bluuebunny/crossref_metadata_2025 huggingface dataset:
Commit, hide and escape: the story ofPlasmodiumgametocytes
Authors: Beri Divya , Balan Balu , Tatu Utpal
Published: July 2018

Malaria is the major cause of mortality and morbidity in tropical countries. The causative agent,Plasmodiumsp., has a complex life cycle and is armed with various mechanisms which ensure its continuous transmission. Gametocytes represent the sexual stage of the parasite and are indispensable for the transmission of the parasite from the human host to the mosquito. Despite its vital role in the parasite's success, it is the least understood stage in the parasite's life cycle. The presence of gametocytes in asymptomatic populations and induction of gametocytogenesis by most antimalarial drugs warrants further investigation into its biology. With a renewed focus on malaria elimination and advent of modern technology available to biologists today, the field of gametocyte biology has developed swiftly, providing crucial insights into the molecular mechanisms driving sexual commitment. This review will summarise key current findings in the field of gametocyte biology and address the associated challenges faced in malaria detection, control and elimination.
Phytoplankton in the embayments of King George Island (Antarctic Peninsula): a review with emphasis on diatoms
Authors: Lange Priscila Kienteca , Ligowski Ryszard , Tenenbaum Denise Rivera
Published: July 2018

Considering that phytoplankton assemblages are good bioindicators of environmental conditions, the sensitivity of the Western Antarctic Peninsula (WAP) to climate change, and the importance of some areas of its islands as Antarctic Specially Managed Areas, this work assembles published datasets on phytoplankton biodiversity and ecology in confined coastal areas (embayments) of King George Island, WAP. Over 33 years (1980–2013), 415 species from 122 genera have been identified to species level, being mostly diatoms (371 species), with 10 new species described with local material (6 diatoms, 4 cyanobacteria). The importance of diatoms was indicated by the frequent occurrence ofCorethron pennatum,Pseudogomphonema kamtshaticum, and abundant benthic genera in the plankton (e.g.Navicula,Cocconeis). The increased contribution of dinoflagellates after 2010 suggests marked changes in the water column. Early-summer blooms differ between the bays' eastern and western shores, with terrestrial melting and wind-driven upwelling inducing the dominance of benthic species at eastern shores, whereas planktonic diatoms (Thalassiosira,Pseudo-nizschia, andChaetoceros) are most abundant along western shores and central areas. The importance of an accurate identification of organisms that are becoming key ecological components of the region is discussed, as recent changes in the microflora may affect the entire marine food web.
ANALYSIS OF THE NETWORK WITH MULTIPLE CLASSES OF POSITIVE CUSTOMERS AND SIGNALS AT A NON-STATIONARY REGIME
Authors: Matalytski M. , Kopats D.
Published: July 2018

The object of research is G-network with positive customers and signals of multiple classes. The present paper describes an analysis of this network at a non-stationary regime, also provided a description of method for finding non-stationary state probabilities.

At the beginning of the article, a description of the network with positive customers and signals is given. A signal when entering the system destroys a positive customer of its type or moves the customer of its type to another system. Streams of positive customers and signals arriving to each of the network systems are independent. Selection of positive customers of all classes for service – randomly. For non-stationary state probabilities of the network, the system of Kolmogorov difference-differential equations (DDE) has been derived. It is solved by a modified method of successive approximations, combined with the method of series. The convergence of successive approximations with time has been proved to the stationary distribution of probabilities, the form of which is indicated in the article, and the sequence of approximations converges to the unique solution of the DDE system. Any successive approximation is representable in the form of a convergent power series with an infinite radius of convergence, the coefficients of which satisfy recurrence relations, which is convenient for computer calculations.

The obtained results can be applied for modeling behavior of computer viruses and attack in computer systems and networks, for example, as model impact of some file viruses on server resources.
Developmental changes in articulation rate and phonic groups during narration in French children aged four to eleven years
Authors: COLLETTA Jean-Marc , PELLENQ Catherine , HADIAN-CEFIDEKHANIE Ali , ROUSSET Isabelle
Published: July 2018

This paper reports on an original study designed to investigate age-related change in the way French children produce speech during oral narrative, considering both prosodic parameters – speaking rate and duration of the prosodic speech unit – and linguistic structure. Eighty-five French children aged four to eleven years were asked to tell a story after they were shown an excerpt from an animated film. All their remarks were transcribed and coded using ELAN as an annotation tool. Each narrative was analyzed for duration, articulation rate, and linguistic components (i.e., number of phonic groups, syllables, words, clauses). All measures were found to increase with age, with the duration of the phonic group and its linguistic structure showing the stronger differences. Results contribute to providing reference data on speech production during childhood, and they suggest the existence of two distinct developmental patterns in narrative production.
Optimal stability estimates for continuity equations
Authors: Seis Christian
Published: July 2018

This review paper is concerned with the stability analysis of the continuity equation in the DiPerna–Lions setting in which the advecting velocity field is Sobolev regular. Quantitative estimates for the equation were derived only recently, but optimality was not discussed. We revisit the results from our 2017 paper, compare the new estimates with previously known estimates for Lagrangian flows and demonstrate how these can be applied to produce optimal bounds in applications from physics, engineering and numerical analysis.
Japanese and Chinese infrastructure development strategies in Central Asia
Authors: Dadabaev Timur
Published: July 2018

