bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrically-tunable positioning of topological defects in liquid crystals
Authors: Sandford O’Neill John J. , Salter Patrick S. , Booth Martin J. , Elston Steve J. , Morris Stephen M. 
Published: May 2020

AbstractTopological defects are a consequence of broken symmetry in ordered systems and are important for understanding a wide variety of phenomena in physics. In liquid crystals (LCs), defects exist as points of discontinuous order in the vector field that describes the average orientation of the molecules in space and are crucial for explaining the fundamental behaviour and properties of these mesophases. Recently, LC defects have also been explored from the perspective of technological applications including self-assembly of nanomaterials, optical-vortex generation and in tunable plasmonic metamaterials. Here, we demonstrate the fabrication and stabilisation of electrically-tunable defects in an LC device using two-photon polymerisation and explore the dynamic behaviour of defects when confined by polymer structures laser-written in topologically discontinuous states. We anticipate that our defect fabrication technique will enable the realisation of tunable, 3D, reconfigurable LC templates towards nanoparticle self-assembly, tunable metamaterials and next-generation spatial light modulators for light-shaping.
Completing density functional theory by machine learning hidden messages from molecules
Authors: Nagai Ryo , Akashi Ryosuke , Sugino Osamu 
Published: May 2020

AbstractKohn–Sham density functional theory (DFT) is the basis of modern computational approaches to electronic structures. Their accuracy heavily relies on the exchange-correlation energy functional, which encapsulates electron–electron interaction beyond the classical model. As its universal form remains undiscovered, approximated functionals constructed with heuristic approaches are used for practical studies. However, there are problems in their accuracy and transferability, while any systematic approach to improve them is yet obscure. In this study, we demonstrate that the functional can be systematically constructed using accurate density distributions and energies in reference molecules via machine learning. Surprisingly, a trial functional machine learned from only a few molecules is already applicable to hundreds of molecules comprising various first- and second-row elements with the same accuracy as the standard functionals. This is achieved by relating density and energy using a flexible feed-forward neural network, which allows us to take a functional derivative via the back-propagation algorithm. In addition, simply by introducing a nonlocal density descriptor, the nonlocal effect is included to improve accuracy, which has hitherto been impractical. Our approach thus will help enrich the DFT framework by utilizing the rapidly advancing machine-learning technique.
Observation of grating diffraction radiation at the KEK LUCX facility
Authors: Aryshev A. , Potylitsyn A. P. , Naumenko G. A. , Shevelev M. , Shkitov D. , Sukhikh L. G. , Terunuma N. , Urakawa J. 
Published: May 2020

AbstractThe development of linac–based narrow–band THz sources with sub–picosecond, $$\mu J$$
μ
J
-level radiation pulses is in demand from the scientific community. Intrinsically monochromatic emitters such as coherent Smith–Purcell radiation sources appear as natural candidates. However, the lack of broad spectral tunability continues to stimulate active research in this field. We hereby present the first experimental investigation of coherent grating diffraction radiation (GDR), for which comparable radiation intensity with central frequency fine–tuning in a much wider spectral range has been confirmed. Additionally, the approach allows for bandwidth selection at the same central frequency. The experimental validation of performance included the basic spectral, spatial and polarization properties. The discussion of the comparison between GDR intensity and other coherent radiation sources is also presented. These results further strengthen the foundation for the design of a tabletop wide–range tunable quasi–monochromatic or multi–colour radiation source in the GHz–THz frequency range.
Multivoxel Pattern of Blood Oxygen Level Dependent Activity can be sensitive to stimulus specific fine scale responses
Authors: Vizioli Luca , De Martino Federico , Petro Lucy S. , Kersten Daniel , Ugurbil Kamil , Yacoub Essa , Muckli Lars 
Published: May 2020

