting cognitive and affective functioning in depressed BD, which, in part, be due to impaired rich club connectivity.
Prevalence and determinants of cognitive impairment in the euthymic phase of bipolar disorders: results from the FACE-BD cohort
Authors: Roux Paul , Etain Bruno , Cannavo Anne-Sophie , Aubin Valérie , Aouizerate Bruno , Azorin Jean-Michel , Bellivier Frank , Belzeaux Raoul , Bougerol Thierry , Cussac Iréna , Courtet Philippe , Kahn Jean-Pierre , Leboyer Marion , M'Bailara Katia , Payet Marion Perrin , Olié Emilie ,   the FondaMental Advanced Centers of Expertise in Bipolar Disorders (FACE-BD) Collaborators, Henry Chantal , Passerieux Christine 
Published: May 2018

AbstractBackgroundCognitive deficits are a well-established feature of bipolar disorders (BD), even during periods of euthymia, but risk factors associated with cognitive deficits in euthymic BD are still poorly understood. We aimed to validate classification criteria for the identification of clinically significant cognitive impairment, based on psychometric properties, to estimate the prevalence of neuropsychological deficits in euthymic BD, and identify risk factors for cognitive deficits using a multivariate approach.MethodsWe investigated neuropsychological performance in 476 euthymic patients with BD recruited via the French network of BD expert centres. We used a battery of tests, assessing five domains of cognition. Five criteria for the identification of neuropsychological impairment were tested based on their convergent and concurrent validity. Uni- and multivariate logistic regressions between cognitive impairment and several clinical and demographic variables were performed to identify risk factors for neuropsychological impairment in BD.ResultsOne cut-off had satisfactory psychometric properties and yielded a prevalence of 12.4% for cognitive deficits in euthymic BD. Antipsychotics use were associated with the presence of a cognitive deficit.ConclusionsThis is the first study to validate a criterion for clinically significant cognitive impairment in BD. We report a lower prevalence of cognitive impairment than previous studies, which may have overestimated its prevalence. Patients with euthymic BD and cognitive impairment may benefit from cognitive remediation.
Focus on the mechatronics design of a new dexterous robotic hand for inside hand manipulation
Authors: Vulliez P. , Gazeau J. P. , Laguillaumie P. , Mnyusiwalla H. , Seguin P. 
Published: May 2018

SUMMARYThis paper presents a novel tendon-driven bio-inspired robotic hand design for in-hand manipulation. Many dexterous robot hands are able to produce adaptive grasping, but only a few human-sized hands worldwide are able to produce fine motions of the object in the hand. One of the challenges for the near future is to develop human-sized robot hands with human dexterity. Most of the existing hands considered in the literature suffer from dry friction which creates unwanted backlash and non-linearities. These problems limit the accurate control of the fingers and the capabilities of the hand. Such was the case with our first fully actuated dexterous robot hand: the Laboratoire de Mécanique des Solides (LMS) hand.The mechanical design of the hand relies on a tendon-based transmission system. Developing a fully actuated dexterous robot hand requires the routing of the tendons through the finger for the actuation of each joint. This paper focuses on the evolution of the tendon routing; from the LMS hand to the new RoBioSS dexterous hand. The motion transmission in the new design creates purely linear coupling relations between joints and actuators. Experimental results using the same protocol for the previous hand and the new hand illustrate the evolution in the quality of the mechanical design. With the improvements of the mechanical behavior of the robotic fingers, the hand control software could be extensively simplified. The choice of a common architecture for all fingers makes it possible to consider the hand as a collaboration of four serial robots. Moreover, with the transparency of the motor-joint transmissions, we could use robust, industrial-grade cascaded feedback loops for the axis controls.An inside-hand manipulation task concerning the manipulation of a bottle cap is presented at the end of the paper. As proof of the robustness of the hand, demonstrations of the hand's capabilities were carried out continuously over three days at SPS IPC Drives international exhibition in Nuremberg, in November 2016.
Cubical geometry in the polygonalisation complex
Authors: BELL MARK C. , DISARLO VALENTINA , TANG ROBERT 
Published: May 2018

