bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-particle imaging of stress-promoters induction reveals the interplay between MAPK signaling, chromatin and transcription factors
Authors: Wosika Victoria , Pelet Serge 
Published: June 2020

AbstractPrecise regulation of gene expression in response to environmental changes is crucial for cell survival, adaptation and proliferation. In eukaryotic cells, extracellular signal integration is often carried out by Mitogen-Activated Protein Kinases (MAPK). Despite a robust MAPK signaling activity, downstream gene expression can display a great variability between single cells. Using a live mRNA reporter, here we monitor the dynamics of transcription in Saccharomyces cerevisiae upon hyper-osmotic shock. We find that the transient activity of the MAPK Hog1 opens a temporal window where stress-response genes can be activated. We show that the first minutes of Hog1 activity are essential to control the activation of a promoter. Chromatin repression on a locus slows down this transition and contributes to the variability in gene expression, while binding of transcription factors increases the level of transcription. However, soon after Hog1 activity peaks, negative regulators promote chromatin closure of the locus and transcription progressively stops.
Semiconductive microporous hydrogen-bonded organophosphonic acid frameworks
Authors: Tholen Patrik , Peeples Craig A. , Schaper Raoul , Bayraktar Ceyda , Erkal Turan Selman , Ayhan Mehmet Menaf , Çoşut Bünyemin , Beckmann Jens , Yazaydin A. Ozgur , Wark Michael , Hanna Gabriel , Zorlu Yunus , Yücesan Gündoğ 
Published: June 2020

AbstractHerein, we report a semiconductive, proton-conductive, microporous hydrogen-bonded organic framework (HOF) derived from phenylphosphonic acid and 5,10,15,20‐tetrakis[p‐phenylphosphonic acid] porphyrin (GTUB5). The structure of GTUB5 was characterized using single crystal X-ray diffraction. A narrow band gap of 1.56 eV was extracted from a UV-Vis spectrum of pure GTUB5 crystals, in excellent agreement with the 1.65 eV band gap obtained from DFT calculations. The same band gap was also measured for GTUB5 in DMSO. The proton conductivity of GTUB5 was measured to be 3.00 × 10−6 S cm−1at 75 °C and 75% relative humidity. The surface area was estimated to be 422 m2 g−1from grand canonical Monte Carlo simulations. XRD showed that GTUB5 is thermally stable under relative humidities of up to 90% at 90 °C. These findings pave the way for a new family of organic, microporous, and semiconducting materials with high surface areas and high thermal stabilities.
Evidence of shock-compressed stishovite above 300 GPa
Authors: Schoelmerich Markus O. , Tschentscher Thomas , Bhat Shrikant , Bolme Cindy A. , Cunningham Eric , Farla Robert , Galtier Eric , Gleason Arianna E. , Harmand Marion , Inubushi Yuichi , Katagiri Kento , Miyanishi Kohei , Nagler Bob , Ozaki Norimasa , Preston Thomas R. , Redmer Ronald , Smith Ray F. , Tobase Tsubasa , Togashi Tadashi , Tracy Sally J. , Umeda Yuhei , Wollenweber Lennart , Yabuuchi Toshinori , Zastrau Ulf , Appel Karen 
Published: June 2020

AbstractSiO2 is one of the most fundamental constituents in planetary bodies, being an essential building block of major mineral phases in the crust and mantle of terrestrial planets (1–10 ME). Silica at depths greater than 300 km may be present in the form of the rutile-type, high pressure polymorph stishovite (P42/mnm) and its thermodynamic stability is of great interest for understanding the seismic and dynamic structure of planetary interiors. Previous studies on stishovite via static and dynamic (shock) compression techniques are contradictory and the observed differences in the lattice-level response is still not clearly understood. Here, laser-induced shock compression experiments at the LCLS- and SACLA XFEL light-sources elucidate the high-pressure behavior of stishovite on the lattice-level under in situ conditions on the Hugoniot to pressures above 300 GPa. We find stishovite is still (meta-)stable at these conditions, and does not undergo any phase transitions. This contradicts static experiments showing structural transformations to the CaCl2, α-PbO2 and pyrite-type structures. However, rate-limited kinetic hindrance may explain our observations. These results are important to our understanding into the validity of EOS data from nanosecond experiments for geophysical applications.
Risk factors for African swine fever incursion in Romanian domestic farms during 2019
Authors: Boklund A. , Dhollander S. , Chesnoiu Vasile T. , Abrahantes J. C. , Bøtner A. , Gogin A. , Gonzalez Villeta L. C. , Gortázar C. , More S. J. , Papanikolaou A. , Roberts H. , Stegeman A. , Ståhl K. , Thulke H. H. , Viltrop A. , Van der Stede Y. , Mortensen S. 
Published: June 2020

