bluuebunny/crossref_metadata_2025 huggingface dataset:
Do Professors Better Maintain Cognitive Functioning in Older	Age?
Authors: Aschwanden Damaris , Schumacher Vera , Zimmermann Kathrin , Werner Christina , Allemand Mathias , Zimprich Daniel , Martin Mike
Published: March 2019

Abstract. Research on cognitive aging demonstrates age-related cognitive decline. Education is a protective factor against cognitive decline, but few studies have examined the cognitive development of highly educated individuals. This study compared the cognitive performance and intellectual engagement of retired professors ( N = 47, Mage = 72.9) and individuals with average education ( N = 236, Mage = 72.7) over 5 years. Although the highly educated sample showed better performance in perceptual speed and working memory, cognitive performance was rather stable over time in both samples. Interestingly, high intellectual engagement enabled individuals with average education to keep up with the performance of the highly educated sample on perceptual speed. These findings raise the question whether intellectual engagement is more beneficial than years of education in perceptual speed.
Talk or Walk? Gait Speed over Self-Report in Association with	Cognitive Speed in Healthy Older Adults
Authors: Costello Matthew C. , Sizemore Shane J. , O’Brien Kimberly E. , Manning Lydia K.
Published: March 2019

Abstract. This study explores the relative value of both subjectively reported cognitive speed and gait speed in association with objectively derived cognitive speed. It also explores how these factors are affected by psychological and physical well-being. A group of 90 cognitively healthy older adults ( M = 73.38, SD = 8.06 years, range = 60–89 years) were tested in a three-task cognitive battery to determine objective cognitive speed as well as measures of gait speed, well-being, and subjective cognitive speed. Analyses indicated that gait speed was associated with objective cognitive speed to a greater degree than was subjective report, the latter being more closely related to well-being than to objective cognitive speed. These results were largely invariant across the 30-year age range of our older adult sample.
Human Influence on Winter Precipitation Trends (1921–2015) over North America and Eurasia Revealed by Dynamical Adjustment
Authors: Guo Ruixia , Deser Clara , Terray Laurent , Lehner Flavio
Published: March 2019

Detecting and attributing a human influence on observed rainfall trends is a major challenge due to the presence of large amplitude internal variability on all time scales and by limited temporal and spatial data coverage. Here we apply a “dynamical adjustment” methodology to a gridded archive of monthly precipitation to estimate an anthropogenic influence on long‐term (1920–2015) trends over North America and Eurasia during winter (November–March). This empirical approach aims to remove atmospheric circulation influences from precipitation variability and trends, thereby revealing the thermodynamically induced component as a residual. The geographical pattern and amplitude of this observed thermodynamic residual precipitation trend are in good agreement with anthropogenically forced trends obtained from ensembles of historical climate model simulations. Such consistency helps to reconcile observations and models and provides compelling evidence for a human influence on century‐scale precipitation trends over North America and Eurasia during the cold season.
Scaling of Drag Coefficients Under Five Tropical Cyclones
Authors: Hsu Je‐Yuan , Lien Ren‐Chieh , D'Asaro Eric A. , Sanford Thomas B.
Published: March 2019

The drag coefficient, often used to parameterize the surface wind stress τ, beneath tropical cyclones (TCs) is a critical but poorly known factor controlling TC intensity. Here, τ is estimated using current measurements taken by 12 Electromagnetic Autonomous Profiling Explorer floats beneath the forward half of five TCs. Combining estimates of τ and aircraft measurements of winds U10, the downwind drag coefficient
and the angle ϕ clockwise orientation from U10 to τ are computed. At |U10| = 25–40 m/s,
and ϕ vary over (0.8–3.1) × 10−3 and −15–40°, respectively. A new nondimensional parameter “effective wind duration,” a function of |U10|, storm translation speed, and positions in TCs, predicts
to within 25%. The largest
and smallest ϕ occur at high winds, in the forward right quadrant of fast‐moving storms. These dependences are explained by variations in surface wave age and breaking under different wave forcing regimes.
Are Midtwentieth Century Forced Changes in North Atlantic Hurricane Potential Intensity Detectable?
Authors: Trenary L. , DelSole T. , Camargo S. J. , Tippett M. K.
Published: March 2019

The impact of anthropogenic forcings on tropical North Atlantic hurricane potential intensity (PI) is evaluated in Climate Model Intercomparison Project 5 models for the period 1958–2005. Eleven models are examined, but only seven models have a forced response that is distinguishable from internal variability. The use of discriminant analysis to optimize detectability does not yield a clear, common climate change signal. Of the seven models with a significant response, one has a negative linear trend while two have a positive linear trend. The trend in PI is not even consistent among reanalyses, although this difference is not statistically significant because of large uncertainties. Furthermore, estimates of PI internal variability have significantly different variances among different reanalysis products. These disagreements between models, reanalysis products, and between models and reanalyses, in conjunction with relatively large uncertainties, highlight the difficulty of detecting and attributing observed changes in North Atlantic hurricane potential intensity.
Atlantic Inflow to the North Sea Modulated by the Subpolar Gyre in a Historical Simulation With MPI‐ESM
Authors: Koul V. , Schrum C. , Düsterhus A. , Baehr J.
Published: March 2019

