bluuebunny/crossref_metadata_2025 huggingface dataset:
Seamless Estimation of Hydrometeorological Risk Across Spatial Scales
Authors: Sieg Tobias , Vogel Kristin , Merz Bruno , Kreibich Heidi
Published: May 2019

Hydrometeorological hazards caused losses of approximately 110 billion U.S. Dollars in 2016 worldwide. Current damage estimations do not consider the uncertainties in a comprehensive way, and they are not consistent between spatial scales. Aggregated land use data are used at larger spatial scales, although detailed exposure data at the object level, such as openstreetmap.org, is becoming increasingly available across the globe. We present a probabilistic approach for object‐based damage estimation which represents uncertainties and is fully scalable in space. The approach is applied and validated to company damage from the flood of 2013 in Germany. Damage estimates are more accurate compared to damage models using land use data, and the estimation works reliably at all spatial scales. Therefore, it can as well be used for pre‐event analysis and risk assessments. This method takes hydrometeorological damage estimation and risk assessments to the next level, making damage estimates and their uncertainties fully scalable in space, from object to country level, and enabling the exploitation of new exposure data.
Seismic and Geodetic Evidences of a Hydrothermal Source in the Md 4.0, 2017, Ischia Earthquake (Italy)
Authors: Calderoni Giovanna , Di Giovambattista Rita , Pezzo Giuseppe , Albano Matteo , Atzori Simone , Tolomei Cristiano , Ventura Guido
Published: May 2019

Seismic events characterize active hydrothermal and volcanic areas and may be due to magma/fluid migration, hydrothermal pressurization, gravitational instability, and local tectonics. On 21 August 2017, an Md 4.0 earthquake occurred at Ischia volcanic island (Italy), within an active hydrothermal system. We analyze seismic, Global Positioning System, and interferometric synthetic aperture radar data to shed light on the source mechanism of such an event. The low‐frequency content (2 Hz), the low stress drop (0.01 MPa), and a low S/P spectral ratio suggest the involvement of fluids in the source mechanism. The focal mechanism suggests a mixed shear‐tensile (opening) rupture with the P first arrivals showing up movements in the nearest stations. Geodetic data describe an E‐W elongated area of coseismic subsidence overlapping a WSW‐ENE fault bounding the hydrothermal reservoir at depth. The modeled deformation field is consistent with a two‐source model consisting of a WSW‐ESE striking, north dipping normal fault, and a closing subhorizontal crack. This closure immediately followed an initial opening related to a fluid pressurization event responsible for the earthquake. We show that moderate magnitude earthquakes in active hydrothermal areas may be associated with the pressurization/depressurization cycles of a hydrothermal reservoir due to self‐sealing processes and not to the arrival of new fluids from depth. Other events like that recorded at Ischia, which have affected the island in historical times, are not necessarily associated with ‘volcanic unrest’ episodes and imply the occurrence of fault‐valve mechanisms. Therefore, the dynamics of hydrothermal systems must be taken into account in the seismic hazard evaluation.
Drizzle and Turbulence Below Closed Cellular Marine Stratocumulus Clouds
Authors: Ghate Virendra P. , Cadeddu Maria P.
Published: May 2019

Drizzle is ubiquitous in marine boundary layer stratocumulus clouds with much of it evaporating before reaching the surface. Ten days of observations made at the Atmospheric Radiation Measurement's Eastern North Atlantic site during closed cellular stratocumulus cloud conditions are used to characterize drizzle below the cloud base and its impact on the boundary layer turbulence. Cloud and drizzle microphysical and macrophysical properties were retrieved by combining the data from vertically pointing Doppler cloud radar, ceilometer, and microwave radiometer. On average, the drizzle shafts were 28.14 km wide, with cloud base rain rate and modal diameter of 0.98 mm/day and 138.62 μm, respectively. The rain rate at the surface was negligible yielding an average diabatic cooling of −28.68 W/m2 in the subcloud layer. The liquid water path and turbulence within the boundary layer increased with an increase in the cloud top radiative cooling; however, none of these variables exhibited any relationship with cloud base rain rate. For a similar amount of radiative cooling at the cloud top, the average variance of vertical velocity in the subcloud layer was about 16% lower during strongly precipitating conditions as compared to lightly precipitating conditions. The reduction in the variance of vertical velocity due to drizzle evaporation was primarily confined to the upper half of the subcloud layer and was due to reduction in the strengths of the downdrafts. Collectively, our results show substantial impact of drizzle evaporation on turbulence below stratocumulus clouds, necessitating its accurate representation in the Earth system models.
Model‐Space Localization in Serial Ensemble Filters
Authors: Shlyaeva Anna , Whitaker Jeffrey S. , Snyder Chris
Published: May 2019

