bluuebunny/crossref_metadata_2025 huggingface dataset:
A stochastic-statistical residential burglary model with independent Poisson clocks
Authors: WANG CHUNTIAN , ZHANG YUAN , BERTOZZI ANDREA L. , SHORT MARTIN B.
Published: February 2020

Residential burglary is a social problem in every major urban area. As such, progress has been to develop quantitative, informative and applicable models for this type of crime: (1) the Deterministic-time-step (DTS) model [Short, D’Orsogna, Pasour, Tita, Brantingham, Bertozzi & Chayes (2008) Math. Models Methods Appl. Sci.18, 1249–1267], a pioneering agent-based statistical model of residential burglary criminal behaviour, with deterministic time steps assumed for arrivals of events in which the residential burglary aggregate pattern formation is quantitatively studied for the first time; (2) the SSRB model (agent-based stochastic-statistical model of residential burglary crime) [Wang, Zhang, Bertozzi & Short (2019) Active Particles, Vol. 2, Springer Nature Switzerland AG, in press], in which the stochastic component of the model is theoretically analysed by introduction of a Poisson clock with time steps turned into exponentially distributed random variables. To incorporate independence of agents, in this work, five types of Poisson clocks are taken into consideration. Poisson clocks (I), (II) and (III) govern independent agent actions of burglary behaviour, and Poisson clocks (IV) and (V) govern interactions of agents with the environment. All the Poisson clocks are independent. The time increments are independently exponentially distributed, which are more suitable to model individual actions of agents. Applying the method of merging and splitting of Poisson processes, the independent Poisson clocks can be treated as one, making the analysis and simulation similar to the SSRB model. A Martingale formula is derived, which consists of a deterministic and a stochastic component. A scaling property of the Martingale formulation with varying burglar population is found, which provides a theory to the finite size effects. The theory is supported by quantitative numerical simulations using the pattern-formation quantifying statistics. Results presented here will be transformative for both elements of application and analysis of agent-based models for residential burglary or in other domains.
ON PHASE SHIFTS IN A NEW KEYNESIAN MODEL ECONOMY
Authors: Li Xue , Haslag Joseph H.
Published: February 2020

The purpose of this paper is to focus directly on the phase shift. For one thing, we ask whether a New Keynesian sticky-price model economy can account for both countercyclical prices and procyclical inflation. We present findings in which the price level is countercyclical and the inflation rate is procyclical. We proceed to use the model economy as an identification mechanism. What set of individual shocks are necessary to account for the phase shift? That set contains the price markup shock. Next, we ask what set of shocks are sufficient to account for the phase shift. This set contains three elements: the price markup and wage markup shocks along with the government spending shock. The results are important as a building block. We infer that price stickiness is an important model feature; without price stickiness, we are in the real business cycle economies that Cooley and Hansen studied. But, it raises further questions. For instance, is price stickiness of the Calvo form—the one used here—necessary to explain the phase shift?
The complexities of selling fruits and vegetables in remote Navajo Nation retail outlets: perspectives from owners and managers of small stores
Authors: Piltch Emily M , Shin Sonya S , Houser Robert F , Griffin Timothy
Published: February 2020

Objective:

Navajo Nation residents experience extreme rates of poverty, food insecurity and diet-related diseases. While many residents travel far to shop at grocery stores, there are small stores closer to home that could provide more healthy options, like fruits and vegetables (F&V). Little is known from the perspective of store owners and managers regarding the barriers and facilitators to offering F&V; the present study contributes to filling that gap.

Design:

Data were collected through structured interviews from a sampling frame of all store owners or managers in the setting (n 29).

Setting:

Small stores in Navajo Nation, New Mexico, USA. Navajo Nation is predominantly rural and the largest federally recognized Native American tribe in the USA.

Participants:

Sixteen managers and six owners at twenty-two stores.

Results:

When asked about the types of foods that were most commonly purchased at their stores, most participants reported snacks and drinks (82 and 68 %, respectively). Many participants reported they would like to offer more fresh F&V. However, barriers included varying perceived customer demand, limited F&V choices from distributors and (for some managers) limited authority over product selection.