While the influence of the subpolar gyre (SPG) on thermohaline variability in the eastern North Atlantic is well documented, the extent and timescale of the influence of the SPG on North Sea is not well understood. This is primarily because earlier investigations on the causes of variability in the North Sea water properties mostly focused on the role of atmosphere and deployed regional models. Here using a historical simulation with the Max Planck Institute Earth System Model (MPI‐ESM), we investigate circulation and water mass variability in key regions, namely, the Rockall Trough and the Faroe‐Scotland Channel, which link the North Atlantic to the North Sea. We find that salinity covaries with advective lags in these three regions and that the northern North Sea salinity follows the Rockall Trough with a lag of 1 year. We show that recurring and persistent excursions of salinity anomalies into the northern North Sea are related to the SPG strength and not to the local acceleration of the inflow. Furthermore, we illustrate that the SPG signal is more pronounced in salinity than in temperature and that this simulated SPG signal has a period of 30–40 years. Overall, our study suggests that, at low frequency, water mass variability originating in the North Atlantic dominates changes in the North Sea water properties over those due to local wind‐driven volume transport.
Upwelling in the Ocean Basins North of the ACC: 1. On the Upwelling Exposed by the Surface Distribution of Δ14C
Authors: Toggweiler J. R. , Druffel Ellen R. M. , Key Robert M. , Galbraith Eric D.
Published: March 2019

The upwelling associated with the ocean's overturning circulation is hard to observe directly. Here, a large data set of surface Δ14C measurements is compiled in order to show where deep water is brought back up to the surface in the ocean basins north of the Antarctic Circumpolar Current (ACC). Maps constructed from the data set show that low‐Δ14C deep water from the ACC is drawn up to the surface in or near the upwelling zones off Northwest Africa and Namibia in the Atlantic, off Costa Rica and Peru in the Pacific, and in the northern Arabian Sea in the Indian Ocean. Deep water also seems to be reaching the surface in the subarctic Pacific gyre near the Kamchatka Peninsula. The low‐Δ14C water drawn up to the surface in the upwelling zones is also shown to spread across the ocean basins. It is easily seen, for example, in the western Atlantic off Florida and in the western Pacific off New Guinea and Palau. The spreading allows one to estimate the volumes of upwelling, which, it turns out, are similar to the volumes of large‐scale upwelling derived from inverse box models. This means that very large volumes of cool subsurface water are reaching the surface in and near the upwelling zones—much larger volumes than would be expected from the local winds.
Modification of Near‐Surface Temperature Over East Asia Associated With Local‐Scale Paddy Irrigation
Authors: Sugimoto Shiori , Takahashi Hiroshi G. , Sekiyama Hirosato
Published: March 2019

This study used two regional climate model experiments to assess the impact of paddy irrigation in the Sichuan Basin, China, on the near‐surface temperature across East Asia: a control experiment (CTL run), which was used to calculate soil moisture using an unmodified land surface scheme and a sensitivity experiment (SEN run) that incorporated an increase in soil moisture over the basin at the beginning of the rice‐growing season. Although the near‐surface temperature in the Sichuan Basin was higher in the CTL run than in the observations, it improved in the SEN run because of a change in the Bowen ratio associated with the increase in soil moisture. In the SEN run, the modification of local‐scale land surface wetness in the basin causes the decrease in the near‐surface temperature over northeastern China and its increase over southern China relative to that in the CTL run because of a change in the cloud convection associated with precipitation, which, in turn, modifies the solar and net radiation at the surface and the partitioning into the sensible and latent heat fluxes. The greenhouse effect associated with an increase in precipitable water in the SEN run also influences near‐surface warming over southeastern China and the ocean north of southwestern Japan, where the impacts of radiation processes and surface heat fluxes on the near‐surface temperature are small. Consequently, these results suggest that local‐scale modifications to land surface wetness in the Sichuan Basin result in changes in the spatial distribution of near‐surface temperatures over a part of East Asia.
Shading by Trees and Fractional Snow Cover Control the Subcanopy Radiation Budget
Authors: Malle Johanna , Rutter Nick , Mazzotti Giulia , Jonas Tobias
Published: March 2019

Radiative processes are substantially altered by the presence of forest canopies, further affecting snow energetics during wintertime. In situ measurements of subcanopy radiation can help improve process‐scale understanding of these complex interactions, which are needed to further constrain and improve land surface models. In this study, a custom‐made cable car was used to measure incoming and outgoing, shortwave and longwave radiation below an evergreen forest stand. Hemispherical photographs taken concurrently from the cable car measured view fractions of shaded snow, sunlit snow, and bare ground. With this setup it was possible to quantify diurnal and seasonal radiation patterns together with their potential drivers at high spatiotemporal resolution. Measurements were performed between January and May 2018, along a 48‐m transect in a discontinuous needleleaf forest in the Swiss Alps. Analysis of diurnal radiation patterns revealed a strong linear relationship (R = 0.94) between outgoing shortwave radiation and sunlit snow‐view fraction, highlighting shading as the main control on the subcanopy shortwave radiation budget. Measurements of outgoing longwave radiation were strongly controlled by the snow cover extent, with locations of diminished snow cover showing an increase in outgoing longwave radiation of up to 60 W/m2. The subcanopy radiation budget was shown to be dominated by shortwave radiation when surrounding canopy structure and the position of the sun allowed for direct insolation of the forest floor, but longwave radiation was the dominating component in the absence of direct insolation.
Microbial Community Responses to Vanadium Distributions in Mining Geological Environments and Bioremediation Assessment
Authors: Zhang Baogang , Wang Song , Diao Muhe , Fu Jie , Xie Miaomiao , Shi Jiaxin , Liu Ziqi , Jiang Yufeng , Cao Xuelong , Borthwick Alistair G. L.
Published: March 2019

