bluuebunny/crossref_metadata_2025 huggingface dataset:
Spreading properties of a three-component reaction-diffusion model for the population of farmers and hunter-gatherers
Authors: Xiao Dongyuan , Mori Ryunosuke
Published: September 2020

In this paper, we investigate the spreading properties of solutions of farmer and hunter-gatherer model which is a three-component reaction-diffusion system. Ecologically, the model describes the geographical spreading of an initially localized population of farmers into a region occupied by hunter-gatherers. This model was proposed by Aoki, Shida and Shigesada in 1996. By numerical simulations and some formal linearization arguments, they concluded that there are four different types of spreading behaviors depending on the parameter values. Despite such intriguing observations, no mathematically rigorous studies have been made to justify their claims. The main difficulty comes from the fact that the comparison principle does not hold for the entire system. In this paper, we give theoretical justification to all of the four types of spreading behaviors observed by Aoki et al. Furthermore, we show that a logarithmic phase drift of the front position occurs as in the scalar KPP equation. We also investigate the case where the motility of the hunter-gatherers is larger than that of the farmers, which is not discussed in the paper of Aoki et al.
Conditional Accountability for the Economy, Insecurity, and Corruption Across Latin American Party Systems
Authors: Singer Matthew M.
Published: September 2020

The association between how citizens perceive economic performance, insecurity, or corruption and how they evaluate the president varies systematically across Latin American countries and within them over time. In particular, while presidential popularity reflects these outcomes in the average Latin American country, survey data from 2006–17 confirm that the connection between government performance and presidential approval is generally stronger when unfragmented party systems or single-party majority governments make assessments of political responsibility easier. While these results suggest that the region’s citizens do not blindly blame the president for outcomes where political responsibility should be shared, they also remind us that there are many countries in the region where fragmented party systems weaken the conditions for effective political accountability.
‘Cyclone Not Above Politics’ : East Pakistan, disaster politics, and the 1970 Bhola Cyclone
Authors: BISWAS SRAVANI , DALY PATRICK
Published: September 2020

On 12 November 1970, the Bhola Cyclone swept across the southern districts of East Pakistan, killing over 300,000 people. Small islands were swept away and dead bodies of humans and cattle lay strewn across the devastated landscape. Following the news of the destruction, journalists, students, artists, and political workers rushed to the affected area with basic relief supplies, without waiting for the Military Law Administration (MLA) to intervene. The cyclone's occurrence just three weeks prior to the first general elections in Pakistan added a new dimension to the already simmering political crisis. The extensive media coverage of the disaster brought the pitiful state of infrastructural development and lack of governance in East Pakistan under local and global scrutiny. The cyclone and the corresponding issues soon became embroiled within the larger political demand for regional autonomy. The MLA came under attack from sections of East Pakistan's politicians, press, and public, as well as international political actors, for its poor disaster governance. This article uses the Bhola Cyclone of 1970 as the lens to explore the complex interconnections between environmental disasters and a key issue of governance. While the Bhola Cyclone has been a subject of recent discussions, this article uses a disaster-politics analytical framework to understand the disaster's role in the subsequent political turbulence and the emergence of Bangladesh.
EEG Power spectra and subcortical pathology in chronic disorders of consciousness
Authors: Lutkenhoff Evan S. , Nigri Anna , Rossi Sebastiano Davide , Sattin Davide , Visani Elisa , Rosazza Cristina , D'Incerti Ludovico , Bruzzone Maria Grazia , Franceschetti Silvana , Leonardi Matilde , Ferraro Stefania , Monti Martin M.
Published: September 2020

Background

Despite a growing understanding of disorders of consciousness following severe brain injury, the association between long-term impairment of consciousness, spontaneous brain oscillations, and underlying subcortical damage, and the ability of such information to aid patient diagnosis, remains incomplete.

Methods

Cross-sectional observational sample of 116 patients with a disorder of consciousness secondary to brain injury, collected prospectively at a tertiary center between 2011 and 2013. Multimodal analyses relating clinical measures of impairment, electroencephalographic measures of spontaneous brain activity, and magnetic resonance imaging data of subcortical atrophy were conducted in 2018.

Results

In the final analyzed sample of 61 patients, systematic associations were found between electroencephalographic power spectra and subcortical damage. Specifically, the ratio of beta-to-delta relative power was negatively associated with greater atrophy in regions of the bilateral thalamus and globus pallidus (both left>right) previously shown to be preferentially atrophied in chronic disorders of consciousness. Power spectrum total density was also negatively associated with widespread atrophy in regions of the left globus pallidus, right caudate, and in the brainstem. Furthermore, we showed that the combination of demographics, encephalographic, and imaging data in an analytic framework can be employed to aid behavioral diagnosis.