Conclusions:

Findings contribute to the discussion on engaging store owners and managers in providing quality, healthy foods close to home in low-income, rural regions.
Lack of effective resistance to the virulent race of Colletotrichum lentis in Lens culinaris Medikus subsp. culinaris
Authors: Gela Tadesse S. , Banniza Sabine , Vandenberg Albert
Published: February 2020

Anthracnose caused by Colletotrichum lentis is an important fungal disease of lentil in western Canada. Two known pathogenic C. lentis races, race 0 and race 1 have been identified and current cultivars of lentil have little or no resistance to the virulent race 0. Seven Lens culinaris subsp. culinaris landrace accessions were previously reported to have resistance to C. lentis race 0. In this study, accession VIR-2633, with reported resistance to both races of C. lentis, and seven accessions were assessed for race 0 resistance relative to LR-59-81, an interspecific line derived from a L. culinaris subsp. culinaris × Lens ervoides cross. The results showed a lack of effective resistance to race 0 among the tested L. culinaris accessions when compared to that of LR-59-81. A few sublines displayed modest improvements in resistance compared to the susceptible check ‘Eston’, but were significantly more susceptible than LR-59-81. Moreover, screening of the sublines of accession VIR-2633 identified 12 sublines with resistance to race 1, but all VIR-2633 sublines were susceptible to race 0. The study underlined the importance of wild lentil germplasm for broadening the genetic base of cultivated lentil and their usefulness in disease screening experiments as positive checks.
Explaining Ethnoreligious Minority Targeting: Variation in U.S. Anti-Semitic Incidents
Authors: Feinberg Ayal
Published: February 2020

Over the last two decades alone, the United States has suffered well over ten thousand religion-motivated hate crimes. While racism and religion-motivated prejudice have received considerable attention following the “Unite the Right” rally in Charlottesville that resulted in deadly violence, there is little systematic scholarship evaluating where and when incidents targeting ethnoreligious minorities by non-state actors are likely to occur. Utilizing the FBI’s reported anti-Semitic hate crime data from 2001–2014, my main theoretical and empirical exercise is to determine which factors best explain where and when American ethnoreligious groups are likely to be targeted. I propose that there are four essential mechanisms necessary to explain variation in minority targeting: “opportunity” (target group concentration), “distinguishability” (target group visibility), “stimuli” (events increasing target group salience) and “organization” (hate group quantity). My models show that variables falling within each of these theoretical concepts significantly explain variation in anti-Semitic incidents in the United States. Of particular importance for scholars and practitioners alike, Israeli military operations and the number of active hate groups within a state play a major role in explaining anti-Semitic incident variation.
Multi‐Centennial‐Scale Variations of South American Summer Monsoon Intensity in the Southern Central Andes (24–27°S) During the Late Holocene
Authors: Kock Sebastian T. , Schittek Karsten , Mächtle Bertil , Maldonado Antonio , Vos Heinz , Lupo Liliana C. , Kulemeyer Julio J. , Wissel Holger , Schäbitz Frank , Lücke Andreas
Published: February 2020

Oxygen isotope records of cushion‐plant peat cellulose from the southern central Andes capture evidence for significant environmental changes. We observe that the δ18Ocell peatland record from Cerro Tuzgle (24°S) is in high conformity with the respective Lagunillas peatland record (27°S). During the late Holocene, two significant fluctuations occurred and are interpreted as regional moisture signals with increased precipitation amounts indicated during multi‐centennial phases from 1,530 to 1,270 cal. yr BP and from 470 to 70 cal. yr BP. These fluctuations can be best explained by changes in the strength of the South American summer monsoon (SASM). This interpretation is further supported by consistency with northern Andean paleoclimate records (10–13°S) and very high correlation (R2 = 0.76) with the Southern Oscillation Index. The congruent precipitation signals suggest the persistent climatic control of the SASM‐strength in this latitudinal band during the last 1,800 years.
Southern Annular Mode Influence on Wintertime Ventilation of the Southern Ocean Detected in Atmospheric O2 and CO2 Measurements
Authors: Nevison Cynthia D. , Munro David R. , Lovenduski Nicole S. , Keeling Ralph F. , Manizza Manfredi , Morgan Eric J. , Rödenbeck Christian
Published: February 2020

The Southern Annular Mode (SAM) is the dominant mode of climate variability in the Southern Ocean, but only a few observational studies have linked variability in SAM to changes in ocean circulation. Atmospheric potential oxygen (APO) combines atmospheric O2/N2 and CO2 data to mask the influence of terrestrial exchanges, yielding a tracer that is sensitive mainly to ocean circulation and biogeochemistry. We show that observed wintertime anomalies of APO are significantly correlated to SAM in 25‐ to 30‐year time series at three Southern Hemisphere sites, while CO2 anomalies are also weakly correlated. We find additional correlations between SAM and O2 air‐sea fluxes in austral winter inferred from both an atmospheric inversion of observed APO and a forced ocean biogeochemistry model simulation. The model results indicate that the correlation with SAM is mechanistically linked to stronger wind speeds and upwelling, which brings oxygen‐depleted deep waters to the surface.
Responses of Australian Dryland Vegetation to the 2019 Heat Wave at a Subdaily Scale
Authors: Qiu Bo , Ge Jun , Guo Weidong , Pitman Andrew J. , Mu Mengyuan
Published: February 2020

