bluuebunny/crossref_metadata_2025_split huggingface dataset:
LSD1-mediated enhancer silencing attenuates retinoic acid signalling during pancreatic endocrine cell development
Authors: Vinckier Nicholas K. , Patel Nisha A. , Geusz Ryan J. , Wang Allen , Wang Jinzhao , Matta Ileana , Harrington Austin R. , Wortham Matthew , Wetton Nichole , Wang Jianxun , Jhala Ulupi S. , Rosenfeld Michael G. , Benner Christopher W. , Shih Hung-Ping , Sander Maike 
Published: April 2020

AbstractDevelopmental progression depends on temporally defined changes in gene expression mediated by transient exposure of lineage intermediates to signals in the progenitor niche. To determine whether cell-intrinsic epigenetic mechanisms contribute to signal-induced transcriptional responses, here we manipulate the signalling environment and activity of the histone demethylase LSD1 during differentiation of hESC-gut tube intermediates into pancreatic endocrine cells. We identify a transient requirement for LSD1 in endocrine cell differentiation spanning a short time-window early in pancreas development, a phenotype we reproduced in mice. Examination of enhancer and transcriptome landscapes revealed that LSD1 silences transiently active retinoic acid (RA)-induced enhancers and their target genes. Furthermore, prolonged RA exposure phenocopies LSD1 inhibition, suggesting that LSD1 regulates endocrine cell differentiation by limiting the duration of RA signalling. Our findings identify LSD1-mediated enhancer silencing as a cell-intrinsic epigenetic feedback mechanism by which the duration of the transcriptional response to a developmental signal is limited.
Goteo.org civic crowdfunding and match-funding data connecting Sustainable Development Goals
Authors: Fuster Morell Mayo , Senabre Hidalgo Enric , Rodríguez Enrique 
Published: April 2020

AbstractThe United Nations’ Sustainable Development Goals (SDGs) highlight priority areas for global sustainable development, such as reducing inequalities and protecting the environment. Digital platforms, such as Goteo.org, facilitate financial support from individuals for SDG-related initiatives through crowdfunding and match-funding campaigns. Match-funding is a type of crowdfunding, where individual donations are matched or multiplied by public and private organizations. There remains a lack of open data, however, to study the effectiveness of match-funding as a way to finance these civic initiatives. The Goteo.org platform’s approach to data transparency and open source principles have allowed these data to be collected, and here we present a dataset for 487 civic crowdfunding campaigns. This dataset presents a unique opportunity to compare the behaviour of different crowdfunding modalities in parallel with the SDGs.
Differential Impact of Sleep Deprivation and Circadian Timing on Reflexive Versus Inhibitory Control of Attention
Authors: Collet Jinny , Ftouni Suzanne , Clough Meaghan , Cain Sean W. , Fielding Joanne , Anderson Clare 
Published: April 2020

AbstractIn a visually stimulating environment with competing stimuli, we continually choose where to allocate attention, and what to ignore. Wake and circadian-dependent modulation of attentional control and resolution of conflict is poorly understood. Twenty-two participants (17males; 25.6 ± 5.6 years) completed ocular motor tasks throughout 40 hours of sleep deprivation under constant routine conditions. A prosaccade task required a reflexive saccade toward a stimulus (no conflict), while an antisaccade task required inhibiting a reflexive saccade to the peripheral stimulus, and looking in the mirror opposite instead (conflict resolution). Antisaccade inhibitory errors showed circadian modulation, being highest in the morning, progressively decreasing until melatonin onset, before returning to the prior morning’s peak throughout the biological night. This diurnal rhythm was blunted by sleep loss (>24 hours), with inhibitory control remaining impaired across the second biological day. For prosaccade, responses slowed down during the biological night. Taken together, we provide evidence for a circadian modulation of attentional bias: the morning being biased toward reflexive responding, and the evening toward higher inhibitory control. Our data show that sleep loss and circadian timing differentially impact attention, depending on whether a response conflict is present (antisaccade) or absent (prosaccade).
Airborne Optical Sectioning for Nesting Observation
Authors: Schedl David C. , Kurmi Indrajit , Bimber Oliver 
Published: April 2020

