bluuebunny/crossref_metadata_2025_split huggingface dataset:
Skeletonema marinoi as a new genetic model for marine chain-forming diatoms
Authors: Johansson Oskar N. , Töpel Mats , Pinder Matthew I. M. , Kourtchenko Olga , Blomberg Anders , Godhe Anna , Clarke Adrian K. 
Published: April 2019

AbstractDiatoms are ubiquitous primary producers in marine ecosystems and freshwater habitats. Due to their complex evolutionary history, much remains unknown about the specific gene functions in diatoms that underlie their broad ecological success. In this study, we have genetically transformed the centric diatom Skeletonema marinoi, a dominant phytoplankton species in temperate coastal regions. Transformation of S. marinoi is the first for a true chain-forming diatom, with the random genomic integration via nonhomologous recombination of a linear DNA construct expressing the resistance gene to the antibiotic zeocin. A set of molecular tools were developed for reliably identifying the genomic insertion site within each transformant, many of which disrupt recognizable genes and constitute null or knock-down mutations. We now propose S. marinoi as a new genetic model for marine diatoms, representing true chain-forming species that play a central role in global photosynthetic carbon sequestration and the biogeochemical cycling of silicates and various nutrients, as well as having potential biotechnological applications.
Profile measurement adopting binocular active vision with normalization object of vector orthogonality
Authors: Xu Guan , Chen Junyi , Li Xiaotao , Su Jian 
Published: April 2019

AbstractActive-vision-based measurement plays an important role in the profile inspection study. The binocular vision, a passive vision, is employed in the active vision system to contribute the benefits of them. The laser plane is calibrated by two 2D targets without texture initially. Then, an L target with feature points is designed to construct the orthogonality object of two vectors. In order to accurately model the binocular-active-vision system, the feature points on the L target are built by two cameras and parameterized by the laser plane. Different from the optimization methods on the basis of the distance object, the laser plane is further refined by the distance-angle object. Thus, an optimization function is created considering both the norms and angles of the vectors. However, the scale of the distance is diverse from the scale of the angle. Therefore, the optimization function is enhanced by the normalization process to balance the different scales. The comparison experiments show that the binocular active vision with the normalization object of vector orthogonality achieves the decreasing distance errors of 25%, 22%, 13% and 4%, as well as the decreasing angle errors of 23%, 20%, 14% and 4%, which indicates an accurate measurement to reconstruct the object profile.
Arctic warming interrupts the Transpolar Drift and affects long-range transport of sea ice and ice-rafted matter
Authors: Krumpen Thomas , Belter H. Jakob , Boetius Antje , Damm Ellen , Haas Christian , Hendricks Stefan , Nicolaus Marcel , Nöthig Eva-Maria , Paul Stephan , Peeken Ilka , Ricker Robert , Stein Rüdiger 
Published: April 2019

AbstractSea ice is an important transport vehicle for gaseous, dissolved and particulate matter in the Arctic Ocean. Due to the recently observed acceleration in sea ice drift, it has been assumed that more matter is advected by the Transpolar Drift from shallow shelf waters to the central Arctic Ocean and beyond. However, this study provides first evidence that intensified melt in the marginal zones of the Arctic Ocean interrupts the transarctic conveyor belt and has led to a reduction of the survival rates of sea ice exported from the shallow Siberian shelves (−15% per decade). As a consequence, less and less ice formed in shallow water areas (<30 m) has reached Fram Strait (−17% per decade), and more ice and ice-rafted material is released in the northern Laptev Sea and central Arctic Ocean. Decreasing survival rates of first-year ice are visible all along the Russian shelves, but significant only in the Kara Sea, East Siberian Sea and western Laptev Sea. Identified changes affect biogeochemical fluxes and ecological processes in the central Arctic: A reduced long-range transport of sea ice alters transport and redistribution of climate relevant gases, and increases accumulation of sediments and contaminates in the central Arctic Ocean, with consequences for primary production, and the biodiversity of the Arctic Ocean.
Ultrasonic tracking of a sinking ball in a vibrated dense granular suspension
Authors: van den Wildenberg S. , Jia X. , Léopoldès J. , Tourin A. 
Published: April 2019

