bluuebunny/crossref_metadata_2025_split huggingface dataset:
A system wide approach to managing zoo collections for visitor attendance and in situ conservation
Authors: Mooney Andrew , Conde Dalia A. , Healy Kevin , Buckley Yvonne M. 
Published: February 2020

AbstractZoos contribute substantial resources to in situ conservation projects in natural habitats using revenue from visitor attendance, as well as other sources. We use a global dataset of over 450 zoos to develop a model of how zoo composition and socio-economic factors directly and indirectly influence visitor attendance and in situ project activity. We find that zoos with many animals, large animals, high species richness (particularly of mammals), and which are dissimilar to other zoos achieve higher numbers of visitors and contribute to more in situ conservation projects. However, the model strongly supports a trade-off between number of animals and body mass indicating that alternative composition strategies, such as having many small animals, may also be effective. The evidence-base presented here can be used to help guide collection planning processes and increase the in situ contributions from zoos, helping to reduce global biodiversity loss.
Liver governs adipose remodelling via extracellular vesicles in response to lipid overload
Authors: Zhao Yue , Zhao Meng-Fei , Jiang Shan , Wu Jing , Liu Jia , Yuan Xian-Wen , Shen Di , Zhang Jing-Zi , Zhou Nan , He Jian , Fang Lei , Sun Xi-Tai , Xue Bin , Li Chao-Jun 
Published: February 2020

AbstractLipid overload results in lipid redistribution among metabolic organs such as liver, adipose, and muscle; therefore, the interplay between liver and other organs is important to maintain lipid homeostasis. Here, we show that liver responds to lipid overload first and sends hepatocyte-derived extracellular vesicles (EVs) targeting adipocytes to regulate adipogenesis and lipogenesis. Geranylgeranyl diphosphate synthase (Ggpps) expression in liver is enhanced by lipid overload and regulates EV secretion through Rab27A geranylgeranylation. Consistently, liver-specific Ggpps deficient mice have reduced fat adipose deposition. The levels of several EV-derived miRNAs in the plasma of non-alcoholic fatty liver disease (NAFLD) patients are positively correlated with body mass index (BMI), and these miRNAs enhance adipocyte lipid accumulation. Thus, we highlight an inter-organ mechanism whereby the liver senses different metabolic states and sends corresponding signals to remodel adipose tissue to adapt to metabolic changes in response to lipid overload.
Chiral terahertz wave emission from the Weyl semimetal TaAs
Authors: Gao Y. , Kaushik S. , Philip E. J. , Li Z. , Qin Y. , Liu Y. P. , Zhang W. L. , Su Y. L. , Chen X. , Weng H. , Kharzeev D. E. , Liu M. K. , Qi J. 
Published: February 2020

AbstractWeyl semimetals host chiral fermions with distinct chiralities and spin textures. Optical excitations involving those chiral fermions can induce exotic carrier responses, and in turn lead to novel optical phenomena. Here, we discover strong coherent terahertz emission from Weyl semimetal TaAs, which is demonstrated as a unique broadband source of the chiral terahertz wave. The polarization control of the THz emission is achieved by tuning photoexcitation of ultrafast photocurrents via the photogalvanic effect. In the near-infrared regime, the photon-energy dependent nonthermal current due to the predominant circular photogalvanic effect can be attributed to the radical change of the band velocities when the chiral Weyl fermions are excited during selective optical transitions between the tilted anisotropic Weyl cones and the massive bulk bands. Our findings provide a design concept for creating chiral photon sources using quantum materials and open up new opportunities for developing ultrafast opto-electronics using Weyl physics.
Pre-processing visualization of hyperspectral fluorescent data with Spectrally Encoded Enhanced Representations
Authors: Shi Wen , Koo Daniel E. S. , Kitano Masahiro , Chiang Hsiao J. , Trinh Le A. , Turcatel Gianluca , Steventon Benjamin , Arnesano Cosimo , Warburton David , Fraser Scott E. , Cutrale Francesco 
Published: February 2020