This paper compares Japanese and Chinese infrastructure development strategies in post-Soviet Central Asia (CA) by analyzing the similarities and differences in the approaches of the two Asian economic powers. This paper develops several arguments with respect to the Japanese and Chinese approaches to infrastructure development in CA. This paper argues that the discourse of mutually exclusive interests in China and Japan's development of various infrastructure-related projects in CA is empirically unproven. Most of the Chinese engagements emphasize the creation of energy and transportation infrastructure (construction), while Japan's main areas of focus are the maintenance, modernization, and rehabilitation of current infrastructure. Thus, this paper suggests that China positions itself as CA's leading economic partner, while Japan is CA's leading assistance provider. These two roles have different implications. Furthermore, the current infrastructure engagements of Japan (from assistance to partnership) and China (from exploitation to contribution to the region) in CA demonstrate both countries’ attempts to adjust and search for new opportunities.
Stellar SiO masers in the Galaxy: The Bulge Asymmetries and Dynamic Evolution (BAaDE) survey
Authors: Sjouwerman L. O. , Pihlström Y. M. , Rich R. M. , Claussen M. J , Morris M. R. ,   the BAaDE collaboration
Published: July 2018

Circumstellar SiO masers can be observed in red giant evolved stars throughout the Galaxy. Since stellar masers are not affected by non-gravitational forces, they serve as point-mass probes of the gravitational potential and form an excellent sample for studies of the Galactic structure and dynamics. Compared to optical studies, the non-obscured masers are in particular valuable when observed close to the highly obscured Galactic Bulge and Plane. Their line-of-sight velocities can easily be obtained with high accuracy, proper motions can be measured and distances can be estimated. Furthermore, when different mass and metallicity effects can be accounted for, such a large sample will highlight asymmetries and evolutionary traces in the sample. In our Bulge Asymmetries and Dynamic Evolution (BAaDE) survey we have searched 20,000 infrared selected evolved stars for 43 GHz SiO masers with the VLA in the northern Bulge and Plane and are in the process of observing another 10,000 stars for 86 GHz SiO masers with ALMA in the southern Bulge. Our instantaneous detection rate in the Bulge is close to 70%, both at 43 and 86 GHz, with occasionally up to 7 simultaneous SiO transitions observed in a single star. Here we will outline the BAaDE survey, its first results and some of the peculiar maser features we have observed. Furthermore we will discuss the prospects for obtaining proper motions and parallaxes for individual maser stars to reconstruct individual stellar orbits.
Expansion of methanol maser rings
Authors: Bartkiewicz Anna , Sanna Alberto , Szymczak Marian , Moscadelli Luca , van Langevelde Huib
Published: July 2018

Ring−like sources of 6.7 GHz methanol maser emission were discovered a decade ago with the European VLBI Network. In the past years we have been incessantly working to understand the nature of these rings. In general, the methanol rings do not coincide with H II regions nor they show 22 GHz water maser emission. Here, we present a proper motion study over a time baseline up to 10.5 years for the first sub-sample of methanol maser rings. Our findings suggest that in three targets G23.207−00.377, G23.389+00.185, and G23.657−00.127, such rings form in outflows or even in winds close to the central sources, and the masers trace slow proper motions of a few km s−1 typically.
Eight new astrometry results of 6.7 GHz CH3OH and 22 GHz H2O masers in the Perseus arm
Authors: Sakai Nobuyuki ,   BeSSeL and VERA projects members
Published: July 2018

We report astrometric results for seven 6.7 GHz CH3OH and one 22 GHz H2O masers in the Perseus arm with VLBA and VERA observations. Among the eight sources, we succeeded in obtaining trigonometric parallaxes for all sources, except G098.03+1.44 at 6.7 GHz band. By combining our results with previous astrometry results (Choi et al. 2014), we determined an arm width of 0.41 kpc and a pitch angle of 8.2 ± 2.5 deg for the Perseus arm. By using a large sample of the Perseus arm (26 sources), we examined the three-dimensional, non-circular motions (defined as U, V and W) of sources in the Perseus arm as a function of the distance (D) perpendicular to the arm. Interestingly, we found a weighted mean of  = 12.7 ± 1.2 km s−1 for 14 sources with D < 0 kpc (i.e. sources on the interior side of the arm) and  = −0.3 ± 1.5 km s−1 for 12 sources with D > 0 kpc (i.e. sources exterior to the arm). These findings might be the first observational indication of the ”damping phase of a spiral arm” suggested by the non-steady spiral arm model of Baba et al. (2013). The small pitch angle of the Perseus arm (< 10 deg) also supports the damping phase, based on ”pitch angle vs. arm amplitude” relation shown in Grøsbol et al. (2004).
ALMA observations of submillimeter H2O and SiO lines in Orion Source I
Authors: Hirota Tomoya , Machida Masahiro N. , Matsushita Yuko , Motogi Kazuhito , Matsumoto Naoko , Kim Mikyoung , Burns Ross A. , Honma Mareki
Published: July 2018

We present observational results of the submillimeter H2O and SiO lines toward a candidate high-mass young stellar object Orion Source I using ALMA. The spatial structures of the high excitation lines at lower-state energies of >2500 K show compact structures consistent with the circumstellar disk and/or base of the northeast-southwest bipolar outflow with a 100 au scale. The highest excitation transition, the SiO (v=4) line at band 8, has the most compact structure. In contrast, lower-excitation transitions are more extended than 200 au tracing the outflow. Almost all the line show velocity gradients perpendicular to the outflow axis suggesting rotation motions of the circumstellar disk and outflow. While some of the detected lines show broad line profiles and spatially extended emission components indicative of thermal excitation, the strong H2O lines at 321 GHz, 474 GHz, and 658 GHz with brightness temperatures of >1000 K show clear signatures of maser action.
Understanding high-mass star formation through KaVA observations of water and methanol masers
Authors: Kim Kee-Tae , Hirota Tomoya , Sugiyama Koichiro , Kim Jungha , Byun Do-Young , Chibueze James , Hachisuka Kazuya , Hu Bo , Hwang Eodam , Kang Ji-Hyun , Kim Jeong-Sook , Kim Mikyoung , Liu Tie , Matsumoto Naoko , Motogi Kazuhito , Oh Chung Sik , Sunada Kazuyoshi , Wu Yuanwei ,   KaVA star formation group
Published: July 2018

