bluuebunny/crossref_metadata_2025_split huggingface dataset:
The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution
Authors: Wei Suyun , Yang Yonghua , Yin Tongming 
Published: March 2020

AbstractSalix suchowensis is an early-flowering shrub willow that provides a desirable system for studies on the basic biology of woody plants. The current reference genome of S. suchowensis was assembled with 454 sequencing reads. Here, we report a chromosome-scale assembly of S. suchowensis generated by combining PacBio sequencing with Hi-C technologies. The obtained genome assemblies covered a total length of 356 Mb. The contig N50 of these assemblies was 263,908 bp, which was ~65-fold higher than that reported previously. The contiguity and completeness of the genome were significantly improved. By applying Hi-C data, 339.67 Mb (95.29%) of the assembled sequences were allocated to the 19 chromosomes of haploid willow. With the chromosome-scale assembly, we revealed a series of major chromosomal fissions and fusions that explain the genome divergence between the sister genera of Salix and Populus. The more complete and accurate willow reference genome obtained in this study provides a fundamental resource for studying many genetic and genomic characteristics of woody plants.
Turbocharging introgression breeding of perennial fruit crops: a case study on apple
Authors: Kumar Satish , Hilario Elena , Deng Cecilia H. , Molloy Claire 
Published: March 2020

AbstractThe allelic diversity of primitive germplasm of fruit crops provides a useful resource for introgressing novel genes to meet consumer preferences and environmental challenges. Pre-breeding facilitates the identification of novel genetic variation in the primitive germplasm and expedite its utilisation in cultivar breeding programmes. Several generations of pre-breeding could be required to minimise linkage drag from the donor parent and to maximise the genomic content of the recipient parent. In this study we investigated the potential of genomic selection (GS) as a tool for rapid background selection of parents for the successive generation. A diverse set of 274 accessions was genotyped using random-tag genotyping-by-sequencing, and phenotyped for eight fruit quality traits. The relationship between ‘own phenotypes’ of 274 accessions and their general combining ability (GCA) was also examined. Trait heritability influenced the strength of correspondence between own phenotype and the GCA. The average (across eight traits) accuracy of predicting own phenotype was 0.70, and the correlations between genomic-predicted own phenotype and GCA were similar to the observed correlations. Our results suggest that genome-assisted parental selection (GAPS) is a credible alternative to phenotypic parental selection, so could help reduce the generation interval to allow faster accumulation of favourable alleles from donor and recipient parents.
Spatial heterogeneity of flesh-cell osmotic potential in sweet cherry affects partitioning of absorbed water
Authors: Grimm Eckhard , Pflugfelder Daniel , Hahn Jan , Schmidt Moritz Jonathan , Dieckmann Hendrik , Knoche Moritz 
Published: March 2020

AbstractA fleshy fruit is commonly assumed to resemble a thin-walled pressure vessel containing a homogenous carbohydrate solution. Using sweet cherry (Prunus avium L.) as a model system, we investigate how local differences in cell water potential affect H2O and D2O (heavy water) partitioning. The partitioning of H2O and D2O was mapped non-destructively using magnetic resonance imaging (MRI). The change in size of mesocarp cells due to water movement was monitored by optical coherence tomography (OCT, non-destructive). Osmotic potential was mapped using micro-osmometry (destructive). Virtual sections through the fruit revealed that the H2O distribution followed a net pattern in the outer mesocarp and a radial pattern in the inner mesocarp. These patterns align with the disposition of the vascular bundles. D2O uptake through the skin paralleled the acropetal gradient in cell osmotic potential gradient (from less negative to more negative). Cells in the vicinity of a vascular bundle were of more negative osmotic potential than cells more distant from a vascular bundle. OCT revealed net H2O uptake was the result of some cells loosing volume and other cells increasing volume. H2O and D2O partitioning following uptake is non-uniform and related to the spatial heterogeneity in the osmotic potential of mesocarp cells.
Petermann-factor sensitivity limit near an exceptional point in a Brillouin ring laser gyroscope
Authors: Wang Heming , Lai Yu-Hung , Yuan Zhiquan , Suh Myoung-Gyun , Vahala Kerry 
Published: March 2020

