bluuebunny/crossref_metadata_2025 huggingface dataset:
COSIM: The necessary evolution of a cross-identification tool along with data evolution
Authors: Brunet Catherine , Allen Mark , Brouty Marianne , Buga Mihaela , Loup Cécile , Oberto Anaïs , Perret Emmanuelle , Vollmer Bernd , Woelfel Fabienne
Published: August 2018

SIMBAD is a bibliographic added-value database on astronomical objects, where the data on individual objects are cross-identified as far as possible. The data comes exclusively from what has been published by the scientific community. To treat large tables, the work is done semi-automatically with the help of a customized software. Since 2014, we are using a new one, called COSIM (Comparison of Objects for SIMBAD). It meets the new requirements which is a consequence of the evolution of the available astronomical data. It has increased in number, accuracy and diversity. On the basis of the data presented in a published table, COSIM searches for objects that are already known in SIMBAD, by name or by coordinates. A combination of scores based on the available and comparable parameters, like the main object type, coordinates, velocity and magnitudes, suggests whether the candidate is good for cross-identification or not. As soon as the result of the search is clear, indicating that there is either no matching candidate or only one good candidate, COSIM creates the commands necessary for updating the SIMBAD database. The documentalists can act on the method of calculation of each score, according to the nature of the objects in the table. Thus, with COSIM the documentalists manage to obtain a good cross-identification level with a minimum risk of omitted or false cross-identifications in a relatively short time compared to the treated data number.
Comparing People with Bibliometrics
Authors: Kurtz Michael J.
Published: August 2018

Bibliometric indicators, citation counts and/or download counts are increasingly being used to inform personnel decisions such as hiring or promotions. These statistics are very often misused. Here we provide a guide to the factors which should be considered when using these so-called quantitative measures to evaluate people. Rules of thumb are given for when begin to use bibliometric measures when comparing otherwise similar candidates.
New ADS Functionality for the Curator
Authors: Accomazzi Alberto , Kurtz Michael J. , Henneken Edwin A. , Grant Carolyn S. , Thompson Donna M. , Chyla Roman , McDonald Steven , Shaulis Taylor J. , Blanco-Cuaresma Sergi , Shapurian Golnaz , Hostetler Timothy W. , Templeton Matthew R.
Published: August 2018

In this paper we provide an update concerning the operations of the NASA Astrophysics Data System (ADS), its services and user interface, and the content currently indexed in its database. As the primary information system used by researchers in Astronomy, the ADS aims to provide a comprehensive index of all scholarly resources appearing in the literature. With the current effort in our community to support data and software citations, we discuss what steps the ADS is taking to provide the needed infrastructurein collaboration with publishers and data providers. A new API provides accessto the ADS search interface, metrics, and libraries allowing users to programmatically automate discovery and curation tasks. The new ADS interface supports a greater integration of content and services with a variety of partners, including ORCID claiming, indexing of SIMBAD objects, and article graphics from a variety of publishers. Finally, we highlight how librarians can facilitate the ingest of gray literature that they curate into our system.
Dossier : La fabrique de la compensation écologique : controverses et pratiques – Introduction. La fabrique de la compensation écologique, un approfondissement de la modernisation écologique ?
Authors: Arnauld de Sartre Xavier , Doussan Isabelle
Published: August 2018

Longtemps peu appliquée, l’obligation de compensation écologique s’est peu à peu imposée, en droit français, aux projets soumis à évaluation environnementale. La loi de 2016 sur la biodiversité la rend obligatoire tout en en faisant un outil de « modernisation écologique ». Les différentes contributions qui composent ce dossier mettent cela en évidence au travers des controverses dont la compensation fait l’objet et des expérimentations qui sont mises en œuvre. La compensation apparaît ainsi comme un outil visant l’intégration de l’environnement dans les politiques publiques et, plus largement, dans l’économie, au travers d’une opération de standardisation de la nature destinée à permettre son déplacement et sa substitution quand elle est affectée. En outre, la loi laisse la gouvernance de la compensation aux experts, au juge et à l’autorégulation par les acteurs de terrain. Les analyses proposées s’inscrivent ainsi dans un contexte plus large qu’elles contribuent à éclairer, celui des profondes transformations de l’action de l’État dans la dynamique de « modernisation écologique ».
La Bile noire et son humour : fin du monde, l’être déchet et la ligue de domination mondiale
Authors: Allen David , Hercouet Fanny
Published: August 2018

L’étude pose la question de l’humour noir et son rapport à la mélancolie clinique. Les witz d’Hamlet sont étudiés comme une possible date de naissance de l’humour noir. Les écrits de Spike Milligan et Peter Cook concernant la fin du monde sont étudiés en tant qu’expression de l’humour mélancolique. Ainsi l’humour noir semble être le terrain sur lequel le mélancolique peut faire le procès de l’homme post Auschwitz, post Hiroshima, une forme de critique encore disponible au sujet moderne.
Illustration clinique de la non fermeture du corps dans la psychose : Robert Schumann, composer ou se décomposer
Authors: Poulain-Berhault Marie
Published: August 2018