Vanadium mining activities can cause contamination of the surrounding geological environment. Vanadium may exist in multiple matrices due to its migration and transformation, forming interactive relationships; however, the connection between vanadium distributions in multiple matrices and microbial community responses remains largely unknown. Vanadium is a redox‐sensitive metal that can be microbiologically reduced and immobilized. To date, bioremediation of vanadium‐contaminated environments by indigenous microorganisms has rarely been evaluated. This paper reports a systematic investigation into vanadium distributions and microbial communities in soils, water, and sediment from Panzhihua, China. Large vanadium contents of 1130.1 ± 9.8 mg/kg and 0.13 ± 0.02 mg/L were found in surface soil and groundwater. Vanadium in surface water tended to precipitate. Microbial communities isolated from similar environments were alike due to similarity in matrix chemistry whereas communities were distinct when compared to different matrices, with lower richness and diversity in groundwater. Proteobacteria was distributed widely and dominated microbial communities within groundwater. Redundancy analysis shows that vanadium and nutrients significantly affected metal‐tolerant bacteria. Long‐term cultivation (240 days) suggests the possibility of vanadium bioremediation by indigenous microorganisms, within acid‐soluble fraction. This active fraction can potentially release mobile vanadium with shifted redox conditions. Vanadium (V) was bio‐reduced to less toxic, mobile vanadium (IV) primarily by enriched Bacillus and Thauera. This study reveals the biogeochemical fate of vanadium in regional geological environments and suggests a bioremediation pathway via native vanadium‐reducing microbes.
Tectonics of the Eastern Kunlun Range: Cenozoic Reactivation of a Paleozoic‐Early Mesozoic Orogen
Authors: Wu Chen , Zuza Andrew V. , Chen Xuanhua , Ding Lin , Levy Drew A. , Liu Changfeng , Liu Wencan , Jiang Tian , Stockli Daniel F.
Published: March 2019

The Eastern Kunlun Range in north Tibet, located along the northern margin of the eastern Tethyan orogenic system, records evidence for continental break‐up and ocean development in the Neoproterozoic, Paleozoic‐early Mesozoic subduction and continental collision, Mesozoic intracontinental extension, and Cenozoic contractional deformation. The Kunlun region is marked by active left‐lateral strike‐slip deformation of Kunlun fault system, one of the major intracontinental strike‐slip faults in Tibet that developed in response India‐Asia. To better constrain the tectonic evolution of the Eastern Kunlun Range and the closure of the various Kunlun oceans, we conducted detailed investigation integrating new geologic mapping, geochronology, and whole‐rock geochemistry with a synthesis of existing datasets across north Tibet. The Eastern Kunlun Range experienced three major deformation events in the Neoproterozoic, early Paleozoic, and Late Paleozoic‐early Mesozoic, which were associated with collision of the Proto‐, Paleo‐, and Neo‐Kunlun arcs, respectively. Our new detrital zircon analyses from Mesoproterozoic‐Cenozoic strata constrain stratigraphic age and sediment provenance and highlight the importance of three periods of arc activity. Our stratigraphic synthesis, including new field observations, provides new insights into connections between sediment dispersal and changes in tectonism and paleogeography. Miocene‐to‐present strike‐slip activity on the Kunlun fault and the associated strain pattern can be explained by clockwise rotation of the Kunlun fault and its wall rock as a bookshelf‐fault system, which has been proposed for northern Tibet as a result of distributed north‐south right‐lateral shear. The development of this fault system was facilitated by the presence of a Triassic suture that provided a preexisting weakness.
Establishing Science Campaigns in Sub-Saharan Africa
Authors: Beighley Edward , Tshimanga Raphael , N’kaya Guy
Published: March 2019

AGU Chapman Conference on Hydrologic Research in the Congo Basin; Washington, D.C., 25–27 September 2018
Everything Is Connected
Authors: Goss Heather
Published: March 2019

The field of hydrology embraces the balance of worldwide systems and local behavior.
Secular Drift of the Auroral Ovals: How Fast Do They Actually Move?
Authors: Tsyganenko N. A.
Published: March 2019

A surprisingly fast secular drift of the Northern geomagnetic dip pole during the last two decades has attracted much interest lately, in particular, evoking speculations about a possibility of a sweeping relocation of the auroral oval. This letter presents first results of a model investigation of this issue, based on an empirical representation of the distant magnetosphere combined with a series of internal geomagnetic field models for 12 epochs, covering the interval from 1965 to 2020. The secular drift of the northern auroral oval was found to result in its net displacement over the 55‐year period, commensurate with the concurrent shifts of the centered, eccentric, and corrected geomagnetic poles, all of them much smaller than the enormous spurt of the northern dip pole. In the Southern Hemisphere, the shift of the auroral oval and of the poles over the same period is much weaker, revealing a remarkable interhemispheric asymmetry.
Double-blind, randomized pilot clinical trial targeting alpha oscillations with transcranial alternating current stimulation (tACS) for the treatment of major depressive disorder (MDD)
Authors: Alexander Morgan L. , Alagapan Sankaraleengam , Lugo Courtney E. , Mellin Juliann M. , Lustenberger Caroline , Rubinow David R. , Fröhlich Flavio
Published: March 2019