AbstractAfrican swine fever (ASF) entered Georgia in 2007 and the EU in 2014. In the EU, the virus primarily spread in wild boar (Sus scrofa) in the period from 2014–2018. However, from the summer 2018, numerous domestic pig farms in Romania were affected by ASF. In contrast to the existing knowledge on ASF transmission routes, the understanding of risk factors and the importance of different transmission routes is still limited. In the period from May to September 2019, 655 Romanian pig farms were included in a matched case-control study investigating possible risk factors for ASF incursion in commercial and backyard pig farms. The results showed that close proximity to outbreaks in domestic farms was a risk factor in commercial as well as backyard farms. Furthermore, in backyard farms, herd size, wild boar abundance around the farm, number of domestic outbreaks within 2 km around farms, short distance to wild boar cases and visits of professionals working on farms were statistically significant risk factors. Additionally, growing crops around the farm, which could potentially attract wild boar, and feeding forage from ASF affected areas to the pigs were risk factors for ASF incursion in backyard farms.
Hyaloid vasculature and mmp2 activity play a role during optic fissure fusion in zebrafish
Authors: Weaver Megan L. , Piedade Warlen P. , Meshram Nishita N. , Famulski Jakub K. 
Published: June 2020

AbstractVertebrate retinal development requires timely and precise fusion of the optic fissure (OF). Failure of this event leads to congenital vision impairment in the form of coloboma. Recent studies have suggested hyaloid vasculature to be involved in OF fusion. In order to examine this link, we analyzed OF fusion and hyaloid vasculogenesis in the zebrafish pax2a noi mutant line. We first determined that pax2a−/− embryos fail to accumulate F-actin in the OF prior to basement membrane (BM) degradation. Furthermore, using 3D and live imaging we observed reduced OF hyaloid vascularization in pax2a−/− embryos. When examining the connection between pax2a loss of function and hyaloid vasculature, we observed significant reduction of talin1 expression, a regulator of hyaloid vasculature. In addition, cranial VEGF expression was found to be reduced in pax2a−/− embryos. Pharmacological inhibition of VEGF signaling phenocopied the pax2a−/− vasculature, F-actin and BM degradation phenotypes. Lastly, we determined that OF associated hyaloid vasculature is a source of mmp2, mmp14a and mmp14b expression and showed that mmp2 is functionally necessary for degradation of OF BM. Taken together we propose a pax2a driven mechanism that ensures proper and timely hyaloid vasculature invasion of the OF in order to facilitate availability of the BM remodeler mmp2.
Conditioning of Superconductive Properties in Graph-Shaped Reticles
Authors: Lucci M. , Cassi D. , Merlo V. , Russo R. , Salina G. , Cirillo M. 
Published: June 2020

AbstractWe report on phenomena observed in planar integrated networks obtained connecting superconducting island by Josephson tunnel junctions. These networks, identifiable as tree-like graphs, have branches consisting of series arrays of Josephson junctions which can be individually current biased and characterized. Both Josephson supercurrents and gap parameters of the arrays embedded in the graph structures display properties significantly different from those of “reference” arrays fabricated on the same chips and having identical geometrical shape. The temperature and magnetic field dependencies of the Josephson current of the embedded arrays both show a singular behavior when a critical value is reached by the Josephson characteristic energy. The gap parameter of the junctions generating the embedded arrays is higher than that of the junctions forming the reference geometrical arrays.
Asymmetry between Activators and Deactivators in Functional Protein Networks
Authors: Tareen Ammar , Wingreen Ned S. , Mukhopadhyay Ranjan 
Published: June 2020