Cet article montre que l’artiste enseigne le clinicien sur le traitement de sa psychose. Le but de est de montrer que la création, précisément la composition musicale, a une fonction pour l’artiste. Robert Schumann tente de border un débordement intérieur avec son art. La méthode choisie consiste à lire le journal intime, la correspondance avec sa femme et ses pairs, et certains articles de la revue pour la musique de Robert Schumann. Cette lecture éclairée par la psychanalyse lacanienne montre que le choix de la musique a eu un effet de fragilisation psychique qui s’est inscrite dans son corps. Son œuvre a été une réponse au réel qui s’est manifesté à lui en différents moments de son existence. Nous montrons que la création est en rapport avec le corps, pas biologique, celui de la libido, des pulsions et de l’angoisse. La création pourrait être un moyen de mettre à distance l’objet pulsionnel et de colmater une part de jouissance envahissante mais elle n’a pas opéré du côté de la suppléance. La composition pour une tentative de fermeture du corps a mené vers une décompensation psychique menant Schumann à tenter de se suicider.
Le rôle des émotions dans les agirs violents en institution
Authors: Vicet Marielle
Published: August 2018

La problématique des violences institutionnelles sur mineurs par des professionnels chargés de leur protection pose la question de l’interprétation de la loi. Le caractère dénégatif de cette souffrance subie et la transgression de la loi qui en résulte, peut entraîner un défaut de signalements d’enfants en danger jusqu’à une institutionnalisation de la violence. Pour repérer les modes pathologiques institutionnels et des passages à l’acte construits par le contexte historique, il est nécessaire de s’intéresser aux trajectoires victimales individuelles et collectives ainsi qu’aux liens entre auteur et victimé grâce, notamment, aux interactions des neurones miroirs de chacun. Cette vulnérabilité liée aux souffrances vécues sur le plan individuel et/ou en lien avec des éléments issus de l’héritage transgénérationnel conduit à la répétition d’agirs violents. L’exemple d’une analyse clinique dégage les principes d’une institutionnalisation de ces violences et les conditions de son dépassement.
Défauts de contenance en protection de l’enfance
Authors: Chapot Mickaël , Charreton Grégory
Published: August 2018

Dans cet article, les auteurs, à partir de leurs pratiques de psychologues dans le champ de la protection de l’enfance, interrogent les effets d’une logique gestionnaire sur les institutions, sur les équipes, sur les professionnels et sur les familles accompagnées. Les changements législatifs de 2002 et 2007 sont analysés selon leurs effets potentiellement désorganisateurs au sein des institutions. L’article propose de mettre en parallèle les effets que peuvent avoir les familles rencontrées par les équipes avec ceux que peuvent occasionner les logiques gestionnaires sur les institutions. À partir du repérage des défauts de contenance engendrés par la difficulté à prendre en compte l’état d’angoisse des institutions, les auteurs proposent des pistes de réflexion afin d’éviter l’installation d’une pensée de l’impossible menaçant la tâche primaire elle-même.
Complications of Volar Plating of Distal Radius Fractures: A Systematic Review
Authors: Alter Todd H. , Sandrowski Kristin , Gallant Gregory , Kwok Moody , Ilyas Asif M.
Published: August 2018

Background In recent years, there has been an increased utilization of volar locking plate fixation of distal radius fractures (DRFs). However, reported long-term complication rates with this technique remain unclear.

Purpose The purpose of this systematic review was to investigate the pooled incidence of complications associated with volar locking plating of DRF.

Methods A search of the Scopus database was performed from 2006 through 2016. Studies were considered eligible if they had a diagnosis of a DRF and were treated with a volar locking plate with an average of 12 months or longer follow-up.

Results The literature search yielded 633 citations, with 55 eligible for inclusion in the review (total n = 3,911). An overall complication rate of 15% was identified, with 5% representing major complications requiring reoperation. The most common complication types identified included nerve dysfunction (5.7%), tendon injury (3.5%), and hardware-related issues (1.6%).

Conclusion Nerve complications were reportedly higher than tendon and hardware-related complications combined. However, despite varying complication rates in the literature, this systematic review reveals an overall low complication rate associated with volar locking plating of DRF.
Cost Analysis of Azithromycin versus Erythromycin in Pregnancies Complicated by Preterm Premature Rupture of Membranes
Authors: Smith Devin , Buhimschi Catalin , Finneran Matthew
Published: August 2018

Objective To quantify the potential cost savings if azithromycin is substituted for erythromycin in women with preterm premature rupture of membranes (PPROM).

Study Design Secondary analysis of a multicentered study investigating magnesium sulfate for the prevention of cerebral palsy in premature infants. All patients with PPROM who received antibiotics for prophylaxis were included in the analysis. The number of expected doses each patient would have received was calculated for erythromycin, multidose azithromycin, and single-dose azithromycin regimens accounting for latency from PPROM to delivery. The wholesale acquisition cost was used to calculate the expected cost of each regimen.

Results There were 981 PPROM patients who received a penicillin class antibiotic and erythromycin. Patients would have received 7,528 intravenous doses and 10,194 oral doses of erythromycin at a combined cost of $357,169. In comparison, patients would have received 6,422 and 3,942 doses at a cost of $15,669 and $9,574 for the multidose and single-dose azithromycin regimens respectively, which represents a more than 95% cost reduction for either regimen compared with erythromycin.