Ensemble‐based data assimilation systems typically use covariance localization to dampen spurious correlations associated with sampling error while increasing the rank of the covariance estimate. Variational methods use model‐space localization, in which localization is applied to ensemble estimates of covariances between model variables and is based on distances between those variables, while ensemble filters apply observation‐space localization to estimates of model‐observation covariances, based on distances between model variables and observations. It has been shown that for nonlocal observations, such as satellite radiances, model‐space localization can be superior. This paper demonstrates a new method for performing model‐space localization in serial ensemble filters using the linearized observation operators (or Jacobians). Results of radiance‐only assimilation in a global forecast system show the benefit of using model‐space localization relative to observation‐space localization. The serial ensemble square root filter with vertical model‐space localization gives results similar to those of the Ensemble Variational system (without outer loops or extra balance constraints) while increasing the runtime compared to the filter with observation‐space localization by a factor between 2 and 8, depending on how sparse the Jacobian matrices are. The results are also similar to another approach to model‐space localization in ensemble filters: ensemble Kalman filter with modulated ensembles.
Soil Physical, Hydraulic, and Thermal Properties in Interior Alaska, USA: Implications for Hydrologic Response to Thawing Permafrost Conditions
Authors: Ebel Brian A. , Koch Joshua C. , Walvoord Michelle A.
Published: May 2019

Boreal forest regions are a focal point for investigations of coupled water and biogeochemical fluxes in response to wildfire disturbances, climate warming, and permafrost thaw. Soil hydraulic, physical, and thermal property measurements for mineral soils in permafrost regions are limited, despite substantial influences on cryohydrogeologic model results. This work expands mineral soil property quantification in cold regions through soil characterization from the discontinuous permafrost zone of interior Alaska, USA. Values extend beyond the range of prior measurement magnitudes in analogous regions, highlighting the importance of this data set. Rocky and silty upland soil landscape classifications and wildfire disturbance provided guiding frameworks for the sampling and analysis for potential implications for the hydrologic response to thawing permafrost. Bulk density (ρb), soil organic matter, soil‐particle size distributions (sand, silt, and gravel fractions), and soil hydraulic properties of van Genuchten parameters alpha and N had moderate evidence of differences between silty and rocky classifications. Burned and unburned sites had only moderate evidence of differences for silt fraction. Field‐saturated hydraulic conductivity (Kfs) was more variable at burned sites compared to unburned sites, which corresponded to observations of greater rooting depths at burned sites and observations of root paths in soil cores for Kfs measurement. Soil thermal properties suggested that gravel content may reduce the accuracy of commonly used estimation methods for thermal conductivity. This work provides soil parameter constraints necessary for hypothesis testing and site‐specific prediction with cryohydrogeologic models to examine controls on active layer and permafrost dynamics in upland boreal forests.
First Analysis of Asteroid Water Reveals Earth-Like Makeup
Authors: Cartier Kimberly
Published: May 2019

Samples returned from the surface of an asteroid show that these small bodies may have more water than previously thought and could have delivered that water to Earth.
Implications of a Varying Observational Network for Accurately Estimating Recent Climate Trends
Authors: Singh Deepti
Published: May 2019