Major depressive disorder (MDD) is one of the most common psychiatric disorders, but pharmacological treatments are ineffective in a substantial fraction of patients and are accompanied by unwanted side effects. Here we evaluated the feasibility and efficacy of transcranial alternating current stimulation (tACS) at 10 Hz, which we hypothesized would improve clinical symptoms by renormalizing alpha oscillations in the left dorsolateral prefrontal cortex (dlPFC). To this end, 32 participants with MDD were randomized to 1 of 3 arms and received daily 40 min sessions of either 10 Hz-tACS, 40 Hz-tACS, or active sham stimulation for 5 consecutive days. Symptom improvement was assessed using the Montgomery–Åsberg Depression Rating Scale (MADRS) as the primary outcome. High-density electroencephalograms (hdEEGs) were recorded to measure changes in alpha oscillations as the secondary outcome. For the primary outcome, we did not observe a significant interaction between treatment condition (10 Hz-tACS, 40 Hz-tACS, sham) and session (baseline to 4 weeks after completion of treatment); however, exploratory analyses show that 2 weeks after completion of the intervention, the 10 Hz-tACS group had more responders (MADRS and HDRS) compared with 40 Hz-tACS and sham groups (n = 30, p = 0.026). Concurrently, we found a significant reduction in alpha power over the left frontal regions in EEG after completion of the intervention for the group that received per-protocol 10 Hz-tACS (n = 26, p < 0.05). Our data suggest that targeting oscillations with tACS has potential as a therapeutic intervention for treatment of MDD.
Correction: Psychiatric disorders in children with 16p11.2 deletion and duplication
Authors: Niarchou Maria , Chawner Samuel J. R. A. , Doherty Joanne L. , Maillard Anne M. , Jacquemont Sébastien , Chung Wendy K. , Green-Snyder LeeAnne , Bernier Raphael A. , Goin-Kochel Robin P. , Hanson Ellen , Linden David E. J. , Linden Stefanie C. , Raymond F. Lucy , Skuse David , Hall Jeremy , Owen Michael J. , van den Bree Marianne B. M.
Published: March 2019

One of the co-authors, Marianne B.M. van den Bree has had her name incorrectly abbreviated by citation manager. It was stated as “Bree MBMVD14”, but has been updated to “van den Bree, M.B.M.” in the HTML, PDF, and XML versions of this article.
Correction: Exploratory genome-wide association analysis of response to ketamine and a polygenic analysis of response to scopolamine in depression
Authors: Guo Wei , Machado-Vieira Rodrigo , Mathew Sanjay , Murrough James W. , Charney Dennis S. , Grunebaum Matthew , Oquendo Maria A. , Kadriu Bashkim , Akula Nirmala , Henter Ioline , Yuan Peixiong , Merikangas Kathleen , Drevets Wayne , Furey Maura , Mann J. John , McMahon Francis J. , Zarate Carlos A. , Shugart Yin Yao
Published: March 2019

Michael F. Grunebaum’s name was misspelled/misstated as “Gruenbaum M.F.” in the original Article. This has now been updated in the HTML and PDF versions of this Article.
A theoretical framework for controlling complex microbial communities
Authors: Angulo Marco Tulio , Moog Claude H. , Liu Yang-Yu
Published: March 2019

Microbes form complex communities that perform critical roles for the integrity of their environment or the well-being of their hosts. Controlling these microbial communities can help us restore natural ecosystems and maintain healthy human microbiota. However, the lack of an efficient and systematic control framework has limited our ability to manipulate these microbial communities. Here we fill this gap by developing a control framework based on the new notion of structural accessibility. Our framework uses the ecological network of the community to identify minimum sets of its driver species, manipulation of which allows controlling the whole community. We numerically validate our control framework on large communities, and then we demonstrate its application for controlling the gut microbiota of gnotobiotic mice infected with Clostridium difficile and the core microbiota of the sea sponge Ircinia oros. Our results provide a systematic pipeline to efficiently drive complex microbial communities towards desired states.
Spontaneous droplets gyrating via asymmetric self-splitting on heterogeneous surfaces
Authors: Li Huizeng , Fang Wei , Li Yanan , Yang Qiang , Li Mingzhu , Li Qunyang , Feng Xi-Qiao , Song Yanlin
Published: March 2019

Droplet impacting and bouncing off solid surface plays a vital role in various biological/physiological processes and engineering applications. However, due to a lack of accurate control of force transmission, the maneuver of the droplet movement and energy conversion is rather primitive. Here we show that the translational motion of an impacting droplet can be converted to gyration, with a maximum rotational speed exceeding 7300 revolutions per minute, through heterogeneous surface wettability regulation. The gyration behavior is enabled by the synergetic effect of the asymmetric pinning forces originated from surface heterogeneity and the excess surface energy of the spreading droplet after impact. The findings open a promising avenue for delicate control of liquid motion as well as actuating of solids.
Genome wide analysis for mouth ulcers identifies associations at immune regulatory loci
Authors: Dudding Tom , Haworth Simon , Lind Penelope A. , Sathirapongsasuti J. Fah ,   23andMe Research Team, Agee Michelle , Alipanahi Babak , Auton Adam , Bell Robert K. , Bryc Katarzyna , Elson Sarah L. , Fontanillas Pierre , Furlotte Nicholas A. , Hicks Barry , Hinds David A. , Huber Karen E. , Jewett Ethan M. , Jiang Yunxuan , Kleinman Aaron , Lin Keng-Han , Litterman Nadia K. , McCeight Jennifer C. , McIntyre Matthew H. , McManus Kimberly F. , Mountain Joanna L. , Noblin Elizabeth S. , Northover Carrie A. M. , Pitts Steven J. , Poznik G. David , Shelton Janie F. , Shringarpure Suyash , Tian Chao , Vacic Vladimir , Wang Xin , Wilson Catherine H. , Tung Joyce Y. , Mitchell Ruth , Colodro-Conde Lucía , Medland Sarah E. , Gordon Scott , Elsworth Benjamin , Paternoster Lavinia , Franks Paul W. , Thomas Steven J. , Martin Nicholas G. , Timpson Nicholas J.
Published: March 2019