Conclusions

These results ground, for the first time, electroencephalographic presentation detected with routine clinical techniques in the underlying brain pathology of disorders of consciousness and demonstrate how multimodal combination of clinical, electroencephalographic, and imaging data can be employed in potentially mitigating the high rates of misdiagnosis typical of this patient cohort.
What drives partisan conflict and consensus on welfare state issues?
Authors: Ennser-Jedenastik Laurenz
Published: September 2020

Left-right partisan conflict has been a key driver of welfare state expansion and retrenchment over time and across countries. Yet, we know very little about how left-right differences in party appeals vary across social policy domains. Why are some issues contentious while there is broad consensus on others? This paper starts from the simple premise that partisan conflict is a function of how popular a certain policy is. Based on this assumption, it argues that the left-right gap should be (1) larger for revenue-side issues than for expenditure-side issues, (2) larger for policies targeted at groups that are viewed as less deserving and (3) larger for more redistributive programs than less redistributive ones (e.g. means-tested versus earnings-related benefits). These expectations are tested on fine-grained policy data coded from 65 Austrian party manifestos issued between 1970 and 2017 (N = 18,219). The analysis strongly supports the revenue–expenditure hypothesis and the deservingness hypothesis, but not the redistribution hypothesis.
Mono versus dual isocentric technique for breast cancer radiotherapy: evaluation of planning, dosimetry and treatment delivery
Authors: Wadasadawala Tabassum , Lewis Shirley , Gaikwad Utpal , Gayake Umesh , Phurailatpam Reena , Tambe Santosh , Sarin Rajiv
Published: September 2020

Aim:

To compare the dosimetry and reproducibility of set-up with monoisocentric technique (MIT) and dual isocentric technique (DIT) in adjuvant breast radiotherapy (RT).

Material and methods:

Breast cancer patients treated with MIT or DIT were retrospectively studied. The organ-at-risk dose was compared between two groups. All patients underwent set-up verification with an electronic portal imaging device, and set-up time was recorded for each fraction. Treatment reproducibility was assessed in terms of systematic and random error.

Results:

Twenty patients were included (11 right and 9 left-sided tumours) and ten received whole breast RT, while the rest received chest wall RT. Overall, the mean heart dose was less with MIT (0.40 versus 0.79, p = <0.001) as well as in left-sided tumours (0.37 versus 0.98, p = 0.003). The maximum dose at the field junction was significantly higher with DIT (43 Gy, 107%, p = 0.003). The maximum total error was 1 cm in lateral for supraclavicular field and 8 mm in superior–inferior in tangents for both techniques. There was no difference in set-up errors between the two techniques.

Findings:

MIT resulted in better dose homogeneity at the field junctions and reduced mean heart dose as compared to DIT. MIT is safe for implementation in clinical practice for breast cancer treatment.

Conclusion:

This study is one of the few studies comparing MIT with DIT in terms of the dosimetry and the first one to compare set-up errors between the two techniques. The ease of set-up and better dosimetry with MIT was achieved.
Survey of rice production practices and perception of weedy red rice (Oryza sativa f. spontanea) in Taiwan
Authors: Huang Yung-Fen , Wu Dong-Hong , Wang Chih-Lu , Du Pei-Rong , Cheng Chih-Yun , Cheng Chia-Chi
Published: September 2020

Rice (Oryza sativa L.) is the primary staple crop in Taiwan, and it can be grown twice a year. The prevalent subspecies grown in Taiwan is Japonica, and a transplanting system is used for rice production. Although the transplanting system is known for efficient weed control at the seedling stage, weedy red rice (WRR, O. sativa f. spontanea) infestation is progressively being reported. Fieldwork and previous studies have suggested that WRR infestation in Taiwan is probably related to growers’ operating practices and their perception of WRR. However, no data are available for a detailed investigation. The present study aimed to collect data on rice growers’ backgrounds, farming practices, and perceptions of WRR to quantify and characterize the patterns of farming operations for rice growers in Taiwan and to investigate factors contributing to WRR infestation. We collected 408 questionnaires completed by rice growers from 17 counties covering all rice production regions in Taiwan. The growers’ median age was 51 to 60 yr, and 75% of respondents had paddies from 0.25 to 2.75 ha in size, which corresponded with nationwide data for farmers’ backgrounds. In general, growers applied similar farming practices for both cropping seasons. Most respondents did not notice WRR infestation or consider it to be a problem: only 9.8% noticed a moderate to severe infestation of WRR in their fields. The major perceived causes of WRR infestation was seed impurity (55.1%) or cultivar degeneration (18.6%). Correlation analysis and farming patterns estimated with a nonnegative matrix factorization algorithm showed that WRR contamination rate was due to the use of dry or wet tillage. The present study provides the first quantitative and qualitative evidence of rice production practices and growers’ perceptions of WRR infestation in Taiwan.
Wave Equation‐Based Local Traveltime Inversion
Authors: Hu Y. , Han L. G. , Liu Y. S. , Jin Z. Y.
Published: September 2020

Full waveform inversion (FWI) is a strongly nonlinear optimization problem, which suffers from cycle skipping when the initial velocity model is not good enough or the seismic data lack low frequencies. Traveltime tomography is often used to invert the low‐wave number components of a velocity model, but traveltime inversion results show a low‐resolution model. To bridge the inversion wave number gap between the traveltime tomography and the FWI, a wave equation‐based local travetime inversion is proposed. In this case, the cross‐correlation algorithm is applied to calculate the traveltime differences between the localized synthetic and observed data. To mitigate traveltime crosstalk noise caused by multiple seismic events, a sliding Gaussian window is applied to transform the seismic data into local domain. In this way, the traveltime information of different seismic events can be simultaneously used to improve the inversion results. The numerical examples show that the combination of Local Traveltime Inversion (LTI) and FWI successfully mitigate the cycle skipping and produce satisfactory inversion results, even if the seismic data lack low frequencies and the initial velocity model is far from the true one.
Response of Landfalling Atmospheric Rivers on the U.S. West Coast to Local Sea Surface Temperature Perturbations
Authors: Chen Xiaodong , Leung L. Ruby
Published: September 2020