Conclusion The use of azithromycin substituted for erythromycin in the standard antibiotic regimen of women with PPROM represents a potential for substantial cost reduction.
Nonsurgical Treatment of Chest Wall Deformities: Contradiction or Complement?
Authors: Häcker Frank-Martin
Published: August 2018

For decades, open surgical repair was the only available method to treat congenital and acquired chest wall deformities (CWDs). In 1998, D. Nuss described a minimally invasive procedure for surgical repair of pectus excavatum (PE), and a few years later H. Abramson reported on his experience with the “reversed Nuss technique” for surgical repair of pectus carinatum (PC). Both procedures are performed with increasing frequency worldwide.

However, nonsurgical measures such as vacuum bell (VB) therapy for conservative treatment of PE and more differentiated bracing systems for conservative treatment of PC were established 15 to 20 years ago. Nowadays, information on new therapeutic modalities circulates not only among surgeons and pediatricians, but also rapidly among patients. In particular, patients who refused operative treatment by previously available procedures now appear at the outpatient clinic and request to be considered for the new methods.

Analyzing the increasing number of studies reporting on conservative treatment of CWDs as well as our own group of patients who visited a busy outpatient clinic in a small country within the last 15 to 20 years, we have to realize that the majority of patients asked for nonsurgical treatment of their CWD. Based on these experiences and results, we have to realize that nonsurgical treatment of CWD is no contradiction but a helpful complement to treat congenital and acquired CWDs and may be applied for the majority of patients suffering from a CWD.
All-Cause Mortality Risk with Direct Oral Anticoagulants and Warfarin in the Primary Treatment of Venous Thromboembolism
Authors: Roetker Nicholas , Lutsey Pamela , Zakai Neil , Alonso Alvaro , Adam Terrence , MacLehose Richard
Published: August 2018

Oral anticoagulants used for the primary treatment of venous thromboembolism (VTE) include warfarin and the more recently introduced direct oral anticoagulants (DOACs), including rivaroxaban, apixaban, dabigatran and edoxaban. Information on the comparative safety of these medications in routine clinical practice is lacking. We identified patients with diagnoses for VTE and prescriptions for oral anticoagulants using claims data from a large U.S. insurance database from 2012 to 2017. Marginal structural logistic models were used to examine associations between type of oral anticoagulant and risk of all-cause mortality. Of 62,431 enrolees in this analysis, 51% were female and the mean age was 61.9 years. Initial oral anticoagulant prescriptions were for warfarin (n = 35,704), rivaroxaban (n = 21,064) and apixaban (n = 5,663). A total of 1,791 deaths occurred within 6 months of the initial oral anticoagulant prescription. Risk of all-cause mortality was not associated with having a prescription for warfarin versus any DOAC or between any head-to-head DOAC comparisons. Also, associations generally did not vary when stratified by VTE type, sex, age, co-morbidities (including renal disease) or anti-platelet medication use. In this observational study, the associations with all-cause mortality comparing DOACs versus warfarin agree with results from previous clinical trials and observational studies, while the associations for head-to-head DOAC comparisons provide new information on the comparative safety of DOACs. Our findings suggest that other criteria such as patient preference, cost, recurrent VTE risk or bleeding risk should be used when determining the choice of anticoagulant for the primary treatment of VTE.
Multiple pulse magnetized electron beam injection in deuterium gas
Authors: Postupaev V. V. , Burdakov A. V. , Ivanov I. A. , Sklyarov V. F. , Arzhannikov A. V. , Burmasov V. S. , Gavrilenko D. Ye. , Kandaurov I. V. , Kurkuchekov V. V. , Mekler K. I. , Polosatkin S. V. , Rovenskikh A. F. , Sudnikov A. V. , Sulyaev Yu. S. , Trunev Yu. A.
Published: August 2018

Results of experiments on injection of a sequence of several electron beam pulses (80–90 keV, 20–75 A, ∼30 μs) into 1019–1021 m−3 deuterium plasma are presented. The first beam pulse was injected into deuterium gas, the following pulses propagated through residual plasma that survived the inter-pulse periods. A typical pulse duration was of the order of 106 ωp−1 that is much longer than most of the interaction-related processes. However, we noticed significant differences in plasma processes between the first pulse and the rest ones. A suggested physical factor behind those differences is longitudinal plasma current that develops during the first beam pulse.
Stochastic sampling of the isothermal-isobaric ensemble: Phase diagram of crystalline solids from molecular dynamics simulation
Authors: Cajahuaringa Samuel , Antonelli Alex
Published: August 2018

A methodology to sample the isothermal-isobaric ensemble using Langevin dynamics is proposed, which combines novel features of geometric integrators for the equations of motion. By employing the Trotter expansion, the methodology generates a robust, symmetric, and accurate numerical algorithm. In order to show that the proposed method correctly samples the phase-space, simulations in the isotropic NPT ensemble were carried out for two analytical examples. Also this method lets us study a solid-solid phase transition by conducting a fully flexible-cell molecular dynamics simulation. Additionally, we present an efficient method to determine the Gibbs free energy in a wide interval of pressure along an isothermal path, which allows us to determine the transition pressure in a driven by pressure solid-solid phase transition. Our calculations show that the methodology is highly suitable for the study of the phase diagram of crystalline solids.
Electrical and anisotropic magnetic properties in layered Mn1/3TaS2 crystals
Authors: Zhang Hongwei , Wei Wensen , Zheng Guolin , Lu Jianwei , Wu Min , Zhu Xiangde , Tang Jin , Ning Wei , Han Yuyan , Ling Langsheng , Yang Jiyong , Gao Wenshuai , Qin Yongliang , Tian Mingliang
Published: August 2018