AbstractWe describe how a new and low-cost aerial scanning technique, airborne optical sectioning (AOS), can support ornithologists in nesting observation. After capturing thermal and color images during a seven minutes drone flight over a 40 × 12 m patch of the nesting site of Austria’s largest heron population, a total of 65 herons and 27 nests could be identified, classified, and localized in a sparse 3D reconstruction of the forest. AOS is a synthetic aperture imaging technique that removes occlusion caused by leaves and branches. It registers recorded images to a common 3D coordinate system to support the reconstruction and analysis of the entire forest volume, which is impossible with conventional 2D or 3D imaging techniques. The recorded data is published with open access.
Gamma-Ray and Radio-Frequency Radiation from Thunderstorms Observed from Space and Ground
Authors: Mailyan B. G. , Nag A. , Dwyer J. R. , Said R. K. , Briggs M. S. , Roberts O. J. , Stanbro M. , Rassoul H. K. 
Published: April 2020

AbstractTerrestrial gamma ray flashes (TGFs) are a class of enigmatic electrical discharges in the Earth’s atmosphere. In this study, we analyze an unprecedentedly large dataset comprised of 2188 TGFs whose signatures were simultaneously measured using space- and ground-based detectors over a five-year period. The Gamma-ray Burst Monitor (GBM) on board the Fermi spacecraft provided the energetic radiation measurements. Radio frequency (RF) measurements were obtained from the Global Lightning Dataset (GLD360). Here we show the existence of two categories of TGFs − those that were accompanied by quasi-simultaneous electromagnetic pulses (EMPs) detected by the GLD360 and those without such simultaneous EMPs. We examined, for the first time, the dependence of the TGF-associated EMP-peak-amplitude on the horizontal offset distance between the Fermi spacecraft and the TGF source. TGFs detected by the GBM with sources at farther horizontal distances are expected to be intrinsically brighter and were found to be associated with EMPs having larger median peak-amplitudes. This provides independent evidence that the EMPs and TGFs are produced by the same phenomenon, rather than the EMPs being from “regular” lightning in TGF-producing thunderstorms.
Brain distribution of geissoschizine methyl ether in rats using mass spectrometry imaging analysis
Authors: Matsumoto Takashi , Ikarashi Yasushi , Takiyama Mikina , Watanabe Junko , Setou Mitsutoshi 
Published: April 2020

AbstractGeissoschizine methyl ether (GM) is one of the main active ingredients responsible for ameliorating the behavioral and psychological symptoms of dementia (BPSD) in Kampo medicine yokukansan. GM is mainly metabolized into hydroxylated forms (HM-1/2). However, the brain distributions of GM and HM has not been reported in vivo. In this study, therefore, the plasma concentrations and brain distribution of these compounds were examined in vivo using rats injected intravenously with GM. Plasma concentrations were analyzed using liquid chromatography-tandem mass spectrometry analysis and brain distribution using mass spectrometry imaging analysis. Plasma GM and HM-1 concentrations decreased in the 4 h after injection, whereas the concentration of plasma HM-2 increased at 4 h. In the 0.25 h-brain, GM signals were diffusely observed throughout the brain, including the cerebral cortex, hippocampus, striatum, thalamus, amygdala, cerebellum, and cerebral ventricle. HM signals were detected only in the ventricles of the brain at 4 h. These results suggest that plasma GM enters the brain and distributes in the parenchyma of various brain regions involved in BPSD, while plasma HM does not enter the brain parenchyma. This study is also the first to visually demonstrate the brain distribution of GM and its metabolite in vivo.
Standardised comparison of limonene-derived monoterpenes identifies structural determinants of anti-inflammatory activity
Authors: Sousa Cátia , Leitão Alcino Jorge , Neves Bruno Miguel , Judas Fernando , Cavaleiro Carlos , Mendes Alexandrina Ferreira 
Published: April 2020