Atmospheric rivers (ARs) play a crucial role in the hydroclimate of the U.S. west coast. While the impact of large‐scale sea surface temperature (SST) patterns on ARs is well recognized, the specific roles of local SST on ARs have not been systematically investigated. This study analyzed the landfalling ARs from two regional climate simulations that differ only in the local SST. With local SST warming, AR frequency increases across the U.S. west coast, with comparable contributions from the spatial expansion of ARs and emergence of new ARs. AR landfalling area, inland intrusion distance, and intensity also increase, with landfalling area showing the largest sensitivity. Although local SST warming only increases the AR moisture by ∼0.4%/K, AR‐related precipitation increases by 3%/K, demonstrating the important impact of local SST warming on intensifying storms. Hence, local SST is important for accurate depiction of ARs and their precipitation in the western United States.
Emergent Constraint on the Frequency of Central Pacific El Niño Under Global Warming by the Equatorial Pacific Cold Tongue Bias in CMIP5/6 Models
Authors: Jiang Wenping , Huang Ping , Li Gen , Huang Gang
Published: September 2020

El Niño, as the dominant interannual variability for global climate, exhibits different spatial “flavors” with distinct global impacts, and the ensemble of current model projects there will be an increase in the frequency of central Pacific El Niño (CP El Niño) in a warmer world. In this study, we identified that future changes in CP El Niño frequency are significantly related to the simulated cold tongue strength in CMIP5/6 models. A model simulating a stronger cold tongue tends to project more frequent CP El Niño events under global warming, due to the positive zonal advection feedback in the central Pacific. Based on this relationship, we calibrate the CP El Niño frequency projections using the emergent constraint concept and reveal that the changes in CP El Niño frequency under global warming as projected in previous multimodel ensembles more likely decrease because of an excessive cold tongue in CMIP5/6 models.
A 60‐Year Cycle in the Meteorite Fall Frequency Suggests a Possible Interplanetary Dust Forcing of the Earth's Climate Driven by Planetary Oscillations
Authors: Scafetta Nicola , Milani Franco , Bianchini Antonio
Published: September 2020

One of the most famous climate oscillations has a period of about 60 years. Although this oscillation might emerge from internal variability, increasing evidence points toward a solar or astronomical origin, as also argued herein. We highlight that the orbital eccentricity of Jupiter presents prominent oscillations with a period of quasi 60 years due to its gravitational coupling with Saturn. This oscillation is found to be well correlated with quite a number of climatic records and also with a 60‐year oscillation present in long meteorite fall records relative to the periods 619–1943 CE. Since meteorite falls are the most macroscopic aspect of incoming space dust and their motion is mostly regulated by Jupiter, we propose that the interplanetary dust influx also presents a 60‐year cycle and could be forcing the climate to oscillate in a similar manner by modulating the formation of the clouds and, therefore, the Earth's albedo.
NOx Emission Changes Over China During the COVID‐19 Epidemic Inferred From Surface NO2 Observations
Authors: Feng Shuzhuang , Jiang Fei , Wang Hengmao , Wang Haikun , Ju Weimin , Shen Yang , Zheng Yanhua , Wu Zheng , Ding Aijun
Published: September 2020

The COVID‐19 epidemic has substantially limited human activities and affected anthropogenic emissions. In this work, daily NOx emissions are inferred using a regional data assimilation system and hourly surface NO2 measurement over China. The results show that because of the coronavirus outbreak, NOx emissions across the whole mainland China dropped sharply after 31 January, began to rise slightly in certain areas after 10 February, and gradually recover across the country after 20 February. Compared with the emissions before the outbreak, NOx emissions fell by more than 60% and ~30% in many large cities and most small to medium cities, respectively. Overall, NOx emissions were reduced by 36% over China, which were mainly contributed by transportation. Evaluations show that the inverted changes over eastern China are credible, whereas those in western China might be underestimated. These findings are of great significance for exploring the reduction potential of NOx emissions in China.
Composite of Typhoon‐Induced Sea Surface Temperature and Chlorophyll‐a Responses in the South China Sea
Authors: Wang Yuntao
Published: September 2020

Sixteen years of data on typhoons in the South China Sea (SCS) are used to investigate their impacts on sea surface temperature (SST) and chlorophyll‐a (Chl‐a). The time series of SST and Chl‐a before and after typhoons are composited for all typhoon locations to assess their responses. Decreases in SST and increases in Chl‐a occur after 73% and 70% of the typhoons, respectively, with overall averaged changes equal to −0.42 ± 0.015°C and 0.056 ± 0.003 log10 mg/m3, respectively. The largest responses are found near the typhoon center, and the extent of changes in these parameters decreases linearly with distance. The SST responds rapidly, starting to drop 2 days ahead of the typhoon passage and continuing to drop until 2 days after its passage. On the other hand, the Chl‐a increases after the typhoon passage, remaining high for 5 days before beginning to return to the initial conditions. Large (weak) changes are associated with typhoons that have high (low) wind speeds and slow (fast) translation speeds. This is especially true for SST, whereas some typhoons with slow translation speeds are characterized by increases in Chl‐a, mostly occurring near the coast. The largest SST and Chl‐a changes induced by a single typhoon are found in the upwelling region off Vietnam. The study offers a comprehensive quantitative analysis that describes the general pattern of SST and Chl‐a responses to typhoons in the SCS.
Drivers of Interannual Sea Level Variability on the Northwestern European Shelf
Authors: Hermans Tim H. J. , Le Bars Dewi , Katsman Caroline A. , Camargo Carolina M. L. , Gerkema Theo , Calafat Francisco M. , Tinker Jonathan , Slangen Aimée B. A.
Published: September 2020

