bluuebunny/crossref_metadata_2025 huggingface dataset:
Star formation history from the cosmic infrared background anisotropies
Authors: Maniyar A. S. , Béthermin M. , Lagache G.
Published: February 2018

We present a linear clustering model of cosmic infrared background (CIB) anisotropies at large scales that is used to measure the cosmic star formation rate density up to redshift 6, the effective bias of the CIB, and the mass of dark matter halos hosting dusty star-forming galaxies. This is achieved using the Planck CIB auto- and cross-power spectra (between different frequencies) and CIB × CMB (cosmic microwave background) lensing cross-spectra measurements, as well as external constraints (e.g. on the CIB mean brightness). We recovered an obscured star formation history which agrees well with the values derived from infrared deep surveys and we confirm that the obscured star formation dominates the unobscured formation up to at least z = 4. The obscured and unobscured star formation rate densities are compatible at 1σ at z = 5. We also determined the evolution of the effective bias of the galaxies emitting the CIB and found a rapid increase from ~0.8 at z = 0 to ~8 at z = 4. At 2 < z < 4, this effective bias is similar to that of galaxies at the knee of the mass functions and submillimetre galaxies. This effective bias is the weighted average of the true bias with the corresponding emissivity of the galaxies. The halo mass corresponding to this bias is thus not exactly the mass contributing the most to the star formation density. Correcting for this, we obtained a value of log(Mh/M⊙) = 12.77−0.125+0.128 for the mass of the typical dark matter halo contributing to the CIB at z = 2. Finally, using a Fisher matrix analysis we also computed how the uncertainties on the cosmological parameters affect the recovered CIB model parameters, and find that the effect is negligible.
Synthesis of Sterically Protected Isoindoles from ortho-Phthalaldehyde
Authors: Nakao Michiyasu , Nishikiori Nanako , Nakamura Akihito , Miyagi Murasaki , Shibata Nao , Kitaike Syuji , Fukui Makoto , Ito Hiro-O , Sano Shigeki
Published: February 2018

o-Phthalaldehyde (OPA) reacts with O-protected tris(hydroxyalkyl)aminomethanes in the presence of 1-propanethiol to afford a novel class of stable isoindoles. Steric protection provided by the bulkiness of C
3-symmetric primary amines derived from tris(hydroxymethyl)aminomethane could be significant for the stabilization of 1-alkylthio-2-alkyl-substituted isoindoles derived from OPA. A plausible reaction mechanism is proposed to explain the formation of the isoindole and an isoindolin-1-one by-product.
Asymmetric Titanium-Catalyzed Cyclopropanation of Nitriles with Grignard Reagents
Authors: Caillé Julien , Setzer Paul , Boeda Fabien , Pearson-Long Morwenna , Bertus Philippe
Published: February 2018

The titanium-catalyzed asymmetric cyclopropanation of cyanoesters­ with Grignard reagents was investigated for the first time. Particularly, the study of the efficiency of Taddol-based titanium complexes­ has shown that the prior preparation of Taddol titanium complexes was not required and a large panel of ligands was evaluated by using this approach. The spirocyclopropanelactams were obtained with good diastereoselectivity and with moderate enantioselectivities from the main diastereoisomer (up to 32%).
Combined Interhemispheric and Transsylvian Approach for Resection of Craniopharyngioma
Authors: Inoue Tomohiro , Ono Hideaki , Tamura Akira , Saito Isamu
Published: February 2018

We present a 37-year-old male case of cystic suprasellar huge craniopharyngioma, who presented with significant memory disturbance due to obstructive hydrocephalus. Combined interhemispheric and pterional approach was chosen to resect huge suprasellar tumor. Interhemispheric trans-lamina terminalis approach was quite effective to resect third ventricular tumor, while pterional approach was useful to dissect tumor out of basilar perforators and stalk.

The link to the video can be found at: https://youtu.be/BoYIPa96kdo.
The “Auto-sliding Graft” Aortic Wrapping Technique
Authors: Estevez-Cid Francisco , Herrera-Norena Jose María , de Sierra Carlos Velasco-García
Published: February 2018

We describe the “auto-sliding graft” technique, a different anastomotic option for reconstructive prosthetic procedures on the ascending aorta especially in patients at risk of circulatory arrest with mild aortic dilatation. This simple technique provides not only an important hemostatic reinforcement for the distal aortic graft anastomosis but also a protective effect on the native ascending aorta beyond the suture line.
Individuelle Therapie
Authors: Maier Klaus-Jürgen , Knobe Matthias
Published: February 2018

Einführung Die Therapie der Altersfrakturen stellt aufgrund der meist vorliegenden Multimorbidität der
geriatrischen Patienten für alle beteiligten Berufsgruppen eine große Herausforderung dar – von der
Indikationsstellung bis zur Nachbehandlung. Im Schwerpunkt beschreiben wir Schritt für Schritt die individuell
abgestimmten Behandlungsmöglichkeiten für typische Altersfrakturen.
Demenzsensible Versorgung
Authors: Spitzner Katja , Morgenstern Ulrike
Published: February 2018