AbstractAt ultra-high field, fMRI voxels can span the sub-millimeter range, allowing the recording of blood oxygenation level dependent (BOLD) responses at the level of fundamental units of neural computation, such as cortical columns and layers. This sub-millimeter resolution, however, is only nominal in nature as a number of factors limit the spatial acuity of functional voxels. Multivoxel Pattern Analysis (MVPA) may provide a means to detect information at finer spatial scales that may otherwise not be visible at the single voxel level due to limitations in sensitivity and specificity. Here, we evaluate the spatial scale of stimuli specific BOLD responses in multivoxel patterns exploited by linear Support Vector Machine, Linear Discriminant Analysis and Naïve Bayesian classifiers across cortical depths in V1. To this end, we artificially misaligned the testing relative to the training portion of the data in increasing spatial steps, then investigated the breakdown of the classifiers’ performances. A one voxel shift led to a significant decrease in decoding accuracy (p < 0.05) across all cortical depths, indicating that stimulus specific responses in a multivoxel pattern of BOLD activity exploited by multivariate decoders can be as precise as the nominal resolution of single voxels (here 0.8 mm isotropic). Our results further indicate that large draining vessels, prominently residing in proximity of the pial surface, do not, in this case, hinder the ability of MVPA to exploit fine scale patterns of BOLD signals. We argue that tailored analytical approaches can help overcoming limitations in high-resolution fMRI and permit studying the mesoscale organization of the human brain with higher sensitivities.
Geophysical monitoring of simulated homicide burials for forensic investigations
Authors: Pringle Jamie K. , Stimpson Ian G. , Wisniewski Kristopher D. , Heaton Vivienne , Davenward Ben , Mirosch Natalie , Spencer Francesca , Jervis Jon R. 
Published: May 2020

AbstractFinding hidden bodies, believed to have been murdered and buried, is problematic, expensive in terms of human resource and currently has low success rates for law enforcement agencies. Here we present, for the first time, ten years of multidisciplinary geophysical monitoring of simulated clandestine graves using animal analogues. Results will provide forensic search teams with crucial information on optimal detection techniques, equipment configuration and datasets for comparison to active and unsolved cold case searches. Electrical Resistivity (ER) surveys showed a naked burial produced large, low-resistivity anomalies for up to four years, but then the body became difficult to image. A wrapped burial had consistent small, high-resistivity anomalies for four years, then large high-resistivity anomalies until the survey period end. Ground Penetrating Radar (GPR) 110–900 MHz surveys showed the wrapped burial could be detected throughout. 225 MHz GPR data was optimal, but the naked burial was poorly imaged after six years. Results suggested conducting both ER and GPR surveys if the burial style was unknown when searching for interred remains. Surveys in winter and spring produced the best datasets, and, as post-burial time increases, surveying in these seasons became increasingly important. This multidisciplinary study provides critical new insights for law enforcement and families of the disappeared worldwide.
Distinct and combined responses to environmental geometry and features in a working-memory reorientation task in rats and chicks
Authors: Lee Sang Ah , Austen Joseph M. , Sovrano Valeria Anna , Vallortigara Giorgio , McGregor Anthony , Lever Colin 
Published: May 2020

AbstractThe original provocative formulation of the ‘geometric module’ hypothesis was based on a working-memory task in rats which suggested that spontaneous reorientation behavior is based solely on the environmental geometry and is impervious to featural cues. Here, we retested that claim by returning to a spontaneous navigation task with rats and domestic chicks, using a single prominent featural cue (a striped wall) within a rectangular arena. Experiments 1 and 2 tested the influence of geometry and features separately. In Experiment 1, we found that both rats and chicks used environmental geometry to compute locations in a plain rectangular arena. In Experiment 2, while chicks failed to spontaneously use a striped wall in a square arena, rats showed a modest influence of the featural cue as a local marker to the goal. The critical third experiment tested the striped wall inside the rectangular arena. We found that although chicks solely relied on geometry, rats navigated based on both environmental geometry and the featural cue. While our findings with rats are contrary to classic claims of an impervious geometric module, they are consistent with the hypothesis that navigation by boundaries and features may involve distinct underlying cognitive computations. We conclude by discussing the similarities and differences in feature-use across tasks and species.
Ciliary vortex flows and oxygen dynamics in the coral boundary layer
Authors: Pacherres Cesar O. , Ahmerkamp Soeren , Schmidt-Grieb Gertraud M. , Holtappels Moritz , Richter Claudio 
Published: May 2020