Sea level on the northwestern European shelf (NWES) varies substantially from year to year. Removing explained parts of interannual sea level variability from observations helps to improve estimates of long‐term sea level trends. To this end, the contributions of different drivers to interannual sea level variability need to be understood and quantified. We quantified these contributions for the entire NWES by performing sensitivity experiments with a high‐resolution configuration of the Regional Ocean Modeling System (ROMS). The lateral and atmospheric boundary conditions were derived from reanalyses. We compared our model results with satellite altimetry data and used our sensitivity experiments to show that nonlinear feedbacks cause only minor interannual sea level variability on the shelf. This indicates that our experiments can be used to separate the effects of different drivers. We find that wind dominates the variability of annual mean sea level in the southern and eastern North Sea (up to 4.7‐cm standard deviation), whereas the inverse barometer effect dominates elsewhere on the NWES (up to 1.7‐cm standard deviation). In contrast, forcing at the lateral ocean boundaries results in small and coherent variability on the shelf (0.5‐cm standard deviation). Variability driven by buoyancy fluxes ranges from 0.5‐ to 1.3‐cm standard deviation. The results of our sensitivity experiments explain the (anti)correlation between interannual sea level variability at different locations on the NWES and can be used to estimate sea level rise from observations in this region with higher accuracy.
Two Centuries of Hydroclimatic Variability Reconstructed From Tree‐Ring Records Over the Amazonian Andes of Peru
Authors: Humanes‐Fuente V. , Ferrero M. E. , Muñoz A. A. , González‐Reyes Á. , Requena‐Rojas E. J. , Barichivich J. , Inga J. G. , Layme‐Huaman E. T.
Published: September 2020

Almost half of the tributaries of the Amazon River originate in the tropical Andes and support large populations in mountain regions and downstream areas. However, it is difficult to assess hydroclimatic conditions or to evaluate future scenarios due to the scarcity of long, high‐quality instrumental records. Data from the Global Precipitation Climatology Project (GPCP) provide a complete record since 1979 and offer a good representation of rainfall over the tropical Andes. Longer records are needed to improve our understanding of rainfall variability and summer monsoon behavior at various scales. We developed the first annually resolved precipitation reconstruction for the tropical Andes in Peru, based on tree‐ring chronologies of Cedrela and Juglans species. The annual (November–October) reconstruction extends the short instrumental records back to 1817, explaining 68% of the total variance of precipitation over the 1979–2007 calibration period. The reconstruction reveals the well‐documented influence of El Niño‐Southern Oscillation (ENSO) on Amazon Rainfall at interannual scales (~19% of total variance) and significant multidecadal variability with alternating periods of about 40 years (~13% of rainfall variability) related to the Atlantic Multidecadal Oscillation (AMO). Both oscillatory modes can explain dry and humid periods observed within the reconstruction and are likely associated with the negative trends of rainfall in the short instrumental records and the increased drought recurrence in recent decades. Our results show that montane tropical tree rings can be used to reconstruct precipitation with exceptionally high fidelity, characterize the interannual to multidecadal variability, and identify remote forcings in the hydroclimate over the Andean Amazon Basin of Peru.
Effects of Cloud Liquid‐Phase Microphysical Processes in Mixed‐Phase Cumuli Over the Tibetan Plateau
Authors: Xu Xiaoqi , Lu Chunsong , Liu Yangang , Gao Wenhua , Wang Yuan , Cheng Yueming , Luo Shi , Van Weverberg Kwinten
Published: September 2020

Numerical simulations often overpredict precipitation over the Tibetan Plateau (TP). To examine the factors causing precipitation overprediction, different parameterizations of liquid‐phase microphysical processes (accretion, autoconversion, and entrainment mixing) are implemented into the Morrison microphysics scheme to simulate a TP precipitation event in summer with the Weather Research and Forecasting (WRF) model. The general spatial distribution and temporal trend of precipitation are captured by all simulations, but the precipitation rate is overpredicted. The results from sensitivity experiments suggest that compared to other examined liquid‐phase processes, the accretion process is more important in precipitation simulation over the TP region. Further investigation with the Heidke skill scores reveals that accretion parameterization that takes into account the raindrop size produces the most accurate results in terms of the total surface precipitation. This parameterization suppresses spurious accretion and does not produce liquid‐phase precipitation until cloud droplets are big enough. It is also confirmed that increasing the model resolution can reduce precipitation overprediction. Results from the case study are confirmed by the use of a 1‐month simulation.
A Monte Carlo Approach to Approximating the Effects of Pore Geometry on the Phase Behavior of Soil Freezing
Authors: Chen Jiangzhi , Mei Shenghua , Irizarry Julia T. , Rempel Alan W.
Published: September 2020