AbstractExceptional points are singularities of open systems, and among their many remarkable properties, they provide a way to enhance the responsivity of sensors. Here we show that the improved responsivity of a laser gyroscope caused by operation near an exceptional point is precisely compensated by increasing laser noise. The noise, of fundamental origin, is enhanced because the laser mode spectrum loses the oft-assumed property of orthogonality. This occurs as system eigenvectors coalesce near the exceptional point and a bi-orthogonal analysis confirms experimental observations. While the results do not preclude other possible advantages of the exceptional-point-enhanced responsivity, they do show that the fundamental sensitivity limit of the gyroscope is not improved through this form of operation. Besides being important to the physics of microcavities and non-Hermitian photonics, these results help clarify fundamental sensitivity limits in a specific class of exceptional-point sensor.
Estimated discharge of antibiotic-resistant bacteria from combined sewer overflows of urban sewage system
Authors: Honda Ryo , Tachi Chihiro , Yasuda Keisuke , Hirata Tatsuki , Noguchi Mana , Hara-Yamamura Hiroe , Yamamoto-Ikemoto Ryoko , Watanabe Toru 
Published: March 2020

AbstractYearly discharge of antibiotic-resistant bacteria (ARB) from combined sewer overflow (CSO) was estimated. The volume of CSO was estimated from operating data of the pumping station. In the target sewer catchment, 23% of the total of the volume of combined sewage was discharged untreated as CSO. Combined sewage contained 3-log larger E. coli than secondary treatment effluent although the abundance of antibiotic-resistant E. coli was not significantly different. In the target-combined sewer catchment, a yearly total of 4.8 × 1016 CFU of E. coli was discharged from 6.1 × 106 m3 of CSO, while 1.3 × 1012 CFU of E. coli from 2.1 × 107 m3 of effluent from the wastewater treatment plant (WWTP). This E. coli discharge was equivalent to 7.9 × 109 CFU/m3 from CSO, and 6.2 × 104 CFU/m3 from WWTP effluent. Consequently, a yearly total discharge of antibiotic-resistant E. coli from CSO was 3.7-log larger than the WWTP effluent. The small-flow CSO events, which had hourly flow rate smaller than five times of the average dry-weather flow, accounted for 43% of the total CSO volume, but 79% of the total discharge of antibiotic-resistant E. coli due to a small dilution factor with stormwater and frequent discharge. Reduction of small-flow CSO events would be important for effective reduction of ARB discharge from CSO.
Diurnal activity in cane toads (Rhinella marina) is geographically widespread
Authors: Pettit Lachlan , Ducatez Simon , DeVore Jayna L. , Ward-Fear Georgia , Shine Richard 
Published: March 2020

AbstractAlthough adult cane toads (Rhinella marina) are generally active only at night, a recent study reported that individuals of this species switched to diurnal activity in response to encountering a novel habitat type (deeply shaded gorges) in the course of their Australian invasion. Our sampling over a broader geographic scale challenges the idea that this behaviour is novel; we documented diurnal behaviour both in the species’ native range and in several sites within the invaded range, in multiple habitat types. Diurnal activity was most common in the tropics and in areas where toads attain high population densities and are in poor body condition, suggesting that the expansion of activity times may be induced by intraspecific competition for food.
Multi-resolution convolutional neural networks for inverse problems
Authors: Wang Feng , Eljarrat Alberto , Müller Johannes , Henninen Trond R. , Erni Rolf , Koch Christoph T. 
Published: March 2020

AbstractInverse problems in image processing, phase imaging, and computer vision often share the same structure of mapping input image(s) to output image(s) but are usually solved by different application-specific algorithms. Deep convolutional neural networks have shown great potential for highly variable tasks across many image-based domains, but sometimes can be challenging to train due to their internal non-linearity. We propose a novel, fast-converging neural network architecture capable of solving generic image(s)-to-image(s) inverse problems relevant to a diverse set of domains. We show this approach is useful in recovering wavefronts from direct intensity measurements, imaging objects from diffusely reflected images, and denoising scanning transmission electron microscopy images, just by using different training datasets. These successful applications demonstrate the proposed network to be an ideal candidate solving general inverse problems falling into the category of image(s)-to-image(s) translation.
The Extracellular Domain of Two-component System Sensor Kinase VanS from Streptomyces coelicolor Binds Vancomycin at a Newly Identified Binding Site
Authors: Lockey Christine , Edwards Richard J. , Roper David I. , Dixon Ann M. 
Published: March 2020