AbstractAre “turn-on” and “turn-off” functions in protein-protein interaction networks exact opposites of each other? To answer this question, we implement a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm, and apply the model to study neutral drift in networks that yield oscillatory dynamics. We study the roles of activators and deactivators, two core components of oscillatory protein interaction networks, and find a striking asymmetry in the roles of activating and deactivating proteins, where activating proteins tend to be synergistic and deactivating proteins tend to be competitive.
Heritability and genome-wide association of swine gut microbiome features with growth and fatness parameters
Authors: Bergamaschi Matteo , Maltecca Christian , Schillebeeckx Constantino , McNulty Nathan P. , Schwab Clint , Shull Caleb , Fix Justin , Tiezzi Francesco 
Published: June 2020

AbstractDespite recent efforts to characterize longitudinal variation in the swine gut microbiome, the extent to which a host’s genome impacts the composition of its gut microbiome is not yet well understood in pigs. The objectives of this study were: i) to identify pig gut microbiome features associated with growth and fatness, ii) to estimate the heritability of those features, and, iii) to conduct a genome-wide association study exploring the relationship between those features and single nucleotide polymorphisms (SNP) in the pig genome. A total of 1,028 pigs were characterized. Animals were genotyped with the Illumina PorcineSNP60 Beadchip. Microbiome samples from fecal swabs were obtained at weaning (Wean), at mid-test during the growth trial (MidTest), and at the end of the growth trial (OffTest). Average daily gain was calculated from birth to week 14 of the growth trial, from weaning to week 14, from week 14 to week 22, and from week 14 to harvest. Backfat and loin depth were also measured at weeks 14 and 22. Heritability estimates (±SE) of Operational Taxonomic Units ranged from 0.025 (±0.0002) to 0.139 (±0.003), from 0.029 (±0.003) to 0.289 (±0.004), and from 0.025 (±0.003) to 0.545 (±0.034) at Wean, MidTest, and OffTest, respectively. Several SNP were significantly associated with taxa at the three time points. These SNP were located in genomic regions containing a total of 68 genes. This study provides new evidence linking gut microbiome composition with growth and carcass traits in swine, while also identifying putative host genetic markers associated with significant differences in the abundance of several prevalent microbiome features.
State-space models reveal a continuing elephant poaching problem in most of Africa
Authors: Schlossberg Scott , Chase Michael J. , Gobush Kathleen S. , Wasser Samuel K. , Lindsay Keith 
Published: June 2020

AbstractThe most comprehensive data on poaching of African elephants comes from the Monitoring the Illegal Killing of Elephants (MIKE) program, which reports numbers of illegally killed carcasses encountered by rangers. Recent studies utilizing MIKE data have reported that poaching of African elephants peaked in 2011 and has been decreasing through 2018. Closer examination of these studies, however, raises questions about the conclusion that poaching is decreasing throughout the continent. To provide more accurate information on trends in elephant poaching, we analyzed MIKE data using state-space models. State-space models account for missing data and the error inherent when sampling carcasses. Using the state-space model, for 2011–2018, we found no significant temporal trends in rates of illegal killing for Southern, Central and Western Africa. Only in Eastern Africa have poaching rates decreased substantially since 2011. For Africa as a whole, poaching did decline for 2011–2018, but the decline was entirely due to Eastern African sites. Our results suggest that poaching for ivory has not diminished across most of Africa since 2011. Continued vigilance and anti-poaching efforts will be necessary to combat poaching and to conserve African elephants.
FACS-Based Functional Protein Screening via Microfluidic Co-encapsulation of Yeast Secretor and Mammalian Reporter Cells
Authors: Yanakieva Desislava , Elter Adrian , Bratsch Jens , Friedrich Karlheinz , Becker Stefan , Kolmar Harald 
Published: June 2020