AbstractThe exchange of metabolites between environment and coral tissue depends on the flux across the diffusive boundary layer (DBL) surrounding the tissue. Cilia covering the coral tissue have been shown to create vortices that enhance mixing in the DBL in stagnant water. To study the role of cilia under simulated ambient currents, we designed a new light-sheet microscopy based flow chamber setup. Microparticle velocimetry was combined with high-resolution oxygen profiling in the coral Porites lutea under varying current and light conditions with natural and arrested cilia beating. Cilia-generated vortices in the lower DBL mitigated extreme oxygen concentrations close to the tissue surface. Under light and arrested cilia, oxygen surplus at the tissue surface increased to 350 µM above ambient, in contrast to 25 µM under ciliary beating. Oxygen shortage in darkness decreased from 120 µM (cilia arrested) to 86 µM (cilia active) below ambient. Ciliary redistribution of oxygen had no effect on the photosynthetic efficiency of the photosymbionts and overall oxygen flux across the DBL indicating that oxygen production and consumption was not affected. We found that corals actively change their environment and suggest that ciliary flows serve predominantly as a homeostatic control mechanism which may play a crucial role in coral stress response and resilience.
The F220C and F45L rhodopsin mutations identified in retinitis pigmentosa patients do not cause pathology in mice
Authors: Lewis Tylor R. , Shores Camilla R. , Cady Martha A. , Hao Ying , Arshavsky Vadim Y. , Burns Marie E. 
Published: May 2020

AbstractRetinitis pigmentosa is a retinal degenerative disease that leads to blindness through photoreceptor loss. Rhodopsin is the most frequently mutated protein in this disease. While many rhodopsin mutations have well-understood consequences that lead to cell death, the disease association of several rhodopsin mutations identified in retinitis pigmentosa patients, including F220C and F45L, has been disputed. In this study, we generated two knockin mouse lines bearing each of these mutations. We did not observe any photoreceptor degeneration in either heterozygous or homozygous animals of either line. F220C mice exhibited minor disruptions of photoreceptor outer segment dimensions without any mislocalization of outer segment proteins, whereas photoreceptors of F45L mice were normal. Suction electrode recordings from individual photoreceptors of both mutant lines showed normal flash sensitivity and photoresponse kinetics. Taken together, these data suggest that neither the F220C nor F45L mutation has pathological consequences in mice and, therefore, may not be causative of retinitis pigmentosa in humans.
Target-site EPSPS Pro-106-Ser mutation in Conyza canadensis biotypes with extreme resistance to glyphosate in Ohio and Iowa, USA
Authors: Beres Zachery T. , Giese Laura A. , Mackey David M. , Owen Micheal D. K. , Page Eric R. , Snow Allison A. 
Published: May 2020

AbstractDocumenting the diversity of mechanisms for herbicide resistance in agricultural weeds is helpful for understanding evolutionary processes that contribute to weed management problems. More than 40 species have evolved resistance to glyphosate, and at least 13 species have a target-site mutation at position 106 of EPSPS. In horseweed (Conyza canadensis), this p106 mutation has only been reported in Canada. Here, we sampled seeds from one plant (= biotype) at 24 sites in Ohio and 20 in Iowa, screened these biotypes for levels of resistance, and sequenced their DNA to detect the p106 mutation. Resistance categories were based on 80% survival at five glyphosate doses: S (0×), R1 (1×), R2 (8×), R3 (20×), or R4 (40×). The p106 mutation was not found in the19 biotypes scored as S, R1, or R2, while all 25 biotypes scored as R3 or R4 had the same proline-to-serine substitution at p106. These findings represent the first documented case of target-site mediated glyphosate resistance in horseweed in the United States, and the first to show that this mutation was associated with very strong resistance. We hypothesize that the p106 mutation has occurred multiple times in horseweed and may be spreading rapidly, further complicating weed management efforts.
Large Magneto-piezoelectric Effect in EuMnBi2 Single Crystal at Low Temperatures
Authors: Shiomi Yuki , Masuda Hidetoshi , Takahashi Hidefumi , lshiwata Shintaro 
Published: May 2020