AbstractThe glycopeptide antibiotic vancomycin has been widely used to treat infections of Gram-positive bacteria including Clostridium difficile and methicillin-resistant Staphylococcus aureus. However, since its introduction, high level vancomycin resistance has emerged. The genes responsible require the action of the two-component regulatory system VanSR to induce expression of resistance genes. The mechanism of detection of vancomycin by this two-component system has yet to be elucidated. Diverging evidence in the literature supports activation models in which the VanS protein binds either vancomycin, or Lipid II, to induce resistance. Here we investigated the interaction between vancomycin and VanS from Streptomyces coelicolor (VanSSC), a model Actinomycete. We demonstrate a direct interaction between vancomycin and purified VanSSC, and traced these interactions to the extracellular region of the protein, which we reveal adopts a predominantly α-helical conformation. The VanSSC-binding epitope within vancomycin was mapped to the N-terminus of the peptide chain, distinct from the binding site for Lipid II. In targeting a separate site on vancomycin, the effective VanS ligand concentration includes both free and lipid-bound molecules, facilitating VanS activation. This is the first molecular description of the VanS binding site within vancomycin, and could direct engineering of future therapeutics.
Engineered cartilage utilizing fetal cartilage-derived progenitor cells for cartilage repair
Authors: Park Do Young , Min Byoung-Hyun , Park So Ra , Oh Hyun Ju , Truong Minh-Dung , Kim Mijin , Choi Ja-Young , Park In-Su , Choi Byung Hyune 
Published: March 2020

AbstractThe aim of this study was to develop a fetal cartilage-derived progenitor cell (FCPC) based cartilage gel through self-assembly for cartilage repair surgery, with clinically useful properties including adhesiveness, plasticity, and continued chondrogenic remodeling after transplantation. Characterization of the gels according to in vitro self-assembly period resulted in increased chondrogenic features over time. Adhesion strength of the cartilage gels were significantly higher compared to alginate gel, with the 2-wk group showing a near 20-fold higher strength (1.8 ± 0.15 kPa vs. 0.09 ± 0.01 kPa, p < 0.001). The in vivo remodeling process analysis of the 2 wk cultured gels showed increased cartilage repair characteristics and stiffness over time, with higher integration-failure stress compared to osteochondral autograft controls at 4 weeks (p < 0.01). In the nonhuman primate investigation, cartilage repair scores were significantly better in the gel group compared to defects alone after 24 weeks (p < 0.001). Cell distribution analysis at 24 weeks showed that human cells remained within the transplanted defects only. A self-assembled, FCPC-based cartilage gel showed chondrogenic repair potential as well as adhesive properties, beneficial for cartilage repair.
Instabilities of Thin Films on a Compliant Substrate: Direct Numerical Simulations from Surface Wrinkling to Global Buckling
Authors: Nikravesh Siavash , Ryu Donghyeon , Shen Yu-Lin 
Published: March 2020

AbstractFor structures consisting of a thin film bonded to a compliant substrate, wrinkling of the thin film is commonly observed as a result of mechanical instability. Although this surface undulation may be an undesirable feature, the development of new functional devices has begun to take advantage of wrinkled surfaces. The wrinkled structure also serves to improve mechanical resilience of flexible devices by suppressing crack formation upon stretching and bending. If the substrate has a reduced thickness, buckling of the entire structure may also occur. It is important to develop numerical design tools for predicting both wrinkle and buckle formations. In this paper we report a comprehensive finite element-based study utilizing embedded imperfections to directly simulate instabilities. The technique overcomes current computational challenges. The temporal evolution of the wrinkling features including wavelength and amplitude, as well as the critical strains to trigger the surface undulation and overall structural buckling, can all be predicted in a straightforward manner. The effects of model dimensions, substrate thickness, boundary condition, and composite film layers are systematically analyzed. In addition to the separate wrinkling and buckling instabilities developed under their respective geometric conditions, we illustrate that concurrent wrinkling and buckling can actually occur and be directly simulated. The correlation between specimen geometry and instability modes, as well as how the deformation increment size can influence the simulation result, are also discussed.
Coronary Plaque Characteristics and Cut-Off Stenosis for Developing Spasm in Patients with Vasospastic Angina
Authors: Jo Sang-Ho , Sim Ju Ho , Baek Sang Hong 
Published: March 2020