Satellite solar‐induced chlorophyll fluorescence (SIF) products from the Global Ozone Monitoring Experiment 2 (GOME‐2) and Orbiting Carbon Observatory 2 (OCO‐2) are used to investigate the responses of vegetation growth to the 2019 heat wave in Australia. Both satellite SIF data sets are more sensitive to water and heat stress than is the greenness‐based vegetation index (enhanced vegetation index). Moreover, the OCO‐2 SIF observations show a more significant reduction and earlier response to the heat stress than does GOME‐2 SIF, indicating that the two satellite SIF data sets differ in how they monitor the drought and heat wave event due to the different timing of observations. Eddy covariance measurements confirm the different responses of dryland vegetation to the 2019 heat wave at a subdaily time scale. The differences in the timing of the satellite SIF products can be used to assess different elements of the impact of heat and water stress on Australian dryland ecosystems.
Upright Convection in Extratropical Cyclones: A Survey Using Ground‐Based Radar Data Over the United States
Authors: Jeyaratnam Jeyavinoth , Booth James F. , Naud Catherine M. , Luo Z. Johnny , Homeyer Cameron R.
Published: February 2020

Upright convection can impact extratropical cyclone (ETC) precipitation and dynamics differently than isentropic ascent, but how often it occurs and how much it contributes to total precipitation within an ETC have not been systematically documented in previous literature. Herein, convection in ETCs is analyzed using ground‐based radar observations over the Eastern United States. Convection occupies 1%–5% of the precipitating region and constitutes 1%–15% of total cyclone precipitation. Furthermore, the location of convective activity occurs preferentially in the warm sector early in a cyclone's life cycle, and then as the storm evolves, more convection occurs along and behind the cold front. The precipitation rates in regions with convection are more likely to be stronger than those in other precipitating regions of the cyclone. However, the cyclones with the largest area‐average precipitation rates include only a small contribution from convection.
Projected Future Changes of Meridional Heat Transport and Heat Balance of the Indian Ocean
Authors: Ma Jie , Feng Ming , Lan Jian , Hu Dunxin
Published: February 2020

An ocean downscaling model product, forced under the Representative Concentration Pathway 8.5 future climate change scenario, has been used to understand the ocean heat balance of the Indian Ocean in a warming climate. Toward the end of the 21th century, the model simulates a significant reduction of Indonesian throughflow (ITF) transport, which reduces the Pacific to Indian Ocean heat transport by 0.20 PW, whereas across 32°S in the Southern Indian Ocean (SIO), the southward heat transport is reduced by 0.28 PW, mainly contributed from the weakening western boundary current, the Agulhas Current (0.21 PW). The projected weakening of the Agulhas Current is to compensate for the reduction of the ITF transport, with additional contribution from the spin‐down of the SIO subtropical gyre. Thus, being amplified by the ocean circulation changes in the SIO, the projected Indian Ocean warming trend will be faster than the direct air‐sea heat flux input.
COSMIC‐2 Radio Occultation Constellation: First Results
Authors: Schreiner W.S. , Weiss J.P. , Anthes R.A. , Braun J. , Chu V. , Fong J. , Hunt D. , Kuo Y.‐H. , Meehan T. , Serafino W. , Sjoberg J. , Sokolovskiy S. , Talaat E. , Wee T.K. , Zeng Z.
Published: February 2020

Initial data from the Formosa Satellite‐7/Constellation Observing System for Meteorology Ionosphere and Climate (FORMOSAT‐7/COSMIC‐2, hereafter C2), a recently launched equatorial constellation of six satellites carrying advanced radio occultation receivers, exhibit high signal‐to‐noise ratio, precision, and accuracy, and the ability to provide high vertical resolution profiles of bending angles and refractivity, which contain information on temperature and water vapor in the challenging tropical atmosphere. After an initial calibration/validation phase, over 100,000 soundings of bending angles and refractivity that passed quality control in October 2019 are compared with independent data, including radiosondes, model forecasts, and analyses. The comparisons show that C2 data meet expectations of high accuracy, precision, and capability to detect superrefraction. When fully operational, the C2 satellites are expected to produce ~5,000 soundings per day, providing freely available observations that will enable improved forecasts of weather, including tropical cyclones, and weather, space weather, and climate research.
Long‐Term Statistics of Observed Bubble Depth Versus Modeled Wave Dissipation
Authors: Strand Kjersti Opstad , Breivik Øyvind , Pedersen Geir , Vikebø Frode Bendiksen , Sundby Svein , Christensen Kai Håkon
Published: February 2020