AbstractObserving and understanding the motion of an intruder through opaque dense suspensions such as quicksand remains a practical and conceptual challenge. Here we use an ultrasonic probe to monitor the sinking dynamics of a steel ball in a dense glass bead packing (3D) saturated by water. We show that the frictional model developed for dry granular media can be used to describe the ball motion induced by horizontal vibration. From this rheology, we infer the static friction coefficient and effective viscosity that decrease when increasing the vibration intensity. Our main finding is that the vibration-induced reduction of the yield stress and increase of the sinking depth are presumably due to micro-slips induced at the grain contacts but without visible plastic deformation due to macroscopic rearrangements, in contrast to dry granular packings. To explain these results, we propose a mechanism of acoustic lubrication that reduces the inter-particle friction and leads to a decrease of the yield stress. This scenario is different from the mechanism of liquefaction usually invoked in loosely packed quicksands where the vibration-induced compaction increases the pore pressure and decreases the confining pressure on the solid skeleton, thus reducing the granular resistance to external load.
Humans best judge how much to cooperate when facing hard problems in large groups
Authors: Guazzini Andrea , Stefanelli Federica , Imbimbo Enrico , Vilone Daniele , Bagnoli Franco , Levnajić Zoran 
Published: April 2019

AbstractWe report the results of a game-theoretic experiment with human players who solve problems of increasing complexity by cooperating in groups of increasing size. Our experimental environment is set up to make it complicated for players to use rational calculation for making the cooperative decisions. This environment is directly translated into a computer simulation, from which we extract the collaboration strategy that leads to the maximal attainable score. Based on this, we measure the error that players make when estimating the benefits of collaboration, and find that humans massively underestimate these benefits when facing easy problems or working alone or in small groups. In contrast, when confronting hard problems or collaborating in large groups, humans accurately judge the best level of collaboration and easily achieve the maximal score. Our findings are independent on groups’ composition and players’ personal traits. We interpret them as varying degrees of usefulness of social heuristics, which seems to depend on the size of the involved group and the complexity of the situation.
Insertional mutagenesis using the Sleeping Beauty transposon system identifies drivers of erythroleukemia in mice
Authors: Loeb Keith R. , Hughes Bridget T. , Fissel Brian M. , Osteen Nyka J. , Knoblaugh Sue E. , Grim Jonathan E. , Drury Luke J. , Sarver Aaron , Dupuy Adam J. , Clurman Bruce E. 
Published: April 2019

AbstractInsertional mutagenesis is a powerful means of identifying cancer drivers in animal models. We used the Sleeping Beauty (SB) transposon/transposase system to identify activated oncogenes in hematologic cancers in wild-type mice and mice that express a stabilized cyclin E protein (termed cyclin ET74AT393A). Cyclin E governs cell division and is misregulated in human cancers. Cyclin ET74AT393A mice develop ineffective erythropoiesis that resembles early-stage human myelodysplastic syndrome, and we sought to identify oncogenes that might cooperate with cyclin E hyperactivity in leukemogenesis. SB activation in hematopoietic precursors caused T-cell leukemia/lymphomas (T-ALL) and pure red blood cell erythroleukemias (EL). Analysis of >12,000 SB integration sites revealed markedly different oncogene activations in EL and T-ALL: Notch1 and Ikaros were most common in T-ALL, whereas ETS transcription factors (Erg and Ets1) were targeted in most ELs. Cyclin E status did not impact leukemogenesis or oncogene activations. Whereas most SB insertions were lost during culture of EL cell lines, Erg insertions were retained, indicating Erg’s key role in these neoplasms. Surprisingly, cyclin ET74AT393A conferred growth factor independence and altered Erg-dependent differentiation in EL cell lines. These studies provide new molecular insights into erythroid leukemia and suggest potential therapeutic targets for human leukemia.
The use of spatially explicit genetic variation data from four deep-sea sponges to inform the protection of Vulnerable Marine Ecosystems
Authors: Zeng Cong , Clark Malcolm R. , Rowden Ashley A. , Kelly Michelle , Gardner Jonathan P. A. 
Published: April 2019

