bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relating retinal blood flow and vessel morphology in sickle cell retinopathy
Authors: Cano Jennifer , Farzad Shayan , Khansari Maziyar M. , Tan Ou , Huang David , Lim Jennifer I. , Shahidi Mahnaz 
Published: September 2019

Abstract
Purpose
The purpose of the current study was to determine associations between retinal blood flow and vessel morphology metrics in sickle cell retinopathy (SCR) and healthy normal control (NC) subjects.

Methods
Optical coherence tomography angiography (OCTA) and Doppler OCT imaging were performed in 12 SCR (15 eyes) and 19 NC (26 eyes) subjects. Vessel tortuosity was measured using a dedicated image analysis algorithm applied to OCTA images. Vessel density and spacing between vessels were determined from OCTA images by a fractal dimension analysis method. Retinal blood flow was quantified using a phase-resolved technique applied to en face Doppler OCT images.

Results
There was a significant association between increased retinal blood flow and increased vessel tortuosity (P = 0.03). Furthermore, increased retinal blood flow was associated with increased vessel density (P = 0.03) and decreased spacing between small vessels (P = 0.01). There was no significant association between retinal blood flow and spacing between large vessels (P = 0.11). Vessel tortuosity and blood flow were increased, whereas spacing between small vessels was decreased in SCR compared to NC group (P ≤ 0.03). There were no significant differences in vessel density or spacing between large vessels between the SCR and NC groups (P ≥ 0.31).

Conclusions
Associations between retinal hemodynamics and vessel morphology were reported, providing better understanding of retinal pathophysiology and insight into potential quantitative biomarkers to evaluate SCR.
The hidden structure of human enamel
Authors: Beniash Elia , Stifler Cayla A. , Sun Chang-Yu , Jung Gang Seob , Qin Zhao , Buehler Markus J. , Gilbert Pupa U. P. A. 
Published: September 2019

AbstractEnamel is the hardest and most resilient tissue in the human body. Enamel includes morphologically aligned, parallel, ∼50 nm wide, microns-long nanocrystals, bundled either into 5-μm-wide rods or their space-filling interrod. The orientation of enamel crystals, however, is poorly understood. Here we show that the crystalline c-axes are homogenously oriented in interrod crystals across most of the enamel layer thickness. Within each rod crystals are not co-oriented with one another or with the long axis of the rod, as previously assumed: the c-axes of adjacent nanocrystals are most frequently mis-oriented by 1°–30°, and this orientation within each rod gradually changes, with an overall angle spread that is never zero, but varies between 30°–90° within one rod. Molecular dynamics simulations demonstrate that the observed mis-orientations of adjacent crystals induce crack deflection. This toughening mechanism contributes to the unique resilience of enamel, which lasts a lifetime under extreme physical and chemical challenges.
Possible role of L-form switching in recurrent urinary tract infection
Authors: Mickiewicz Katarzyna M. , Kawai Yoshikazu , Drage Lauren , Gomes Margarida C. , Davison Frances , Pickard Robert , Hall Judith , Mostowy Serge , Aldridge Phillip D. , Errington Jeff 
Published: September 2019

AbstractRecurrent urinary tract infection (rUTI) is a major medical problem, especially in the elderly and infirm, but the nature of the reservoir of organisms responsible for survival and recolonisation after antibiotic treatment in humans is unclear. Here, we demonstrate the presence of cell-wall deficient (L-form) bacteria in fresh urine from 29 out of 30 older patients with rUTI. In urine, E. coli strains from patient samples readily transition from the walled state to L-form during challenge with a cell wall targeting antibiotic. Following antibiotic withdrawal, they then efficiently transition back to the walled state. E. coli switches between walled and L-form states in a zebrafish larva infection model. The results suggest that L-form switching is a physiologically relevant phenomenon that may contribute to the recurrence of infection in older patients with rUTI, and potentially other infections.
Multiplexed and high-throughput neuronal fluorescence imaging with diffusible probes
Authors: Guo Syuan-Ming , Veneziano Remi , Gordonov Simon , Li Li , Danielson Eric , Perez de Arce Karen , Park Demian , Kulesa Anthony B. , Wamhoff Eike-Christian , Blainey Paul C. , Boyden Edward S. , Cottrell Jeffrey R. , Bathe Mark 
Published: September 2019