AbstractMagneto-piezoelectric effect (MPE) refers to generation of strain in response to electric currents in magnetic metals which lack both time-reversal and space-inversion symmetries. A recent experimental paper demonstrated the MPE in the antiferromagnetic metal EuMnBi2 at 77 K, but the limited temperature range of the MPE measurement hampered detailed discussion on the MPE. Here we extend the measurement temperature range down to liquid He temperature, and studied the dependences of the MPE on the laser position, frequency and amplitude of electric currents, and temperature in the very low temperature range. We show that the MPE signal is enhanced at low temperatures and reaches a maximum magnitude in the antiferromagnetically ordered states of both Eu and Mn ions. An effective piezoelectric coefficient for the MPE at 4.5 K is estimated to be as large as 3500 pC/N, which is much larger than piezoelectric coefficients of typical piezoelectric ceramics, although the magnitude of real MPE displacements should be limited due to strong Joule heating at high electric currents. The present results may open up a new strategy to realize new lead-free piezoelectric materials.
Enzymatic Cleavage of 3’-Esterified Nucleotides Enables a Long, Continuous DNA Synthesis
Authors: LinWu Shiuan-Woei , Tsai Ting-Yueh , Tu Yu-Hsuan , Chi Hung-Wen , Tsao Yu-Ping , Chen Ya-Chen , Wang Hsiang-Ming , Chang Wei-Hsin , Chiou Chung-Fan , Lee Johnsee , Chen Cheng-Yao 
Published: May 2020

AbstractThe reversible dye-terminator (RDT)-based DNA sequencing-by-synthesis (SBS) chemistry has driven the advancement of the next-generation sequencing technologies for the past two decades. The RDT-based SBS chemistry relies on the DNA polymerase reaction to incorporate the RDT nucleotide (NT) for extracting DNA sequence information. The main drawback of this chemistry is the “DNA scar” issue since the removal of dye molecule from the RDT-NT after each sequencing reaction cycle leaves an extra chemical residue in the newly synthesized DNA. To circumvent this problem, we designed a novel class of reversible (2-aminoethoxy)-3-propionyl (Aep)-dNTPs by esterifying the 3’-hydroxyl group (3’-OH) of deoxyribonucleoside triphosphate (dNTP) and examined the NT-incorporation activities by A-family DNA polymerases. Using the large fragment of both Bacillus stearothermophilus (BF) and E. coli DNA polymerase I (KF) as model enzymes, we further showed that both proteins efficiently and faithfully incorporated the 3’-Aep-dNMP. Additionally, we analyzed the post-incorporation product of N + 1 primer and confirmed that the 3’-protecting group of 3’-Aep-dNMP was converted back to a normal 3’-OH after it was incorporated into the growing DNA chain by BF. By applying all four 3’-Aep-dNTPs and BF for an in vitro DNA synthesis reaction, we demonstrated that the enzyme-mediated deprotection of inserted 3’-Aep-dNMP permits a long, continuous, and scar-free DNA synthesis.
Individual and cohort-specific gut microbiota patterns associated with tissue-specific insulin sensitivity in overweight and obese males
Authors: Hermes Gerben D. A. , Reijnders Dorien , Kootte Ruud S. , Goossens Gijs H. , Smidt Hauke , Nieuwdorp Max , Blaak Ellen E. , Zoetendal Erwin G. 
Published: May 2020

AbstractA growing body of evidence suggests that the human gut microbiota plays a role in the development of obesity and related metabolic diseases. However, there is little consensus between studies, which could be due to biological as well as technical variation. In addition, little human data are available to investigate whether tissue-specific insulin sensitivity is related to specific microbial patterns. We examined this relation in two independent cohorts of overweight and obese pre-diabetic men, using phylogenetic microarray data and hepatic, peripheral and adipose tissue insulin sensitivity that were determined by a two-step hyperinsulinemic-euglycemic clamp with [6,6-2H2]-glucose tracer infusion. Despite a prominent subject-specific microbiota, we found significant associations of microbial taxa with tissue-specific insulin sensitivity using regression analysis. Using random forests we found moderate associations with other measures of glucose homeostasis in only one of the cohorts (fasting glucose concentrations AUC = 0.66 and HbA1c AUC = 0.65). However, all findings were cohort-specific due to pronounced variation in microbiota between cohorts, suggesting the existence of alternative states for dysbiosis in metabolic syndrome patients. Our findings suggest individual or group related dynamics, instead of universal microbiota signals, related to the host when the overweight or obese state has already developed and argue that care should be taken with extrapolating significant correlations from single cohorts, into generalized biological relevance.
Sex- and age-specific variations, temporal trends and metabolic determinants of serum uric acid concentrations in a large population-based Austrian cohort
Authors: Zitt Emanuel , Fischer Anton , Lhotta Karl , Concin Hans , Nagel Gabriele 
Published: May 2020