AbstractCoronary plaque distribution, frequency and cut-off value of percent stenosis for developing vasospasm are uncertain in patients with vasospastic angina (VA). We enrolled 2960 patients who received coronary angiography (CAG) and ergonovine provocation test prospectively in 11 university hospitals in Korea. A total of 1836 patients with VA and 867 without VA were included. Plaque and % stenosis were defined as ≥1% luminal narrowing and mean of each segmental stenosis. Overall frequency of plaque and % diameter stenosis was compared among VA-patients with index coronary spasm positive, those with index arterial spasm negative/other arterial spasm positive (INOP) and non-VA patients. Diameter stenosis associated with the spasm positivity was investigated. Overall plaque frequency and % stenosis were higher in VA patients than non-VA patients. Plaque frequency was 27.6% (243/881) in spasm positive at LAD, 16.4% (157/955) in LAD INOP and 12.6% (109/867) in non-VA with statistic difference (P < 0.001). Same trend for higher rate was observed in LCx and RCA. For % stenosis, 36.6 vs 32.4% (p = 0.010) in LAD, 36.1 vs. 28% (p < 0.001) in LCx and 35.3 vs.30.0% (p = 0.047) in RCA, respectively. Diameter stenosis of LAD with spasm positive vs. LAD INOP vs. non-VA were 38.3%, 34.0%, 32% (P = 0.002) with similar pattern in LCx and RCA. By multivariate logistic regression analysis, coronary stenosis of LAD ≥ 35% or LCx ≥35% or RCA ≥ 40% were independent predictor of developing spasm (OR 2.019, 95% CI 1.315–3.100, P = 0.001). In conclusions, spastic coronary artery had more plaque frequency, higher % stenosis than in non-spastic coronary in VA patients. The spasm related and unrelated coronary in VA patients had more plaque than in matched and unmatched coronary arteries in non-VA patients. Coronary stenosis ≥35% in LAD and LCx was an independent predictor of developing spasm.
The rubber hand illusion in hypnosis provides new insights into the sense of body ownership
Authors: Fiorio Mirta , Modenese Michele , Cesari Paola 
Published: March 2020

AbstractBody ownership can be experimentally investigated with the rubber hand illusion (RHI), in which watching a rubber hand stroked synchronously with one’s own hidden hand induces a feeling of ownership over the rubber hand. The aim of this study was to investigate response to the RHI in high (N = 21) and low (N = 19) hypnotizable individuals in normal waking state and in hypnosis. Response to the RHI was measured via a question on the illusory feeling of ownership and with proprioceptive drift. The Highs expressed an overall feeling of more ownership over the rubber hand in both the normal waking state and hypnosis, although both groups gave higher ownership scores after synchronous than after asynchronous stroking and the difference between conditions was similar across groups. Conversely, the proprioceptive drift appeared to be differentially modulated by hypnosis and hypnotic suggestibility: it was increased in the Highs and decreased in the Lows after hypnosis induction. These findings hint at an interplay between hypnotic suggestibility and hypnosis in modulating response to the RHI. The selective breakdown of proprioceptive drift among the Lows suggests resistance to recalibrate one’s own limb in hypnosis.
Anti-inflammatory Effect of Curcuma longa and Allium hookeri Co-treatment via NF-κB and COX-2 Pathways
Authors: Lee Soon-Young , Cho Seung-Sik , Li YongChun , Bae Chun-Sik , Park Kyung Mok , Park Dae-Hun 
Published: March 2020