Gridded data sets that are widely used to characterize recent historical trends in regional and global climate are derived from a temporally varying and spatially inhomogeneous observational network. Lin and Huybers (2018, https://doi.org/10.1029/2018GL079709) demonstrate that such network variations underlying two widely used precipitation data sets have biased trends in mean and extreme rainfall over India. I highlight similar concerns raised by studies over other regions and discuss the implications for climate change research. Evaluating uncertainties arising from such nonclimatic factors requires access to underlying station data that is currently unavailable for several vulnerable regions but is critical for accurately characterizing recent climate change and evaluating climate models.
The Impact of Modified Fractional Cloud Condensate to Precipitation Conversion Parameter in Revised Simplified Arakawa‐Schubert Convection Parameterization Scheme on the Simulation of Indian Summer Monsoon and Its Forecast Application on an Extreme Rainfall Event Over Mumbai
Authors: Ganai Malay , Krishna R. P. M. , Tirkey Snehlata , Mukhopadhyay P. , Mahakur M. , Han Ji‐Young
Published: May 2019

The impact of modified fractional conversion parameter (from cloud condensate to precipitation) in the revised simplified Arakawa‐Schubert (RSAS) convection scheme in Climate Forecast System version 2 on the simulation of Indian summer monsoon (ISM) is examined. While the default fractional conversion parameter is constant in RSAS, the modified parameter has the form of an exponential function of temperature above the freezing level, whereas below the freezing, level it is kept constant. The model simulation indicates RSAS with modified conversion parameter (RSAS_mod) shows a better fidelity in capturing the mean monsoon features over the ISM region. The spatial distribution of precipitation shows notable improvement over the ISM region. Most of the global general circulation models has a tendency to grossly overestimate (underestimate) the convective (large‐scale) rainfall over the ISM region, which has somewhat improved in RSAS_mod simulation. It is suggested that reduced rate of conversion of cloud condensate to convective precipitation above the freezing level leads to suppression of convective precipitation, which further increases the detrained moisture from the upper‐level, resulting enhancement in large‐scale precipitation. Further, improvement has been noted in outgoing longwave radiation, wind circulation, total cloud fraction, and dynamical and thermodynamical processes in RSAS_mod simulation. The modified conversion parameter helps in improving the feedback between moisture and convective processes through better lower tropospheric moistening. In addition to mean summer monsoon, the RSAS_mod indicates its potential in predicting an extreme rainfall event over Mumbai in high‐resolution global forecast system at T1534 horizontal resolution. However, its fidelity needs to be further tested for more number of heavy rainfall events.
Spatial and Diurnal Variations of Summer Hourly Rainfall Over Three Super City Clusters in Eastern China and Their Possible Link to the Urbanization
Authors: Fu Xinshu , Yang Xiu‐Qun , Sun Xuguang
Published: May 2019

Three super city clusters in eastern China, that is, Beijing‐Tianjin‐Hebei (BTH), Yangtze River Delta (YRD), and Pearl River Delta (PRD), have been developed in recent decades. The spatial and diurnal variations of summer hourly rainfall over these city clusters and their possible link to the urbanization are investigated in this study, with the Climate Prediction Center Morphing technique (CMORPH) satellite precipitation estimates at high spatial‐temporal resolutions for 2004‐2009. Although the summer rainfall in eastern China is mainly characterized by large‐scale pattern, significant regional rainfall features over the three city clusters can be clearly observed, which are related to the clustered urbanization. Large hourly rainfall intensity is found over the city clusters or downwind from them. Those regions with large hourly rainfall intensity are named as the city cluster impacted regions (CCIRs), contrast to the surrounding mountainous regions where high frequency and large amount but low hourly intensity of rainfall occur. Location and geometry of each CCIR are unique because of the distinctive geography and structures among city clusters. The CCIR situates right over YRD, but it is shifted to the downwind region with an elongated shape for BTH and a circular shape for PRD. More heavy rain but less light rain occurs over the CCIRs than the surrounding regions. Diurnal variations of light rain amount and frequency can be influenced by both mountain and urbanization, and a diurnal cycle amplitude increase related to the urbanization is detected only over the CCIR of YRD where the terrains are mostly low and flat.
Author Correction: Improving pharmacogenetic prediction of extrapyramidal symptoms induced by antipsychotics
Authors: Boloc Daniel , Gortat Anna , Cheng-Zhang Jia Qi , García-Cerro Susana , Rodríguez Natalia , Parellada Mara , Saiz-Ruiz Jeronimo , Cuesta Manolo J. , Gassó Patricia , Lafuente Amalia , Bernardo Miquel , Mas Sergi
Published: May 2019