AbstractHyperspectral fluorescence imaging is gaining popularity for it enables multiplexing of spatio-temporal dynamics across scales for molecules, cells and tissues with multiple fluorescent labels. This is made possible by adding the dimension of wavelength to the dataset. The resulting datasets are high in information density and often require lengthy analyses to separate the overlapping fluorescent spectra. Understanding and visualizing these large multi-dimensional datasets during acquisition and pre-processing can be challenging. Here we present Spectrally Encoded Enhanced Representations (SEER), an approach for improved and computationally efficient simultaneous color visualization of multiple spectral components of hyperspectral fluorescence images. Exploiting the mathematical properties of the phasor method, we transform the wavelength space into information-rich color maps for RGB display visualization. We present multiple biological fluorescent samples and highlight SEER’s enhancement of specific and subtle spectral differences, providing a fast, intuitive and mathematical way to interpret hyperspectral images during collection, pre-processing and analysis.
Ranking environmental degradation trends of plastic marine debris based on physical properties and molecular structure
Authors: Min Kyungjun , Cuiffi Joseph D. , Mathers Robert T. 
Published: February 2020

AbstractAs plastic marine debris continues to accumulate in the oceans, many important questions surround this global dilemma. In particular, how many descriptors would be necessary to model the degradation behavior of ocean plastics or understand if degradation is possible? Here, we report a data-driven approach to elucidate degradation trends of plastic debris by linking abiotic and biotic degradation behavior in seawater with physical properties and molecular structures. The results reveal a hierarchy of predictors to quantify surface erosion as well as combinations of features, like glass transition temperature and hydrophobicity, to classify ocean plastics into fast, medium, and slow degradation categories. Furthermore, to account for weathering and environmental factors, two equations model the influence of seawater temperature and mechanical forces.
X-ray Phase Contrast osteo-articular imaging: a pilot study on cadaveric human hands
Authors: Rougé-Labriet Hélène , Berujon Sebastien , Mathieu Hervé , Bohic Sylvain , Fayard Barbara , Ravey Jean-Noel , Robert Yohann , Gaudin Philippe , Brun Emmanuel 
Published: February 2020

AbstractX-ray Phase Contrast Imaging (PCI) is an emerging modality whose availability in clinics for mammography and lung imaging is expected to materialize within the coming years. In this study, we evaluate the PCI Computed Tomography (PCI-CT) performances with respect to current conventional imaging modalities in the context of osteo-articular disorders diagnosis. X-ray PCI-CT was performed on 3 cadaveric human hands and wrists using a synchrotron beam. Conventional CT, MRI and Ultrasound were also performed on these three samples using routine procedures as well as research protocols. Six radiologists and rheumatologists independently evaluated qualitatively and semi quantitatively the 3D images’ quality. Medical interpretations were also made from the images. PCI-CT allows the simultaneous visualization of both the high absorbing and the softer tissues. The 6 reader evaluations characterized PCI-CT as a visualization tool with improved performances for all tissue types (significant p-values), which provides sharper outlines and clearer internal structures than images obtained using conventional modalities. The PCI-CT images contain overall more information, especially at smaller scales with for instance more visible micro-calcifications in our chondrocalcinosis case. Despite a reduced number of samples used, this pilot study highlights the possible medical benefits of PCI for osteo-articular disorders evaluation. Although PCI-CT is not yet available in hospitals, the improved visualization capabilities demonstrated so far and the enhanced tissue measurement quality let suggest strong diagnosis benefits for rheumatology in case of a widespread application of PCI.
Nerve damage induced skeletal muscle atrophy is associated with increased accumulation of intramuscular glucose and polyol pathway intermediates
Authors: Langer Henning Tim , Afzal Shoaib , Kempa Stefan , Spuler Simone 
Published: February 2020

AbstractPerturbations in skeletal muscle metabolism have been reported for a variety of neuromuscular diseases. However, the role of metabolism after constriction injury to a nerve and the associated muscle atrophy is unclear. We have analyzed rat tibialis anterior (TA) four weeks after unilateral constriction injury to the sciatic nerve (DMG) and in the contralateral control leg (CTRL) (n = 7) to investigate changes of the metabolome, immunohistochemistry and protein levels. Untargeted metabolomics identified 79 polar metabolites, 27 of which were significantly altered in DMG compared to CTRL. Glucose concentrations were increased 2.6-fold in DMG, while glucose 6-phosphate (G6-P) was unchanged. Intermediates of the polyol pathway were increased in DMG, particularly fructose (1.7-fold). GLUT4 localization was scattered as opposed to clearly at the sarcolemma. Despite the altered localization, we found GLUT4 protein levels to be increased 7.8-fold while GLUT1 was decreased 1.7-fold in nerve damaged TA. PFK1 and GS levels were both decreased 2.1-fold, indicating an inability of glycolysis and glycogen synthesis to process glucose at sufficient rates. In conclusion, chronic nerve constriction causes increased GLUT4 levels in conjunction with decreased glycolytic activity and glycogen storage in skeletal muscle, resulting in accumulation of intramuscular glucose and polyol pathway intermediates.
First continuous pre-Jaramillo to Jaramillo terrestrial vertebrate succession from Europe
Authors: Piñero Pedro , Agustí Jordi , Oms Oriol , Blain Hugues-Alexandre , Furió Marc , Laplana César , Sevilla Paloma , Rosas Antonio , Vallverdú Josep 
Published: February 2020