AbstractWe introduce the polygonalisation complex of a surface, a cube complex whose vertices correspond to polygonalisations. This is a geometric model for the mapping class group and it is motivated by works of Harer, Mosher and Penner. Using properties of the flip graph, we show that the midcubes in the polygonalisation complex can be extended to a family of embedded and separating hyperplanes, parametrised by the arcs in the surface.We study the crossing graph of these hyperplanes and prove that it is quasi-isometric to the arc complex. We use the crossing graph to prove that, generically, different surfaces have different polygonalisation complexes. The polygonalisation complex is not CAT(0), but we can characterise the vertices where Gromov's link condition fails. This gives a tool for proving that, generically, the automorphism group of the polygonalisation complex is the (extended) mapping class group of the surface.
IZAPAN WRITING: CLASSIFICATION AND PRELIMINARY OBSERVATIONS
Authors: Mora-Marín David F. 
Published: May 2018

AbstractThis paper reviews the limited evidence for the classification of the script attested at the site of Izapa. Sufficient data for assessing the nature of key formal traits exists, thanks to the more recent documentation of the sculptural corpus (Clark and Moreno 2007). After a review of the archaeological and historical linguistic context, the paper examines the history of research on the classification of the writing systems of Mesoamerica (Justeson 1986; Justeson and Mathews 1990; Justeson et al. 1985; Prem 1973), focusing on the Southeastern Tradition. Three diagnostic traits allow for a narrow assignation of Izapa's script, perhaps unsurprisingly, to the Greater Izapan or Maya-Izapa sub-tradition (Justeson and Mathews 1990; Justeson et al. 1985) of the Southeastern Tradition: the superfixed placement of the bar-and-dot numeral with respect to the day sign cartouche, positional notation for counting, and the use of day sign pedestals. Other traits include the conflation and embedding of signs. The paper concludes that the evidence is, at present, insufficient to distinguish between the two likely options, Mixe-Zoquean and Mayan. Finally, a preliminary signary is provided in the Appendix.
HOUSEHOLDERS AS WATER MANAGERS: A COMPARISON OF DOMESTIC-SCALE WATER MANAGEMENT PRACTICES FROM TWO CENTRAL MAYA LOWLAND SITES
Authors: Brewer Jeffrey L. 
Published: May 2018

AbstractMultiple studies conducted over the past few decades have recognized the necessity of rainwater collection and storage as a critical aspect in the evolution of Maya civilization. Few of these efforts, however, have emphasized the importance of managing water resources at the household level. Data are presented from two central lowland sites—the dispersed hinterland community of Medicinal Trail and the urban center of Yaxnohcah—that elucidate the function of small reservoirs and associated landscape modifications in residential water management. Despite differing physical geographies and trajectories of urban development, residents of both communities were clearly engaged in water management activities based, at least in part, on the creation and use of small reservoirs. Decentralized household water management practices appear to have been temporally and spatially widespread components of Maya civilization beginning in the Preclassic period.
Evaluation of mobile applications related to nutrition
Authors: Braz Vitória Negri , Lopes Maria Helena Baena de Moraes 
Published: May 2018

AbstractObjectiveTo verify the reliability of information, the sources of information used and the user opinions of the free mobile applications (apps) with nutritional information available in Brazil.DesignDescriptive, cross-sectional study.SettingWe evaluated the content about nutrition of free apps available on the App Store of iPhone 5S with software iOS 8.4.1 and on the Play Store of the Android platform, version 2.3.6. For this, we compared the nutrition information provided by the app with (i) the Brazilian Food Composition Table (TACO), of 2011; (ii) food composition table: support for nutritional decision, of 2002; and (iii) the National Study of Family Expenditure: food composition tables, of 1999. The evaluation included the description and quantity of macro- and micronutrients in foods. In addition, we evaluated the trustworthiness of information about food energy values and analysed the comments and ratings made by users.SubjectsMobile apps related to nutrition.ResultsWe assessed sixteen apps for mobile devices. Considering the foods selected (a basic Brazilian food basket for the month of August 2015), the apps presented partially adequate or inadequate information about food composition (macro- and micronutrients). The adequacy of the food energy values ranged from 0 to 57·1 %. Despite this, the apps received positive ratings by users.ConclusionsThe mobile apps about nutrition currently available and evaluated in the present study in Brazil are not useful for nutritional guidance because most of them are not based on reliable sources of information.
New constraints on Lyman-α opacity using 92 quasar lines of sight
Authors: Bosman Sarah E. I. , Fan Xiaohui , Jiang Linhua , Reed Sophie , Matsuoka Yoshiki , Becker George , Rorai Alberto 
Published: May 2018