AbstractIn this study, we present a straightforward approach for functional cell-based screening by co-encapsulation of secretor yeast cells and reporter mammalian cells in millions of individual agarose-containing microdroplets. Our system is compatible with ultra-high-throughput selection utilizing standard fluorescence-activated cell sorters (FACS) without need of extensive adaptation and optimization. In a model study we co-encapsulated murine interleukin 3 (mIL-3)-secreting S. cerevisiae cells with murine Ba/F3 reporter cells, which express green fluorescent protein (GFP) upon stimulation with mIL-3, and could observe specific and robust induction of fluorescence signal compared to a control with yeast cells secreting a non-functional mIL-3 mutant. We demonstrate the successful enrichment of activating mIL-3 wt-secreting yeast cells from a 1:10,000 dilution in cells expressing the inactive cytokine variant by two consecutive cycles of co-encapsulation and FACS. This indicates the suitability of the presented strategy for functional screening of high-diversity yeast-based libraries and demonstrates its potential for the efficient isolation of clones secreting bioactive recombinant proteins.
β-carboline chemical signals induce reveromycin production through a LuxR family regulator in Streptomyces sp. SN-593
Authors: Panthee Suresh , Kito Naoko , Hayashi Teruo , Shimizu Takeshi , Ishikawa Jun , Hamamoto Hiroshi , Osada Hiroyuki , Takahashi Shunji 
Published: June 2020

AbstractActinomycetes bacteria produce diverse bioactive molecules that are useful as drug seeds. To improve their yield, researchers often optimize the fermentation medium. However, exactly how the extracellular chemicals present in the medium activate secondary metabolite gene clusters remains unresolved. BR-1, a β-carboline compound, was recently identified as a chemical signal that enhanced reveromycin A production in Streptomyces sp. SN-593. Here we show that BR-1 specifically bound to the transcriptional regulator protein RevU in the reveromycin A biosynthetic gene cluster, and enhanced RevU binding to its promoter. RevU belongs to the LuxR family regulator that is widely found in bacteria. Interestingly, BR-1 and its derivatives also enhanced the production of secondary metabolites in other Streptomyces species. Although LuxR-N-acyl homoserine lactone systems have been characterized in Gram-negative bacteria, we revealed LuxR-β-carboline system in Streptomyces sp. SN-593 for the production of secondary metabolites. This study might aid in understanding hidden chemical communication by β-carbolines.
Bee venom-derived antimicrobial peptide melectin has broad-spectrum potency, cell selectivity, and salt-resistant properties
Authors: Ko Su Jin , Park Eunji , Asandei Alina , Choi Jee-Young , Lee Seung-Chul , Seo Chang Ho , Luchian Tudor , Park Yoonkyung 
Published: June 2020

AbstractAntimicrobial peptides have attracted attention as alternatives to conventional antibiotics. Previously, a novel antimicrobial peptide, melectin, consisting of 18 amino acids was isolated from the venom of a bee, Melecta albifrons. Here, we investigated the antibacterial activity of melectin against drug-resistant bacteria. Melectin showed broad-spectrum antimicrobial activity but low cytotoxicity and no hemolytic activity. Melectin maintained its antimicrobial activity at physiological salt concentrations. Melectin is an α-helical structure that binds to the bacterial membrane via electrostatic interactions and kills bacteria in a short time by bacterial membrane targeting. Collectively, our results suggest that melectin has antibacterial activity and anti-inflammatory activity.
Evaluation of deep convolutional neural networks for automatic classification of common maternal fetal ultrasound planes
Authors: Burgos-Artizzu Xavier P. , Coronado-Gutiérrez David , Valenzuela-Alcaraz Brenda , Bonet-Carne Elisenda , Eixarch Elisenda , Crispi Fatima , Gratacós Eduard 
Published: June 2020

AbstractThe goal of this study was to evaluate the maturity of current Deep Learning classification techniques for their application in a real maternal-fetal clinical environment. A large dataset of routinely acquired maternal-fetal screening ultrasound images (which will be made publicly available) was collected from two different hospitals by several operators and ultrasound machines. All images were manually labeled by an expert maternal fetal clinician. Images were divided into 6 classes: four of the most widely used fetal anatomical planes (Abdomen, Brain, Femur and Thorax), the mother’s cervix (widely used for prematurity screening) and a general category to include any other less common image plane. Fetal brain images were further categorized into the 3 most common fetal brain planes (Trans-thalamic, Trans-cerebellum, Trans-ventricular) to judge fine grain categorization performance. The final dataset is comprised of over 12,400 images from 1,792 patients, making it the largest ultrasound dataset to date. We then evaluated a wide variety of state-of-the-art deep Convolutional Neural Networks on this dataset and analyzed results in depth, comparing the computational models to research technicians, which are the ones currently performing the task daily. Results indicate for the first time that computational models have similar performance compared to humans when classifying common planes in human fetal examination. However, the dataset leaves the door open on future research to further improve results, especially on fine-grained plane categorization.
Orientation control of ideal blue phase photonic crystals
Authors: Otón Eva , Yoshida Hiroyuki , Morawiak Przemysław , Strzeżysz Olga , Kula Przemysław , Ozaki Masanori , Piecek Wiktor 
Published: June 2020