One of the funding sources (FEDER-Unión Europea) was not previously acknowledged in this Article. This study was supported by the Spanish Ministry of Health, Instituto de Salud Carlos III (FIS, Fondo de Investigacion Sanitaria PI13/00812, PI16/0122) and FEDER-Unión Europea.
Whole-genome sequencing reveals novel tandem-duplication hotspots and a prognostic mutational signature in gastric cancer
Authors: Xing Rui , Zhou Yong , Yu Jun , Yu Yingyan , Nie Yongzhan , Luo Wen , Yang Chao , Xiong Teng , Wu William K. K. , Li Zhongwu , Bing Yang , Lin Shuye , Zhang Yaping , Hu Yingqi , Li Lin , Han Lijuan , Yang Chen , Huang Shaogang , Huang Suiping , Zhou Rui , Li Jing , Wu Kaichun , Fan Daiming , Tang Guangbo , Dou Jianhua , Zhu Zhenggang , Ji Jiafu , Fang Xiaodong , Lu Youyong
Published: May 2019

Genome-wide analysis of genomic signatures might reveal novel mechanisms for gastric cancer (GC) tumorigenesis. Here, we analysis structural variations (SVs) and mutational signatures via whole-genome sequencing of 168 GCs. Our data demonstrates diverse models of complex SVs operative in GC, which lead to high-level amplification of oncogenes. We find varying proportion of tandem-duplications (TDs) among individuals and identify 24 TD hotspots involving well-established cancer genes such as CCND1, ERBB2 and MYC. Specifically, we nominate a novel hotspot involving the super-enhancer of ZFP36L2 presents in approximately 10% GCs from different cohorts, the oncogenic role of which is further confirmed by experimental data. In addition, our data reveal a mutational signature, specifically occurring in noncoding region, significantly enriched in tumors with cadherin 1 mutations, and associated with poor prognoses. Collectively, our data suggest that TDs might serve as an important mechanism for cancer gene activation and provide a novel signature for stratification.
Four-fold increase in solar forcing on snow in western U.S. burned forests since 1999
Authors: Gleason Kelly E. , McConnell Joseph R. , Arienzo Monica M. , Chellman Nathan , Calvin Wendy M.
Published: May 2019

Forest fires are increasing across the American West due to climate warming and fire suppression. Accelerated snow melt occurs in burned forests due to increased light transmission through the canopy and decreased snow albedo from deposition of light-absorbing impurities. Using satellite observations, we document up to an annual 9% growth in western forests burned since 1984, and 5 day earlier snow disappearance persisting for >10 years following fire. Here, we show that black carbon and burned woody debris darkens the snowpack and lowers snow albedo for 15 winters following fire, using measurements of snow collected from seven forested sites that burned between 2002 and 2016. We estimate a 372 to 443% increase in solar energy absorbed by snowpacks occurred beneath charred forests over the past two decades, with enhanced post-fire radiative forcing in 2018 causing earlier melt and snow disappearance in > 11% of forests in the western seasonal snow zone.
Differences in S/G ratio in natural poplar variants do not predict catalytic depolymerization monomer yields
Authors: Anderson Eric M. , Stone Michael L. , Katahira Rui , Reed Michelle , Muchero Wellington , Ramirez Kelsey J. , Beckham Gregg T. , Román-Leshkov Yuriy
Published: May 2019

The ratio of syringyl (S) and guaiacyl (G) units in lignin has been regarded as a major factor in determining the maximum monomer yield from lignin depolymerization. This limit arises from the notion that G units are prone to C-C bond formation during lignin biosynthesis, resulting in less ether linkages that generate monomers. This study uses reductive catalytic fractionation (RCF) in flow-through reactors as an analytical tool to depolymerize lignin in poplar with naturally varying S/G ratios, and directly challenges the common conception that the S/G ratio predicts monomer yields. Rather, this work suggests that the plant controls C-O and C-C bond content by regulating monomer transport during lignin biosynthesis. Overall, our results indicate that additional factors beyond the monomeric composition of native lignin are important in developing a fundamental understanding of lignin biosynthesis.
The emergence of cost effective battery storage
Authors: Comello Stephen , Reichelstein Stefan
Published: May 2019