AbstractIn this paper, the early Pleistocene small vertebrate sequence of Quibas-Sima (Quibas karstic complex, Murcia, SE Spain) is presented. The available magnetostratigraphic information together with the small vertebrate association, allow to reliably constrain the age of the different units. The basal unit of the section has recorded a reversed polarity assigned to the pre-Jaramillo Matuyama (C1r.2r, i.e., between 1.2 and 1.07 Ma). The intermediate units have recorded a normal polarity correlated directly with the Jaramillo subchron (C1r.1n, between 1.07 and 0.99 Ma), while the upper units record the post-Jaramillo reverse polarity (C1r.1r, i.e., between 0.99 and 0.78). Jaramillo subchron is especially significant regarding the earliest hominin dispersal in Western Europe. However, vertebrate faunas unambiguously correlatable with Jaramillo subchron are extremely rare in Europe. Thereby, the study of the Quibas-Sima sequence allows to characterize the vertebrate association synchronous to this paleomagnetic episode in southern Iberian Peninsula, and contributes to increase knowledge of the biotic and climatic events that took place in southern Europe at the beginning of the Early-Middle Pleistocene transition, prior to the Matuyama-Brunhes boundary. A continuous small vertebrate succession has been reported, including representatives of the families Bufonidae, Pelodytidae, Testudinidae, Gekkonidae, Blanidae, Lacertidae, Colubridae, Viperidae, Soricidae, Erinaceidae, Rhinolophidae, Vespertilionidae, Muridae, Gliridae, Sciuridae, Leporidae and Ochotonidae The ecological affinities of the faunal association suggest a progressive reduction in forest cover in the onset of the Jaramillo subchron.
Antiviral activity of iridoid glycosides extracted from Fructus Gardeniae against influenza A virus by PACT-dependent suppression of viral RNA replication
Authors: Guo Shanshan , Bao Lei , Li Chun , Sun Jing , Zhao Ronghua , Cui Xiaolan 
Published: February 2020

AbstractEpidemic and pandemic influenza A virus (IAV) poses a significant threat to human populations worldwide. Iridoid glycosides are principal bioactive components from the Gardenia jasminoides J. Ellis fruit that exhibit antiviral activity against several strains of IAV. In the present study, we evaluated the protective effect of Fructus Gardeniae iridoid glycoside extracts (IGEs) against IAV by cytopathogenic effect(CPE), MTT and a plaque formation assay in vitro and examined the reduction in the pulmonary index (PI), restoration of body weight, reduction in mortality and increases in survival time in vivo. As a host factor, PACT provides protection against the pathogenic influenza A virus by interacting with IAV polymerase and activating the IFN-I response. To verify the whether IGEs suppress IAV replication in a PACT-dependent manner, IAV RNA replication, expression of PACT and the phosphorylation of eIF2α in A549 cells were detected; the levels of IFNβ, PACT and PKR in mouse lung tissues were determined; and the activity of IAV polymerase was evaluated in PACT-compromised cells. The results indicated that IGEs sufficiently alleviated cell damage and suppressed IAV replication in vitro, protecting mice from IAV-induced injury and lethal IAV infection. These anti-IAV effects might be related to disrupted interplay between IVA polymerase and PACT and/or prevention of a PACT-dependent overactivated IFN-I antiviral response. Taken together, our findings reveal a new facet of the mechanisms by which IGEs fight the influenza A virus in a PACT-dependent manner.
Taming age mortality in semi-captive Asian elephants
Authors: Crawley Jennie A. H. , Lahdenperä Mirkka , Min Oo Zaw , Htut Win , Nandar Hnin , Lummaa Virpi 
Published: February 2020