AbstractThe large scatter in Lyman-α opacity at z > 5.3 has been an ongoing mystery, prompting a flurry of numerical models. A uniform ultra-violet background has been ruled out at those redshifts, but it is unclear whether any proposed models produce sufficient inhomogeneities. In this paper we provide an update on the measurement which first highlighted the issue: Lyman-α effective optical depth along high-z quasar lines of sight. We nearly triple on the previous sample size in such a study thanks to the cooperation of the DES-VHS, SHELLQs, and SDSS collaborations as well as new reductions and spectra. We find that a uniform UVB model is ruled out at 5.1 < z < 5.3, as well as higher redshifts, which is perplexing. We provide the first such measurements at z ∼ 6. None of the numerical models we confronted to this data could reproduce the observed scatter.
Foreground Mitigation in the Epoch of Reionization
Authors: Chapman Emma 
Published: May 2018

AbstractThe EoR foregrounds can be up to three magnitudes greater than the cosmological signal we wish to detect. Multiple methods have been developed in order to extract the cosmological signal, falling roughly into three categories: foreground removal, foreground suppression and foreground avoidance. These main approaches are briefly discussed in this review and consideration taken to the future application of these methods as a multi-layered approach.
Analysing 21cm signal with artificial neural network
Authors: Shimabukuro Hayato , Semelin Benoit 
Published: May 2018

AbstractThe 21cm signal at epoch of reionization (EoR) should be observed within next decade. We expect that cosmic 21cm signal at the EoR provides us both cosmological and astrophysical information. In order to extract fruitful information from observation data, we need to develop inversion method. For such a method, we introduce artificial neural network (ANN) which is one of the machine learning techniques. We apply the ANN to inversion problem to constrain astrophysical parameters from 21cm power spectrum. We train the architecture of the neural network with 70 training datasets and apply it to 54 test datasets with different value of parameters. We find that the quality of the parameter reconstruction depends on the sensitivity of the power spectrum to the different parameter sets at a given redshift and also find that the accuracy of reconstruction is improved by increasing the number of given redshifts. We conclude that the ANN is viable inversion method whose main strength is that they require a sparse extrapolation of the parameter space and thus should be usable with full simulation.
Intensity Mapping Foreground Cleaning with Generalized Needlet Internal Linear Combination
Authors: Olivari L. C. , Remazeilles M. , Dickinson C. 
Published: May 2018

AbstractIntensity mapping (IM) is a new observational technique to survey the large-scale structure of matter using spectral emission lines. IM observations are contaminated by instrumental noise and astrophysical foregrounds. The foregrounds are at least three orders of magnitude larger than the searched signals. In this work, we apply the Generalized Needlet Internal Linear Combination (GNILC) method to subtract radio foregrounds and to recover the cosmological HI and CO signals within the IM context. For the HI IM case, we find that GNILC can reconstruct the HI plus noise power spectra with 7.0% accuracy forz= 0.13 − 0.48 (960 − 1260 MHz) and ℓ ≲ 400, while for the CO IM case, we find that it can reconstruct the CO plus noise power spectra with 6.7% accuracy forz= 2.4 − 3.4 (26 − 34 GHz) and ℓ ≲ 3000.
EoR imaging with the SKA: the challenge of foreground removal
Authors: Bonaldi Anna 
Published: May 2018