AbstractMint species are widely used in traditional and conventional medicine as topical analgesics for osteoarthritic pain and for disorders of the gastrointestinal and respiratory tracts which are all associated with chronic inflammation. To identify the structural determinants of anti-inflammatory activity and potency which are required for chemical optimization towards development of new anti-inflammatory drugs, a selected group of monoterpenes especially abundant in mint species was screened by measuring bacterial lipopolysacharide (LPS)-induced nitric oxide (NO) production in murine macrophages. Nine compounds significantly decreased LPS-induced NO production by more than 30%. IC50 values were calculated showing that the order of potency is: (S)-(+)-carvone > (R)-(−)-carvone > (+)-dihydrocarveol > (S)-8-hydroxycarvotanacetone > (R)-8-hydroxycarvotanacetone > (+)-dihydrocarvone > (−)-carveol > (−)-dihydrocarveol > (S)-(-)-pulegone. Considering the carbon numbering relative to the common precursor, limonene, the presence of an oxygenated group at C6 conjugated to a double bond at C1 and an isopropenyl group and S configuration at C4 are the major chemical features relevant for activity and potency. The most potent compound, (S)-(+)-carvone, significantly decreased the expression of NOS2 and IL-1β in macrophages and in a cell model of osteoarthritis using primary human chondrocytes. (S)-(+)-carvone may be efficient in halting inflammation-related diseases, like osteoarthritis.
Multi-layered Free-form 3D Cell-printed Tubular Construct with Decellularized Inner and Outer Esophageal Tissue-derived Bioinks
Authors: Nam Hyoryung , Jeong Hun-Jin , Jo Yeonggwon , Lee Jae Yeon , Ha Dong-Heon , Kim Ji Hyun , Chung Jae Hee , Cho Young-Sam , Cho Dong-Woo , Lee Seung-Jae , Jang Jinah 
Published: April 2020

AbstractThe incidences of various esophageal diseases (e.g., congenital esophageal stenosis, tracheoesophageal fistula, esophageal atresia, esophageal cancer) are increasing, but esophageal tissue is difficult to be recovered because of its weak regenerative capability. There are no commercialized off-the-shelf alternatives to current esophageal reconstruction and regeneration methods. Surgeons usually use ectopic conduit tissues including stomach and intestine, presumably inducing donor site morbidity and severe complications. To date, polymer-based esophageal substitutes have been studied as an alternative. However, the fabrication techniques are nearly limited to creating only cylindrical outer shapes with the help of additional apparatus (e.g., mandrels for electrospinning) and are unable to recapitulate multi-layered characteristic or complex-shaped inner architectures. 3D bioprinting is known as a suitable method to fabricate complex free-form tubular structures with desired pore characteristic. In this study, we developed a extrusion-based 3D printing technique to control the size and the shape of the pore in a single extrusion process, so that the fabricated structure has a higher flexibility than that fabricated in the conventional process. Based on this suggested technique, we developed a bioprinted 3D esophageal structure with multi-layered features and converged with biochemical microenvironmental cues of esophageal tissue by using decellularizedbioinks from mucosal and muscular layers of native esophageal tissues. The two types of esophageal tissue derived-decellularized extracellular matrix bioinks can mimic the inherent components and composition of original tissues with layer specificity. This structure can be applied to full-thickness circumferential esophageal defects and esophageal regeneration.
Extreme events are more likely to affect the breeding success of lesser kestrels than average climate change
Authors: Marcelino J. , Silva J. P. , Gameiro J. , Silva A. , Rego F. C. , Moreira F. , Catry I. 
Published: April 2020

AbstractClimate change is predicted to severely impact interactions between prey, predators and habitats. In Southern Europe, within the Mediterranean climate, herbaceous vegetation achieves its maximum growth in middle spring followed by a three-month dry summer, limiting prey availability for insectivorous birds. Lesser kestrels (Falco naumanni) breed in a time-window that matches the nestling-rearing period with the peak abundance of grasshoppers and forecasted climate change may impact reproductive success through changes in prey availability and abundance. We used Normalised Difference Vegetation Index (NDVI) as a surrogate of habitat quality and prey availability to investigate the impacts of forecasted climate change and extreme climatic events on lesser kestrel breeding performance. First, using 14 years of data from 15 colonies in Southwestern Iberia, we linked fledging success and climatic variables with NDVI, and secondly, based on these relationships and according to climatic scenarios for 2050 and 2070, forecasted NDVI and fledging success. Finally, we evaluated how fledging success was influenced by drought events since 2004. Despite predicting a decrease in vegetation greenness in lesser kestrel foraging areas during spring, we found no impacts of predicted gradual rise in temperature and decline in precipitation on their fledging success. Notwithstanding, we found a decrease of 12% in offspring survival associated with drought events, suggesting that a higher frequency of droughts might, in the future, jeopardize the recent recovery of the European population. Here, we show that extreme events, such as droughts, can have more significant impacts on species than gradual climatic changes, especially in regions like the Mediterranean Basin, a biodiversity and climate change hotspot.
Millennial scale maximum intensities of typhoon and storm wave in the northwestern Pacific Ocean inferred from storm deposited reef boulders
Authors: Minamidate Kenta , Goto Kazuhisa , Watanabe Masashi , Roeber Volker , Toguchi Ken , Sannoh Masami , Nakashima Yosuke , Kan Hironobu 
Published: April 2020