Menschen mit Demenz im OP Die Zahl älterer Patienten wächst stetig an, was gleichzeitig zu einer Zunahme
an demenzkranken Patienten führt. Viele Faktoren im Klinikalltag bewirken, dass ihre besonderen Bedürfnisse
nicht ausreichend berücksichtigt werden. Wie die Versorgung im Akutkrankenhaus und speziell im OP für Menschen
mit Demenz angemessener gestaltet werden kann, schildern unsere Autorinnen.
Quo vadis Datenlinkage in Deutschland? Eine erste Bestandsaufnahme
Authors: March Stefanie , Antoni Manfred , Kieschke Joachim , Kollhorst Bianca , Maier Birga , Müller Gabriele , Sariyar Murat , Schulz Mandy , Enno Swart , Zeidler Jan , Hoffmann Falk
Published: February 2018

Die Verknüpfung verschiedener Datenquellen, genannt Datenlinkage oder auch Record Linkage, zur Beantwortung von wissenschaftlichen Fragestellungen findet in den letzten Jahren in Deutschland vermehrt Anwendung. Jedoch mangelt es bisher an publizierten Erfahrungen. Neue Projekte erarbeiten sich in der Regel autark voneinander das notwendige Handwerkszeug. Daher hat sich eine Gruppe von Forschern zusammengefunden, um ihre Erfahrungen zum Datenlinkage in Deutschland als mögliche Hilfestellung bzw. Anregung für Projekte, Gutachter sowie Datenschützer und Ethikkommissionen zusammenzustellen. Ziel dieser ersten Bestandsaufnahme zum Datenlinkage ist es deshalb, eine Unterstützung für zukünftige Projekte zu liefern, die Daten aus Deutschland auf individueller Ebene verknüpfen möchten. Neben den (datenschutz-)rechtlichen Rahmenbedingungen werden dabei auch praxisorientiert die Arten des Datenlinkage, deren Anwendungsfelder und Ansätze zur Vermeidung von Fehlern anhand von Beispielen dargestellt.
Multimodale Schmerztherapie bei traumatisierten Patienten
Authors: Söllner Wolfgang , Venkat Sandra
Published: February 2018

In Schmerzzentren werden häufig Patienten mit Traumatisierung in Kindheit und Jugend und teilweise auch anhaltenden posttraumatischen Belastungsstörungen behandelt. Die Traumatisierung wird oft erst im Rahmen einer multimodalen Schmerztherapie (MMST) erkannt. Die Mitarbeiter von Schmerzeinrichtungen, die eine MMST anbieten, sollten über den Umgang und die Behandlung von traumatisierten Schmerzpatienten geschult werden. Ein zweizeitiges Behandlungsverfahren wird vorgeschlagen: Nach einer MMST sollte eine weiterführende traumatherapeutisch fokussierte psychosomatische Behandlung angeschlossen werden.
Solar Collector Simulator (SolCoSi): A new validated model for predicting the thermal performance of flat plate solar collectors
Authors: Pérez-Espinosa R. , García-Valladares O.
Published: February 2018

A Solar Collector Simulator (SolCoSi) to evaluate the thermal performance of flat plate solar collectors has been successfully carried out. The model discretizes the flat plate solar collectors in the axial and longitudinal directions, and it can be used in order to evaluate the thermal efficiency curve, the incident angle modifier, the stagnation temperature, and the temperature distribution in fluid flow and solids. SolCoSi enables an analysis of different geometries, fluid types, working conditions, and different components and materials: selective surfaces, covers, insulations, air gaps, fins, risers, etc. The numerical model has been validated against a wide range of experimental data (seven different commercial flat plate solar collectors with 70 experimental thermal efficiency data points), and it was also compared with an available free software. Using a comprehensive statistical analysis, based on weighted linear regressions with an outlier detection/rejection algorithm at 95% of confidence level, the prediction performance of the numerical model was evaluated. Linear relationships between thermal efficiency (predicted) and experimental thermal efficiency data were statistically demonstrated. An average deviation error of ±2.55% was consistently computed between the numerical model and experimental data, which demonstrates the good capability of the model developed for predicting the thermal performance of flat plate solar collectors. The physical model developed and validated is available as a free access online software on the website: http://solcosi.ier.unam.mx/.
Temperature and magnetic field dependencies of the Young's modulus in magnetostrictive Fe-Ga alloys
Authors: Li Jiheng , Li Mingming , Mu Xing , Bao Xiaoqian , Gao Xuexu
Published: February 2018

Anomalous temperature dependences of Young's modulus were observed in the as-cast and directionally solidified Fe100-xGax alloys (x = 20, 22, 24, 27). However, the absence of the anomalous temperature dependence of Young's modulus in the DO19 and L12 ordered Fe73Ga27 alloys revealed that the anomalous temperature dependences of Young's modulus of Fe-Ga alloys with different structures were only related with the structure transformation during the heating process. The relationship between the variations of Young's modulus and structural transformation in the Fe78Ga22 alloy indicated that the lattice shrinkage owing to the structural transformations of A2 → DO3 and BCC(A2/DO3) → L12 was offset by the lattice expansion of the A2 phase caused by the thermal effect, which lead to a near constant coefficient of Young's modulus in the temperature range from 500 °C to 560 °C. In addition, the variability of Young's modulus as high as 12.8% was obtained in the as-directional solidified Fe73Ga27 alloy.
The hydrophilic-to-hydrophobic transition in glassy silica is driven by the atomic topology of its surface
Authors: Yu Yingtian , Krishnan N. M. Anoop , Smedskjaer Morten M. , Sant Gaurav , Bauchy Mathieu
Published: February 2018