AbstractSynapses contain hundreds of distinct proteins whose heterogeneous expression levels are determinants of synaptic plasticity and signal transmission relevant to a range of diseases. Here, we use diffusible nucleic acid imaging probes to profile neuronal synapses using multiplexed confocal and super-resolution microscopy. Confocal imaging is performed using high-affinity locked nucleic acid imaging probes that stably yet reversibly bind to oligonucleotides conjugated to antibodies and peptides. Super-resolution PAINT imaging of the same targets is performed using low-affinity DNA imaging probes to resolve nanometer-scale synaptic protein organization across nine distinct protein targets. Our approach enables the quantitative analysis of thousands of synapses in neuronal culture to identify putative synaptic sub-types and co-localization patterns from one dozen proteins. Application to characterize synaptic reorganization following neuronal activity blockade reveals coordinated upregulation of the post-synaptic proteins PSD-95, SHANK3 and Homer-1b/c, as well as increased correlation between synaptic markers in the active and synaptic vesicle zones.
The Chinese public’s awareness and attitudes toward genetically modified foods with different labeling
Authors: Zhao Yawei , Deng Haiyan , Yu Changxin , Hu Ruifa 
Published: September 2019

AbstractsThis paper analyzes the awareness and attitudes of the Chinese public toward genetically modified (GM) foods with different types of labeling and evaluates the impact of public confidence in the government management of GM food labeling has on their attitude. From 2015 to 2016, we conducted a series of surveys to collect data from 1730 respondents, which included consumers, farmers, media, and local agricultural officials in agricultural departments. The results show ~60% of the Chinese public do not know that they usually consume or purchase GM products or products containing GM ingredients. Nearly 80% of the Chinese public are accepting foods labeled as not containing GM ingredients, 57% are accepting foods without labeling, and ~40% are accepting GM-labeled foods. The respondents with a lack of confidence in the government are less likely to embrace GM foods. Those that are more aware of GM products are more likely to accept GM labeled foods. The group having the most positive attitude toward GM-labeled foods is the media, followed by agricultural officials, while the group having the most negative attitude toward GM labeled foods is farmers. Our findings provide an empirical basis to inform GM food labeling policy discussions and possible revisions, which may promote the development of GM foods in China.
Oxytocin modulates the temporal dynamics of resting EEG networks
Authors: Schiller Bastian , Koenig Thomas , Heinrichs Markus 
Published: September 2019

AbstractOxytocin is a key modulator of social interaction, but we possess little knowledge of its underlying effects on neuropsychological processes. We used a spatio-temporal EEG microstates analysis to reveal oxytocin’s effects on the temporal dynamics of intrinsically generated activity in neural networks. Given oxytocin’s known anxiolytic effects, we hypothesized that it increases the temporal stability of the four archetypal EEG resting networks. Eighty-six male participants had received oxytocin or placebo intranasally before we recorded their resting EEG. As hypothesized, oxytocin globally increased the average duration of the four archetypal resting networks and specifically decreased the occurrence and coverage of an autonomic processing-related network to benefit greater coverage of an attention-related network. Moreover, these neurophysiological changes were more pronounced in participants with high anxiety levels and strong subjectively experienced effects of the oxytocin administration. In sum, our study shows that oxytocin reduces rapid switching among neural resting networks by increasing their temporal stability. Specifically, it seems to reduce the brain’s need for preparing the internally-oriented processing of autonomic information, thus enabling the externally-oriented processing of social information. Changes in the temporal dynamics of resting networks might underlie oxytocin’s anxiolytic effects - potentially informing innovative psychobiological treatment strategies.
RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat
Authors: Iquebal Mir Asif , Sharma Pradeep , Jasrotia Rahul Singh , Jaiswal Sarika , Kaur Amandeep , Saroha Monika , Angadi U. B. , Sheoran Sonia , Singh Rajender , Singh G. P. , Rai Anil , Tiwari Ratan , Kumar Dinesh 
Published: September 2019