AbstractTyphoons and associated storm waves in the northwestern Pacific Ocean commonly cause coastal disasters. The possibility remains that an even stronger typhoon than the strongest one observed to date might have occurred before. The development of a method to estimate a maximum intensity of past typhoons over thousands of years is important for paleoclimatology, paleoceanography and disaster prevention. Numerous storm wave boulders exist on reefs in the Ryukyu Islands, Japan, which have been deposited to their present position by the cumulative effects of the past storm waves. These boulders can be used as proxies for the hydrodynamic conditions of the largest waves from past events. Here, we present numerical computations for storm waves and boulder transport with the boulder distribution as a constraint factor to estimate the maximum intensities of storm waves and their causative typhoon events over the past 3500 years. Though the intensities of the maximum estimated waves and associated typhoon events were slightly stronger than those recorded over the past ~70 years in the Ryukyu Islands, our results suggest that no abnormally intense typhoon has struck the Ryukyu Islands in the past 3500 years. The potential impact from tsunamis remains uncertain; however, our results are meteorologically reasonable.
Antimicrobial activity of a silver-microfibrillated cellulose biocomposite against susceptible and resistant bacteria
Authors: Garza-Cervantes Javier Alberto , Mendiola-Garza Gricelda , de Melo Eduardo Macedo , Dugmore Tom I. J. , Matharu Avtar S. , Morones-Ramirez Jose Ruben 
Published: April 2020

AbstractAntibiotic Microbial Resistance (AMR) is a major global challenge as it constitutes a severe threat to global public health if not addressed. To fight against AMR bacteria, new antimicrobial agents are continually needed, and their efficacy must be tested. Historically, many transition metals have been employed, but their cytotoxicity is an issue and hence must be reduced, typically by combination with organic polymers. Cellulose of natural origin, especially those derived from unavoidable residues in the food supply chain, appears to be a good capping agent for the green synthesis of silver nanoparticles. Herein, we describe a green synthesis method to produce a novel biocomposite, using ascorbic acid as reducing agent and microfibrillated cellulose as a capping agent and demonstrate this material to be an efficient antimicrobial agent. Silver nanoparticles were obtained in the cellulose matrix with an average size of 140 nm and with antimicrobial activity against both sensitive and resistant Gram positive (using 1500 ppm) as well as sensitive and resistant Gram negative (using 125 ppm) bacteria. Also, an inverted disk-diffusion methodology was applied to overcome the low-solubility of cellulose compounds. This novel silver nanoparticle-cellulose biocomposite synthesized by a green methodology shows the potential to be applied in the future development of biomedical instruments and therapeutics.
The Effect of Force-Field Parameters on Cytochrome P450-Membrane Interactions: Structure and Dynamics
Authors: Mustafa Ghulam , Nandekar Prajwal P. , Mukherjee Goutam , Bruce Neil J. , Wade Rebecca C. 
Published: April 2020