The surface reactivity and hydrophilicity of silicate materials are key properties for various industrial applications. However, the structural origin of their affinity for water remains unclear. Here, based on reactive molecular dynamics simulations of a series of artificial glassy silica surfaces annealed at various temperatures and subsequently exposed to water, we show that silica exhibits a hydrophilic-to-hydrophobic transition driven by its silanol surface density. By applying topological constraint theory, we show that the surface reactivity and hydrophilic/hydrophobic character of silica are controlled by the atomic topology of its surface. This suggests that novel silicate materials with tailored reactivity and hydrophilicity could be developed through the topological nanoengineering of their surface.
Enhanced magnetoelectric effect in M-type hexaferrites by Co substitution into trigonal bi-pyramidal sites
Authors: Beevers J. E. , Love C. J. , Lazarov V. K. , Cavill S. A. , Izadkhah H. , Vittoria C. , Fan R. , van der Laan G. , Dhesi S. S.
Published: February 2018

The magnetoelectric effect in M-type Ti-Co doped strontium hexaferrite has been studied using a combination of magnetometry and element specific soft X-ray spectroscopies. A large increase (>×30) in the magnetoelectric coefficient is found when Co2+ enters the trigonal bi-pyramidal site. The 5-fold trigonal bi-pyramidal site has been shown to provide an unusual mechanism for electric polarization based on the displacement of magnetic transition metal (TM) ions. For Co entering this site, an off-centre displacement of the cation may induce a large local electric dipole as well as providing an increased magnetostriction enhancing the magnetoelectric effect.
Electron effective mass in In0.33Ga0.67N determined by mid-infrared optical Hall effect
Authors: Armakavicius Nerijus , Stanishev Vallery , Knight Sean , Kühne Philipp , Schubert Mathias , Darakchieva Vanya
Published: February 2018

Mid-infrared optical Hall effect measurements are used to determine the free charge carrier parameters of an unintentionally doped wurtzite-structure c-plane oriented In0.33Ga0.67N epitaxial layer. Room temperature electron effective mass parameters of m⊥*=(0.205±0.013) m0 and m∥*=(0.204±0.016) m0 for polarization perpendicular and parallel to the c-axis, respectively, were determined. The free electron concentration was obtained as (1.7 ± 0.2) × 1019 cm−3. Within our uncertainty limits, we detect no anisotropy for the electron effective mass parameter and we estimate the upper limit of the possible effective mass anisotropy as 7%. We discuss the influence of conduction band nonparabolicity on the electron effective mass parameter as a function of In content. The effective mass parameter is consistent with a linear interpolation scheme between the conduction band mass parameters in GaN and InN when the strong nonparabolicity in InN is included. The In0.33Ga0.67N electron mobility parameter was found to be anisotropic, supporting previous experimental findings for wurtzite-structure GaN, InN, and AlxGa1−xN epitaxial layers with c-plane growth orientation.
Observations of electron heating during 28 GHz microwave power application in proto-MPEX
Authors: Biewer T. M. , Bigelow T. S. , Caneses J. F. , Diem S. J. , Green D. L. , Kafle N. , Rapp J. ,   Proto-MPEX Team
Published: February 2018

The Prototype Material Plasma Exposure Experiment at the Oak Ridge National Laboratory utilizes a variety of power systems to generate and deliver a high heat flux plasma onto the surface of material targets. In the experiments described here, a deuterium plasma is produced via a ∼100 kW, 13.56 MHz RF helicon source, to which ∼20 kW of 28 GHz microwave power is applied. The electron density and temperature profiles are measured using a Thomson scattering (TS) diagnostic, and indicate that the electron density is centrally peaked. In the core of the plasma column, the electron density is higher than the cut-off density (∼0.9 × 1019 m−3) for the launched mixture of X- and O-mode electron cyclotron heating waves to propagate. TS measurements indicate electron temperature increases from ∼5 eV to ∼20 eV during 28 GHz power application when the neutral deuterium pressure is reduced below 0.13 Pa (∼1 mTorr.).
Research on radiation characteristics of dipole antenna modulation by sub-wavelength inhomogeneous plasma layer
Authors: Kong Fanrong , Chen Peiqi , Nie Qiuyue , Zhang Xiaoning , Zhang Zhen , Jiang Binhao
Published: February 2018

The modulation and enhancement effect of sub-wavelength plasma structures on compact antennas exhibits obvious technological advantage and considerable progress. In order to extend the availability of this technology under complex and actual environment with inhomogeneous plasma structure, a numerical simulation analysis based on finite element method has been conducted in this paper. The modulation function of the antenna radiation with sub-wavelength plasma layer located at different positions was investigated, and the inhomogeneous plasma layer with multiple electron density distribution profiles were employed to explore the effect of plasma density distribution on the antenna radiation. It has been revealed that the optical near-field modulated distance and reduced plasma distribution are more beneficial to enhance the radiation. On the basis above, an application-focused research about communication through the plasma sheath surrounding a hypersonic vehicle has been carried out aiming at exploring an effective communication window. The relevant results devote guiding significance in the field of antenna radiation modulation and enhancement, as well as the development of communication technology in hypersonic flight.
New Fourier transform containing a pair of complex Euler Γ-functions with a monomial: Mathematical and physical applications
Authors: Yahiaoui Sid-Ahmed , Bentaiba Mustapha
Published: February 2018