AbstractUnderstanding factors preventing populations of endangered species from being self-sustaining is vital for successful conservation, but we often lack sufficient data to understand dynamics. The global Asian elephant population has halved since the 1950s, however >25% currently live in captivity and effective management is essential to maintain viable populations. Here, we study the largest semi-captive Asian elephant population, those of the Myanma timber industry (~20% global captive population), whose population growth is heavily limited by juvenile mortality. We assess factors associated with increased mortality of calves aged 4.0–5.5 years, the taming age in Myanmar, a process affecting ~15,000 captive elephants to varying degrees worldwide. Using longitudinal survival data of 1,947 taming-aged calves spanning 43 years, we showed that calf mortality risk increased by >50% at the taming age of four, a peak not seen in previous studies on wild African elephants. Calves tamed at younger ages experienced higher mortality risk, as did calves with less experienced mothers. Taming-age survival greatly improved after 2000, tripling since the 1970’s. Management should focus on reducing risks faced by vulnerable individuals such as young and first-born calves to further improve survival. Changes associated with reduced mortality here are important targets for improving the sustainability of captive populations.
Integrative network modeling reveals mechanisms underlying T cell exhaustion
Authors: Bolouri Hamid , Young Mary , Beilke Joshua , Johnson Rebecca , Fox Brian , Huang Lu , Santini Cristina Costa , Hill Christopher Mark , Vries Anne-Renee van der Vuurst de , Shannon Paul T. , Dervan Andrew , Sivakumar Pallavur , Trotter Matthew , Bassett Douglas , Ratushny Alexander 
Published: February 2020

AbstractFailure to clear antigens causes CD8+ T cells to become increasingly hypo-functional, a state known as exhaustion. We combined manually extracted information from published literature with gene expression data from diverse model systems to infer a set of molecular regulatory interactions that underpin exhaustion. Topological analysis and simulation modeling of the network suggests CD8+ T cells undergo 2 major transitions in state following stimulation. The time cells spend in the earlier pro-memory/proliferative (PP) state is a fixed and inherent property of the network structure. Transition to the second state is necessary for exhaustion. Combining insights from network topology analysis and simulation modeling, we predict the extent to which each node in our network drives cells towards an exhausted state. We demonstrate the utility of our approach by experimentally testing the prediction that drug-induced interference with EZH2 function increases the proportion of pro-memory/proliferative cells in the early days post-activation.
Attenuation of bile acid-mediated FXR and PXR activation in patients with Crohn’s disease
Authors: Wilson Aze , Almousa Ahmed , Teft Wendy A. , Kim Richard B. 
Published: February 2020

AbstractBile acids are endogenous ligands of nuclear receptors pregnane X (PXR) and farnesoid X (FXR). PXR and FXR regulate pathways that are impaired in inflammatory bowel disease (IBD). Decreases in PXR and FXR activity are documented in IBD; however reasons for this are unknown. We aimed to assess the effect of Crohn’s disease (CD) on the plasma bile acid composition in vivo and the resultant impact on PXR and FXR activation. A cross-sectional study evaluated the plasma concentrations of 12 bile acids in addition to 4β-hydroxycholesterol (4βOHC), an in vivo probe of the PXR target-gene cytochrome 3A4 (CYP3A4) and the FXR target-gene, fibroblast growth factor (FGF) 19 in individuals with (n = 74) and without (n = 71) CD. An in vitro model was used to assess the impact of CD-specific changes in the plasma bile acid composition on PXR and FXR activation. Decreases in glycochenodeoxycholic acid, taurocholic acid and lithocholic acid were seen in CD with increases in glycodeoxycholic acid and glycocholic acid relative to the total plasma bile acid profile. In vitro, increasing concentrations of bile acids applied in the same ratio as seen in the study cohorts resulted in decreased activation of both PXR and FXR in the CD model. In vivo, plasma 4βOHC (CD = 18.68 ng/ml ± 13.02 ng/ml, non-CD = 46.38 ng/ml ± 40.70 ng/ml, p ≤ 0.0001) and FGF19 (CD = 0.276 pg/L ± 0.189 pg/L, non-CD = 0.485 pg/L ± 0.42 pg/L, p = 0.0002) concentrations were lower in CD versus controls. Ultimately, CD-specific changes in the plasma bile acid composition lead to reduced activation of FXR and PXR target genes in vitro and in vivo.
A frugal implementation of Surface Enhanced Raman Scattering for sensing Zn2+ in freshwaters – In depth investigation of the analytical performances
Authors: Brackx Gwennhaël , Guinoiseau Damien , Duponchel Ludovic , Gélabert Alexandre , Reichel Victoria , Zrig Samia , Meglio Jean-Marc Di , Benedetti Marc F. , Gaillardet Jérôme , Charron Gaëlle 
Published: February 2020