AbstractThe United Nations General Assembly has called for greater protection of the world’s deep-sea species and of features such as Vulnerable Marine Ecosystems (VMEs). Sponges are important components of VMEs and information about their spatially explicit genetic diversity can inform management decisions concerning the placement of protected areas. We employed a spatially explicit hierarchical testing framework to examine genetic variation amongst archived samples of four deep-sea sponges in the New Zealand region. For Poecillastra laminaris Sollas 1886, significant mitochondrial (COI, Cytb) and nuclear DNA (microsatellite) genetic differences were observed between provinces, amongst north-central-south regions and amongst geomorphic features. For Penares sp. no significant structure was detected (COI, 12S) across the same areas. For both Neoaulaxinia persicum Kelly, 2007 (COI, 12S) and Pleroma menoui Lévi & Lévi 1983 (COI) there was no evidence of genetic differentiation within their northern only regional distributions. Of 10 separate species-by-marker tests for isolation-by-distance and isolation-by-depth, only the isolation-by-depth test for N. persicum for COI was significant. The use of archived samples highlights how historical material may be used to support national and international management decisions. The results are discussed in the broader context of existing marine protected areas, and possible future design of spatial management measures for protecting VMEs in the New Zealand region.
Research of activity of Main Belt Comets 176P/LINEAR, 238P/Read and 288P/(300163) 2006 VW139
Authors: Shi Jianchun , Ma Yuehua , Liang He , Xu Ruiqi 
Published: April 2019

AbstractAs a new class of comet, main belt comets (MBCs) have attracted more and more attention in recent years. To study activity and physical properties of three MBCs 176P/LINEAR, 238P/Read and 288P/(300163) 2006 VW139, we carried out broadband CCD photometry of three MBCs on UT 2016 November 18–19 with the 1-m optical telescope at Lulin Observatory in Taiwan. By comparing cometary surface brightness profiles to stellar surface brightness profiles, and by comparing cometary absolute magnitude to the expected magnitude of inactive nucleus, we found that 176P/LINEAR was inactive, while 238P/Read and 288P/(300163) 2006 VW139 were active. By photometric studies, we obtained the Afρ values and the dust production rates. Finally, the activity of three MBCs were discussed. Our photometric results show that the total dust mass of 238P/Read and 288P/(300163) 2006 VW139 obtained in this work are of the same magnitude as the majority of known MBCs.
Integrating gene regulatory pathways into differential network analysis of gene expression data
Authors: Grimes Tyler , Potter S. Steven , Datta Somnath 
Published: April 2019

AbstractThe advent of next-generation sequencing has introduced new opportunities in analyzing gene expression data. Research in systems biology has taken advantage of these opportunities by gleaning insights into gene regulatory networks through the analysis of gene association networks. Contrasting networks from different populations can reveal the many different roles genes fill, which can lead to new discoveries in gene function. Pathologies can also arise from aberrations in these gene-gene interactions. Exposing these network irregularities provides a new avenue for understanding and treating diseases. A general framework for integrating known gene regulatory pathways into a differential network analysis between two populations is proposed. The framework importantly allows for any gene-gene association measure to be used, and inference is carried out through permutation testing. A simulation study investigates the performance in identifying differentially connected genes when incorporating known pathways, even if the pathway knowledge is partially inaccurate. Another simulation study compares the general framework with four state-of-the-art methods. Two RNA-seq datasets are analyzed to illustrate the use of this framework in practice. In both examples, the analysis reveals genes and pathways that are known to be biologically significant along with potentially novel findings that may be used to motivate future research.
A Pilot Randomised Double-Blind Study of the Tolerability and efficacy of repetitive Transcranial Magnetic Stimulation on Persistent Post-Concussion Syndrome
Authors: Moussavi Zahra , Suleiman Abdelbaset , Rutherford Grant , Ranjbar Pouya Omid , Dastgheib Zeinab , Zhang Weijia , Salter Jennifer , Wang Xikui , Mansouri Behzad , Lithgow Brian 
Published: April 2019