AbstractThree-dimensional (3D) photonic crystals like Blue Phases, self-assemble in highly organized structures with a sub-micrometer range periodicity, producing selective Bragg reflections in narrow bands. Current fabrication techniques are emerging at a fast pace, however, manufacturing large 3D monocrystals still remains a challenge, and controlling the crystal orientation of large crystals has not yet been achieved. In this work, we prepared ideal 3D Blue Phase macrocrystals with a controlled crystal orientation. We designed a method to obtain large monocrystals at a desired orientation and lattice size (or reflection wavelength) by adjusting the precursor materials formulation and a simple surface treatment. Moreover, using the same method, it is possible to predict unknown lattice orientations of Blue Phases without resorting to Kossel analysis. Producing large 3D photonic crystals that are also functional tunable structures is likely to have a direct impact on new photonic applications, like microcavity lasers, displays, 3D lasers, or biosensors.
Predictive value of heart rate deceleration capacity on coronary artery lesion in acute phase of Kawasaki disease
Authors: Lu Yaheng , Guo Yonghong , Si Feifei , Chen Tingting , Jin Mei , Wen Yizhou , Wang Xianmin 
Published: June 2020

AbstractThis study was to investigate the correlation of vagal activity with coronary artery lesion (CAL) in Kawasaki disease (KD) children, and assess the predictive value of heart rate deceleration capacity (DC) for CAL in acute phase of KD.50 KD children with CAL, 130 KD children without CAL, 30 children with acute upper respiratory infection and 100 healthy children were recruited and indicators reflecting vagal activity including DC were measstuogram. KD children with CAL showed decreased vagal activity with significantly lower values of DC. DC was negatively correlated with levels of N-terminal pro-brain natriuretic peptide (NT-proBNP) and C-reactive protein (CRP) in KD children. DC was a usable cardiac electrophysiological index to predict CAL in children with KD, with an area under the receiver operating characteristic curve (AUC) of 0.741. The cut-off value of DC for predicting CAL in KD children was 4.37 ms. DC was an independent predictor of CAL in children with KD, evaluated by multiple logistic regression analysis, KD children with DC ≤ 4.37 ms had an increased risk of CAL, with odds ratios (OR) of 5.94. Our study illustrates DC could be used to predict CAL in acute phase of KD.
CD47 is a negative regulator of intestinal epithelial cell self-renewal following DSS-induced experimental colitis
Authors: He Yueqin , Sun Xinlei , Rong Weiwei , Yang Rong , Liang Hongwei , Qi Ying , Li Limin , Zen Ke 
Published: June 2020

AbstractCD47 deficient mice are resistant to dextran sulfate sodium (DSS)-induced experimental colitis. The underlying mechanism, however, remains incompletely understood. In this study, we characterized the role of CD47 in modulating homeostasis of gastrointestinal tract. We found that CD47 expression in both human and mouse intestinal epithelium was upregulated in colitic condition compared to that under normal condition. In line with this, CD47 deficiency protected mice from DSS-induced colitis. Analysis based on both intestinal organoid and cultured cell assays showed that CD47 deficiency accelerated intestinal epithelial cell proliferation and migration. Mechanistically, western blot and functional assays indicated that CD47 deficiency promoting mouse intestinal epithelial cell proliferation and migration follow cell injury is likely through upregulating expression of four Yamanaka transcriptional factors Oct4, Sox2, Klf4 and c-Myc (OSKM in abbreviation). Our studies thus reveal CD47 as a negative regulator in intestinal epithelial cell renewal during colitis through downregulating OSKM transcriptional factors.