Energy storage will be key to overcoming the intermittency and variability of renewable energy sources. Here, we propose a metric for the cost of energy storage and for identifying optimally sized storage systems. The levelized cost of energy storage is the minimum price per kWh that a potential investor requires in order to break even over the entire lifetime of the storage facility. We forecast the dynamics of this cost metric in the context of lithium-ion batteries and demonstrate its usefulness in identifying an optimally sized battery charged by an incumbent solar PV system. Applying the model to residential solar customers in Germany, we find that behind-the-meter storage is economically viable because of the large difference between retail rates and current feed-in tariffs. In contrast, investment incentives for battery systems in California derive principally from a state-level subsidy program.
A generic approach towards afterglow luminescent nanoparticles for ultrasensitive in vivo imaging
Authors: Jiang Yuyan , Huang Jiaguo , Zhen Xu , Zeng Ziling , Li Jingchao , Xie Chen , Miao Qingqing , Chen Jie , Chen Peng , Pu Kanyi
Published: May 2019

Afterglow imaging with long-lasting luminescence after cessation of light excitation provides opportunities for ultrasensitive molecular imaging; however, the lack of biologically compatible afterglow agents has impeded exploitation in clinical settings. This study presents a generic approach to transforming ordinary optical agents (including fluorescent polymers, dyes, and inorganic semiconductors) into afterglow luminescent nanoparticles (ALNPs). This approach integrates a cascade photoreaction into a single-particle entity, enabling ALNPs to chemically store photoenergy and spontaneously decay it in an energy-relay process. Not only can the afterglow profiles of ALNPs be finetuned to afford emission from visible to near-infrared (NIR) region, but also their intensities can be predicted by a mathematical model. The representative NIR ALNPs permit rapid detection of tumors in living mice with a signal-to-background ratio that is more than three orders of magnitude higher than that of NIR fluorescence. The biodegradability of the ALNPs further heightens their potential for ultrasensitive in vivo imaging.
Local sleep-like events during wakefulness and their relationship to decreased alertness in astronauts on ISS
Authors: Petit Gaetan , Cebolla Ana Maria , Fattinger Sara , Petieau Mathieu , Summerer Leopold , Cheron Guy , Huber Reto
Published: May 2019

Adequate sleep quantity and quality is required to maintain vigilance, cognitive and learning processes. A decrease of sleep quantity preflight and on the International Space Station (ISS) has been reported. Recent counter-measures have been implemented to better regulate sleep opportunities on ISS. In our study, astronauts were allocated enough time for sleep the night before the recordings. However, for proper sleep recovery, the quality of sleep is also critical. Unfortunately, data on sleep quality have yet to be acquired from the ISS. Here, we investigate sleep pressure markers during wakefulness in five astronauts throughout their 6-month space mission by the mean of electroencephalographic recordings. We show a global increase of theta oscillations (5–7 Hz) on the ISS compared to on Earth before the mission. We also show that local sleep-like events, another marker of sleep pressure, are more global in space (p < 0.001). By analysing the performances of the astronauts during a docking simulation, we found that local sleep-like events are more global when reaction times are slower (R2 = 0.03, p = 0.006) and there is an increase of reaction times above 244 ms after 2 months in space (p = 0.012). Our analyses provide first evidence for increased sleep pressure in space and raise awareness on possible impacts on visuomotor performances in space.
Effects of targeted memory reactivation during sleep at home depend on sleep disturbances and habituation
Authors: Göldi Maurice , Rasch Björn
Published: May 2019