Despite their importance in the formation and evolution of stellar clusters and galaxies, the formation of high-mass stars remains poorly understood. We recently started a systematic observational study of the 22 GHz water and 44 GHz class I methanol masers in high-mass star-forming regions as a four-year KaVA large program. Our sample consists of 87 high-mass young stellar objects (HM-YSOs) in various evolutionary phases, many of which are associated with two or more different maser species. The primary scientific goals are to measure the spatial distributions and 3-dimensional velocity fields of multiple maser species, and understand the dynamical evolution of HM-YSOs and their circumstellar structures, in conjunction with follow-up observations with JVN/EAVN (6.7 GHz class II methanol masers), VERA, and ALMA. In this paper we present details of our KaVA large program, including the first-year results and observing/data analysis plans for the second year and beyond.
VLBI astrometry of a water maser source in the Sgr B2 complex with VERA
Authors: Sakai Daisuke , Oyama Tomoaki , Nagayama Takumi , Honma Mareki , Kobayashi Hideyuki
Published: July 2018

We have conducted astrometric observations toward a 22 GHz water maser source associated with the Sgr B2 complex in the Galactic center region with VERA (VLBI exploration of Radio Astrometry). We measured a trigonometric parallax and absolute proper motion of the Sgr B2 complex with respect to an extra-galactic source by observing the water maser source at 10 epochs from 2014 to 2017. The measured distance was 7.52+3.01−1.67 kpc for the Sgr B2M region.

We also succeeded to measure internal motions of maser spots in Sgr B2M, and N region. The number of spots which we could measure the internal motions is about 400. The distribution of the maser spots shows that the maser spots are associated with envelope of HII region seen in radio continuum image obtained with VLA and ALMA. We discuss relative motions between Sgr B2M, and N by using the internal motion.
A Legacy in Fossils: a Tribute to Stan(ley) Wood – Preface
Authors: Fraser Nicholas C. , Smithson Timothy R. , Clack Jennifer A.
Published: July 2018

Stan Wood had a gift for finding exceptional Early Carboniferous fossils. Among them are 32 type specimens. His discoveries significantly changed our understanding of the history of life on Earth. Many of the fossils he collected are on display in museums across the UK and the localities he discovered continue to yield important new material. Here we briefly review some of Stan Wood's key achievements and describe the legacy he left.
Investigation of the Abnormal Quasi 2‐Day Wave Activities During the Sudden Stratospheric Warming Period of January 2006
Authors: Gu Sheng‐Yang , Dou Xiankang , Pancheva Dora , Yi Wen , Chen Tingdi
Published: July 2018

A quasi 2‐day wave (QTDW) during the austral summer period usually coincides with a sudden stratospheric warming (SSW) event in the winter hemisphere, while the SSW influences on QTDWs are not totally understood. In this work, the hourly Navy Operational Global Atmospheric Prediction System‐Advanced Level Physics High Altitude reanalysis data sets during January/February 2006 are utilized to study the contribution of a major SSW on the anomalous QTDW activities during the same period. Our new findings are generalized as follows: (1) The summer easterly is enhanced during a SSW event due to the interhemispheric coupling, which is clearly indicated by the anomalous cross‐equator circulation from the winter to summer mesosphere. (2) The enhanced summer easterly could sustain critical layers for QTDWs with larger phase speeds (e.g., smaller zonal wave number or shortwave period) and strengthen the summer easterly barotropic/baroclinic instabilities, which are essential for the QTDW amplification through wave‐mean flow interactions. This is why a strong westward QTDW with zonal wave number 2 is identified besides the conventionally dominant wave mode of wave number 3, and their periods are only ~42–45 hr during January 2006. (3) The strong winter planetary waves during SSW periods facilitate the occurrence of the nonlinear interaction between QTDWs and stationary planetary waves, which is strongly suggested by the abnormal temporal variations of wave number 2 and wave number 3 QTDWs. We conclude that the anomalous QTDW behaviors in summer mesosphere during January 2006 are associated with the major SSW event in the winter stratosphere.
Prevalence of Power Law Profiles in Passive Margin Escarpments
Authors: Banerjee Argha , Shirsat Tejal , Kumari Reshama
Published: July 2018

An analysis of elevation data from several great escarpment regions across the globe revealed a prevalence of inverse power law forms among the escarpment profiles. The best fit power law exponent varies among profiles and has a global median value of 0.9 and standard deviation of 1.8. The power law form is consistent with the shape of a detachment‐limited escarpment that is retreating headward while maintaining a constant shape. Such a constant‐shape evolution requires the local denudation rate to be equal to the product of escarpment retreat rate and local slope. The available basin‐averaged denudation rate data from several great escarpment regions are consistent with this constraint, and this allows estimation of the recent retreat rates of the escarpments within the constant‐shape assumption.
A Model for the Downstream Evolution of Temperate Ice and Subglacial Hydrology Along Ice Stream Shear Margins
Authors: Meyer Colin R. , Yehya Alissar , Minchew Brent , Rice James R.
Published: July 2018