Mouth ulcers are the most common ulcerative condition and encompass several clinical diagnoses, including recurrent aphthous stomatitis (RAS). Despite previous evidence for heritability, it is not clear which specific genetic loci are implicated in RAS. In this genome-wide association study (n = 461,106) heritability is estimated at 8.2% (95% CI: 6.4%, 9.9%). This study finds 97 variants which alter the odds of developing non-specific mouth ulcers and replicate these in an independent cohort (n = 355,744) (lead variant after meta-analysis: rs76830965, nearIL12A, OR 0.72 (95% CI: 0.71, 0.73);P = 4.4e−483). Additional effect estimates from three independent cohorts with more specific phenotyping and specific study characteristics support many of these findings. In silico functional analyses provide evidence for a role of T cell regulation in the aetiology of mouth ulcers. These results provide novel insight into the pathogenesis of a common, important condition.
Assessing the causal association of glycine with risk of cardio-metabolic diseases
Authors: Wittemans Laura B. L. , Lotta Luca A. , Oliver-Williams Clare , Stewart Isobel D. , Surendran Praveen , Karthikeyan Savita , Day Felix R. , Koulman Albert , Imamura Fumiaki , Zeng Lingyao , Erdmann Jeanette , Schunkert Heribert , Khaw Kay-Tee , Griffin Julian L. , Forouhi Nita G. , Scott Robert A. , Wood Angela M. , Burgess Stephen , Howson Joanna M. M. , Danesh John , Wareham Nicholas J. , Butterworth Adam S. , Langenberg Claudia
Published: March 2019

Circulating levels of glycine have previously been associated with lower incidence of coronary heart disease (CHD) and type 2 diabetes (T2D) but it remains uncertain if glycine plays an aetiological role. We present a meta-analysis of genome-wide association studies for glycine in 80,003 participants and investigate the causality and potential mechanisms of the association between glycine and cardio-metabolic diseases using genetic approaches. We identify 27 genetic loci, of which 22 have not previously been reported for glycine. We show that glycine is genetically associated with lower CHD risk and find that this may be partly driven by blood pressure. Evidence for a genetic association of glycine with T2D is weaker, but we find a strong inverse genetic effect of hyperinsulinaemia on glycine. Our findings strengthen evidence for a protective effect of glycine on CHD and show that the glycine-T2D association may be driven by a glycine-lowering effect of insulin resistance.
Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression
Authors: Greenwald William W. , Li He , Benaglio Paola , Jakubosky David , Matsui Hiroko , Schmitt Anthony , Selvaraj Siddarth , D’Antonio Matteo , D’Antonio-Chronowska Agnieszka , Smith Erin N. , Frazer Kelly A.
Published: March 2019

While genetic variation at chromatin loops is relevant for human disease, the relationships between contact propensity (the probability that loci at loops physically interact), genetics, and gene regulation are unclear. We quantitatively interrogate these relationships by comparing Hi-C and molecular phenotype data across cell types and haplotypes. While chromatin loops consistently form across different cell types, they have subtle quantitative differences in contact frequency that are associated with larger changes in gene expression and H3K27ac. For the vast majority of loci with quantitative differences in contact frequency across haplotypes, the changes in magnitude are smaller than those across cell types; however, the proportional relationships between contact propensity, gene expression, and H3K27ac are consistent. These findings suggest that subtle changes in contact propensity have a biologically meaningful role in gene regulation and could be a mechanism by which regulatory genetic variants in loop anchors mediate effects on expression.
The Wolbachia mobilome in Culex pipiens includes a putative plasmid
Authors: Reveillaud Julie , Bordenstein Sarah R. , Cruaud Corinne , Shaiber Alon , Esen Özcan C. , Weill Mylène , Makoundou Patrick , Lolans Karen , Watson Andrea R. , Rakotoarivony Ignace , Bordenstein Seth R. , Eren A. Murat
Published: March 2019

Wolbachia is a genus of obligate intracellular bacteria found in nematodes and arthropods worldwide, including insect vectors that transmit dengue, West Nile, and Zika viruses. Wolbachia’s unique ability to alter host reproductive behavior through its temperate bacteriophage WO has enabled the development of new vector control strategies. However, our understanding of Wolbachia’s mobilome beyond its bacteriophages is incomplete. Here, we reconstruct near-complete Wolbachia genomes from individual ovary metagenomes of four wild Culex pipiens mosquitoes captured in France. In addition to viral genes missing from the Wolbachia reference genome, we identify a putative plasmid (pWCP), consisting of a 9.23-kbp circular element with 14 genes. We validate its presence in additional Culex pipiens mosquitoes using PCR, long-read sequencing, and screening of existing metagenomes. The discovery of this previously unrecognized extrachromosomal element opens additional possibilities for genetic manipulation of Wolbachia.
Pure PEDOT:PSS hydrogels
Authors: Lu Baoyang , Yuk Hyunwoo , Lin Shaoting , Jian Nannan , Qu Kai , Xu Jingkun , Zhao Xuanhe
Published: March 2019