Targeted memory reactivation (TMR) during sleep improves memory consolidation. However, it is still unknown whether TMR also benefits memory in real-life conditions. We tested whether TMR during sleep enhances Dutch-German vocabulary learning when applied during multiple nights at home in an unsupervised fashion. During 3 consecutive nights, 66 healthy young participants used an mp3-player to play Dutch words during sleep, without any control of sleep or awakenings by tones (unsupervised TMR). Unsupervised TMR benefitted overall memory scores only in a subgroup of participants, who reported no disturbances by TMR during sleep. Participants who reported general disturbances of sleep showed no benefit, while TMR specifically impaired memory in a third group who reported specific disturbances by the played words during sleep. Separate analysis per night indicated that memory benefits by TMR were significant in the entire sample in the third night only. Our results indicate that sleep disturbances and habituation might be critical factors for the success of unsupervised TMR in a home setting. Habituation to the TMR process as well as automatic sleep monitoring and avoidance of auditory-induced awakenings might be a precondition to successful application of TMR to language learning in real-life.
Diversity of N-acyl homoserine lactones in activated sludge detected by Fourier transform mass spectrometry
Authors: Honda Ryo , Phan Phuong-Thanh , Tobino Tomohiro , Prasertkulsak Sirilak , Panchavinin Smarch , Hong Phuc-Nguon , Taing Chanreaksmey , Noguchi Mana , Chiemchaisri Wilai , Chiemchaisri Chart
Published: May 2019

Quorum sensing is recently considered to play important roles in biological wastewater treatment processes. This study aimed to investigate diversity of N-acyl homoserine lactones (AHL) among biological wastewater treatment processes and their locations. We analyzed and quantified 10 AHL in activated sludge at wastewater treatment plants (WWTPs) by Fourier transform mass spectrometry (FTMS) and by bioassay on thin-layer chromatography (TLC). Sludge samples were taken at seven WWTPs in Japan and in Thailand, which were chosen to compare different process types including a pilot-scale membrane bioreactor process. Various AHL were detected in activated sludge, suggesting the presence of quorum sensing activity in many practical WWTPs. Detection of AHL by LC-FTMS was much more sensitive than by TLC bioassay, because TLC bioassay was implied to be affected by the presence of quorum quenching molecules in activated sludge. With LC-FTMS analysis, AHL, which has short straight chain in the acyl group, were more abundant. Especially, C4-HSL, C7-HSL, and C8-HSL were detected widely independent of locations and process types. AO processes had higher AHL productivity than other processes.
Publisher Correction: Medusozoan genomes inform the evolution of the jellyfish body plan
Authors: Khalturin Konstantin , Shinzato Chuya , Khalturina Maria , Hamada Mayuko , Fujie Manabu , Koyanagi Ryo , Kanda Miyuki , Goto Hiroki , Anton-Erxleben Friederike , Toyokawa Masaya , Toshino Sho , Satoh Noriyuki
Published: May 2019

The version of this article originally published was not open access, but should have been open access. The error has been corrected, and the paper is now open access with a CC-BY license.
A long-term dataset of lake surface water temperature over the Tibetan Plateau derived from AVHRR 1981–2015
Authors: Liu Baojian , Wan Wei , Xie Hongjie , Li Huan , Zhu Siyu , Zhang Guoqing , Wen Lijuan , Hong Yang
Published: May 2019

Lake surface water temperature (LSWT) is of vital importance for hydrological and meteorological studies. The LSWT ground measurements in the Tibetan Plateau (TP) were quite scarce because of its harsh environment. Thermal infrared remote sensing is a reliable way to calculate historical LSWT. In this study, we present the first and longest 35-year (1981–2015) daytime lake-averaged LSWT data of 97 large lakes (>80 km2 each) in the TP using the 4-km Advanced Very High Resolution Radiometer (AVHRR) Global Area Coverage (GAC) data. The LSWT dataset, taking advantage of observations from NOAA’s afternoon satellites, includes three time scales, i.e., daily, 8-day-averaged, and monthly-averaged. The AVHRR-derived LSWT has a similar accuracy (RMSE = 1.7 °C) to that from other data products such as MODIS (RMSE = 1.7 °C) and ARC-Lake (RMSE = 2.0 °C). An inter-comparison of different sensors indicates that for studies such as those considering long-term climate change, the relative bias of different AVHRR sensors cannot be ignored. The proposed dataset should be, to some extent, a valuable asset for better understanding the hydrologic/climatic property and its changes over the TP.
A high throughput imaging database of toxicological effects of nanomaterials tested on HepaRG cells
Authors: Joossens Elisabeth , Macko Peter , Palosaari Taina , Gerloff Kirsten , Ojea-Jiménez Isaac , Gilliland Douglas , Novak Jaroslav , Fortaner Torrent Salvador , Gineste Jean-Michel , Römer Isabella , Briffa Sophie Marie , Valsami-Jones Eugenia , Lynch Iseult , Whelan Maurice
Published: May 2019