AbstractAlthough inflammation is a host defense mechanism, chronic inflammation mediates several diseases, including cancer, allergy, asthma, and autoimmune diseases, and reportedly, it is associated with a 60% mortality rate. There are several reports on the anti-inflammatory effects of Curcuma longa and Allium hookeri. However, although they can be used as culinary materials and have biological effects, they are not effective anti-inflammatory agents. In this study, we evaluated the synergic effect of C. longa and A. hookeri in order to confirm the possibility of a new anti-inflammatory agent. Based on cell viability and cytokine analyses, the appropriate ratio of C. longa and A. hookeri was confirmed using an air pouch animal model. Then, the anti-inflammatory effect of C. longa and A. hookeri co-treatment was evaluated by measuring the immune cell count and cytokines in the exudate and by comparing the morphological changes and cytokines in inflamed skin samples. Additionally, we evaluated the NF-κB/COX-2 pathway and iNOS levels. The active constituents detected in C. longa were demethoxycurcumin and bisdemethoxycurcumin, and that detected in A. hookeri was methylsulfonylmethane. An in vitro assessment determined the appropriate drug ratio as 3:7. In a carrageenan-induced inflammatory model, co-treatment effectively suppressed inflammatory cytokines, including IFN-γ, IL-1β, IL-6, IL-13, and IL-17, and recovered inflammation-related morphological changes in the skin. The anti-inflammatory effect of the co-treatment was mediated through the NF-κB/COX-2 pathway and iNOS inhibition. We concluded that co-treatment with C. longa and A. hookeri synergistically inhibited inflammation via the NF-κB/COX-2/iNOS pathway.
Iridophoroma associated with the Lemon Frost colour morph of the leopard gecko (Eublepharis macularius)
Authors: Szydłowski Paweł , Madej Jan Paweł , Duda Magdalena , Madej Janusz A. , Sikorska-Kopyłowicz Agnieszka , Chełmońska-Soyta Anna , Ilnicka Lucyna , Duda Przemysław 
Published: March 2020

AbstractThe Lemon Frost is a new colour morph of the leopard gecko, which emerged in ca. 2015 as a result of selective breeding and spontaneous mutation. According to multiple breeders observation of Lemon Frost inbreeding with wild-type leopard geckos, Lemon Frost seems to be a codominant trait. Additionally breeders observed another, presumably associated trait - tumour-like skin lesions. Three private-owned Lemon Frost morph leopard geckos with tumour-like skin lesions were admitted to our clinic for examination, which included histopathology, X-ray and ultrasonography. The histopathological investigation of the biopsies indicated malignant iridophoroma; however, no changes were observed in diagnostic imaging. This research is the first report of clinical and histopathological findings of iridophoroma in leopard geckos.
Surface-based analysis increases the specificity of cortical activation patterns and connectivity results
Authors: Brodoehl Stefan , Gaser Christian , Dahnke Robert , Witte Otto W. , Klingner Carsten M. 
Published: March 2020

AbstractSpatial smoothing of functional magnetic resonance imaging (fMRI) data can be performed on volumetric images and on the extracted surface of the brain. Smoothing on the unfolded cortex should theoretically improve the ability to separate signals between brain areas that are near together in the folded cortex but are more distant in the unfolded cortex. However, surface-based method approaches (SBA) are currently not utilized as standard procedure in the preprocessing of neuroimaging data. Recent improvements in the quality of cortical surface modeling and improvements in its usability nevertheless advocate this method. In the current study, we evaluated the benefits of an up-to-date surface-based smoothing in comparison to volume-based smoothing. We focused on the effect of signal contamination between different functional systems using the primary motor and primary somatosensory cortex as an example. We were particularly interested in how this signal contamination influences the results of activity and connectivity analyses for these brain regions. We addressed this question by performing fMRI on 19 subjects during a tactile stimulation paradigm and by using simulated BOLD responses. We demonstrated that volume-based smoothing causes contamination of the primary motor cortex by somatosensory cortical responses, leading to false positive motor activation. These false positive motor activations were not found by using surface-based smoothing for reasonable kernel sizes. Accordingly, volume-based smoothing caused an exaggeration of connectivity estimates between these regions. In conclusion, this study showed that surface-based smoothing decreases signal contamination considerably between neighboring functional brain regions and improves the validity of activity and connectivity results.