AbstractThis study investigates the effect of Repetitive Transcranial Magnetic Stimulation (rTMS) on persistent post-concussion syndrome (PCS). The study design was a randomized (coin toss), placebo controlled, and double-blind study. Thirty-seven participants with PCS were assessed for eligibility; 22 were randomised and 18 completed the study requirements. Half the participants with PCS were given an Active rTMS intervention and the other half given Sham rTMS over 3 weeks. Follow ups were at the end of treatment and at 30 and 60 days. The primary outcome measure was the Rivermead Post-Concussion Symptoms Questionnaire (RPQ3 & RPQ13). The results indicate participants with more recent injuries (<12 month), who received Active rTMS, showed significant improvements compared to those of: 1) the same subgroup who received Sham, and 2) those with a longer duration of injury (>14 months) who received Active rTMS. This improvement predominantly manifested in RPQ13 in the follow up periods 1 and 2 months after the intervention (RPQ13 change (mean ± SD): at 1 month, Active = −21.8 ± 6.6, Sham = −2.2 ± 9.8; at 2 months, Active = −21.2 ± 5.3, Sham = −5.4 ± 13.7). No improvement was found in the subgroup with longer duration injuries. The results support rTMS as a tolerable and potentially effective treatment option for individuals with a recent (<1 year) concussion.
Mitochondrial DNA mutations and respiratory chain dysfunction in idiopathic and connective tissue disease-related lung fibrosis
Authors: Jaeger Veronika K. , Lebrecht Dirk , Nicholson Andrew G. , Wells Athol , Bhayani Harshil , Gazdhar Amiq , Tamm Michael , Venhoff Nils , Geiser Thomas , Walker Ulrich A. 
Published: April 2019

AbstractReactive oxygen species (ROS) are implicated in the aetiology of interstitial lung disease (ILD). We investigated the role of large-scale somatically acquired mutations in mitochondrial DNA (mtDNA) and consecutive respiratory chain dysfunction as a trigger of ROS-formation and lung fibrosis. Mitochondria were analysed in lung biopsies from 30 patients with idiopathic or connective tissue disease (CTD)-related ILD and 13 controls. In 17 patients we had paired biopsies from upper and lower lobes. Control samples were taken from lung cancer resections without interstitial fibrosis. Malondialdehyde, a marker of ROS-formation, was elevated in ILD-biopsies (p = 0.044). The activity of the mitochondrial respiratory chain (cytochrome c-oxidase/succinate dehydrogenase [COX/SDH]-ratio) was depressed in ILD (median = 0.10,) compared with controls (0.12, p < 0.001), as was the expression of mtDNA-encoded COX-subunit-2 protein normalized for the nucleus-encoded COX-subunit-4 (COX2/COX4-ratio; ILD-median = 0.6; controls = 2.2; p < 0.001). Wild-type mtDNA copies were slightly elevated in ILD (p = 0.088). The common mtDNA deletion was only present at low levels in controls (median = 0%) and at high levels in ILD (median = 17%; p < 0.001). In ILD-lungs with paired biopsies, lower lobes contained more malondialdehyde and mtDNA deletions than upper lobes and had lower COX2/COX4-ratios and COX/SDH-ratios (all p < 0.001). Acquired mtDNA-mutations and consecutive respiratory chain dysfunction may both trigger and perpetuate ROS-formation in ILD.
Halve the dose while maintaining image quality in paediatric Cone Beam CT
Authors: Oenning Anne Caroline , Pauwels Ruben , Stratis Andreas , De Faria Vasconcelos Karla , Tijskens Elisabeth , De Grauwe Annelore ,   Dimitra research group, Chaussain Catherine , Bosmans Hilde , Bogaerts Ria , Politis Constantinus , Nicolielo Laura , Zhang Guozhi , Vranckx Myrthel , Ockerman Anna , Baatout Sarah , Belmans Niels , Moreels Marjan , Hedesiu Mihaela , Virag Pirsoka , Baciut Mihaela , Marcu Maria , Almasan Oana , Roman Raluca , Barbur Ioan , Dinu Cristian , Rotaru Horatiu , Hurubeanu Lucia , Istouan Vlad , Lucaciu Ondine , Leucuta Daniel , Crisan Bogdan , Bogdan Loredana , Candea Ciprian , Bran Simion , Baciut Grigore , Jacobs Reinhilde , Salmon Benjamin 
Published: April 2019