The large amount of existing nanomaterials demands rapid and reliable methods for testing their potential toxicological effect on human health, preferably by means of relevant in vitro techniques in order to reduce testing on animals. Combining high throughput workflows with automated high content imaging techniques allows deriving much more information from cell-based assays than the typical readouts (i.e. one measurement per well) with optical plate-readers. We present here a dataset including data based on a maximum of 14 different read outs (including viable cell count, cell membrane permeability, apoptotic cell death, mitochondrial membrane potential and steatosis) of the human hepatoma HepaRG cell line treated with a large set of nanomaterials, coatings and supernatants at different concentrations. The database, given its size, can be utilized in the development of in silico hazard assessment and prediction tools or can be combined with toxicity results from other in vitro test systems.
The Effect of Ganoderma Microsporum immunomodulatory proteins on alleviating PM2.5-induced inflammatory responses in pregnant rats and fine particulate matter-induced neurological damage in the offsprings
Authors: Tseng Chia-Yi , Yu Jia-Yu , Chuang Yu-Chen , Lin Chia-Ying , Wu Chun-Hao , Liao Chia-Wei , Yang Fu-Hua , Chao Ming-Wei
Published: May 2019

Fine particulate matter 2.5 (PM2.5) induces free radicals and oxidative stress in animals, leading to a range of illnesses. In this study, Ganoderma Microsporum immunomodulatory (GMI) proteins were administered to alleviate PM2.5-induced inflammatory responses in mother rats, and PM2.5-induced inflammatory responses and neurological damage in their offspring. The results suggested that GMI administration decreased the risk of neurological disorders in mother rats and their offspring by reducing the white blood cell count, lessening inflammatory responses and PM2.5-induced memory impairment, and preventing dendritic branches in the hippocampi from declining and microRNAs from PM2.5-induced modulation.
Charge-Dependent Regulation in DNA Adsorption on 2D Clay Minerals
Authors: Xie Hongyi , Wan Zhengqing , Liu Song , Zhang Yi , Tan Jieqiong , Yang Huaming
Published: May 2019

DNA purification is essential for the detection of human clinical specimens. A non-destructive, controllable, and low reagent consuming DNA extraction method is described. Negatively charged DNA is absorbed onto a negatively charged montmorillonite to achieve non-destructive DNA extraction based on cation bridge construction and electric double layer formation. Different valence cation modified montmorillonite forms were used to validate the charge-dependent nature of DNA adsorption on montmorillonite. Electric double layer thickness thinning/thickening with the high/lower valence cations exists, and the minerals tended to be sedimentation-stable due to the Van der Waals attraction/electrostatic repulsion. Li-modified montmorillonite with the lowest charge states showed the best DNA adsorption efficiency of 8–10 ng/μg. Charge-dependent regulating research provides a new perspective for controllable DNA extraction and a deep analysis of interface engineering mechanisms.
Mapping the spectrum of 3D communities in human chromosome conformation capture data
Authors: Lee Sang Hoon , Kim Yeonghoon , Lee Sungmin , Durang Xavier , Stenberg Per , Jeon Jae-Hyung , Lizana Ludvig
Published: May 2019