We report electrical transport and anisotropic magnetic properties of Mn-intercalated 2H-TaS2, a layered transition-metal dichalcogenide with a hexagonal structure. The single crystal MnxTaS2 with x = 1/3 exhibits a transition from paramagnetism to ferromagnetism near 70 K, below which both the magnetoresistance and magnetization properties present strong anisotropic behavior. Its anisotropic magnetoresistance effect and in-plane soft ferromagnetic property suggests that this layered material would be a good candidate for exploring the physics of two-dimensional ferromagnetism.
Stethoscope-type 3ω independent detector for fast measurement of material thermal conductivity
Authors: Zheng Xinghua , Yue Peng , Li Shen , Wang Liang , Yang Xiao , Chen Haisheng
Published: August 2018

As one of the most basic properties of materials, thermal conductivity is a key parameter to investigate the analysis and design of the particular thermal process, such as the analysis of the thermal/cool energy storage and release process, the thermal/cool energy storage system design, and so on. Also, it is the foundation of energy technology development. In order to overcome the problem that the measurement frequency of a polyimide substrate independent detector is lower and the measurement time is longer, based on the relationship among 3ω detection frequency, thermal wave penetration depth, and thermal properties of the substrate material, this paper developed a stethoscope-type 3ω independent detector based on a sapphire substrate for fast measurement of material thermal conductivity. Nickel, with a high resistance temperature coefficient, was used as the metal detector. The influence of the width of the nickel metal detector and the thickness of the sapphire substrate on the measurement accuracy was analyzed by introducing an effective heat flow ratio. The sapphire substrate independent detector was calibrated by using copper, aluminum, 304 stainless steel, quartz glass, ethylene glycol, and plexiglass with known thermal conductivities. The experiment shows that the measurement frequency of the stethoscope detector can be ten times higher than that of a Kapton film independent detector. Its measurement time is only one tenth of that of the Kapton film independent detector.
Conceptual design for resistive bolometer system with multiple apertures for measurement of total radiated power in JT-60SA
Authors: Sano Ryuichi , Fukumoto Masakatsu , Nakano Tomohide , Oyama Naoyuki
Published: August 2018

A field of view (FoV) of the resistive bolometer systems specialized for the total radiated power analysis has been designed with bolometer systems having multiple-apertures in JT-60SA. The multi-aperture bolometer system can reduce the required number of bolometer channels for the determination of the total radiated power. The FoV design has been carried out to minimize unobserved and overlapping regions with the following requirements: (i) independent determination of the divertor and the main plasma radiation, (ii) limitation of the use of only three diagnostic ports, and (iii) a redundant FoV design. With the designed FoV, the whole plasma of JT-60SA is viewed by only five bolometers and five replicated bolometers having the same FoV for redundancy. A signal evaluation with the designed FoV with a predetermined radiation profile indicates that even the lowest performing bolometer exhibits a signal to noise (S/N) ratio of 300 or more. The evaluated S/N ratio is high enough for the total radiated power analysis. Using the designed FoV, the total radiated power over the plasma profile can be determined within 5.3% using only five bolometers.
Harmonizing accuracy and efficiency: A pragmatic approach to fragmentation of large molecules
Authors: Khire Subodh S. , Bartolotti Libero J. , Gadre Shridhar R.
Published: August 2018

Fragmentation methods offer an attractive alternative for ab initio treatment of large molecules and molecular clusters. However, balancing the accuracy and efficiency of these methods is a tight-rope-act. With this in view, we present an algorithm for automatic molecular fragmentation within Molecular Tailoring Approach (MTA) achieving this delicate balance. The automated code is tested out on a variety of molecules and clusters at the Hartree-Fock (HF)- and Møller-Plesset second order perturbation theory as well as density functional theory employing augmented Dunning basis sets. The results show remarkable accuracy and efficiency vis-à-vis the respective full calculations. Thus the present work forms an important step toward the development of an MTA-based black box code for implementation of HF as well as correlated quantum chemical calculations on large molecular systems.
Sensing and cooling of a nanomechanical resonator with an electron beam stimulated internal feedback and a capacitive force
Authors: Descombin A. , Perisanu S. , Poncharal P. , Vincent P. , Purcell S. T. , Ayari A.
Published: August 2018

A model for the cooling properties of a nanocantilever by a free electron beam is presented for a capacitive interaction. The optimal parameters for position sensing and cooling applications are estimated from previous experimental conditions. In particular, we demonstrate that a purely capacitive force and an electron beam stimulated internal feedback can lower the temperature of a nanocantilever by several orders of magnitude, in striking contrast with the conventional electrostatic damping regime. We propose a step by step protocol to extract the interdependent parameters of the experiments. This work will aid future developments of ultra-sensitive force sensors in electron microscopes.
Design of a custom insertable probe platform for measurements of C-2W inner divertor plasma parameters
Authors: DuBois A. M. , Sokolov V. , Knapp K. , Thompson M. C. ,   TAE Team
Published: August 2018