Antarctic mass balance and contribution to sea level rise are dominated by the flow of ice through narrow conduits called ice streams. These regions of relatively fast flow drain over 90% of the ice sheet and generate significant amounts of frictional heat at the ice stream margins where there is a transition to slow flow in the ridge. This heat can generate temperate ice and a sharp transition in flow speed between the stream and the ridge. Within zones of temperate ice, meltwater is produced and drains to the bed. Here we model the downstream development of a temperate zone along an ice stream shear margin and the flow of meltwater through temperate ice into a subglacial hydrologic system. The hydrology sets the basal effective pressure, defined as the difference between ice overburden and water pressure. Using the southern shear margin of Bindschadler Ice Stream as a case study, our model results indicate an abrupt transition from a distributed to channelized hydrologic system within a few ice thicknesses of the point where the temperate zone initiates. This transition leads to a strengthening of the till due to reduced pore pressure because the water pressure in the channel is lower than in the distributed system, a potential mechanism by which hydrology can prevent lateral migration of shear margins.
The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract
Authors: Lin Xiaoxi B , Wang Tuo , Stothard Paul , Corander Jukka , Wang Jun , Baines John F , Knowles Sarah C L , Baltrūnaitė Laima , Tasseva Guergana , Schmaltz Robert , Tollenaar Stephanie , Cody Liz A , Grenier Theodore , Wu Wei , Ramer-Tait Amanda E , Walter Jens
Published: July 2018

The eco-evolutionary interactions among members of the vertebrate gut microbiota that ultimately result in host-specific communities are poorly understood. Here we show that Lactobacillus reuteri coexists with species that belong to the Lactobacillus johnsonii cluster (L. johnsonii, L. gasseri, and L taiwanensis) in a taxonomically wide range of rodents, suggesting cohabitation over evolutionary times. The two dominant Lactobacillus species found in wild mice establish a commensalistic relationship in gastric biofilms when introduced together into germ-free mice in which L. reuteri facilitates colonization of L. taiwanensis. Genomic analysis revealed allopatric diversification in strains of both species that originated from geographically separated locations (Scotland and France). Allopatry of the strains resulted in reduced formation of mixed biofilms in vitro, indicating that interspecies interactions in gastric Lactobacillus-biofilms are the result of an adaptive evolutionary process that occurred in a biogeographical context. In summary, these findings suggest that members within the vertebrate gut microbiota can evolve inter-dependencies through ecological facilitation, which could represent one mechanism by which host-specific bacterial communities assemble across vertebrate species and an explanation for their spatial and biogeographic patterns.
Recurrent homozygous deletion of DROSHA and microduplication of PDE4DIP in pineoblastoma
Authors: Snuderl Matija , Kannan Kasthuri , Pfaff Elke , Wang Shiyang , Stafford James M. , Serrano Jonathan , Heguy Adriana , Ray Karina , Faustin Arline , Aminova Olga , Dolgalev Igor , Stapleton Stacie L. , Zagzag David , Chiriboga Luis , Gardner Sharon L. , Wisoff Jeffrey H. , Golfinos John G. , Capper David , Hovestadt Volker , Rosenblum Marc K. , Placantonakis Dimitris G. , LeBoeuf Sarah E. , Papagiannakopoulos Thales Y. , Chavez Lukas , Ahsan Sama , Eberhart Charles G. , Pfister Stefan M. , Jones David T. W. , Karajannis Matthias A.
Published: July 2018

Pineoblastoma is a rare and highly aggressive brain cancer of childhood, histologically belonging to the spectrum of primitive neuroectodermal tumors. Patients with germline mutations in DICER1, a ribonuclease involved in microRNA processing, have increased risk of pineoblastoma, but genetic drivers of sporadic pineoblastoma remain unknown. Here, we analyzed pediatric and adult pineoblastoma samples (n = 23) using a combination of genome-wide DNA methylation profiling and whole-exome sequencing or whole-genome sequencing. Pediatric and adult pineoblastomas showed distinct methylation profiles, the latter clustering with lower-grade pineal tumors and normal pineal gland. Recurrent variants were found in genes involved in PKA- and NF-κB signaling, as well as in chromatin remodeling genes. We identified recurrent homozygous deletions of DROSHA, acting upstream of DICER1 in microRNA processing, and a novel microduplication involving chromosomal region 1q21 containing PDE4DIP (myomegalin), comprising the ancient DUF1220 protein domain. Expresion of PDE4DIP and DUF1220 proteins was present exclusively in pineoblastoma with PDE4DIP gain.
Abnormal RNA stability in amyotrophic lateral sclerosis
Authors: Tank E. M. , Figueroa-Romero C. , Hinder L. M. , Bedi K. , Archbold H. C. , Li X. , Weskamp K. , Safren N. , Paez-Colasante X. , Pacut C. , Thumma S. , Paulsen M. T. , Guo K. , Hur J. , Ljungman M. , Feldman E. L. , Barmada S. J.
Published: July 2018

Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) share key features, including accumulation of the RNA-binding protein TDP-43. TDP-43 regulates RNA homeostasis, but it remains unclear whether RNA stability is affected in these disorders. We use Bru-seq and BruChase-seq to assess genome-wide RNA stability in ALS patient-derived cells, demonstrating profound destabilization of ribosomal and mitochondrial transcripts. This pattern is recapitulated by TDP-43 overexpression, suggesting a primary role for TDP-43 in RNA destabilization, and in postmortem samples from ALS and FTD patients. Proteomics and functional studies illustrate corresponding reductions in mitochondrial components and compensatory increases in protein synthesis. Collectively, these observations suggest that TDP-43 deposition leads to targeted RNA instability in ALS and FTD, and may ultimately cause cell death by disrupting energy production and protein synthesis pathways.
Lgl1 controls NG2 endocytic pathway to regulate oligodendrocyte differentiation and asymmetric cell division and gliomagenesis
Authors: Daynac Mathieu , Chouchane Malek , Collins Hannah Y. , Murphy Nicole E. , Andor Noemi , Niu Jianqin , Fancy Stephen P. J. , Stallcup William B. , Petritsch Claudia K.
Published: July 2018