Hydrogels of conducting polymers, particularly poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS), provide a promising electrical interface with biological tissues for sensing and stimulation, owing to their favorable electrical and mechanical properties. While existing methods mostly blend PEDOT:PSS with other compositions such as non-conductive polymers, the blending can compromise resultant hydrogels’ mechanical and/or electrical properties. Here, we show that designing interconnected networks of PEDOT:PSS nanofibrils via a simple method can yield high-performance pure PEDOT:PSS hydrogels. The method involves mixing volatile additive dimethyl sulfoxide (DMSO) into aqueous PEDOT:PSS solutions followed by controlled dry-annealing and rehydration. The resultant hydrogels exhibit a set of properties highly desirable for bioelectronic applications, including high electrical conductivity (~20 S cm−1 in PBS, ~40 S cm−1 in deionized water), high stretchability (> 35% strain), low Young’s modulus (~2 MPa), superior mechanical, electrical and electrochemical stability, and tunable isotropic/anisotropic swelling in wet physiological environments.
Author Correction: Indirect tail states formation by thermal-induced polar fluctuations in halide perovskites
Authors: Wu Bo , Yuan Haifeng , Xu Qiang , Steele Julian A. , Giovanni David , Puech Pascal , Fu Jianhui , Ng Yan Fong , Jamaludin Nur Fadilah , Solanki Ankur , Mhaisalkar Subodh , Mathews Nripan , Roeffaers Maarten B. J. , Grätzel Michael , Hofkens Johan , Sum Tze Chien
Published: March 2019

The original version of this article incorrectly listed the present address of Bo Wu as ‘Present address: Institute of Electronic Paper Displays, South China Academy of Advanced Optoelectronics, South China Normal University, Guangzhou, Guangdong Province 510006, China’. This is the author’s primary affiliation. This has been corrected in both the PDF and HTML versions of the article.
PIMKL: Pathway-Induced Multiple Kernel Learning
Authors: Manica Matteo , Cadow Joris , Mathis Roland , Rodríguez Martínez María
Published: March 2019

Reliable identification of molecular biomarkers is essential for accurate patient stratification. While state-of-the-art machine learning approaches for sample classification continue to push boundaries in terms of performance, most of these methods are not able to integrate different data types and lack generalization power, limiting their application in a clinical setting. Furthermore, many methods behave as black boxes, and we have very little understanding about the mechanisms that lead to the prediction. While opaqueness concerning machine behavior might not be a problem in deterministic domains, in health care, providing explanations about the molecular factors and phenotypes that are driving the classification is crucial to build trust in the performance of the predictive system. We propose Pathway-Induced Multiple Kernel Learning (PIMKL), a methodology to reliably classify samples that can also help gain insights into the molecular mechanisms that underlie the classification. PIMKL exploits prior knowledge in the form of a molecular interaction network and annotated gene sets, by optimizing a mixture of pathway-induced kernels using a Multiple Kernel Learning (MKL) algorithm, an approach that has demonstrated excellent performance in different machine learning applications. After optimizing the combination of kernels to predict a specific phenotype, the model provides a stable molecular signature that can be interpreted in the light of the ingested prior knowledge and that can be used in transfer learning tasks.
Succinyl-proteome profiling of Pyricularia oryzae, a devastating phytopathogenic fungus that causes rice blast disease
Authors: Wang Jiaoyu , Li Ling , Chai Rongyao , Zhang Zhen , Qiu Haiping , Mao Xueqin , Hao Zhongna , Wang Yanli , Sun Guochang
Published: March 2019

Pyricularia oryzae is the pathogen for rice blast disease, which is a devastating threat to rice production worldwide. Lysine succinylation, a newly identified post-translational modification, is associated with various cellular processes. Here, liquid chromatography tandem-mass spectrometry combined with a high-efficiency succinyl-lysine antibody was used to identify the succinylated peptides in P. oryzae. In total, 2109 lysine succinylation sites in 714 proteins were identified. Ten conserved succinylation sequence patterns were identified, among which, K*******Ksuc, and K**Ksuc, were two most preferred ones. The frequency of lysine succinylation sites, however, greatly varied among organisms, including plants, animals, and microbes. Interestingly, the numbers of succinylation site in each protein of P. oryzae were significantly greater than that of most previous published organisms. Gene ontology and KEGG analysis showed that these succinylated peptides are associated with a wide range of cellular functions, from metabolic processes to stimuli responses. Further analyses determined that lysine succinylation occurs on several key enzymes of the tricarboxylic acid cycle and glycolysis pathway, indicating that succinylation may play important roles in the regulation of basal metabolism in P. oryzae. Furthermore, more than 40 pathogenicity-related proteins were identified as succinylated proteins, suggesting an involvement of succinylation in pathogenicity. Our results provide the first comprehensive view of the P. oryzae succinylome and may aid to find potential pathogenicity-related proteins to control the rice blast disease. Significance Plant pathogens represent a great threat to world food security, and enormous reduction in the global yield of rice was caused by P. oryzae infection. Here, the succinylated proteins in P. oryzae were identified. Furthermore, comparison of succinylation sites among various species, indicating that different degrees of succinylation may be involved in the regulation of basal metabolism. This data facilitates our understanding of the metabolic pathways and proteins that are associated with pathogenicity.
Lissajous Scanning Two-photon Endomicroscope for In vivo Tissue Imaging
Authors: Kim Daniel Youngsuk , Hwang Kyungmin , Ahn Jinhyo , Seo Yeong-Hyeon , Kim Jae-Beom , Lee Soyoung , Yoon Jin-Hui , Kong Eunji , Jeong Yong , Jon Sangyong , Kim Pilhan , Jeong Ki-Hun
Published: March 2019