Freezing in porous media is associated with a host of dynamic phenomena that stem from the presence and mobility of premelted liquid at subzero temperatures. Accurate assessments of the progressive liquid‐ice phase transition is required for predictive models of frost damage, glacier‐till coupling, and many other cold regions processes, as well as for evaluating the capacity for water storage in near‐surface extraterrestrial environments. We use a Monte Carlo approach to sample the pore space in a synthetic 3D packing of poly‐dispersed spherical particles and evaluate local geometrical constraints that allow us to assess changes in the relative proportions of pore fluid and ice. By approximating the phase boundary geometry in fine‐grained pores while considering both the curvature of the liquid‐ice interface and wetting interactions with matrix particles, our model predicts changes in phase equilibrium in granular media over a broad temperature range, where present accounting for the colligative effects of chloride and perchlorate solutes. In addition to formulating the constitutive behavior needed to better understand properties and processes in frozen soils, our results also provide insight into other aspects of phase equilibria in porous media, including the formation of methane hydrates in permafrost and marine sediments, and the partitioning between liquid water and vapor in the vadose zone.
The Spatial Dynamics of Droughts and Water Scarcity in England and Wales
Authors: Dobson Barnaby , Coxon Gemma , Freer Jim , Gavin Helen , Mortazavi‐Naeini Mohammad , Hall Jim W.
Published: September 2020

Water scarcity occurs when water demand exceeds natural water availability over a range of spatial and temporal scales. Though meteorological and hydrological droughts have been analyzed over large spatial scales, the impacts of water scarcity have typically been addressed at a catchment scale. Here we explore how droughts and water scarcity interact over a larger and more complex spatial domain, by combining climate, hydrological, and water resource system models at a national scale across England and Wales. This approach is essential in a highly connected and heterogeneous region like England and Wales, where we represent 80 different catchments; 70 different water resource zones; 16 water utility companies; and the water supply for over 50 million people. We find that if a reservoir's storage is in its first percentile (i.e., the volume that is exceeded 99% of the time), then there is, on average, a 40% chance that reservoirs in neighboring catchments will also be at or below their first percentile storage volume. The coincidence of low reservoir storage decays relatively quickly, stabilizing after about 100–150 km, implying that if interbasin transfers are to be provided to enhance drought resilience, they will need to be at least this length. Based on a large ensemble of future climate simulations, we show that extreme droughts in precipitation, streamflow, and reservoir storage volume are projected to worsen in every catchment. The probability of a year with water use restrictions doubles by 2050 and is four times worse by 2100.
Implications of Using Global Digital Elevation Models for Flood Risk Analysis in Cities
Authors: McClean Fergus , Dawson Richard , Kilsby Chris
Published: September 2020

As urban populations grow, it is increasingly important to accurately characterize flood risk in cities and built up areas. Global digital elevation models (GDEMs) have recently enabled flood risk analysis at broad scale and worldwide, but their accuracy and its impact on modeled flood risk in cities has not been fully investigated. We compare flood extents, hydrographs, depths, and impacts between hydrodynamic simulations, using five spaceborne GDEM products and an airborne LIDAR product. Benchmark observations of a historical flood event in Carlisle (UK) were used to assess the accuracy of each simulation. GDEM simulations are shown to perform significantly less accurately than the airborne LIDAR‐based simulations. No DEM outperforms the others across all metrics; the MERIT DEM is the best predictor of flood extent, but TanDEM‐X performs best for discharge. However, the impacts of flooding from GDEM simulations are consistently overestimated, 2 to 3 times higher than those from LIDAR simulations. Until a high resolution, accurate, global DEM is available, multiple products should be used concurrently to enable the full uncertainty range to be quantified and communicated, to ensure flood risk management decisions are not misinformed.
Gene co-expression networks in peripheral blood capture dimensional measures of emotional and behavioral problems from the Child Behavior Checklist (CBCL)
Authors: Hess Jonathan L. , Nguyen Nicholas H. , Suben Jesse , Meath Ryan M. , Albert Avery B. , Van Orman Sarah , Anders Kristin M. , Forken Patricia J. , Roe Cheryl A. , Schulze Thomas G. , Faraone Stephen V. , Glatt Stephen J.
Published: September 2020

The U.S. National Institute of Mental Health (NIMH) introduced the research domain criteria (RDoC) initiative to promote the integration of information across multiple units of analysis (i.e., brain circuits, physiology, behavior, self-reports) to better understand the basic dimensions of behavior and cognitive functioning underlying normal and abnormal mental conditions. Along those lines, this study examined the association between peripheral blood gene expression levels and emotional and behavioral problems in school-age children. Children were chosen from two age- and sex-matched groups: those with or without parental reports of any prior or current psychiatric diagnosis. RNA-sequencing was performed on whole blood from 96 probands aged 6–12 years who were medication-free at the time of assessment. Module eigengenes were derived using weighted gene co-expression network analysis (WGCNA). Associations were tested between module eigengene expression levels and eight syndrome scales from parent ratings on the Child Behavior Checklist (CBCL). Nine out of the 36 modules were significantly associated with at least one syndrome scale measured by the CBCL (i.e., aggression, social problems, attention problems, and/or thought problems) after accounting for covariates and correcting for multiple testing. Our study demonstrates that variation in peripheral blood gene expression relates to emotional and behavioral profiles in children. If replicated and validated, our results may help in identifying problem or at-risk behavior in pediatric populations, and in elucidating the biological pathways that modulate complex human behavior.
Heme oxygenase 1 protects human colonocytes against ROS formation, oxidative DNA damage and cytotoxicity induced by heme iron, but not inorganic iron
Authors: Seiwert Nina , Wecklein Sabine , Demuth Philipp , Hasselwander Solveig , Kemper Talke A. , Schwerdtle Tanja , Brunner Thomas , Fahrer Jörg
Published: September 2020