Oligodendrocyte progenitor cells (OPC) undergo asymmetric cell division (ACD) to generate one OPC and one differentiating oligodendrocyte (OL) progeny. Loss of pro-mitotic proteoglycan and OPC marker NG2 in the OL progeny is the earliest immunophenotypic change of unknown mechanism that indicates differentiation commitment. Here, we report that expression of the mouse homolog of Drosophila tumor suppressor Lethal giant larvae 1 (Lgl1) is induced during OL differentiation. Lgl1 conditional knockout OPC progeny retain NG2 and show reduced OL differentiation, while undergoing more symmetric self-renewing divisions at the expense of asymmetric divisions. Moreover, Lgl1 and hemizygous Ink4a/Arf knockouts in OPC synergistically induce gliomagenesis. Time lapse and total internal reflection microscopy reveals a critical role for Lgl1 in NG2 endocytic routing and links aberrant NG2 recycling to failed differentiation. These data establish Lgl1 as a suppressor of gliomagenesis and positive regulator of asymmetric division and differentiation in the healthy and demyelinated murine brain.
Differential temporal salience of earning and saving
Authors: Hu Kesong , De Rosa Eve , Anderson Adam K.
Published: July 2018

People are often characterized as poor savers. Here we examined whether cues associated with earning and saving have differential salience for attention and action. We first modeled earning and saving after positive and negative variants of monetary reinforcement, i.e., gains versus avoiding loss. Despite their equivalent absolute magnitude in a monetary incentive task, colors predicting saving were judged to appear after those that predicted earning in a temporal-order judgment task. This saving posteriority effect also occurred when savings were framed as earnings that come slightly later. Colors predicting savings, whether they acquired either negative or positive value, persisted in their posteriority. An attentional asymmetry away from money-saved relative to money-earned, potentially contributes to decreased everyday salience and future wealth.
Collective magnetism in an artificial 2D XY spin system
Authors: Leo Naëmi , Holenstein Stefan , Schildknecht Dominik , Sendetskyi Oles , Luetkens Hubertus , Derlet Peter M. , Scagnoli Valerio , Lançon Diane , Mardegan José R. L. , Prokscha Thomas , Suter Andreas , Salman Zaher , Lee Stephen , Heyderman Laura J.
Published: July 2018

Two-dimensional magnetic systems with continuous spin degrees of freedom exhibit a rich spectrum of thermal behaviour due to the strong competition between fluctuations and correlations. When such systems incorporate coupling via the anisotropic dipolar interaction, a discrete symmetry emerges, which can be spontaneously broken leading to a low-temperature ordered phase. However, the experimental realisation of such two-dimensional spin systems in crystalline materials is difficult since the dipolar coupling is usually much weaker than the exchange interaction. Here we realise two-dimensional magnetostatically coupled XY spin systems with nanoscale thermally active magnetic discs placed on square lattices. Using low-energy muon-spin relaxation and soft X-ray scattering, we observe correlated dynamics at the critical temperature and the emergence of static long-range order at low temperatures, which is compatible with theoretical predictions for dipolar-coupled XY spin systems. Furthermore, by modifying the sample design, we demonstrate the possibility to tune the collective magnetic behaviour in thermally active artificial spin systems with continuous degrees of freedom.
Simplified ChIP-exo assays
Authors: Rossi Matthew J. , Lai William K. M. , Pugh B. Franklin
Published: July 2018

ChIP-seq and ChIP-exo identify where proteins bind along any genome in vivo. Although ChIP-seq is widely adopted in academic research, it has inherently high noise. In contrast, ChIP-exo has relatively low noise and achieves near-base pair resolution. Consequently, and unlike other genomic assays, ChIP-exo provides structural information on genome-wide binding proteins. Construction of ChIP-exo libraries is technically difficult. Here we describe greatly simplified ChIP-exo methods, each with use-specific advantages. This is achieved through assay optimization and use of Tn5 tagmentation and/or single-stranded DNA ligation. Greater library yields, lower processing time, and lower costs are achieved. In comparing assays, we reveal substantial limitations in other ChIP-based assays. Importantly, the new ChIP-exo assays allow high-resolution detection of some protein-DNA interactions in organs and in as few as 27,000 cells. It is suitable for high-throughput parallelization. The simplicity of ChIP-exo now makes it a highly appropriate substitute for ChIP-seq, and for broader adoption.
High-throughput discovery of organic cages and catenanes using computational screening fused with robotic synthesis
Authors: Greenaway R. L. , Santolini V. , Bennison M. J. , Alston B. M. , Pugh C. J. , Little M. A. , Miklitz M. , Eden-Rump E. G. B. , Clowes R. , Shakil A. , Cuthbertson H. J. , Armstrong H. , Briggs M. E. , Jelfs K. E. , Cooper A. I.
Published: July 2018

Supramolecular synthesis is a powerful strategy for assembling complex molecules, but to do this by targeted design is challenging. This is because multicomponent assembly reactions have the potential to form a wide variety of products. High-throughput screening can explore a broad synthetic space, but this is inefficient and inelegant when applied blindly. Here we fuse computation with robotic synthesis to create a hybrid discovery workflow for discovering new organic cage molecules, and by extension, other supramolecular systems. A total of 78 precursor combinations were investigated by computation and experiment, leading to 33 cages that were formed cleanly in one-pot syntheses. Comparison of calculations with experimental outcomes across this broad library shows that computation has the power to focus experiments, for example by identifying linkers that are less likely to be reliable for cage formation. Screening also led to the unplanned discovery of a new cage topology—doubly bridged, triply interlocked cage catenanes.
Spatial frequency sensitivity in macaque midbrain
Authors: Chen Chih-Yang , Sonnenberg Lukas , Weller Simone , Witschel Thede , Hafed Ziad M.
Published: July 2018