An endomicroscope opens new frontiers of non-invasive biopsy for in vivo imaging applications. Here we report two-photon laser scanning endomicroscope for in vivo cellular and tissue imaging using a Lissajous fiber scanner. The fiber scanner consists of a piezoelectric (PZT) tube, a single double-clad fiber (DCF) with high fluorescence collection, and a micro-tethered-silicon-oscillator (MTSO) for the separation of biaxial resonant scanning frequencies. The endomicroscopic imaging exhibits 5 frames/s with 99% in scanning density by using the selection rule of scanning frequencies. The endomicroscopic scanner was compactly packaged within a stainless tube of 2.6 mm in diameter with a high NA gradient-index (GRIN) lens, which can be easily inserted into the working channel of a conventional laparoscope. The lateral and axial resolutions of the endomicroscope are 0.70 µm and 7.6 μm, respectively. Two-photon fluorescence images of a stained kidney section and miscellaneous ex vivo and in vivo organs from wild type and green fluorescent protein transgenic (GFP-TG) mice were successfully obtained by using the endomicroscope. The endomicroscope also obtained label free images including autofluorescence and second-harmonic generation of an ear tissue of Thy1-GCaMP6 (GP5.17) mouse. The Lissajous scanning two-photon endomicroscope can provide a compact handheld platform for in vivo tissue imaging or optical biopsy applications.
miR-124 dosage regulates prefrontal cortex function by dopaminergic modulation
Authors: Kozuka Takashi , Omori Yoshihiro , Watanabe Satoshi , Tarusawa Etsuko , Yamamoto Haruka , Chaya Taro , Furuhashi Mayu , Morita Makiko , Sato Tetsuya , Hirose Shinichi , Ohkawa Yasuyuki , Yoshimura Yumiko , Hikida Takatoshi , Furukawa Takahisa
Published: March 2019

MicroRNA-124 (miR-124) is evolutionarily highly conserved among species and one of the most abundantly expressed miRNAs in the developing and mature central nervous system (CNS). Previous studies reported that miR-124 plays a role in CNS development, such as neuronal differentiation, maturation, and survival. However, the role of miR-124 in normal brain function has not yet been revealed. Here, we subjected miR-124-1+/− mice, to a comprehensive behavioral battery. We found that miR-124-1+/− mice showed impaired prepulse inhibition (PPI), methamphetamine-induced hyperactivity, and social deficits. Whole cell recordings using prefrontal cortex (PFC) slices showed enhanced synaptic transmission in layer 5 pyramidal cells in the miR-124-1+/− PFC. Based on the results of behavioral and electrophysiological analysis, we focused on genes involved in the dopaminergic system and identified a significant increase of Drd2 expression level in the miR-124-1+/− PFC. Overexpression or knockdown of Drd2 in the control or miR-124-1+/− PFC demonstrates that aberrant Drd2 signaling leads to impaired PPI. Furthermore, we identified that expression of glucocorticoid receptor gene Nr3c1, which enhances Drd2 expression, increased in the miR-124-1+/− PFC. Taken together, the current study suggests that miR-124 dosage modulates PFC function through repressing the Drd2 pathway, suggesting a critical role of miR-124 in normal PFC function.
PLD-dependent phosphatidic acid microdomains are signaling platforms for podosome formation
Authors: Bolomini-Vittori Matteo , Mennens Svenja F. B. , Joosten Ben , Fransen Jack , Du Guangwei , van den Dries Koen , Cambi Alessandra
Published: March 2019

Local membrane phospholipid enrichment serves as docking platform for signaling proteins involved in many processes including cell adhesion and migration. Tissue-resident dendritic cells (DCs) assemble actomyosin-based structures called podosomes, which mediate adhesion and degradation of extracellular matrix for migration and antigen sampling. Recent evidence suggested the involvement of phospholipase D (PLD) and its product phosphatidic acid (PA) in podosome formation, but the spatiotemporal control of this process is poorly characterized. Here we determined the role of PLD1 and PLD2 isoforms in regulating podosome formation and dynamics in human primary DCs by combining PLD pharmacological inhibition with a fluorescent PA sensor and fluorescence microscopy. We found that ongoing PLD2 activity is required for the maintenance of podosomes, whereas both PLD1 and PLD2 control the early stages of podosome assembly. Furthermore, we captured the formation of PA microdomains accumulating at the membrane cytoplasmic leaflet of living DCs, in dynamic coordination with nascent podosome actin cores. Finally, we show that both PLD1 and PLD2 activity are important for podosome-mediated matrix degradation. Our results provide novel insight into the isoform-specific spatiotemporal regulation of PLD activity and further our understanding of the role of cell membrane phospholipids in controlling localized actin polymerization and cell protrusion.
Dynamic plant height QTL revealed in maize through remote sensing phenotyping using a high-throughput unmanned aerial vehicle (UAV)
Authors: Wang Xiaqing , Zhang Ruyang , Song Wei , Han Liang , Liu Xiaolei , Sun Xuan , Luo Meijie , Chen Kuan , Zhang Yunxia , Yang Hao , Yang Guijun , Zhao Yanxin , Zhao Jiuran
Published: March 2019