AbstractDrought is one of the major impediments in wheat productivity. Traditional breeding and marker assisted QTL introgression had limited success. Available wheat genomic and RNA-seq data can decipher novel drought tolerance mechanisms with putative candidate gene and marker discovery. Drought is first sensed by root tissue but limited information is available about how roots respond to drought stress. In this view, two contrasting genotypes, namely, NI5439 41 (drought tolerant) and WL711 (drought susceptible) were used to generate ~78.2 GB data for the responses of wheat roots to drought. A total of 45139 DEGs, 13820 TF, 288 miRNAs, 640 pathways and 435829 putative markers were obtained. Study reveals use of such data in QTL to QTN refinement by analysis on two model drought-responsive QTLs on chromosome 3B in wheat roots possessing 18 differentially regulated genes with 190 sequence variants (173 SNPs and 17 InDels). Gene regulatory networks showed 69 hub-genes integrating ABA dependent and independent pathways controlling sensing of drought, root growth, uptake regulation, purine metabolism, thiamine metabolism and antibiotics pathways, stomatal closure and senescence. Eleven SSR markers were validated in a panel of 18 diverse wheat varieties. For effective future use of findings, web genomic resources were developed. We report RNA-Seq approach on wheat roots describing the drought response mechanisms under field drought conditions along with genomic resources, warranted in endeavour of wheat productivity.
Network-based Responses to the Psychomotor Vigilance Task during Lapses in Adolescents after Short and Extended Sleep
Authors: DiFrancesco M. W. , Van Dyk T. , Altaye M. , Drummond S. P. A. , Beebe D. W. 
Published: September 2019

AbstractNeuroimaging studies of the Psychomotor Vigilance Task (PVT) have revealed brain regions involved in attention lapses in sleep-deprived and well-rested adults. Those studies have focused on individual brain regions, rather than integrated brain networks, and have overlooked adolescence, a period of ongoing brain development and endemic short sleep. This study used functional MRI (fMRI) and a contemporary analytic approach to assess time-resolved peri-stimulus response of key brain networks when adolescents complete the PVT, and test for differences across attentive versus inattentive periods and after short sleep versus well-rested states. Healthy 14–17-year-olds underwent a within-subjects randomized protocol including 5-night spans of extended versus short sleep. PVT was performed during fMRI the morning after each sleep condition. Event-related independent component analysis (eICA) identified coactivating functional networks and corresponding time courses. Analysis of salient time course characteristics tested the effects of sleep condition, lapses, and their interaction. Seven eICA networks were identified supporting attention, executive control, motor, visual, and default-mode functions. Attention lapses, after either sleep manipulation, were accompanied by broadly increased response magnitudes post-stimulus and delayed peak responses in some networks. Well-circumscribed networks respond during the PVT in adolescents, with timing and intensity impacted by attentional lapses regardless of experimentally shortened or extended sleep.
Systematic Analysis of Pigeons’ Discrimination of Pixelated Stimuli: A Hierarchical Pattern Recognition System Is Not Identifiable
Authors: Delius Juan D. , Delius Julia A. M. 
Published: September 2019

AbstractPigeons learned to discriminate two different patterns displayed with miniature light-emitting diode arrays. They were then tested with 84 interspersed, non-reinforced degraded pattern pairs. Choices ranged between 100% and 50% for one or other of the patterns. Stimuli consisting of few pixels yielded low choice scores whereas those consisting of many pixels yielded a broad range of scores. Those patterns with a high number of pixels coinciding with those of the rewarded training stimulus were preferred and those with a high number of pixels coinciding with the non-rewarded training pattern were avoided; a discrimination index based on this correlated 0.74 with the pattern choices. Pixels common to both training patterns had a minimal influence. A pixel-by-pixel analysis revealed that eight pixels of one pattern and six pixels of the other pattern played a prominent role in the pigeons’ choices. These pixels were disposed in four and two clusters of neighbouring locations. A summary index calculated on this basis still only yielded a weak 0.73 correlation. The individual pigeons’ data furthermore showed that these clusters were a mere averaging mirage. The pigeons’ performance depends on deep learning in a midbrain-based multimillion synapse neuronal network. Pixelated visual patterns should be helpful when simulating perception of patterns with artificial networks.
Migratory strategies of juvenile northern fur seals (Callorhinus ursinus): bridging the gap between pups and adults
Authors: Zeppelin Tonya , Pelland Noel , Sterling Jeremy , Brost Brian , Melin Sharon , Johnson Devin , Lea Mary-Anne , Ream Rolf 
Published: September 2019