Visual brain areas exhibit tuning characteristics well suited for image statistics present in our natural environment. However, visual sensation is an active process, and if there are any brain areas that ought to be particularly in tune with natural scene statistics, it would be sensory-motor areas critical for guiding behavior. Here we found that the rhesus macaque superior colliculus, a structure instrumental for rapid visual exploration with saccades, detects low spatial frequencies, which are the most prevalent in natural scenes, much more rapidly than high spatial frequencies. Importantly, this accelerated detection happens independently of whether a neuron is more or less sensitive to low spatial frequencies to begin with. At the population level, the superior colliculus additionally over-represents low spatial frequencies in neural response sensitivity, even at near-foveal eccentricities. Thus, the superior colliculus possesses both temporal and response gain mechanisms for efficient gaze realignment in low-spatial-frequency-dominated natural environments.
Abrupt high-latitude climate events and decoupled seasonal trends during the Eemian
Authors: Salonen J. Sakari , Helmens Karin F. , Brendryen Jo , Kuosmanen Niina , Väliranta Minna , Goring Simon , Korpela Mikko , Kylander Malin , Philip Annemarie , Plikk Anna , Renssen Hans , Luoto Miska
Published: July 2018

The Eemian (the Last Interglacial; ca. 129–116 thousand years ago) presents a testbed for assessing environmental responses and climate feedbacks under warmer-than-present boundary conditions. However, climate syntheses for the Eemian remain hampered by lack of data from the high-latitude land areas, masking the climate response and feedbacks in the Arctic. Here we present a high-resolution (sub-centennial) record of Eemian palaeoclimate from northern Finland, with multi-model reconstructions for July and January air temperature. In contrast with the mid-latitudes of Europe, our data show decoupled seasonal trends with falling July and rising January temperatures over the Eemian, due to orbital and oceanic forcings. This leads to an oceanic Late-Eemian climate, consistent with an earlier hypothesis of glacial inception in Europe. The interglacial is further intersected by two strong cooling and drying events. These abrupt events parallel shifts in marine proxy data, linked to disturbances in the North Atlantic oceanic circulation regime.
Author Correction: Zebrafish and medaka offer insights into the neurobehavioral correlates of vertebrate magnetoreception
Authors: Myklatun Ahne , Lauri Antonella , Eder Stephan H. K. , Cappetta Michele , Shcherbakov Denis , Wurst Wolfgang , Winklhofer Michael , Westmeyer Gil G.
Published: July 2018

Text for Correction
Spin inversion in graphene spin valves by gate-tunable magnetic proximity effect at one-dimensional contacts
Authors: Xu Jinsong , Singh Simranjeet , Katoch Jyoti , Wu Guanzhong , Zhu Tiancong , Žutić Igor , Kawakami Roland K.
Published: July 2018

Graphene has remarkable opportunities for spintronics due to its high mobility and long spin diffusion length, especially when encapsulated in hexagonal boron nitride (h-BN). Here, we demonstrate gate-tunable spin transport in such encapsulated graphene-based spin valves with one-dimensional (1D) ferromagnetic edge contacts. An electrostatic backgate tunes the Fermi level of graphene to probe different energy levels of the spin-polarized density of states (DOS) of the 1D ferromagnetic contact, which interact through a magnetic proximity effect (MPE) that induces ferromagnetism in graphene. In contrast to conventional spin valves, where switching between high- and low-resistance configuration requires magnetization reversal by an applied magnetic field or a high-density spin-polarized current, we provide an alternative path with the gate-controlled spin inversion in graphene.
Machine learning hydrogen adsorption on nanoclusters through structural descriptors
Authors: Jäger Marc O. J. , Morooka Eiaki V. , Federici Canova Filippo , Himanen Lauri , Foster Adam S.
Published: July 2018

Catalytic activity of the hydrogen evolution reaction on nanoclusters depends on diverse adsorption site structures. Machine learning reduces the cost for modelling those sites with the aid of descriptors. We analysed the performance of state-of-the-art structural descriptors Smooth Overlap of Atomic Positions, Many-Body Tensor Representation and Atom-Centered Symmetry Functions while predicting the hydrogen adsorption (free) energy on the surface of nanoclusters. The 2D-material molybdenum disulphide and the alloy copper–gold functioned as test systems. Potential energy scans of hydrogen on the cluster surfaces were conducted to compare the accuracy of the descriptors in kernel ridge regression. By having recourse to data sets of 91 molybdenum disulphide clusters and 24 copper–gold clusters, we found that the mean absolute error could be reduced by machine learning on different clusters simultaneously rather than separately. The adsorption energy was explained by the local descriptor Smooth Overlap of Atomic Positions, combining it with the global descriptor Many-Body Tensor Representation did not improve the overall accuracy. We concluded that fitting of potential energy surfaces could be reduced significantly by merging data from different nanoclusters.
Recurrent loss of heterozygosity correlates with clinical outcome in pancreatic neuroendocrine cancer
Authors: Lawrence Ben , Blenkiron Cherie , Parker Kate , Tsai Peter , Fitzgerald Sandra , Shields Paula , Robb Tamsin , Yeong Mee Ling , Kramer Nicole , James Sarah , Black Mik , Fan Vicky , Poonawala Nooriyah , Yap Patrick , Coats Esther , Woodhouse Braden , Ramsaroop Reena , Yozu Masato , Robinson Bridget , Henare Kimiora , Koea Jonathan , Johnston Peter , Carroll Richard , Connor Saxon , Morrin Helen , Elston Marianne , Jackson Christopher , Reid Papaarangi , Windsor John , MacCormick Andrew , Babor Richard , Bartlett Adam , Damianovich Dragan , Knowlton Nicholas , Grimmond Sean , Findlay Michael , Print Cristin
Published: July 2018