One of the goals of this paper is to propose an elementary method to find a general formula for a new Fourier transform containing a pair of complex Euler Γ-functions with a monomial sm in terms of Gauss’s hypergeometric functions 2F1. Some mathematical results have been obtained and discussed using this transform. Furthermore, physical applications in the phase space quantum mechanics requiring the expectation values of position and momentum operators for a quantum system endowed with position-dependent effective mass are presented.
Irreversible inactivation of ISG15 by a viral leader protease enables alternative infection detection strategies
Authors: Swatek Kirby N. , Aumayr Martina , Pruneda Jonathan N. , Visser Linda J. , Berryman Stephen , Kueck Anja F. , Geurink Paul P. , Ovaa Huib , van Kuppeveld Frank J. M. , Tuthill Tobias J. , Skern Tim , Komander David
Published: February 2018

Significance

An understanding of the mechanisms by which viruses evade host immunity is essential to the development of antiviral drugs and viral detection strategies. Ubiquitin and ubiquitin-like modifications are crucial in cellular innate immune and infection responses and are often suppressed by viral proteins. We here identify a previously unknown mechanism of viral evasion. A viral protease, Lb
pro
, removes ubiquitin and the ubiquitin-like protein ISG15 incompletely from proteins. While this strategy efficiently and irreversibly shuts down these modification systems, it enables repurposing of tools and technologies developed for ubiquitin research in virus detection. Specifically, we show that foot-and-mouth disease virus infection can be detected using an anti-GlyGly antibody developed for ubiquitin mass spectrometry research.
Bone degradation machinery of osteoclasts: An HIV-1 target that contributes to bone loss
Authors: Raynaud-Messina Brigitte , Bracq Lucie , Dupont Maeva , Souriant Shanti , Usmani Shariq M. , Proag Amsha , Pingris Karine , Soldan Vanessa , Thibault Christophe , Capilla Florence , Al Saati Talal , Gennero Isabelle , Jurdic Pierre , Jolicoeur Paul , Davignon Jean-Luc , Mempel Thorsten R. , Benichou Serge , Maridonneau-Parini Isabelle , Vérollet Christel
Published: February 2018

Significance

Bone deficits are frequent complications observed in HIV-1–infected patients. Our study demonstrates that HIV-1 infects osteoclasts, the cells specialized in bone degradation, using different models including HIV-1–infected humanized mice. We decipher the cellular mechanisms by which HIV-1 contributes to enhanced bone degradation in human osteoclasts, showing that the virus modifies the structure and function of the sealing zone, the bone resorption machinery of osteoclasts. We identify the viral protein Nef as the key factor responsible for such effects. As a proof-of-concept, we correlate bone deficit in transgenic Nef-expressing mice with enhanced osteoclast activity. Therefore, our findings provide formal evidence that osteoclasts constitute HIV-1 host target cells, contributing to bone deficits in vivo.
Climate-mediated hybrid zone movement revealed with genomics, museum collection, and simulation modeling
Authors: Ryan Sean F. , Deines Jillian M. , Scriber J. Mark , Pfrender Michael E. , Jones Stuart E. , Emrich Scott J. , Hellmann Jessica J.
Published: February 2018

Significance

The biological consequences of climate change are determined by the responses of individual species and interactions among species. Hybridization, or interbreeding between related species, is an interaction that affects how species evolve in response to environmental change. Here we provide evidence that climatic warming has caused a geographic shift of a butterfly hybrid zone and that strong selection and/or genetic incompatibilities maintain species boundaries during this movement. Through simulations, we show that as climate change progresses, the rate and geographic configuration of future hybrid zone movement will vary across space and time. This geographic variation in future hybrid zone movement may lead to divergent ecological and evolutionary outcomes, and thus has implications for local conservation and management.
STED nanoscopy of the centrosome linker reveals a CEP68-organized, periodic rootletin network anchored to a C-Nap1 ring at centrioles
Authors: Vlijm Rifka , Li Xue , Panic Marko , Rüthnick Diana , Hata Shoji , Herrmannsdörfer Frank , Kuner Thomas , Heilemann Mike , Engelhardt Johann , Hell Stefan W. , Schiebel Elmar
Published: February 2018

Significance

The integrity of the centrosome linker that joints both centrosomes of a cell into one microtubule-organizing unit plays important roles in cell organization, chromosome segregation, and cancer development. However, little is known about the structure of the linker. Here, we show by stimulated emission depletion microscopy that the centrosome linker consists of a vast network of repeating rootletin units with a C-Nap1 ring at centrioles as organizer and CEP68 as filament modulator. Rootletin filaments originating from the two centrosomes form a web-like, interdigitating filamentous network, explaining the flexible nature of the centrosome linker and the ability of the kinesin motor Eg5 to disrupt the linker function by force.
Metabolic division of labor in microbial systems
Authors: Tsoi Ryan , Wu Feilun , Zhang Carolyn , Bewick Sharon , Karig David , You Lingchong
Published: February 2018

Significance

If contained in a single population a complex metabolic pathway can impose a burden on the host, decreasing the system’s overall productivity. This limitation can be overcome by division of labor (DOL), where distinct populations perform different steps of the pathway, thus reducing the burden on each population. By compartmentalizing reactions, however, DOL reduces their efficiency by introducing a transport barrier for metabolites and enzymes. It remains unclear how the trade-off between reducing burden and decreasing reaction efficiency dictates the potential benefit of DOL. Through the analysis of different metabolic pathways we derive a general criterion establishing when DOL outperforms a single population. Our results can guide rational engineering of metabolic pathways and provide insights into operation of natural pathways.
Three-dimensional virtual histology enabled through cytoplasm-specific X-ray stain for microscopic and nanoscopic computed tomography
Authors: Busse Madleen , Müller Mark , Kimm Melanie A. , Ferstl Simone , Allner Sebastian , Achterhold Klaus , Herzen Julia , Pfeiffer Franz
Published: February 2018