AbstractLittle is known about sex- and age-specific variations and temporal trends in serum uric acid (SUA) concentrations, the prevalence of hyperuricemia and its association with metabolic risk factors in the general population. Between January 1, 1985 and June 30, 2005 146,873 participants (42% women) were recruited. Prevalence of hyperuricemia was estimated applying a common (SUA > 360 µmol/L) and sex-specific cut-off points (women > 340 µmol/L, men > 420 µmol/L). At baseline, mean age was 41.2 years in men and 51.5 years in women, mean SUA concentration was 314.8 µmol/L and 243.6 µmol/L, respectively. Applying a common cut-off point, the prevalence of hyperuricemia was 18.5% in men and 4.4% in women and by sex-specific cut-off points it was 15.1% and 13.8%, respectively. SUA levels increased by 6.7 µmol/L per decade in men, but remained constant in women until the age of 50 years with a sharp increase by approximately 22 µmol/L per decade thereafter. In men and women, hyperuricemia was associated with obesity, hypertriglyceridemia and elevated gamma-glutamyl transferase. With increasing age SUA levels and the prevalence of hyperuricemia rise in a sex-specific manner. Above the age of 65 years, the sex-specific prevalence of hyperuricemia in women outreaches that in men.
18F-FDG positron emission tomography and diffusion-weighted magnetic resonance imaging for response evaluation of nanoparticle-mediated photothermal therapy
Authors: Simón Marina , Jørgensen Jesper Tranekjær , Norregaard Kamilla , Kjaer Andreas 
Published: May 2020

AbstractNanoparticle-mediated photothermal cancer therapy (PTT) is a treatment which creates localized damage to tumors via nanoparticles that generate heat when irradiated with near infrared light. Substantial work has been dedicated to developing efficient heat-transducing nanoparticles that can be delivered systemically to the tumor. However, less attention has been given to clinically relevant assessment methods of treatment outcome that could be used for personalizing the therapy. Here, we compare 18F-FDG positron emission tomography combined with computed tomography (PET/CT) and diffusion-weighted imaging (DWI) for early evaluation and prognosis of PTT in tumor-bearing mice using silica-gold nanoshells (NS). The NS-treated mice experienced inhibited tumor growth and significantly prolonged survival compared to control mice. One day after PTT, PET/CT and DWI scans showed a decrease in tumor 18F-FDG uptake of ~90% and an increase of ~50% in apparent diffusion coefficient (ADC) values respectively, compared to baseline. No significant changes were observed for control groups. Additionally, the changes in 18F-FDG uptake and ADC values correlated significantly with survival, demonstrating that both methods can be used for early evaluation of PTT although 18F-FDG PET/CT showed the strongest prognostic value. Based on these results, both modalities should be considered for therapy monitoring of PTT when clinically translated.
The coenzyme thiamine diphosphate displays a daily rhythm in the Arabidopsis nucleus
Authors: Noordally Zeenat B. , Trichtinger Celso , Dalvit Ivan , Hofmann Manuel , Roux Céline , Zamboni Nicola , Pourcel Lucille , Gas-Pascual Elisabet , Gisler Alexandra , Fitzpatrick Teresa B. 
Published: May 2020

AbstractIn plants, metabolic homeostasis—the driving force of growth and development—is achieved through the dynamic behavior of a network of enzymes, many of which depend on coenzymes for activity. The circadian clock is established to influence coordination of supply and demand of metabolites. Metabolic oscillations independent of the circadian clock, particularly at the subcellular level is unexplored. Here, we reveal a metabolic rhythm of the essential coenzyme thiamine diphosphate (TDP) in the Arabidopsis nucleus. We show there is temporal separation of the clock control of cellular biosynthesis and transport of TDP at the transcriptional level. Taking advantage of the sole reported riboswitch metabolite sensor in plants, we show that TDP oscillates in the nucleus. This oscillation is a function of a light-dark cycle and is independent of circadian clock control. The findings are important to understand plant fitness in terms of metabolite rhythms.