Pancreatic neuroendocrine tumors (pNETs) are uncommon cancers arising from pancreatic islet cells. Here we report the analysis of gene mutation, copy number, and RNA expression of 57 sporadic well-differentiated pNETs. pNET genomes are dominated by aneuploidy, leading to concordant changes in RNA expression at the level of whole chromosomes and chromosome segments. We observed two distinct patterns of somatic pNET aneuploidy that are associated with tumor pathology and patient prognosis. Approximately 26% of the patients in this series had pNETs with genomes characterized by recurrent loss of heterozygosity (LoH) of 10 specific chromosomes, accompanied by bi-allelicMEN1inactivation and generally poor clinical outcome. Another ~40% of patients had pNETs that lacked this recurrent LoH pattern but had chromosome 11 LoH, bi-allelicMEN1inactivation, and universally good clinical outcome. The somatic aneuploidy allowed pathogenic germline variants (e.g.,ATM) to be expressed unopposed, with RNA expression patterns showing inactivation of downstream tumor suppressor pathways. No prognostic associations were found with tumor morphology, single gene mutation, or expression of RNAs reflecting the activity of immune, differentiation, proliferative or tumor suppressor pathways. In pNETs, single gene mutations appear to be less important than aneuploidy, withMEN1the only statistically significant recurrently mutated driver gene. In addition, only one pNET in the series had clearly actionable single nucleotide variants (SNVs) (inPTENandFLCN) confirmed by corroborating RNA expression changes. The two clinically relevant patterns of LoH described here define a novel oncogenic mechanism and a plausible route to genomic precision oncology for this tumor type.
Corrosion avoidance in lightweight materials for automotive applications
Authors: Liu Ming , Guo Yang , Wang Jeff , Yergin Mark
Published: July 2018

Due to increasing vehicle greenhouse gas emission regulations across the globe, the automotive industry is facing pressure to improving fuel economy. The key to achieving this is reducing vehicle mass and developing alternative energy vehicles, thereby reducing environmental impact. Lightweighting has become one of the most important aspects to consider in the design and manufacture of modern vehicles, while electric vehicles require a different approach to design and build. All the aforementioned factors have a significant impact on materials selection and usage, and corrosion is a vital consideration. In this article, we discuss and summarize some of the challenges and demands of future fuel-efficient vehicles, from the perspective of corrosion avoidance
Temporal intensity correlation of bunched light from a warm atomic vapor with a ladder-type two-photon transition
Authors: Park Jiho , Jeong Taek , Moon Han Seb
Published: July 2018

We report the temporal intensity correlation (TIC) of scattered photons (SPs) generated via a two-photon transition in a Doppler-broadened warm atomic vapor of the 5S1/2 − 5P3/2 − 5D5/2 transition of 87Rb atoms. Through the investigation of the TICs of the SPs obtained via both one- and two-photon transitions, the second-order correlation values g(2)(0) (i.e., at zero time delay) of both SPs were measured as approximately 1.75, respectively. The widths of the g(2)(τ) spectra were measured as 26 ns (corresponding to the natural lifetime of the 5P3/2 state) for the one-photon transition and 1.8 ns (corresponding to the Doppler width of the warm atomic vapor) for the two-photon transition. We confirmed that the coherence time of the SPs can vary in accordance with the photons emitted from the one- or two-photon transitions in the ladder-type atomic system. The correlated SPs obtained via the two-photon transition contributed to almost all the velocity classes of the atoms in the Doppler-broadened atomic ensemble.
Human coelomic fluid investigation: A MS-based analytical approach to prenatal screening
Authors: Aiello Donatella , Giambona Antonino , Leto Filippo , Passarello Cristina , Damiani Gianfranca , Maggio Aurelio , Siciliano Carlo , Napoli Anna
Published: July 2018

Coelomic fluid (CF) is the earliest dynamic and complex fluid of the gestational sac. CF contains maternal cells and proteins produced by embryonic cells, tissues and excretions. The biochemical composition of CF is modified throughout the first trimester of pregnancy and its protein profile reflects both physiological/pathological changes affecting the embryo and mother. Identification of variations in the balance of proteins might indicate particular types of pathologies, or ascertain specific genetic disorders. A platform utilizing protein enrichment procedures coupled with shotgun identification and iTRAQ differentiation provided the identification and quantitation of 88 unique embryonic proteins. It is relevant to note that chromosome X protein CXorf23 was found suggesting the embryo sex. Foetal sex was determined by Quantitative Fluorescent Polymerase Chain Reaction (QF-PCR) on coelomic cells, foetal tissues and maternal white blood cells, with a 100% concordance rate between iTRAQ-MS/MS and QF-PCR data. The functional associations among the identified proteins were investigated using STRING database. Open Targets Platform showed as significant the following therapeutic areas: nervous, respiratory, eye and head system disease.
A hand-held device for rapid single tube detection of hepatitis-C virus
Authors: Jogezai Naqeebullah , Shabbir Muhammad Imran
Published: July 2018

A Single Tube Analysis system using LAMP, LED and ION-sensing (STALLION) for pathogen derived RNA/DNA.
Degradation of RhB by a sono-Fenton-like process with an iron-foam in the presence of oxalic acid
Authors: Li Guangming , Qiu Shan , Ma Fang , Ji Yawan , Jiang Xiaofeng
Published: July 2018