Abstract21-cm observations of the Cosmic dawn (CD) and Epoch of Reionization (EoR) are one of the high priority science objectives for SKA Low. One of the most difficult aspects of the 21-cm measurement is the presence of foreground emission, due to our Galaxy and extragalactic sources, which is about four orders of magnitude brighter than the cosmological signal. While end-to-end simulations are being produced to investigate in details the foreground subtraction strategy, it is useful to complement this thorough but time-consuming approach with simpler, quicker ways to evaluate performance and identify possible critical steps. In this work, I present a forecast method, based on Bonaldi et al. (2015), Bonaldi & Ricciardi (2011), to understand the level of residual contamination after a component separation step, and its impact on our ability to investigate CD and EoR.
Resolving the structure of the Galactic foreground using Herschel measurements and the Kriging technique
Authors: Pinter S. , Bagoly Z. , Balázs L. G. , Horvath I. , Racz I. I. , Zahorecz S. , Tóth L. V. 
Published: May 2018

AbstractInvestigating the distant extragalactic Universe requires a subtraction of the Galactic foreground. One of the major difficulties deriving the fine structure of the galactic foreground is the embedded foreground and background point sources appearing in the given fields. It is especially so in the infrared. We report our study subtracting point sources from Herschel images with Kriging, an interpolation method where the interpolated values are modelled by a Gaussian process governed by prior covariances. Using the Kriging method on Herschel multi-wavelength observations the structure of the Galactic foreground can be studied with much higher resolution than previously, leading to a better foreground subtraction at the end.
Reionization and Cosmic Dawn: theory and simulations
Authors: Mesinger Andrei 
Published: May 2018

AbstractWe highlight recent progress in the sophistication and diversification of the simulations of cosmic dawn and reionization. The application of these modeling tools to recent observations has allowed us narrow down the timing of reionization. The midpoint of reionization is constrained to z = 7.6−0.7+0.8 (1 σ), with the strongest constraints coming from the optical depth to the CMB measured with the Planck satellite and the first detection of ongoing reionization from the spectra of the z = 7.1 QSOs ULASJ1120+0641. However, we still know virtually nothing about the astrophysical sources during the first billion years. The revolution in our understanding will be led by upcoming interferometric observations of the cosmic 21-cm signal. The properties of the sources and sinks of UV and X-ray photons are encoded in the 3D patterns of the signal. The development of Bayesian parameter recovery techniques, which tap into the wealth of the 21-cm signal, will soon usher in an era of precision astrophysical cosmology.
Foreground mitigation strategy for measuring the 21 cm-LAE cross-correlation
Authors: Yoshiura Shintaro , Line Jack L. B. , Kubota Kenji , Hasegawa Kenji , Takahashi Keitaro 
Published: May 2018

AbstractThe cross power spectrum of the 21 cm signal and Lyman-α emitters (LAEs) is a probe of the Epoch of Reionization. Astrophysical foregrounds do not correlate with the LAE distribution, though the foregrounds contribute to the error. To study the impact of foregrounds on the measurement, we assume realistic observation by the Murchison Widefield Array using a catalogue of radio galaxies, a LAE survey by the Subaru Hyper Supreme-Cam and the redshift of LAEs is determined by the Prime Focus Spectrograph. The HI distribution is estimated from a radiative transfer simulation with models based on results of radiation hydrodynamics simulation. Using these models, we found that the error of cross power spectrum is dominated by foreground terms. Furthermore, we estimate the effects of foreground removal, and find 99% of the foreground removal is required to detect the 21 cm-LAE signal at k ∼ 0.4 h Mpc−1.
Precision Calibration for HERA and 21 cm Cosmology
Authors: Dillon Joshua S. 
Published: May 2018

AbstractHere I discuss progress in both the theory and practice of data analysis for the Hydrogen Epoch of Reionization Array (HERA), focusing on techniques to calibrate the instrumental response and preserve the spectral smoothness that is essential to separating the cosmological 21 cm signal from foregrounds that are five orders of magnitude brighter. I explain how mis-calibration can create ruinous spectral structure and how we take advantage of HERA’s highly-redundant configuration for calibration. This proceeding draws from a talk I gave on October 3, 2017. Slides for it and all my talks are available atjoshdillon.net.