The consumption of red meat is probably carcinogenic to humans and is associated with an increased risk to develop colorectal cancer (CRC). Red meat contains high amounts of heme iron, which is thought to play a causal role in tumor formation. In this study, we investigated the genotoxic and cytotoxic effects of heme iron (i.e., hemin) versus inorganic iron in human colonic epithelial cells (HCEC), human CRC cell lines and murine intestinal organoids. Hemin catalyzed the formation of reactive oxygen species (ROS) and induced oxidative DNA damage as well as DNA strand breaks in both HCEC and CRC cells. In contrast, inorganic iron hardly affected ROS levels and only slightly increased DNA damage. Hemin, but not inorganic iron, caused cell death and reduced cell viability. This occurred preferentially in non-malignant HCEC, which was corroborated in intestinal organoids. Both hemin and inorganic iron were taken up into HCEC and CRC cells, however with differential kinetics and efficiency. Hemin caused stabilization and nuclear translocation of Nrf2, which induced heme oxygenase-1 (HO-1) and ferritin heavy chain (FtH). This was not observed after inorganic iron treatment. Chemical inhibition or genetic knockdown of HO-1 potentiated hemin-triggered ROS generation and oxidative DNA damage preferentially in HCEC. Furthermore, HO-1 abrogation strongly augmented the cytotoxic effects of hemin in HCEC, revealing its pivotal function in colonocytes and highlighting the toxicity of free intracellular heme iron. Taken together, this study demonstrated that hemin, but not inorganic iron, induces ROS and DNA damage, resulting in a preferential cytotoxicity in non-malignant intestinal epithelial cells. Importantly, HO-1 conferred protection against the detrimental effects of hemin.
CPEB3-mediated MTDH mRNA translational suppression restrains hepatocellular carcinoma progression
Authors: Zhang He , Zou Chendan , Qiu Zini , E Fang , Li Qiang , Chen Miao , Wang Dayong , Tan Qinrui , Yin Wanli , Matunda Cedric , Wang Hefei , Zhang Yongjian , Zhan Chao , Wang Chuxuan , Wu Yue , Xuan Xiuchen , Wang Yayan , Zou Chaoxia , Lv Guixiang , Gao Xu
Published: September 2020

Cytoplasmic polyadenylation element-binding protein 3 (CPEB3) is a sequence-specific RNA-binding protein. We had reported that CPEB3 is involved in hepatocellular carcinoma (HCC) progression. However, the underlying mechanisms of CPEB3 in HCC remain unclear. In this study, we firstly performed RNA immunoprecipitation to uncover the transcriptome-wide CPEB3-bound mRNAs (CPEB3 binder) in HCC. Bioinformatic analysis indicates that CPEB3 binders are closely related to cancer progression, especially HCC metastasis. Further studies confirmed that metadherin (MTDH) is a direct target of CPEB3. CPEB3 can suppress the translation of MTDH mRNA in vivo and in vitro. Besides, luciferase assay demonstrated that CPEB3 interacted with 3′-untranslated region of MTDH mRNA and inhibited its translation. Subsequently, CPEB3 inhibited the epithelial–mesenchymal transition and metastasis of HCC cells through post-transcriptional regulation of MTDH. In addition, cpeb3 knockout mice are more susceptible to carcinogen-induced hepatocarcinogenesis and subsequent lung metastasis. Our results also indicated that CPEB3 was a good prognosis marker, which is downregulated in HCC tissue. In conclusion, our results demonstrated that CPEB3 played an important role in HCC progression and targeting CPEB3-mediated mRNA translation might be a favorable therapeutic approach.
Correction: Exosomal miR-25-3p from mesenchymal stem cells alleviates myocardial infarction by targeting proapoptotic proteins and EZH2
Authors: Peng Yi , Zhao Ji-Ling , Peng Zhi-Yong , Xu Wei-Fang , Yu Guo-Long
Published: September 2020

Since online publication of this article, the authors noticed that an incorrect image was used during the compilation of Fig. 2a, which was caused during manuscript preparation. The correct Fig. 2a is shown below.
A20 promotes melanoma progression via the activation of Akt pathway
Authors: Ma Jinyuan , Wang Huina , Guo Sen , Yi Xiuli , Zhao Tao , Liu Yu , Shi Qiong , Gao Tianwen , Li Chunying , Guo Weinan
Published: September 2020