AbstractIn species exhibiting differential migration by sex and age, understanding what differences exist, and the adaptive reasons for these differences is critical for determining how demographic groups will respond to environmental variability and anthropogenic perturbations. We used satellite-telemetered movement and diving data to investigate differential migration and its ontogeny in a highly migratory North Pacific Ocean predator, the northern fur seal (Callorhinus ursinus; NFS), with a focus on understudied juvenile (1- to 2-year-old) animals. We instrumented 71 juvenile NFS in two years (2006–07 and 2007–08) at three major North American breeding sites and compared their migratory strategies with pups and adults. Although sexual dimorphism is strong in adult NFS, only weak differences in body mass between sexes were found in juveniles, which had similar body mass to pups (~3–4 months). However, unlike widely-dispersed pups, juvenile male and female NFS dispersed in different directions, and used different habitats characterized by distinct hydrography and prey assemblages during migration, similar to breeding adults. Juvenile diving behavior differed only modestly among habitats and between sexes, consistent with weak differences in body mass. Evidence of habitat sexual segregation by juvenile NFS contradicts previous hypotheses that physiological differences predominantly drive the ontogeny of differential migration.
Vegetation dynamics in Alpine glacier forelands tackled from space
Authors: Fischer Andrea , Fickert Thomas , Schwaizer Gabriele , Patzelt Gernot , Groß Günther 
Published: September 2019

AbstractMonitoring of plant succession in glacier forelands has so far been restricted to field sampling. In this study, in situ vegetation sampling along a chronosequence between Little Ice Age (LIA) maximum extent and the recent glacier terminus at Jamtalferner in the Austrian Alps is compared to time series of the Normalized Difference Vegetation Index (NDVI) calculated from 13 Landsat scenes (1985–2016). The glacier terminus positions at 16 dates between the LIA maximum and 2015 were analysed from historical maps, orthophotos and LiDAR images. We sampled plots of different ages since deglaciation, from very recent to approx. 150 years: after 100 years, roughly 80% of the ground is covered by plants and ground cover does not increase significantly thereafter. The number of species increases from 10–20 species on young sites to 40–50 species after 100 years. The NDVI increases with the time of exposure from a mean of 0.11 for 1985–1991 to 0.20 in 2009 and 0.27 in 2016. As the increase in ground cover is clearly reproduced by the NDVI (R² ground cover/NDVI 0.84) – even for sparsely vegetated areas –, we see a great potential of satellite-borne NDVI to perform regional characterizations of glacier forelands for hydrological, ecological and hazard management-related applications.
Responses of neurons in the rat’s inferior colliculus to a sound are affected by another sound in a space-dependent manner
Authors: Chot Mathiang G. , Tran Sarah , Zhang Huiming 
Published: September 2019

AbstractThe perception of a sound can be influenced by another sound in a space-dependent manner. An understanding of this perceptual phenomenon depends on knowledge about how the spatial relationship between two sounds affects neural responses to the sounds. We used the rat as a model system and equal-probability two-tone sequences as stimuli to evaluate how spatial separation between two asynchronously recurring sounds affected responses to the sounds in midbrain auditory neurons. We found that responses elicited by two tone bursts when they were colocalized at the ear contralateral to the neuron were different from the responses elicited by the same sounds when they were separated with one at the contralateral ear while the other at another location. For neurons with transient sound-driven firing and not responsive to stimulation presented at the ipsilateral ear, the response to a sound with a fixed location at the contralateral ear was enhanced when the second sound was separated. These neurons were likely important for detecting a sound in the presence of a spatially separated competing sound. Our results suggest that mechanisms underlying effects of spatial separation on neural responses to sounds may include adaptation and long-lasting binaural excitatory/inhibitory interaction.
Protein quantification and visualization via ultraviolet-dependent labeling with 2,2,2-trichloroethanol
Authors: Chopra Anand , Willmore William G. , Biggar Kyle K. 
Published: September 2019