A custom motor controlled probe system has been designed to make spatially resolved measurements of temperature, density, flow, and plasma potential in the C-2W inner divertors. Measurements in the inner divertors, which have a 1.7 m radius and are located on either end of the confinement vessel, are critical in order to gauge exactly how local settings affect the plasma conditions, confinement, and stability in the field-reversed configuration core. The inner Divertor Insertable Probe Platform (iDIPP) system consists of a custom motor controlled linear rack and pinion transporter that has a 1.9 m travel length in order to reach the center of the divertor. Mounted to the end of the transporter is a 1 m long segmented probe shaft made of individually floating stainless steel rings to prevent shorting out the electrode plates, which are biased up to 5 kV/m. A variety of interchangeable probe tips, including a triple Langmuir probe, a baffled probe, and a Gundestrup probe, can plug into the end of the probe shaft. Custom UHV coiled cabling comprised of 9 shielded conductors expands/retracts with the motion of the transporter in/out of the divertor. The physics motivating plasma parameter measurements in the inner divertors and the details of the design of the iDIPP system will be discussed.
Toward quasi-DC conductivity of warm dense matter measured by single-shot terahertz spectroscopy
Authors: Ofori-Okai B. K. , Descamps A. , Lu J. , Seipp L. E. , Weinmann A. , Glenzer S. H. , Chen Z.
Published: August 2018

We present an experimental setup capable of measuring the near DC conductivity of laser generated warm dense matter using single-shot terahertz time-domain spectroscopy. The setup uses a reflective echelon and balanced detection to record THz waveforms with a minimum detectable signal of 0.2% in a single laser pulse. We describe details of the experimental setup and the data analysis procedure and present single-shot terahertz transmission data on aluminum that has been laser heated to an electron temperature of 0.5 eV.
Revisiting lattice thermal transport in PbTe: The crucial role of quartic anharmonicity
Authors: Xia Yi
Published: August 2018

We perform a first-principles study of lattice thermal transport in PbTe by explicitly considering anharmonicity up to 4th order. To determine the temperature-dependent lattice constant of PbTe beyond quasiharmonic approximation, we introduce a simple yet effective scheme to account for anharmonic phonon renormalization at finite temperature. Moreover, we explicitly compute mode-resolved phonon lifetimes by including both three- and four-phonon scatterings. We find that (1) anharmonic phonon renormalization leads to strong vibrational frequency shifts which improve the agreement between simulated and experimental lattice constants; (2) these frequency shifts lead to a significant increase in lattice thermal conductivity (κl) because of reduced phonon scattering phase space; and (3) four-phonon scatterings are responsible for severe reduction in κl on top of three-phonon scatterings, making κl consistent with experiments. Our results suggest that the predicted κl and its temperature dependence without considering thermal expansion, anharmonic phonon renormalization and four-phonon scatterings could accidentally agree with experiments due to error cancellation. Our study not only deepens the understanding of lattice thermal transport in PbTe but also exemplifies a widely applicable approach to investigate lattice dynamics and thermal transport properties from first-principles calculations including high-order anharmonicity.
Dynamic behavior of CH3NH3PbI3 perovskite twin domains
Authors: Liu Yongtao , Collins Liam , Belianinov Alex , Neumayer Sabine M. , Ievlev Anton V. , Ahmadi Mahshid , Xiao Kai , Retterer Scott T. , Jesse Stephen , Kalinin Sergei V. , Hu Bin , Ovchinnikova Olga S.
Published: August 2018

The recent discovery of twin domains in MAPbI3 perovskites has initiated contentious discussion on the ferroic nature of hybrid perovskites. Ferroelectric polarization is thought to facilitate the dissociation of photoinduced electron-hole pairs, helping to explain the extraordinary photovoltaic performance exhibited by this class of materials. Alternate to ferroelectricity, which has yet to be unambiguously established despite considerable efforts to do so, ferroelasticity was also proposed in these materials. Meanwhile, given the coupling of ionic states and ferroelectricity and the interconnected nature of defect chemistry and ferroelasticity, the electrochemical reactivity can no longer be ignored. In this work, using band excitation piezoresponse force microscopy, we reveal the variation in elasticity between adjacent domains, indicating the ferroelasticity and the difference in the crystallographic states of the twin domain. Moreover, using band excitation contact Kelvin probe force microscopy, we dynamically map the evolution of the twinning structure under electric bias. These results help decipher the effect of the twin domains on ionic mobility and ion diffusion pathways. Combining these results, we reveal the interaction of twin domains and ionic activity in this material. Overall, this work provides insights into the twinning structure in MAPbI3 and its potential effects on the hybrid perovskite optoelectronics.
Local structural changes during the disordered substitutional alloy transition in Bi2Te3 by high-pressure XAFS
Authors: Guo Zhiying , Zhu Hailiang , Dong Juncai , Jia Quanjie , Gong Yu , Wang Yan , Li Haijing , An Pengfei , Yang Dongliang , Zhao Yidong , Xing Haiying , Li Xiaodong , Chen Dongliang
Published: August 2018