Melanoma is the most life-threatening skin cancer with increasing incidence around the world. Although recent advances in targeted therapy and immunotherapy have brought revolutionary progress of the treatment outcome, the survival of patients with advanced melanoma remains unoptimistic, and metastatic melanoma is still an incurable disease. Therefore, to further understand the mechanism underlying melanoma pathogenesis could be helpful for developing novel therapeutic strategy. A20 is a crucial ubiquitin-editing enzyme implicated immunity regulation, inflammatory responses and cancer pathogenesis. Herein, we report that A20 played an oncogenic role in melanoma. We first found that the expression of A20 was significantly up-regulated in melanoma cell lines. Then, we showed that knockdown of A20 suppressed melanoma cell proliferation in vitro and melanoma growth in vivo through the regulation of cell-cycle progression. Moreover, A20 could potentiate the invasive and migratory capacities of melanoma cell in vitro and melanoma metastasis in vivo by promoting epithelial–mesenchymal transition (EMT). Mechanistically, we found that Akt activation mediated the oncogenic effect of A20 on melanoma development, with the involvement of glycolysis. What’s more, the up-regulation of A20 conferred the acquired resistance to Vemurafenib in BRAF-mutant melanoma. Taken together, we demonstrated that up-regulated A20 promoted melanoma progression via the activation of Akt pathway, and that A20 could be exploited as a potential therapeutic target for melanoma treatment.
A novel lncRNA LNC_000052 leads to the dysfunction of osteoporotic BMSCs via the miR-96-5p–PIK3R1 axis
Authors: Li Mingyang , Cong Rong , Yang Liyu , Yang Lei , Zhang Yiqi , Fu Qin
Published: September 2020

Bone marrow-derived mesenchymal stem cells (BMSCs) in postmenopausal osteoporosis models exhibit loss of viability and multipotency. Identification of the differentially expressed RNAs in osteoporotic BMSCs could reveal the mechanisms underlying BMSC dysfunction under physiological conditions, which might improve stem cell therapy and tissue regeneration. In this study, we performed high-throughput RNA sequencing and showed that the novel long non-coding RNA (lncRNA) LNC_000052 and its co-expressed mRNA PIK3R1 were upregulated in osteoporotic BMSCs. Knockdown of LNC_000052 could promote BMSC proliferation, migration, osteogenesis, and inhibit apoptosis via the PI3K/Akt signaling pathway. We found that both LNC_000052 and PIK3R1 shared a miRNA target, miR-96-5p, which was downregulated in osteoporotic BMSCs. Their binding sites were confirmed by dual-luciferase assays. Downregulation of miR-96-5p could restrain the effects of LNC_000052 knockdown while upregulation of miR-96-5p together with LNC_000052 knockdown could improve the therapeutic effects of BMSCs. In summary, the LNC_000052–miR-96-5p–PIK3R1 axis led to dysfunction of osteoporotic BMSCs and might be a novel therapeutic target for stem cell therapy and tissue regeneration.
Dental cell type atlas reveals stem and differentiated cell types in mouse and human teeth
Authors: Krivanek Jan , Soldatov Ruslan A. , Kastriti Maria Eleni , Chontorotzea Tatiana , Herdina Anna Nele , Petersen Julian , Szarowska Bara , Landova Marie , Matejova Veronika Kovar , Holla Lydie Izakovicova , Kuchler Ulrike , Zdrilic Ivana Vidovic , Vijaykumar Anushree , Balic Anamaria , Marangoni Pauline , Klein Ophir D. , Neves Vitor C. M. , Yianni Val , Sharpe Paul T. , Harkany Tibor , Metscher Brian D. , Bajénoff Marc , Mina Mina , Fried Kaj , Kharchenko Peter V. , Adameyko Igor
Published: September 2020

Understanding cell types and mechanisms of dental growth is essential for reconstruction and engineering of teeth. Therefore, we investigated cellular composition of growing and non-growing mouse and human teeth. As a result, we report an unappreciated cellular complexity of the continuously-growing mouse incisor, which suggests a coherent model of cell dynamics enabling unarrested growth. This model relies on spatially-restricted stem, progenitor and differentiated populations in the epithelial and mesenchymal compartments underlying the coordinated expansion of two major branches of pulpal cells and diverse epithelial subtypes. Further comparisons of human and mouse teeth yield both parallelisms and differences in tissue heterogeneity and highlight the specifics behind growing and non-growing modes. Despite being similar at a coarse level, mouse and human teeth reveal molecular differences and species-specific cell subtypes suggesting possible evolutionary divergence. Overall, here we provide an atlas of human and mouse teeth with a focus on growth and differentiation.
Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico
Authors: Broom Aron , Rakotoharisoa Rojo V. , Thompson Michael C. , Zarifi Niayesh , Nguyen Erin , Mukhametzhanov Nurzhan , Liu Lin , Fraser James S. , Chica Roberto A.
Published: September 2020

The creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity. Here, we use room-temperature X-ray crystallography to study changes in the conformational ensemble during evolution of the designed Kemp eliminase HG3 (kcat/KM 146 M−1s−1). We observe that catalytic residues are increasingly rigidified, the active site becomes better pre-organized, and its entrance is widened. Based on these observations, we engineer HG4, an efficient biocatalyst (kcat/KM 103,000 M−1s−1) containing key first and second-shell mutations found during evolution. HG4 structures reveal that its active site is pre-organized and rigidified for efficient catalysis. Our results show how directed evolution circumvents challenges inherent to enzyme design by shifting conformational ensembles to favor catalytically-productive sub-states, and suggest improvements to the design methodology that incorporate ensemble modeling of crystallographic data.
Effective interactions mediated between two permeable disks in an active fluid
Authors: Sebtosheikh Mahmoud , Naji Ali
Published: September 2020