Plant height (PH) is a key factor in maize (Zea maysL.) yield, biomass, and plant architecture. We investigated the PH of diverse maize inbred lines (117 temperate lines, 135 tropical lines) at four growth stages using unmanned aerial vehicle high-throughput phenotypic platforms (UAV-HTPPs). We extracted PH data using an automated pipeline based on crop surface models and orthomosaic model. The correlation between UAV and manually measured PH data reached 0.95. Under temperate field conditions, temperate maize lines grew faster than tropical maize lines at early growth stages, but tropical lines grew faster at later growth stages and ultimately became taller than temperate lines. A genome-wide association study identified 68 unique quantitative trait loci (QTLs) for seven PH-related traits, and 35% of the QTLs coincided with those previously reported to control PH. Generally, different QTLs controlled PH at different growth stages, but eight QTLs simultaneously controlled PH and growth rate at multiple growth stages. Based on gene annotations and expression profiles, we identified candidate genes controlling PH. The PH data collected by the UAV-HTPPs were credible and the genetic mapping power was high. Therefore, UAV-HTPPs have great potential for use in studies on PH.
Partially spatially coherent digital holographic microscopy and machine learning for quantitative analysis of human spermatozoa under oxidative stress condition
Authors: Dubey Vishesh , Popova Daria , Ahmad Azeem , Acharya Ganesh , Basnet Purusotam , Mehta Dalip Singh , Ahluwalia Balpreet Singh
Published: March 2019

Semen quality assessed by sperm count and sperm cell characteristics such as morphology and motility, is considered to be the main determinant of men’s reproductive health. Therefore, sperm cell selection is vital in assisted reproductive technology (ART) used for the treatment of infertility. Conventional bright field optical microscopy is widely utilized for the imaging and selection of sperm cells based on the qualitative analysis by experienced clinicians. In this study, we report the development of a highly sensitive quantitative phase microscopy (QPM) using partially spatially coherent light source, which is a label-free, non-invasive and high-resolution technique to quantify various biophysical parameters. The partial spatial coherence nature of light source provides a significant improvement in spatial phase sensitivity and hence reconstruction of the phase of the entire sperm cell is demonstrated, which was otherwise not possible using highly spatially coherent light source. High sensitivity of the system enables quantitative phase imaging of the specimens having very low refractive index contrast with respect to the medium like tail of the sperm cells. Further, it also benefits with accurate quantification of 3D-morphological parameters of sperm cells which might be helpful in the infertility treatment. The quantitative analysis of more than 2500 sperm cells under hydrogen peroxide (H2O2) induced oxidative stress condition is demonstrated. It is further correlated with motility of sperm cell to study the effect of oxidative stress on healthy sperm cells. The results exhibit a decrease in the maximum phase values of the sperm head as well as decrease in the sperm cell’s motility with increasing oxidative stress, i.e., H2O2concentration. Various morphological and texture parameters were extracted from the phase maps and subsequently support vector machine (SVM) based machine learning algorithm is employed for the classification of the control and the stressed sperms cells. The algorithm achieves an area under the receiver operator characteristic (ROC) curve of 89.93% based on the all morphological and texture parameters with a sensitivity of 91.18%. The proposed approach can be implemented for live sperm cells selection in ART procedure for the treatment of infertility.
The 1997 Mars Pathfinder Spacecraft Landing Site: Spillover Deposits from an Early Mars Inland Sea
Authors: Rodriguez J. A. P. , Baker V. R. , Liu T. , Zarroca M. , Travis B. , Hui T. , Komatsu G. , Berman D. C. , Linares R. , Sykes M. V. , Banks M. E. , Kargel J. S.
Published: March 2019

The Martian outflow channels comprise some of the largest known channels in the Solar System. Remote-sensing investigations indicate that cataclysmic floods likely excavated the channels ~3.4 Ga. Previous studies show that, in the southern circum-Chryse region, their flooding pathways include hundreds of kilometers of channel floors with upward gradients. However, the impact of the reversed channel-floor topography on the cataclysmic floods remains uncertain. Here, we show that these channel floors occur within a vast basin, which separates the downstream reaches of numerous outflow channels from the northern plains. Consequently, floods propagating through these channels must have ponded, producing an inland sea, before reaching the northern plains as enormous spillover discharges. The resulting paleohydrological reconstruction reinterprets the 1997 Pathfinder landing site as part of a marine spillway, which connected the inland sea to a hypothesized northern plains ocean. Our flood simulation shows that the presence of the sea would have permitted the propagation of low-depth floods beyond the areas of reversed channel-floor topography. These results explain the formation at the landing site of possible fluvial features indicative of flow depths at least an order of magnitude lower than those apparent from the analyses of orbital remote-sensing observations.
Wide-field choroidal thickness in myopes and emmetropes
Authors: Hoseini-Yazdi Hosein , Vincent Stephen J. , Collins Michael J. , Read Scott A. , Alonso-Caneiro David
Published: March 2019

There is a paucity of knowledge regarding the normal in-vivo thickness of the choroid beyond the macula (~17°). In this study, the choroidal thickness of 27 healthy young adults was examined across the macular (the central 5 mm including the fovea, parafovea, and perifovea) and extra-macular (a 5–14 mm annulus including the near-periphery and periphery) regions using wide-field optical coherence tomography, and compared between emmetropes (n = 14) and myopes (n = 13). The choroid progressively thinned beyond the parafovea (350 ± 86 µm) towards the periphery (264 ± 44 µm), and was thickest superiorly (355 ± 76 µm) and thinnest nasally (290 ± 79 µm). Choroidal thickness also varied with refractive error; myopes exhibited a thinner choroid than emmetropes in the macular region (311 ± 88 vs. 383 ± 66 µm), however, this difference diminished towards the periphery (251 ± 48 vs. 277 ± 37 µm). Meridional variations in choroidal thickness were not different between myopes and emmetropes. In conclusion, the choroid was thickest within the perifovea; thinned substantially towards the periphery, and exhibited the minimum and maximum peripheral thinning superiorly and nasally across a 55° region respectively. Choroidal thinning associated with myopia was more pronounced in the macular than extra-macular regions.