AbstractThe simulation of membrane proteins requires compatible protein and lipid force fields that reproduce the properties of both the protein and the lipid bilayer. Cytochrome P450 enzymes are bitopic membrane proteins with a transmembrane helical anchor and a large cytosolic globular domain that dips into the membrane. As such, they are representative and challenging examples of membrane proteins for simulations, displaying features of both peripheral and integral membrane proteins. We performed molecular dynamics simulations of three cytochrome P450 isoforms (2C9, 2C19 and 1A1) in a 2-oleoyl-1-palmitoyl-sn-glycerol-3-phosphocholine bilayer using two AMBER force field combinations: GAFF-LIPID with ff99SB for the protein, and LIPID14 with ff14SB for the protein. Comparison of the structural and dynamic properties of the proteins, the lipids and the protein-membrane interactions shows differing sensitivity of the cytochrome P450 isoforms to the choice of force field, with generally better agreement with experiment for the LIPID14 + ff14SB combination.
On the Thermal Performance of a Fractal Microchannel Subjected to Water and Kerosene Carbon Nanotube Nanofluid
Authors: Lyu Zongjie , Pourfattah Farzad , Arani Ali Akbar Abbasian , Asadi Amin , Foong Loke Kok 
Published: April 2020

AbstractUsing single layer microchannels accompanied by nanofluids is one of the most practical solutions in thermal management of high power density devices. The main challenge in cooling systems of electronic devices is to provide a uniform temperature distribution. In the present study, fluid flow and heat transfer in a fractal microchannel heatsink have been simulated employing the computational fluid dynamics (CFD) method. The fractal microchannel is used to achieve uniform temperature distribution. Thermal performance of single-walled carbon nanotubes (SWCNT) and multi-walled carbon nanotubes (MWCNT) dispersed in the two base fluids of water and kerosene in a fractal microchannel at Reynolds (Re) numbers of 1500 to 3000 are investigated. It should be noted that the nanofluids have been simulated by the two-phase mixture model. The results indicated that the use of fractals silicon microchannel leads to having a uniform temperature distribution. Based on the results, at maximum Re number when the working fluid is water, Nu number and pumping power are 20.9 and 0.033 W whereas, in kerosene flow at the same condition, Nu number and pumping power are 6 and 0.054 W, respectively. According to the obtained results, using the SWCNT nanoparticle compared with the MWCNT nanoparticle leads to a significant enhancement in the Nusselt (Nu) number. This difference is more pronounced by increasing the Re number and nanoparticle volume fraction. In addition, the results indicated that at the same Re number and nanoparticle volume fraction, the performance evaluation criterion of the water-based nanofluid is 4 times higher than that of the kerosene-based nanofluid. So the use of the water as the working fluid with the SWCNT nanoparticle for cooling in the fractal silicon microchannel is recommended.
Deep learned tissue “fingerprints” classify breast cancers by ER/PR/Her2 status from H&E images
Authors: Rawat Rishi R. , Ortega Itzel , Roy Preeyam , Sha Fei , Shibata Darryl , Ruderman Daniel , Agus David B. 
Published: April 2020

AbstractBecause histologic types are subjective and difficult to reproduce between pathologists, tissue morphology often takes a back seat to molecular testing for the selection of breast cancer treatments. This work explores whether a deep-learning algorithm can learn objective histologic H&E features that predict the clinical subtypes of breast cancer, as assessed by immunostaining for estrogen, progesterone, and Her2 receptors (ER/PR/Her2). Translating deep learning to this and related problems in histopathology presents a challenge due to the lack of large, well-annotated data sets, which are typically required for the algorithms to learn statistically significant discriminatory patterns. To overcome this limitation, we introduce the concept of “tissue fingerprints,” which leverages large, unannotated datasets in a label-free manner to learn H&E features that can distinguish one patient from another. The hypothesis is that training the algorithm to learn the morphological differences between patients will implicitly teach it about the biologic variation between them. Following this training internship, we used the features the network learned, which we call “fingerprints,” to predict ER, PR, and Her2 status in two datasets. Despite the discovery dataset being relatively small by the standards of the machine learning community (n = 939), fingerprints enabled the determination of ER, PR, and Her2 status from whole slide H&E images with 0.89 AUC (ER), 0.81 AUC (PR), and 0.79 AUC (Her2) on a large, independent test set (n = 2531). Tissue fingerprints are concise but meaningful histopathologic image representations that capture biological information and may enable machine learning algorithms that go beyond the traditional ER/PR/Her2 clinical groupings by directly predicting theragnosis.