AbstractThe incorporation of 2,2,2-trichloroethanol in polyacrylamide gels allows for fluorescent visualization of proteins following electrophoresis. Ultraviolet-light exposure, in the presence of this trichlorinated compound, results in a covalent modification of the tryptophan indole ring that shifts the fluorescent emission into the visible range. Based on this principle, we used 2,2,2-trichloroethanol to develop a microplate format protein quantification assay based on the fluorescent signal generated by modified proteins. We also demonstrated a specific fluorescent emission of 2,2,2-trichloroethanol-labeled protein at 450 nm, with a 310 nm excitation, resulting from modification of both tryptophan and tyrosine residues. Following optimization, this protein quantification assay displayed superior sensitivity when compared to UV absorbance at 280 nm (A280), and enabled quantification beyond the linear range permitted by the Bradford method. This 100 μL assay displayed a sensitivity of 10.5 μg in a range up to at least 200 μg. Furthermore, we extended the utility of this method through the development of a 20 μL low-volume assay, with a sensitivity of 8.7 μg tested up to 100 μg, which enabled visualization of proteins following SDS-PAGE. Collectively, these results demonstrate the utility of 2,2,2-trichloroethanol-based protein quantification and demonstrates the protein visualization in polyacrylamide gels based on 2,2,2-trichloroethanol-labeling pre-electrophoresis.
The influence of heterogeneous learning ability on the evolution of cooperation
Authors: Li Xiaogang , Geng Yini , Shen Chen , Shi Lei 
Published: September 2019

AbstractIn this paper, we design a simple coevolution model to investigate the role of heterogeneous learning ability on the evolution of cooperation. The model weakens the winner’s learning ability in order to keep its current advantage. Conversely, it strengthens the loser’s learning ability for increasing the chance to update its strategy. In particular, we consider this coevolutionary model separately applying to both cooperators and defectors (rule I), only cooperators (rule II), as well as only defectors (rule III) in spatial prisoner’s dilemma game. Through numerical simulations, we find that cooperation can be promoted in rule II, whereas, cooperation is hampered in rule I and rule III. We reveal its potential reason from the viewpoint of enduring and expanding periods in game dynamics. Our results thus provide a deeper understanding regarding the heterogeneous learning ability on game theory.
Overshooting in simulations of compressible convection
Authors: Käpylä P. J. 
Published: September 2019

Context.Convective motions that overshoot into regions that are formally convectively stable cause extended mixing.Aims.We aim to determine the scaling of the overshooting depth (dos) at the base of the convection zone as a function of imposed energy flux (ℱn) and to estimate the extent of overshooting at the base of the solar convection zone.Methods.Three-dimensional Cartesian simulations of hydrodynamic compressible non-rotating convection with unstable and stable layers were used. The simulations used either a fixed heat conduction profile or a temperature- and density-dependent formulation based on Kramers opacity law. The simulations covered a range of almost four orders of magnitude in the imposed flux, and the sub-grid scale diffusivities were varied so as to maintain approximately constant supercriticality at each flux.Results.A smooth heat conduction profile (either fixed or through Kramers opacity law) leads to a relatively shallow power law withdos∝ ℱn0.08for low ℱn. A fixed step-profile of the heat conductivity at the bottom of the convection zone leads to a somewhat steeper dependency ondos∝ ℱn0.12in the same regime. Experiments with and without subgrid-scale entropy diffusion revealed a strong dependence on the effective Prandtl number, which is likely to explain the steep power laws as a function of ℱnreported in the literature. Furthermore, changing the heat conductivity artificially in the radiative and overshoot layers to speed up thermal saturation is shown to lead to a substantial underestimation of the overshooting depth.Conclusions.Extrapolating from the results obtained with smooth heat conductivity profiles, which are the most realistic set-up we considered, suggest that the overshooting depth for the solar energy flux is about 20% of the pressure scale height at the base of the convection zone. This is two to four times higher than the estimates from helioseismology. However, the current simulations do not include rotation or magnetic fields, which are known to reduce convective overshooting.