Air bubble penetration depths are investigated with a bottom‐mounted echosounder at a seabed observatory in northern Norway. We compare a 1‐year time series of observed bubble depth against modeled and estimated turbulent kinetic energy flux from breaking waves as well as wind speed and sea state. We find that the hourly mean and maximum bubble depths are highly variable, reaching 18 and 38 m, respectively, and strongly correlated with wind and sea state. The bubble depth is shallowest during summer following the seasonal variations in wind speed and wave height. Summertime shallowing of the mixed layer depth is not limiting the penetration depth. A strong relationship between bubble depth and modeled turbulent kinetic energy flux from breaking waves is found, similar in strength to the relationship between bubble depth and wind speed. The wind sea is more strongly correlated with bubble depth than the total significant wave height, and the swell is only weakly correlated, suggesting that the wave model does a reasonable separation of swell and wind sea.
Boosting Effect of Tropical Cyclone “Fani” on the Onset of the South China Sea Summer Monsoon in 2019
Authors: Liu Boqi , Zhu Congwen
Published: February 2020

The late onset of the South China Sea (SCS) summer monsoon (SCSSM) has traditionally been attributed to El Niño events. However, the SCSSM built up around Pentad 26 in 2019, which was 10 days earlier than expected following the 2018/2019 El Niño event. The present study showed that the early onset of the SCSSM in 2019 could be ascribed to tropical cyclone (TC) Fani over the Bay of Bengal (BOB) from 27 April to 3 May 2019. Before the landfall in Pentad 24, the anomalous condensation heating released by the TC not only shifted the South Asian High (SAH) northward but also reinforced the upper‐level barotropic trough to the west of the Tibetan Plateau (TP) at midlatitudes. This phenomenon facilitated the early establishment of monsoon convection by intensifying the upper‐level pumping over the SCS. In addition, the TC carried abundant moisture to the eastern TP and the SCS when it landed in eastern India in Pentad 25 and strengthened the local rainfall in front of the deeper midlatitudinal trough in the upper troposphere over the TP, which in turn released more condensation heating to warm the tropospheric atmosphere. Afterwards, this warmer air advected downstream to the north of the SCS by the basic flow, resulting in the further northward shift of the SAH and the stronger monsoon onset convection over the SCS. Such an upscaling effect of the TC prevented the onset time of the 2019 SCSSM from being accurately forecasted by the ECMWF S2S model.
QBO Modulation of the MJO‐Related Precipitation in East Asia
Authors: Kim Hera , Son Seok‐Woo , Yoo Changhyun
Published: February 2020

This study revisits precipitation change in East Asia caused by the Madden‐Julian oscillation (MJO) and its interannual variation due to the quasi‐biennial oscillation (QBO). Specifically, boreal‐winter precipitation, derived from weather stations across China, Korea, and Japan, is examined for MJO phases 2–3 and 6–8. Consistent with previous findings, precipitation in southern China and southern Japan increases by up to 36% during MJO phases 2–3, when the MJO convection is located in the Indian Ocean. In contrast, during MJO phases 6–8, precipitation decreases by 13%. More importantly, these MJO‐related precipitation anomalies become larger and more organized when the QBO is in its easterly phase. The difference in precipitation anomalies between the QBO easterly and westerly phases is approximately 40% for MJO phases 2–3 and 70% for MJO phases 6–8 from southern China to Japan. This result reaffirms that the QBO can affect surface weather in the northern extratropics through MJO teleconnection.
LncRNA RUNX1-IT1 which is downregulated by hypoxia-driven histone deacetylase 3 represses proliferation and cancer stem-like properties in hepatocellular carcinoma cells
Authors: Sun Liankang , Wang Liang , Chen Tianxiang , Shi Yu , Yao Bowen , Liu Zhikui , Wang Yufeng , Li Qing , Liu Runkun , Niu Yongshen , Tu Kangsheng , Liu Qingguang
Published: February 2020