AbstractCone beam CT (CBCT) for dentomaxillofacial paediatric assessment has been widely used despite the uncertainties of the risks of the low-dose radiation exposures. The aim of this work was to investigate the clinical performance of different CBCT acquisition protocols towards the optimization of paediatric exposures. Custom-made anthropomorphic phantoms were scanned using a CBCT unit in six protocols. CT slices were blinded, randomized and presented to three observers, who scored the image quality using a 4-point scale along with their level of confidence. Sharpness level was also measured using a test object containing an air/PMMA e,dge. The effective dose was calculated by means of a customized Monte Carlo (MC) framework using previously validated paediatric voxels models. The results have shown that the protocols set with smaller voxel size (180 µm), even when decreasing exposure parameters (kVp and mAs), showed high image quality scores and increased sharpness. The MC analysis showed a gradual decrease in effective dose when exposures parameters were reduced, with an emphasis on an average reduction of 45% for the protocol that combined 70 kVp, 16 mAs and 180 µm voxel size. In contrast, both “ultra-low dose” protocols that combined a larger voxel size (400 µm) with lower mAs (7.4 mAs) demonstrated the lowest scores with high levels of confidence unsuitable for an anatomical approach. In conclusion, a significant decrease in the effective dose can be achieved while maintaining the image quality required for paediatric CBCT.
Potassium doping increases biochar carbon sequestration potential by 45%, facilitating decoupling of carbon sequestration from soil improvement
Authors: Mašek Ondřej , Buss Wolfram , Brownsort Peter , Rovere Massimo , Tagliaferro Alberto , Zhao Ling , Cao Xinde , Xu Guangwen 
Published: April 2019

AbstractNegative emissions technologies offer an important tool to limit the global warming to <2 °C. Biochar is one of only a few such technologies, and the one at highest technology readiness level. Here we show that potassium as a low-concentration additive in biochar production can increase biochar’s carbon sequestration potential; by up to 45% in this study. This translates to an increase in the estimated global biochar carbon sequestration potential to over 2.6 Gt CO2-C(eq) yr−1, thus boosting the efficiency of utilisation of limited biomass and land resources, and considerably improving the economics of biochar production and atmospheric carbon sequestration. In addition, potassium doping also increases plant nutrient content of resulting biochar, making it better suited for agricultural applications. Yet, more importantly, due to its much higher carbon sequestration potential, AM-enriched biochar facilitates viable biochar deployment for carbon sequestration purposes with reduced need to rely on biochar’s abilities to improve soil properties and crop yields, hence opening new potential areas and scenarios for biochar applications.
Sustained effects of corrupted feedback on perceptual inference
Authors: Varrier R. S. , Stuke H. , Guggenmos M. , Sterzer P. 
Published: April 2019

AbstractFeedback is central to most forms of learning, and its reliability is therefore critical. Here, we investigated the effects of corrupted, and hence unreliable, feedback on perceptual inference. Within the framework of Bayesian inference, we hypothesised that corrupting feedback in a demanding perceptual task would compromise sensory information processing and bias inference towards prior information if available. These hypotheses were examined by a simulation and in two behavioural experiments with visual detection (experiment 1) and discrimination (experiment 2) tasks. Both experiments consisted of two sessions comprising intervention runs with either corrupted or uncorrupted (correct) feedback, and pre- and post-intervention tests to assess the effects of feedback. In the tests alone, additional prior beliefs were induced through predictive auditory cues to assess sustained effects of feedback on the balance between sensory evidence and prior beliefs. Both experiments and the simulation showed the hypothesised decrease in performance and increased reliance on prior beliefs after corrupted but not uncorrupted feedback. Exploratory analyses indicated reduced confidence regarding perceptual decisions during delivery of corrupted feedback. Our results suggest that corrupted feedback on perceptual decisions leads to sustained changes in perceptual inference, characterised by a shift from sensory likelihood to prior beliefs when those are accessible.