A2B3-type 3D topological insulators, Bi2Te3 and Sb2Te3, have been reported to transform into disordered substitutional alloys under high pressure. However, γ → δ phase transition and the local structure changes around Bi during the formation of the disordered Bi-Te binary alloy in Bi2Te3 still remain unclear. Here, high-pressure X-ray absorption fine structure (XAFS) combined with high-pressure X-ray diffraction has been used to explore the local structural transformations in the three structural phase transitions of Bi2Te3. The Bi L3-X-ray absorbing near edge structure (XANES) spectra of δ-Bi2Te3 clearly showed that a new absorption feature at energy of about 13 465 eV would emerge during the γ → δ phase transition. Through simulation of the XANES spectra by varying the cluster size, we confirmed that the new absorption peak arises from the medium-range order in bcc structure. The Bi L3-EXAFS results in δ phase reveal that the Bi atoms in the third shell exhibit abnormal elongations with pressure until merging with the shrinking Te shell. Our findings indicate a two-step structural transition of the disordered substitutional alloys via an ordered bcc intermediate phase.
Vegfaa instructs cardiac muscle hyperplasia in adult zebrafish
Authors: Karra Ravi , Foglia Matthew J. , Choi Wen-Yee , Belliveau Christine , DeBenedittis Paige , Poss Kenneth D.
Published: August 2018

Significance

The human heart is unable to meaningfully recover lost cardiac muscle after injury. As a result, injuries such as myocardial infarction cause irreversible damage that increases the risk for heart failure. Replacing lost or dysfunctional cardiac tissue can potentially reverse or prevent heart failure. Here we demonstrate that experimentally increasing expression of the angiogenic factorvegfaaalone is able to induce a cardiac growth program in zebrafish. We also show evidence that the site ofvegfaaexpression is important for patterning the cardiac growth response. This work identifies Vegfa as a growth factor capable of activating genetic programs for heart regeneration and has generalizable implications for therapeutic administration of cardiac growth factors.
Linguistic effect on speech perception observed at the brainstem
Authors: Zhao T. Christina , Kuhl Patricia K.
Published: August 2018

Significance

Early linguistic experience affects perception and cortical processing of speech, even in infants. The current study examined whether linguistic effects extend to brainstem speech encoding, where responses are rapid, automatic, and preattentive. We focused on transient consonants and measured perception behaviorally and the corresponding complex auditory brainstem response (cABR) onset using simultaneous electroencephalography/magnetoencephalography (EEG/MEG) in native Spanish and English speakers. We demonstrate that the latency of an EEG-cABR onset peak predicts consonant perception and that the perception differs according to language background. MEG-cABR analysis demonstrates deep sources for the onset, providing complimentary support for a brainstem origin. Effects of early linguistic experience on speech perception can be observed at the earlier stage of speech encoding at the brainstem.
Evidence for the impact of the 8.2-kyBP climate event on Near Eastern early farmers
Authors: Roffet-Salque Mélanie , Marciniak Arkadiusz , Valdes Paul J. , Pawłowska Kamilla , Pyzel Joanna , Czerniak Lech , Krüger Marta , Roberts C. Neil , Pitter Sharmini , Evershed Richard P.
Published: August 2018

Significance

This study reveals that animal fats preserved in pottery vessels from the United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage site of Çatalhöyük recorded the abrupt 8.2-thousand years B.P. climatic event in their hydrogen isotopic compositions. In addition, significant changes are observed in the archaeology and faunal assemblage of the site, showing how the early farming community at Çatalhöyük had to adapt to climate change. Significantly, this contribution shows that individual biomolecules preserved in ancient animal fats can be used to reconstruct paleoclimate records and thus, provides a powerful tool for the detection of climatic events at well-dated onsite terrestrial locations (i.e., at the very settlements where human populations lived).
Electron tomography reveals details of the internal microstructure of desalination membranes
Authors: Culp Tyler E. , Shen Yue-xiao , Geitner Michael , Paul Mou , Roy Abhishek , Behr Michael J. , Rosenberg Steve , Gu Junsi , Kumar Manish , Gomez Enrique D.
Published: August 2018

Significance

The development of membrane materials is limited by our lack of tools to characterize their complex microstructure. We demonstrate how a combination of careful sample preparation, electron tomography, and quantitative analysis of 3D models can provide unique insights into the morphology of polyamide active layers used in reverse osmosis membranes. Extracting the 3D morphology is required to obtain accurate estimates of the top surface area and internal void fraction. Furthermore, mapping the internal heterogeneity shows that polymer density is highest near the top surface and suggests new models of how microstructure and membrane performance is connected.
Spectroscopic ruler for measuring active-site distortions based on Raman optical activity of a hydrogen out-of-plane vibration
Authors: Haraguchi Shojiro , Shingae Takahito , Fujisawa Tomotsumi , Kasai Noritaka , Kumauchi Masato , Hanamoto Takeshi , Hoff Wouter D. , Unno Masashi
Published: August 2018

Significance

Many biological cofactors, including light-absorbing chromophores in photoreceptors, are modulated upon insertion into a protein. The steric contribution can cause structural distortions in the cofactor, and such effects are considered to be crucial for biological function. For example, the out-of-plane distortion of chromophores is a key factor in controlling their absorption spectra. In spite of the functional importance, such structural distortions are difficult to measure experimentally. In this study, we used a unique capability of Raman optical activity (ROA) to address the above-mentioned issue. This study applied ROA spectroscopy to a photoreceptor protein and indicates that a hydrogen out-of-plane ROA band provides a spectroscopic ruler for the out-of-plane distortion of the chromophore that is embedded in a protein environment.
Proteomic analysis of monolayer-integrated proteins on lipid droplets identifies amphipathic interfacial α-helical membrane anchors
Authors: Pataki Camille I. , Rodrigues João , Zhang Lichao , Qian Junyang , Efron Bradley , Hastie Trevor , Elias Joshua E. , Levitt Michael , Kopito Ron R.
Published: August 2018