We study steady-state properties of a bath of active Brownian particles (ABPs) in two dimensions in the presence of two fixed, permeable (hollow) disklike inclusions, whose interior and exterior regions can exhibit mismatching motility (self-propulsion) strengths for the ABPs. We show that such a discontinuous motility field strongly affects spatial distribution of ABPs and thus also the effective interaction mediated between the inclusions through the active bath. Such net interactions arise from soft interfacial repulsions between ABPs that sterically interact with and/or pass through permeable membranes assumed to enclose the inclusions. Both regimes of repulsion and attractive (albeit with different mechanisms) are reported and summarized in overall phase diagrams.
Epidemiology and risk factors for avascular necrosis in childhood systemic lupus erythematosus in a Taiwanese population
Authors: Tsai Hsin-Lin , Chang Jei-Wen , Lu Jen-Her , Liu Chin-Su
Published: September 2020

Childhood-onset systemic lupus erythematosus (SLE) is associated with greater disease activity, more aggressive course, and high rates of organ damage. The prolonged use of corticosteroids in childhood SLE contributes to increased morbidity, including avascular necrosis (AVN). We conducted this retrospective study using claims data from the Taiwan National Health Insurance Research Database, enrolling 1,472 children with newly-diagnosed SLE between 2005 and 2013. The mean age at the diagnosis of SLE was 15.5 ± 3.3 years, and the female to male ratio was 6.2:1. Thirty-nine patients (2.6%) developed symptomatic AVN during a mean follow-up of 4.6 ± 2.5 years. In multivariate analysis, the risk of AVN was higher in the patients with a daily prednisolone dose between 7.5 mg and 30 mg (HR 7.435, 95% CI 2.882–19.178, p < 0.001) and over 30 mg (HR 9.366, 95% CI 2.225–39.418, p = 0.002) than in those with a dose ≤ 7.5 mg/day. In addition, AVN was inversely correlated with the use of hydroxychloroquine > 627 days (HR 0.335, 95% CI 0.162–0.694, p = 0.003). In conclusion, high daily doses of prednisolone were associated with a significant risk of AVN, whereas the use of hydroxychloroquine > 627 days conferred an advantage. We suggest that the judicious use of corticosteroids combined with hydroxychloroquine might be a promising preventive strategy for AVN.
Optimization of human papillomavirus-based pseudovirus techniques for efficient gene transfer
Authors: Gilson Timra D. , Gibson Ryan T. , Androphy Elliot J.
Published: September 2020

Human papillomavirus (HPV) L1 and L2 capsid proteins self-assemble into virions capable of efficiently packaging either its 8 kilobase genome or non-viral DNA. The ability of HPV capsids to package non-viral DNA makes these a useful tool for delivering plasmids to study proteins of interest in a variety of cell types. We describe optimization of current methods and present new protocols for using HPV capsids to deliver non-viral DNA thereby providing an alternative to DNA transfection. Using keratinocyte generated extracellular matrices can enhance infection efficiency in keratinocytes, hepatocytes and neuronal cells. Furthermore, we describe a suspension-based efficient technique for infecting different cell types.
Whitefly genomes contain ribotoxin coding genes acquired from plants
Authors: Lapadula Walter J. , Mascotti María L. , Juri Ayub Maximiliano
Published: September 2020

Ribosome inactivating proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of 28S rRNA. These enzymes are widely distributed among plants and bacteria. Previously, we have described for the first time RIP genes in mosquitoes belonging to the Culicidae family. We showed that these genes are derived from a single event of horizontal gene transfer (HGT) from a prokaryotic donor. Mosquito RIP genes are evolving under purifying selection, strongly suggesting that these toxins have acquired a functional role. In this work, we show the existence of two RIP encoding genes in the genome of the whitefly Bemisia tabaci, a hemiptera species belonging to the Aleyrodidae family distantly related to mosquitoes. Contamination artifacts were ruled out analyzing three independent B. tabaci genome databases. In contrast to mosquito RIPs, whitefly genes harbor introns and according to transcriptomic evidence are transcribed and spliced. Phylogeny and the taxonomic distribution strongly support that whitefly RIP genes are derived from an independent HGT event from a plant source. These results, along with our previous description of RIPs in Diptera, suggest that the acquired genes are functional in these insects and confer some fitness advantage.
Animated virtual characters to explore audio-visual speech in controlled and naturalistic environments
Authors: Thézé Raphaël , Gadiri Mehdi Ali , Albert Louis , Provost Antoine , Giraud Anne-Lise , Mégevand Pierre
Published: September 2020

Natural speech is processed in the brain as a mixture of auditory and visual features. An example of the importance of visual speech is the McGurk effect and related perceptual illusions that result from mismatching auditory and visual syllables. Although the McGurk effect has widely been applied to the exploration of audio-visual speech processing, it relies on isolated syllables, which severely limits the conclusions that can be drawn from the paradigm. In addition, the extreme variability and the quality of the stimuli usually employed prevents comparability across studies. To overcome these limitations, we present an innovative methodology using 3D virtual characters with realistic lip movements synchronized on computer-synthesized speech. We used commercially accessible and affordable tools to facilitate reproducibility and comparability, and the set-up was validated on 24 participants performing a perception task. Within complete and meaningful French sentences, we paired a labiodental fricative viseme (i.e. /v/) with a bilabial occlusive phoneme (i.e. /b/). This audiovisual mismatch is known to induce the illusion of hearing /v/ in a proportion of trials. We tested the rate of the illusion while varying the magnitude of background noise and audiovisual lag. Overall, the effect was observed in 40% of trials. The proportion rose to about 50% with added background noise and up to 66% when controlling for phonetic features. Our results conclusively demonstrate that computer-generated speech stimuli are judicious, and that they can supplement natural speech with higher control over stimulus timing and content.