Significance

Three-dimensional histology of soft-tissue samples has proven to provide crucial benefits for the understanding of tissue structure. Nevertheless, the low attenuation of soft tissue has impaired the use of computed tomography (CT) as a tool for the nondestructive and 3D visualization of external and internal structural details. We present a cytoplasm-specific staining method tailored for X-ray CT that enables a routine and efficient 3D volume screening at high resolutions. Our technique is fully compatible with conventional histology and allows further histological investigations, as demonstrated for a mouse kidney. The comparative analysis of our CT data with conventional 2D histology highlights the future applicability of the cytoplasm-specific X-ray staining method for modern histological and histopathological investigations using laboratory X-ray CT devices.
Within- and across-trial dynamics of human EEG reveal cooperative interplay between reinforcement learning and working memory
Authors: Collins Anne G. E. , Frank Michael J.
Published: February 2018

Significance

A major factor that improves learning in artificial agents is the use of multiple algorithms in parallel to benefit from their complementary strengths across different environments. The human brain performs a similar optimization, balancing the use of resource-intensive but immediately accessible information in working memory and a more reliable slow but steady reinforcement learning to build habits. These parallel computations are evident in neural signal dynamics that unfold across both short- and long-term time scales, which reveal that the two processes compete for decisions but cooperate for learning. These findings further our understanding of human learning and may inspire better artificial learners.
Bacmeta: simulator for genomic evolution in bacterial metapopulations
Authors: Sipola Aleksi , Marttinen Pekka , Corander Jukka
Published: February 2018

The advent of genomic data from densely sampled bacterial populations has created a need for flexible simulators by which models and hypotheses can be efficiently investigated in the light of empirical observations. Bacmeta provides fast stochastic simulation of neutral evolution within a large collection of interconnected bacterial populations with completely adjustable connectivity network. Stochastic events of mutations, recombinations, insertions/deletions, migrations and micro-epidemics can be simulated in discrete non-overlapping generations with a Wright–Fisher model that operates on explicit sequence data of any desired genome length. Each model component, including locus, bacterial strain, population and ultimately the whole metapopulation, is efficiently simulated using C++ objects and detailed metadata from each level can be acquired. The software can be executed in a cluster environment using simple textual input files, enabling, e.g. large-scale simulations and likelihood-free inference.

Availability and implementation

Bacmeta is implemented with C++ for Linux, Mac and Windows. It is available at https://bitbucket.org/aleksisipola/bacmeta under the BSD 3-clause license.

Supplementary information

Supplementary data are available at Bioinformatics online.
PennDiff: detecting differential alternative splicing and transcription by RNA sequencing
Authors: Hu Yu , Lin Jennie , Hu Jian , Hu Gang , Wang Kui , Zhang Hanrui , Reilly Muredach P , Li Mingyao
Published: February 2018

Motivation

Alternative splicing and alternative transcription are a major mechanism for generating transcriptome diversity. Differential alternative splicing and transcription (DAST), which describe different usage of transcript isoforms across different conditions, can complement differential expression in characterizing gene regulation. However, the analysis of DAST is challenging because only a small fraction of RNA-seq reads is informative for isoforms. Several methods have been developed to detect exon-based and gene-based DAST, but they suffer from power loss for genes with many isoforms.

Results

We present PennDiff, a novel statistical method that makes use of information on gene structures and pre-estimated isoform relative abundances, to detect DAST from RNA-seq data. PennDiff has several advantages. First, grouping exons avoids multiple testing for ‘exons’ originated from the same isoform(s). Second, it utilizes all available reads in exon-inclusion level estimation, which is different from methods that only use junction reads. Third, collapsing isoforms sharing the same alternative exons reduces the impact of isoform expression estimation uncertainty. PennDiff is able to detect DAST at both exon and gene levels, thus offering more flexibility than existing methods. Simulations and analysis of a real RNA-seq dataset indicate that PennDiff has well-controlled type I error rate, and is more powerful than existing methods including DEXSeq, rMATS, Cuffdiff, IUTA and SplicingCompass. As the popularity of RNA-seq continues to grow, we expect PennDiff to be useful for diverse transcriptomics studies.

Availability and implementation

PennDiff source code and user guide is freely available for download at https://github.com/tigerhu15/PennDiff.

Supplementary information

Supplementary data are available at Bioinformatics online.
Age Differences in Beliefs About Emotion Regulation Strategies
Authors: Livingstone Kimberly M , Castro Vanessa L , Isaacowitz Derek M
Published: February 2018

Objectives

Age shifts in emotion regulation may be rooted in beliefs about different strategies. We test whether there are age differences in the beliefs people hold about specific emotion regulation strategies derived from the process model of emotion regulation and whether profiles of emotion beliefs vary by age.

Method

An adult life-span sample (N = 557) sorted 13 emotion regulation strategies either by (a) how effective the strategies would be or (b) how likely they would be to use them, in 15 negative emotion-eliciting situations.