Hepatocellular carcinoma (HCC) is characterised by a hypoxic microenvironment and a high rate of heterogeneity and recurrence, and the presence of cancer stem cells (CSCs) in HCC may well explain both of these pathological properties. There is mounting evidence that long non-coding RNAs (lncRNAs) participate in carcinogenesis and maintain cancer stemness of HCC cells. However, the expression modes, regulatory mechanisms and potential roles of stemness-related lncRNAs in HCC are still obscure. LncRNA RUNX1-IT1 is the intronic transcript 1 of the RUNX1, which is also known as chromosome 21 open-reading frame 96 (C21orF96). Although the functions of the RUNX1 have been identified in different diseases, the function and its potential mechanisms of the lncRNA RUNX1-IT1 in HCC still remains to be largely unknown. In this study, we verified that the expression of LncRNA RUNX1-IT1 was decreased in GEO data set, HCC samples and correlated with unfavourable clinicopathologic characteristics and poor prognosis. RUNX1-IT1 repressed HCC cell proliferation, cell cycle progression, invasion and cancer stemness and induced apoptosis in vitro. Overexpression of RUNX1-IT1 impaired the growth, metastasis and stem-like features of HCC cells in vivo. Mechanistically, RUNX1-IT1 directly bound to miR-632 and acted as competing endogenous RNA to facilitate the expression of the miR-632 target gene GSK-3β and subsequently modulate the WNT/β-catenin pathway in HCC cells. Furthermore, hypoxia-driven histone deacetylase 3 (HDAC3), as an upstream regulatory mechanism, was critical for the downregulation of RUNX1-IT1 in HCC. Thus, lncRNA RUNX1-IT1, as a regulator of hypoxia, may function as a potential therapeutic target for conquering HCC.
mTORC1 coordinates an immediate unfolded protein response-related transcriptome in activated B cells preceding antibody secretion
Authors: Gaudette Brian T. , Jones Derek D. , Bortnick Alexandra , Argon Yair , Allman David
Published: February 2020

How activated B cells build biosynthetic pathways and organelle structures necessary for subsequent robust antibody secretion is still unclear. The dominant model holds that nascent plasma cells adapt to increased antibody synthesis by activating the unfolded protein response (UPR) under the control of the transcription factor Xbp1. Here, by analyzing gene expression in activated B cells with or without plasma cell-inductive signals, we find that follicular B cells up-regulate a wide array of UPR-affiliated genes before initiating antibody secretion; furthermore, initial transcription of these loci requires the mTORC1 kinase adaptor, Raptor, but not Xbp1. Transcriptomic analyses of resting marginal zone B cells, which generate plasma cells with exceptionally rapid kinetics, reinforce these results by revealing the basal expression of UPR-affiliated mRNA networks without detectable Xbp1 activity. We thus conclude that B cells utilize mTORC1 to prepare for subsequent plasma cell function, before the onset of antibody synthesis.
Clonal competition within complex evolutionary hierarchies shapes AML over time
Authors: Sandén Carl , Lilljebjörn Henrik , Orsmark Pietras Christina , Henningsson Rasmus , Saba Karim H. , Landberg Niklas , Thorsson Hanna , von Palffy Sofia , Peña-Martinez Pablo , Högberg Carl , Rissler Marianne , Gisselsson David , Lazarevic Vladimir , Juliusson Gunnar , Ågerstam Helena , Fioretos Thoas
Published: February 2020

Clonal heterogeneity and evolution has major implications for disease progression and relapse in acute myeloid leukemia (AML). To model clonal dynamics in vivo, we serially transplanted 23 AML cases to immunodeficient mice and followed clonal composition for up to 15 months by whole-exome sequencing of 84 xenografts across two generations. We demonstrate vast changes in clonality that both progress and reverse over time, and define five patterns of clonal dynamics: Monoclonal, Stable, Loss, Expansion and Burst. We also show that subclonal expansion in vivo correlates with a more adverse prognosis. Furthermore, clonal expansion enabled detection of very rare clones with AML driver mutations that were undetectable by sequencing at diagnosis, demonstrating that the vast majority of AML cases harbor multiple clones already at diagnosis. Finally, the rise and fall of related clones enabled deconstruction of the complex evolutionary hierarchies of the clones that compete to shape AML over time.
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

Zoos 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

Lipid 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

Weyl 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

Hyperspectral 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

As 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

X-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

Perturbations 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.
Author Correction: Application of interspecific Somatic Cell Nuclear Transfer (iSCNT) in sturgeons and an unexpectedly produced gynogenetic sterlet with homozygous quadruple haploid
Authors: Fatira Effrosyni , Havelka Miloš , Labbé Catherine , Depincé Alexandra , Iegorova Viktoriia , Pšenička Martin , Saito Taiju
Published: February 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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

In 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

Epidemic 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

Understanding 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

Failure 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

Bile 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

Surface 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

We 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

Filament-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.