Significance

Biological membranes are semipermeable barriers that are composed primarily of phospholipid bilayers or monolayers and proteins. Proteins embedded within membranes are extremely diverse in structure and function. Some membrane-integrated proteins do not fully span phospholipid bilayers but play key roles in organizing membrane surfaces. How these monolayer-integrated proteins interact with membranes has not been systematically investigated, primarily because they are very difficult to distinguish from the far more common class of proteins that fully traverse the phospholipid bilayer. We describe an approach to systematically identify monolayer-integrated proteins and demonstrate that interfacial α-helices are a structural motif that directs membrane integration for this important class of membrane protein.
Deciphering the super relaxed state of human β-cardiac myosin and the mode of action of mavacamten from myosin molecules to muscle fibers
Authors: Anderson Robert L. , Trivedi Darshan V. , Sarkar Saswata S. , Henze Marcus , Ma Weikang , Gong Henry , Rogers Christopher S. , Gorham Joshua M. , Wong Fiona L. , Morck Makenna M. , Seidman Jonathan G. , Ruppel Kathleen M. , Irving Thomas C. , Cooke Roger , Green Eric M. , Spudich James A.
Published: August 2018

Significance

Cardiac muscle contraction is powered by ATP hydrolysis during cycles of interaction between myosin-containing thick filaments and actin-containing thin filaments. This generates force in the cardiac muscle necessary for pumping blood through the body. Mutations in myosin alter this force generation leading to hypercontractility and hypertrophic cardiomyopathy (HCM). An energy-conserving, super relaxed state (SRX) of myosin, which has a very low ATPase activity, has previously been described in muscle fibers. Destabilization of the SRX has been proposed to be a chief cause of HCM. This work sheds light on the biochemical and molecular nature of SRX and demonstrates the mechanism of action of mavacamten, a cardiac inhibitor in phase 2 clinical trials. Mavacamten exerts its effects primarily by stabilizing the SRX of β-cardiac myosin.
PathwayConnector: finding complementary pathways to enhance functional analysis
Authors: Minadakis George , Zachariou Margarita , Oulas Anastasis , Spyrou George M
Published: August 2018

PathwayConnector is a web-tool that facilitates the construction of complementary pathway-to-pathway networks and subnetworks of them, based on a reference pathway network derived from the rich information available either in KEGG or Reactome database for pathway mapping. Specifically, for a given set of pathways, PathwayConnector (i) finds all the direct connections between them, (ii) adds a minimum set of complementary pathways required to achieve connectivity between the pathways, leading to informative fully connected networks and (ii) provides a series of clustering methods for the further grouping of pathways in to sub-clusters. The proposed web-tool is a simple yet informative tool towards identifying connected groups of pathways that are significantly related to specific diseases.

Availability and implementation

http://bioinformatics.cing.ac.cy/PathwayConnector

Supplementary information

Supplementary data are available at Bioinformatics online.
Constructing equivalence-preserving Dirac variational integrators with forces
Authors: Parks Helen , Leok Melvin
Published: August 2018

The dynamical motion of mechanical systems possesses underlying geometric structures and preserving these structures in numerical integration improves the qualitative accuracy and reduces the long-time error of the simulation. For a single mechanical system, structure preservation can be achieved by adopting the variational integrator construction (Marsden, J. & West, M. (2001) Discrete mechanics and variational integrators. Acta Numer., 10, 357–514). This construction has been generalized to more complex systems involving forces or constraints as well as to the setting of Dirac mechanics (Leok, M. & Ohsawa, T. (2011) Variational and geometric structures of discrete Dirac measures. Found. Comput. Math., 11, 529–562). Forced Lagrange–Dirac systems are described by a Lagrangian and an external force pair, and two pairs of Lagrangians and external forces are said to be equivalent if they yield the same equations of motion. However, the variational discretization of a forced Lagrange–Dirac system discretizes the Lagrangian and forces separately, and will generally depend on the choice of representation. In this paper we derive a class of Dirac variational integrators with forces that yield well-defined numerical methods that are independent of the choice of representation. We present a numerical simulation to demonstrate how such equivalence-preserving discretizations avoid spurious solutions that otherwise arise from poorly chosen representations.
The repeatability of cognitive performance: a meta-analysis
Authors: Cauchoix M. , Chow P. K. Y. , van Horik J. O. , Atance C. M. , Barbeau E. J. , Barragan-Jason G. , Bize P. , Boussard A. , Buechel S. D. , Cabirol A. , Cauchard L. , Claidière N. , Dalesman S. , Devaud J. M. , Didic M. , Doligez B. , Fagot J. , Fichtel C. , Henke-von der Malsburg J. , Hermer E. , Huber L. , Huebner F. , Kappeler P. M. , Klein S. , Langbein J. , Langley E. J. G. , Lea S. E. G. , Lihoreau M. , Lovlie H. , Matzel L. D. , Nakagawa S. , Nawroth C. , Oesterwind S. , Sauce B. , Smith E. A. , Sorato E. , Tebbich S. , Wallis L. J. , Whiteside M. A. , Wilkinson A. , Chaine A. S. , Morand-Ferron J.
Published: August 2018