Results

Younger adults ranked attentional and cognitive distraction more effective than older adults, and preferred avoidance, distraction, and rumination more (and attentional deployment less) than middle-aged and older adults. Latent profile analysis on preferences identified three distinct strategy profiles: Classically adaptive regulators preferred a variety of strategies; situation modifiers showed strong preferences for changing situations; a small percentage of people preferred avoidance and rumination. Middle-aged and older adults were more likely than younger adults to be classically adaptive regulators (as opposed to situation modifiers or avoiders/ruminators).

Discussion

These findings provide insight into the reasons people of different ages may select and implement different emotion regulation strategies, which may influence their emotional well-being.
Curiosity, interdisciplinarity, and giving back†
Authors: Ommer Rosemary E
Published: February 2018

The pursuit of interdisciplinarity in the marine sciences is at last beginning to come into its own, but the kind of interdisciplinarity that bridges the social, human, health, and natural science realms remains rare. This article traces the evolution of my own history of interdisciplinarity from its early days when I worked in two disciplines, to the present when I have worked with many others to bring together the natural sciences, social sciences, humanities, and earth/ocean sciences in large projects that illuminate the interconnectedness of all these parts of knowledge acquisition. In the process, I have broadened my intellectual vision both in scope and scale, uncovering the many ways in which, quite pragmatically, the very local and the international are more tightly interconnected than is often realized, with all the implications for fisheries governance that that implies. This, then, is both a story and, I hope, a pathway to a rewarding way for young and middle-career fisheries scholars to pursue their research.
Word of Mouth versus Word of Mouse: Speaking about a Brand Connects You to It More Than Writing Does
Authors: Shen Hao , Sengupta Jaideep
Published: February 2018

This research merges insights from the communications literature with that on the self-brand connection to examine a novel question: how does speaking versus writing about a liked brand influence the communicator’s own later reactions to that brand? Our conceptualization argues that because oral communication involves a greater focus on social interaction with the communication recipient than does written communication, oral communicators are more likely to express self-related thoughts than are writers, thereby increasing their self-brand connection (SBC). We also assess the implications of this conceptualization, including the identification of theoretically derived boundary conditions for the speech/writing difference, and the downstream effects of heightened SBC. Results from five studies provide support for our predictions, informing both the basic literature on communications, and the body of work on consumer word of mouth.
‘The Desert is Our Neighbour’: A Postcolonial Feminist Ethic of Narrative Encounter in Helen Oyeyemi’s Mr Fox
Authors: Radford CL Wren
Published: February 2018

Helen Oyeyemi’s Mr Fox rewrites gothic and fairytale tropes to expose patriarchal and colonial lines in sand encoded in fiction that legitimise the subjugation of women. Drawing on the work of Mayra Rivera, Sara Ahmed, and Kamala Visweswaran, this article argues that Oyeyemi’s work enacts a postcolonial feminist ethic of encounter that foregrounds and challenges gendered and colonial power relations. The article examines Oyeyemi’s metafictive storytelling, her use and critique of feminist revisioning and voicing, and genre play as strategies that call into question processes of representation and meaning-making in encountering others.
Pattern-Triggered Immunity Alters the Transcriptional Regulation of Virulence-Associated Genes and Induces the Sulfur Starvation Response in Pseudomonas syringae pv. tomato DC3000
Authors: Lovelace Amelia H. , Smith Amy , Kvitko Brian H.
Published: February 2018

Pattern-triggered immunity (PTI) can confer broad defense against diverse microbes and pathogens with disparate lifestyles through the detection of microbial extracellular signatures by surface-exposed pattern recognition receptors. However, unlike recognition of pathogen effectors by cytosolic resistance proteins, PTI is typically not associated with a host-cell programmed cell death response. Although host PTI signaling has been extensively studied, the mechanisms by which it restricts microbial colonization are poorly understood. We sought to gain insight into the mechanisms of PTI action by using bacterial transcriptomics analysis during exposure to PTI. Here, we describe a method for bacterial cell extraction from inoculated leaves that was used to analyze a time course of genome-wide transcriptional responses in the pathogen Pseudomonas syringae pv. tomato DC3000 during early naïve host infection and exposure to pre-induced PTI in Arabidopsis thaliana. Our analysis revealed early transcriptional regulation of important bacterial metabolic processes and host interaction pathways. We observed peak induction of P. syringae virulence genes at 3 h postinoculation and that exposure to PTI was associated with significant reductions in the expression of virulence genes. We also observed the induction of P. syringae sulfur starvation response genes such as sulfate and sulfonate importers only during exposure to PTI.
Recent progress of laser spectroscopy experiments on antiprotonic helium
Authors: Hori Masaki
Published: February 2018

The Atomic Spectroscopy and Collisions Using Slow Antiprotons (ASACUSA) collaboration is currently carrying out laser spectroscopy experiments on antiprotonic helium

atoms at CERN’s Antiproton Decelerator facility. Two-photon spectroscopic techniques have been employed to reduce the Doppler width of the measured

resonance lines, and determine the atomic transition frequencies to a fractional precision of 2.3–5 parts in 10
9
. More recently, single-photon spectroscopy of buffer-gas cooled

has reached a similar precision. By comparing the results with three-body quantum electrodynamics calculations, the antiproton-to-electron mass ratio was determined as

, which agrees with the known proton-to-electron mass ratio with a precision of 8×10
−10
. The high-quality antiproton beam provided by the future Extra Low Energy Antiproton Ring (ELENA) facility should enable further improvements in the experimental precision.