The decolorization of rhodamine B (RhB) using ultrasound (US) combined with a Fenton-like process has been investigated.
Synthesis, structure and electrical conductivity of a new perovskite type barium cobaltate BaCoO1.80(OH)0.86
Authors: Waidha Aamir Iqbal , Lepple Maren , Wissel Kerstin , Benes Alexander , Wollstadt Stephan , Slater Peter R. , Fortes A. D. , Clemens Oliver
Published: July 2018

BaCoO1.80(OH)0.86, a new member of the perovskite family showing ordering of vacancies and protons.
Aggregation and sedimentation of shattered graphene oxide nanoparticles in dynamic environments: a solid-body rotational approach
Authors: Babakhani Peyman , Bridge Jonathan , Phenrat Tanapon , Doong Ruey-an , Whittle Karl R.
Published: July 2018

Nanoparticle (NP) aggregation is typically investigated in either quiescent or turbulent mixing conditions; neither is fully representative of dynamic natural environments.
Apparent diffusion coefficients in sewer force main biofilms treated with iron salts
Authors: Kiilerich Bruno , Wagner Michael , Nielsen Asbjørn H. , Vollertsen Jes
Published: July 2018

Iron treatment of wastewater in sewer force mains for sulfide abatement reduces biofilm diffusivity.
Phenolics from Eugenia jambolana seeds with advanced glycation endproduct formation and alpha-glucosidase inhibitory activities
Authors: Liu Feifei , Ma Hang , Wang Guihua , Liu Weixi , Seeram Navindra P. , Mu Yu , Xu Yingjie , Huang Xueshi , Li Liya
Published: July 2018

Jamun seed phenolics exhibit antidiabetic potential through inhibiting AGE formation and α-glucosidase activity.
Crystallisation of freeze-dried sucrose in model mixtures that represent the amorphous sugar matrices present in confectionery
Authors: Jawad Rim , Elleman Carole , Martin Gary P. , Royall Paul G.
Published: July 2018

Sucrose crystallization is highly dependent on the presence of other common food ingredients within an amorphous freeze-dried matrix.
Metalloenzymes in natural product biosynthetic pathways
Authors: Ryan Katherine S. , Drennan Catherine L.
Published: July 2018

The Natural Product Reports themed issue on ‘Metalloenzymes in natural product biosynthetic pathways’ is introduced by the Guest Editors, Katherine Ryan and Catherine Drennan.
Nacre-like laminate nitrogen-doped porous carbon/carbon nanotubes/graphene composite for excellent comprehensive performance supercapacitors
Authors: Chen Zeyu , Zhao Siqi , Zhou Yang , Yu Chuying , Zhong Wenbin , Yang Wantai
Published: July 2018

Nitrogen doped nacre-like laminate structure (PGMC) was prepared by alternatively stacked graphene sheets and porous carbon interspersed by MWNTs, promising for applications in high comprehensive performance supercapacitors.
Reduction of graphene oxide alters its cyto-compatibility towards primary and immortalized macrophages
Authors: Wu Yakun , Wang Fanfan , Wang Shunhao , Ma Juan , Xu Ming , Gao Ming , Liu Rui , Chen Wei , Liu Sijin
Published: July 2018

Graphene oxide (GO) and its derivatives (e.g., reduced graphene oxide, RGO) have shown great promise in biomedicine.
Nanoscale surface dynamics of Bi2Te3(111): observation of a prominent surface acoustic wave and the role of van der Waals interactions
Authors: Tamtögl Anton , Campi Davide , Bremholm Martin , Hedegaard Ellen M. J. , Iversen Bo B. , Bianchi Marco , Hofmann Philip , Marzari Nicola , Benedek Giorgio , Ellis John , Allison William
Published: July 2018

A prominent surface acoustic wave dominates the vibrational dynamics of Bi2Te3(111). Theoretical calculations reveal the crucial role of vdW interactions.
The chemical fingerprint of hair melanosomes by infrared nano-spectroscopy
Authors: Stanic Vesna , Maia Francisco Carlos Barbosa , Freitas Raul de Oliveira , Montoro Fabiano Emmanuel , Evans-Lutterodt Kenneth
Published: July 2018

In situ characterization of the sheep hair melanosomes was performed with a spatial resolution of 25 nm using infrared nano-spectroscopy.
A broadband, self-biased photodiode based on antimony telluride (Sb2Te3) nanocrystals/silicon heterostructures
Authors: Parbatani Asish , Song Eui Sang , Yang Fan , Yu Bin
Published: July 2018

Low bulk band gaps and conductive surface electronic states of tetradymite topological insulators (TTI) make them potential candidates for next generation ultra-broadband photodevices.
Au nanocrystal superlattices: nanocrystallinity, vicinal surfaces, and growth processes
Authors: Smilgies Detlef-M. , Li Ruipeng , Pileni Marie Paule
Published: July 2018

Vicinal Au supracrystal surfaces were prepared from Ausingle single domain nanocrystals (NCs), whereas by replacing Ausingle with their polycrystalline counterparts common low-energy supracrystal surfaces were produced.
Peripheral cyclic β-amino acids balance the stability and edge-protection of β-sandwiches
Authors: Olajos Gábor , Hetényi Anasztázia , Wéber Edit , Szögi Titanilla , Fülöp Lívia , Martinek Tamás A.
Published: July 2018

cis-2-Aminocyclohexanecarboxylic acid replacements at the edges of β-sandwiches reduce β-sheet propensities just enough to prevent aggregation but still maintain a compact structure.