AbstractSurface Enhanced Raman Scattering (SERS) has been widely praised for its extreme sensitivity but has not so far been put to use in routine analytical applications, with the accessible scale of measurements a limiting factor. We report here on a frugal implementation of SERS dedicated to the quantitative detection of Zn2+ in water, Zn being an element that can serve as an indicator of contamination by heavy metals in aquatic bodies. The method consists in randomly aggregating simple silver colloids in the analyte solution in the presence of a complexometric indicator of Zn2+, recording the SERS spectrum with a portable Raman spectrometer and analysing the data using multivariate calibration models. The frugality of the sensing procedure enables us to acquire a dataset much larger than conventionally done in the field of SERS, which in turn allows for an in-depth statistical analysis of the analytical performances that matter to end-users. In pure water, the proposed sensor is sensitive and accurate in the 160–2230 nM range, with a trueness of 96% and a precision of 4%. Although its limit of detection is one order of magnitude higher than those of golden standard techniques for quantifying metals, its sensitivity range matches Zn levels that are relevant to the health of aquatic bodies. Moreover, its frugality positions it as an interesting alternative to monitor water quality. Critically, the combination of the simple procedure for sample preparation, abundant SERS material and affordable portable instrument paves the way for a realistic deployment to the water site, with each Zn reading three to five times cheaper than through conventional techniques. It could therefore complement current monitoring methods in a bid to solve the pressing needs for large scale water quality data.
Applicability of Anatomical Landmarks for Chest Compression Depth in Cardiopulmonary Resuscitation for Children
Authors: Kim Yong Hwan , Lee Jun Ho , Lee Dong Woo , Song Yun Gyu , Lee Kyoung Yul , Lee Young Hwan , Hwang Seong Youn , Yeom Seok Ran 
Published: February 2020

AbstractWe evaluated the applicability of the neck and sternal notch (SN) as anatomical landmarks for paediatric chest compression (CC) depth using chest computed tomography. The external anteroposterior diameter (EAPD) of the neck and chest at the SN level, mid-point between two landmarks (mid-landmark), and EAPD of the chest at the lower half of the sternum (EDLH) were measured. To estimate the depths of the landmarks from a virtual point at the same height as the position for CC, we calculated the differences between the EAPDs of the neck, SN, mid-landmark, and EDLH. We analysed the relationship between the depths of the landmarks and one-third EDLH using Bland–Altman plots. In all, 506 paediatric patients aged 1–9 years were enrolled. The depths of the neck, SN, and mid-landmark were 53.7 ± 10.0, 37.8 ± 8.5, and 45.8 ± 9.0 mm, respectively. The mean one-third EDLH was 46.8 ± 7.0 mm. The means of the differences between the depths of the neck and one-third EDLH, depths of the SN and one-third EDLH, and depths of the mid-landmark and one-third EDLH were 9.0, −6.9, and 1.0 mm, respectively. The SN and neck are inappropriate landmarks to guide compression depth in paediatric CPR.
Identification and characterization of novel filament-forming proteins in cyanobacteria
Authors: Springstein Benjamin L. , Woehle Christian , Weissenbach Julia , Helbig Andreas O. , Dagan Tal , Stucken Karina 
Published: February 2020

AbstractFilament-forming proteins in bacteria function in stabilization and localization of proteinaceous complexes and replicons; hence they are instrumental for myriad cellular processes such as cell division and growth. Here we present two novel filament-forming proteins in cyanobacteria. Surveying cyanobacterial genomes for coiled-coil-rich proteins (CCRPs) that are predicted as putative filament-forming proteins, we observed a higher proportion of CCRPs in filamentous cyanobacteria in comparison to unicellular cyanobacteria. Using our predictions, we identified nine protein families with putative intermediate filament (IF) properties. Polymerization assays revealed four proteins that formed polymersin vitroand three proteins that formed polymersin vivo. Fm7001 fromFischerella muscicolaPCC 7414 polymerizedin vitroand formed filamentsin vivoin several organisms. Additionally, we identified a tetratricopeptide repeat protein - All4981 - inAnabaenasp. PCC 7120 that polymerized into filamentsin vitroandin vivo. All4981 interacts with known cytoskeletal proteins and is indispensable forAnabaenaviability. Although it did not form filamentsin vitro, Syc2039 fromSynechococcus elongatusPCC 7942 assembled into filamentsin vivoand a Δsyc2039mutant was characterized by an impaired cytokinesis. Our results expand the repertoire of known prokaryotic filament-forming CCRPs and demonstrate that cyanobacterial CCRPs are involved in cell morphology, motility, cytokinesis and colony integrity.