This article is part of the Theo Murphy meeting issue ‘Antiproton physics in the ELENA era’.
The strong grip of childhood conditions in older Europeans
Authors: Tampubolon Gindo , Fajarini Maria
Published: February 2018

Among older Europeans grip strength has been found to be marked by a disadvantaged adulthood. Across the Channel, among older Britons gait speed as another measure of physical function has been found to be marked by disadvantaged childhood. Using the Survey of Health, Ageing, and Retirement in Europe (2004-2013), we studied whether childhood poverty led to Europeans aged 50 to 104 years having a weaker grip. We then drew their trajectories of repeatedly measured grip strength to discern a steeper decline among the childhood poor. Retrospective childhood poverty some four to nine decades in the past was treated as a latent construct following the above literature; attrition during repeated measurements is handled using inverse proportional to attrition weighting. The data showed the childhood poor to have a weaker grip for half a century in later life. However, they do not show a steeper decline. Most important, by contributing to levels of grip strength in later life, adult condition holds the potential to shape the strong and long arm of childhood condition. The results are another impetus to eliminate childhood poverty to ensure healthy ageing Europeans.
Dissociable effects of prediction and integration during language comprehension: Evidence from a large-scale study using brain potentials
Authors: Nieuwland Mante S. , Barr Dale J. , Bartolozzi Federica , Busch-Moreno Simon , Darley Emily , Donaldson David I. , Ferguson Heather J. , Fu Xiao , Heyselaar Evelien , Huettig Falk , Husband E. Matthew , Ito Aine , Kazanina Nina , Kogan Vita , Kohút Zdenko , Kulakova Eugenia , Mézière Diane , Politzer-Ahles Stephen , Rousselet Guillaume , Rueschemeyer Shirley-Ann , Segaert Katrien , Tuomainen Jyrki , Wolfsthurn Sarah Von Grebmer Zu
Published: February 2018

Composing sentence meaning is easier for predictable words than for unpredictable words. Are predictable words genuinely predicted, or simply more plausible and therefore easier to integrate with sentence context? We addressed this persistent and fundamental question using data from a recent, large-scale (N= 334) replication study, by investigating the effects of word predictability and sentence plausibility on the N400, the brain’s electrophysiological index of semantic processing. A spatiotemporally fine-grained mixed effects multiple regression analysis revealed overlapping effects of predictability and plausibility on the N400, albeit with distinct spatiotemporal profiles. Our results challenge the view that the predictability-dependent N400 reflects the effects ofeitherpredictionorintegration, and suggest that semantic facilitation of predictable words arises from a cascade of processes that activate and integrate word meaning with context into a sentence-level meaning.
Characterizing higher order structures of chromatin in human cells
Authors: Schwartz Uwe , Németh Attila , Diermeier Sarah , Exler Josef , Hansch Stefan , Maldonado Rodrigo , Heizinger Leonhard , Merkl Rainer , Läengst Gernot
Published: February 2018

Packaging of DNA into chromatin regulates DNA accessibility and, consequently, all DNA-dependent processes, such as transcription, recombination, repair, and replication. The nucleosome is the basic packaging unit of DNA forming arrays that are suggested, by biochemical studies, to fold hierarchically into ordered higher-order structures of chromatin. This defined organization of chromatin has been recently questioned using microscopy techniques, proposing a rather irregular structure. To gain more insight into the principles of chromatin organization, we applied an in situ differential MNase-seq strategy and analyzed in silico the results of complete and partial digestions of human chromatin. We investigated whether different levels of chromatin packaging exist in the cell. Thus, we assessed the accessibility of chromatin within distinct domains of kb to Mb genomic regions by utilizing statistical data analyses and computer modelling. We found no difference in the degree of compaction between domains of euchromatin and heterochromatin or between other sequence and epigenomic features of chromatin. Thus, our data suggests the absence of differentially compacted domains of higher-order structures of chromatin. Moreover, we identified only local structural changes, with individual hyper-accessible nucleosomes surrounding regulatory elements, such as enhancers and transcription start sites. The regulatory sites per se are occupied with structurally altered nucleosomes, exhibiting increased MNase sensitivity. Our findings provide biochemical evidence that supports an irregular model of large-scale chromatin organization.
Heterocyclic sterol probes for live monitoring of sterol trafficking and lysosomal storage disorders
Authors: Králová Jarmila , Jurášek Michal , Krčová Lucie , Dolenský Bohumil , Novotný Ivan , Dušek Michal , Rottnerová Zdeňka , Kahle Michal , Drašar Pavel , Bartůněk Petr , Král Vladimír
Published: February 2018

The monitoring of intracellular cholesterol homeostasis and trafficking is of great importance because their imbalance leads to many pathologies. Reliable tools for cholesterol detection are in demand. This study presents the design and synthesis of fluorescent probes for cholesterol recognition and demonstrates their selectivity by a variety of methods. The construction of dedicated library of 14 probes was based on heterocyclic (pyridine)-sterol derivatives with various attached fluorophores. The most promising probe, a P1-BODIPY conjugate FP-5, was analyzed in detail and showed an intensive labeling of cellular membranes followed by intracellular redistribution into various cholesterol rich organelles and vesicles. FP-5 displayed a stronger signal, with faster kinetics, than the commercial TF-Chol probe. In addition, cells with pharmacologically disrupted cholesterol transport, or with a genetic mutation of cholesterol transporting protein NPC1, exhibited strong and fast FP-5 labeling in the endo/lysosomal compartment, co-localizing with filipin staining of cholesterol. Hence, FP-5 has high potential as a new probe for monitoring cholesterol trafficking and its disorders.