Behavioural and cognitive processes play important roles in mediating an individual's interactions with its environment. Yet, while there is a vast literature on repeatable individual differences in behaviour, relatively little is known about the repeatability of cognitive performance. To further our understanding of the evolution of cognition, we gathered 44 studies on individual performance of 25 species across six animal classes and used meta-analysis to assess whether cognitive performance is repeatable. We compared repeatability (R) in performance (1) on the same task presented at different times (temporal repeatability), and (2) on different tasks that measured the same putative cognitive ability (contextual repeatability). We also addressed whetherRestimates were influenced by seven extrinsic factors (moderators): type of cognitive performance measurement, type of cognitive task, delay between tests, origin of the subjects, experimental context, taxonomic class and publication status. We found support for both temporal and contextual repeatability of cognitive performance, with meanRestimates ranging between 0.15 and 0.28. Repeatability estimates were mostly influenced by the type of cognitive performance measures and publication status. Our findings highlight the widespread occurrence of consistent inter-individual variation in cognition across a range of taxa which, like behaviour, may be associated with fitness outcomes.

This article is part of the theme issue ‘Causes and consequences of individual differences in cognitive abilities’.
A distributed brain network predicts general intelligence from resting-state human neuroimaging data
Authors: Dubois Julien , Galdi Paola , Paul Lynn K. , Adolphs Ralph
Published: August 2018

Individual people differ in their ability to reason, solve problems, think abstractly, plan and learn. A reliable measure of this general ability, also known as intelligence, can be derived from scores across a diverse set of cognitive tasks. There is great interest in understanding the neural underpinnings of individual differences in intelligence, because it is the single best predictor of long-term life success. The most replicated neural correlate of human intelligence to date is total brain volume; however, this coarse morphometric correlate says little about function. Here, we ask whether measurements of the activity of the resting brain (resting-state fMRI) might also carry information about intelligence. We used the final release of the Young Adult Human Connectome Project (N= 884 subjects after exclusions), providing a full hour of resting-state fMRI per subject; controlled for gender, age and brain volume; and derived a reliable estimate of general intelligence from scores on multiple cognitive tasks. Using a cross-validated predictive framework, we predicted 20% of the variance in general intelligence in the sampled population from their resting-state connectivity matrices. Interestingly, no single anatomical structure or network was responsible or necessary for this prediction, which instead relied on redundant information distributed across the brain.

This article is part of the theme issue ‘Causes and consequences of individual differences in cognitive abilities’.
Heritabilities and co-variation among cognitive traits in red junglefowl
Authors: Sorato Enrico , Zidar Josefina , Garnham Laura , Wilson Alastair , Løvlie Hanne
Published: August 2018

Natural selection can act on between-individual variation in cognitive abilities, yet evolutionary responses depend on the presence of underlying genetic variation. It is, therefore, crucial to determine the relative extent of genetic versus environmental control of these among-individual differences in cognitive traits to understand their causes and evolutionary potential. We investigated heritability of associative learning performance and of a cognitive judgement bias (optimism), as well as their covariation, in a captive pedigree-bred population of red junglefowl (Gallus gallus,n> 300 chicks over 5 years). We analysed performance in discriminative and reversal learning (two facets of associative learning), and cognitive judgement bias, by conducting animal models to disentangle genetic from environmental contributions. We demonstrate moderate heritability for reversal learning, and weak to no heritability for optimism and discriminative learning, respectively. The two facets of associative learning were weakly negatively correlated, consistent with hypothesized trade-offs underpinning individual cognitive styles. Reversal, but not discriminative learning performance, was associated with judgement bias; less optimistic individuals reversed a previously learnt association faster. Together these results indicate that genetic and environmental contributions differ among traits. While modular models of cognitive abilities predict a lack of common genetic control for different cognitive traits, further investigation is required to fully ascertain the degree of covariation between a broader range of cognitive traits and the extent of any shared genetic control.

This article is part of the theme issue ‘Causes and consequences of individual differences in cognitive abilities’.
An intraspecific appraisal of the social intelligence hypothesis
Authors: Ashton Benjamin J. , Thornton Alex , Ridley Amanda R.
Published: August 2018

The prevailing hypotheses for the evolution of cognition focus on either the demands associated with group living (the social intelligence hypothesis (SIH)) or ecological challenges such as finding food. Comparative studies testing these hypotheses have generated highly conflicting results; consequently, our understanding of the drivers of cognitive evolution remains limited. To understand how selection shapes cognition, research must incorporate an intraspecific approach, focusing on the causes and consequences of individual variation in cognition. Here, we review the findings of recent intraspecific cognitive research to investigate the predictions of the SIH. Extensive evidence from our own research on Australian magpies (
Cracticus tibicen dorsalis
), and a number of other taxa, suggests that individuals in larger social groups exhibit elevated cognitive performance and, in some cases, elevated reproductive fitness. Not only do these findings demonstrate how the social environment has the potential to shape cognitive evolution, but crucially, they demonstrate the importance of considering both genetic
and
developmental factors when attempting to explain the causes of cognitive variation.

This article is part of the theme issue ‘Causes and consequences of individual differences in cognitive abilities’.