Significance statement

Cholesterol is a vital steroid molecule with many important functions in animal cells. Although its dysregulation is associated with an expanding list of clinically important pathologies, the study of its role is limited by a lack of reliable tools for live intracellular monitoring. This study demonstrates the applicability of a novel class of heterocyclic sterol probes. These probes exhibit fast cellular uptake with effective fluorescence labeling of sterol species in a variety of living cells, without a need for artificial carriers. When applied to Niemann-Pick disease type C1 cells, they identified massive accumulation of cholesterol in the endosome/lysosome compartment. Thus, several probes from the same series can also be used for visualizing lysosomal storage disorders and sterol transporting pathologies.
Tdrd6a regulates the aggregation of Buc into functional subcellular compartments that drive germ cell specification
Authors: Roovers Elke F. , Kaaij Lucas J.T. , Redl Stefan , Bronkhorst Alfred W. , Wiebrands Kay , de Jesus Domingues António M. , Huang Hsin-Yi , Han Chung-Ting , Salvenmoser Willi , Grün Dominic , Butter Falk , van Oudenaarden Alexander , Ketting René F.
Published: February 2018

In recent years, it has become clear that phase separation represents an important class of subcellular compartmentalization. However, relatively little is known about how the formation or disassembly of such compartments is regulated. In zebrafish, the Balbiani body (Bb) and the germ plasm (Gp) are phase-separated structures essential for germ cell specification and home to many germ cell-specific mRNAs and proteins. Throughout development, these structures range from a single large aggregate (Bb), to a dispersed state and back to relatively large assemblies (Gp). Formation of the Bb requires Bucky ball (Buc), a protein with prion-like properties. We found that the multi-tudor domain-containing protein Tdrd6a interacts directly with Buc, affecting its mobility and aggregation properties. Importantly, lack of this regulatory interaction leads to significant defects in germ cell development. Our work presents a new mechanism for how prion-like protein-aggregations can be regulated and highlights the biological relevance of such regulatory events.
Bayesian phylodynamic inference with complex models
Authors: Volz Erik M. , Siveroni Igor
Published: February 2018

Population genetic modeling can enhance Bayesian phylogenetic inference by providing a realistic prior on the distribution of branch lengths and times of common ancestry.The parameters of a population genetic model may also have intrinsic importance, and simultaneous estimation of a phylogeny and model parameters has enabled phylodynamic inference of population growth rates, reproduction numbers, and effective population size through time. Phylodynamic inference based on pathogen genetic sequence data has emerged as useful supplement to epidemic surveillance, however commonly-used mechanistic models that are typically fitted to non-genetic surveillance data are rarely fitted to pathogen genetic data due to a dearth of software tools, and the theory required to conduct such inference has been developed only recently. We present a framework for coalescent-based phylogenetic and phylodynamic inference which enables highly-flexible modeling of demographic and epidemiological processes. This approach builds upon previous structured coalescent approaches and includes enhancements for computational speed, accuracy, and stability. A flexible markup language is described for translating parametric demographic or epidemiological models into a structured coalescent model enabling simultaneous estimation of demographic or epidemiological parameters and time-scaled phylogenies. We demonstrate the utility of these approaches by fitting compartmental epidemiological models to Ebola virus and Influenza A virus sequence data, demonstrating how important features of these epidemics, such as the reproduction number and epidemic curves, can be gleaned from genetic data. These approaches are provided as an open-source packagePhyDynfor the BEAST phylogenetics platform.
Matching drug transcriptional signatures to rare losses disrupting synaptic gene networks identifies known and novel candidate drugs for schizophrenia
Authors: Merico Daniele , Wang Xiao , Yuen Ryan K. C. , Scherer Stephen W. , Bassett Anne S.
Published: February 2018

Schizophrenia is a complex neuropsychiatric disorder. The etiology is not fully understood, but genetics plays an important role. Pathway analysis of genetic variants have suggested a central role for neuronal synaptic processes. Currently available antipsychotic medications successfully control positive symptoms (hallucinations and delusions) largely by inhibiting the dopamine D2 receptors; however, these drugs have more limited impact on negative symptoms (social withdrawal, flat affections, anhedonia) and cognitive deterioration. Drug development efforts have focused on a wide range of neurotransmitter systems and other agents, with conflicting or inconclusive results. New drug development paradigms are needed. A recent analysis, using common variant association results to match drugs based on their transcriptional perturbation signature, found drugs enriched in known antipsychotics plus novel candidates.

We followed a similar approach, but started our analysis from a synaptic gene network implicated by rare copy number loss variants. We found that a significant number of antipsychotics (p-value = 0.0002) and other psychoactive drugs (p-value = 0.0004) upregulate synaptic network genes. Based on global gene expression similarity, active drugs formed two main clusters: one with many known antipsychotics and antidepressants, the other with various drug categories including two nootropics. We specifically recommend further examination of nootropics with limited side effects (meclofenoxate, piracetam and vinpocetine) for combination therapy with antipsychotics to improve cognitive performance. Detailed experimental follow-up is required to further evaluate other candidate drugs lacking an official nervous system indication, although, for at least a few of these, psychoactive effects have been reported in the literature.