Several experiments show that the three dimensional (3D) organization of chromosomes affects genetic processes such as transcription and gene regulation. To better understand this connection, researchers developed the Hi-C method that is able to detect the pairwise physical contacts of all chromosomal loci. The Hi-C data show that chromosomes are composed of 3D compartments that range over a variety of scales. However, it is challenging to systematically detect these cross-scale structures. Most studies have therefore designed methods for specific scales to study foremost topologically associated domains (TADs) and A/B compartments. To go beyond this limitation, we tailor a network community detection method that finds communities in compact fractal globule polymer systems. Our method allows us to continuously scan through all scales with a single resolution parameter. We found: (i) polymer segments belonging to the same 3D community do not have to be in consecutive order along the polymer chain. In other words, several TADs may belong to the same 3D community. (ii) CTCF proteins—a loop-stabilizing protein that is ascribed a big role in TAD formation—are well correlated with community borders only at one level of organization. (iii) TADs and A/B compartments are traditionally treated as two weakly related 3D structures and detected with different algorithms. With our method, we detect both by simply adjusting the resolution parameter. We therefore argue that they represent two specific levels of a continuous spectrum 3D communities, rather than seeing them as different structural entities.
Effects of water depth on GBD associated with total dissolved gas supersaturation in Chinese sucker (Myxocyprinus asiaticus) in upper Yangtze River
Authors: Cao Lu , Li Yong , An Ruidong , Wang Yuanming , Li Kefeng , Buchmann Kurt
Published: May 2019

Spillway water falling from hydroelectric power plant dams in the upper Yangtze River creates a high pressure in plunge pools below the dams allowing gasses to be dissolved at high rates. The resulting supersaturation persists many miles downstream the dam which may elicit mortality in river fishes associated with gas bubble disease (GBD). We have in a two-year study (2014–15) evaluated the effect of water depth on development of GBD in an endemic and endangered fish species, the Chinese sucker Myxocyprinus asiaticus, 24 km downstream of Xiangjaiba dam. Mortality and incidence of GBD were recorded and it was seen that water depth and survival time/GBD development was positively correlated. The physiological mechanisms explaining increased resistance to GBD with increased water depths (and thereby higher hydrostatic pressure) are discussed. The results may be applied in future management of fish resources in order to protect endangered endemic fishes in rivers affected by dam constructions.
Genetic Predisposition Impacts Clinical Changes in a Lifestyle Coaching Program
Authors: Zubair Niha , Conomos Matthew P. , Hood Leroy , Omenn Gilbert S. , Price Nathan D. , Spring Bonnie J. , Magis Andrew T. , Lovejoy Jennifer C.
Published: May 2019

Both genetic and lifestyle factors contribute to an individual’s disease risk, suggesting a multi-omic approach is essential for personalized prevention. Studies have examined the effectiveness of lifestyle coaching on clinical outcomes, however, little is known about the impact of genetic predisposition on the response to lifestyle coaching. Here we report on the results of a real-world observational study in 2531 participants enrolled in a commercial “Scientific Wellness” program, which combines multi-omic data with personalized, telephonic lifestyle coaching. Specifically, we examined: 1) the impact of this program on 55 clinical markers and 2) the effect of genetic predisposition on these clinical changes. We identified sustained improvements in clinical markers related to cardiometabolic risk, inflammation, nutrition, and anthropometrics. Notably, improvements in HbA1c were akin to those observed in landmark trials. Furthermore, genetic markers were associated with longitudinal changes in clinical markers. For example, individuals with genetic predisposition for higher LDL-C had a lesser decrease in LDL-C on average than those with genetic predisposition for average LDL-C. Overall, these results suggest that a program combining multi-omic data with lifestyle coaching produces clinically meaningful improvements, and that genetic predisposition impacts clinical responses to lifestyle change.
Terahertz Radiation from Combined Metallic Slit Arrays
Authors: Li Dazhi , Nakajima Makoto , Tani Masahiko , Yang Jinfeng , Kitahara Hideaki , Hashida Masaki , Asakawa Makoto , Liu Wenxin , Wei Yanyu , Yang Ziqiang
Published: May 2019

We report an approach to efficiently generate terahertz radiation from a combined periodic structure. The proposed configuration is composed of two metallic slit arrays deliberately designed with different periodic length, slit width and depth. We found that the combination of the two slit arrays could provide special electromagnetic modes, which exhibit nonradiative property above the surface of one slit array and radiative property inside the other one. An electron beam holding proper energy could resonate with those modes to generate strong and directional electromagnetic radiations in the terahertz regime, indicating that the approach has the potential in developing high-performance terahertz radiation sources.
CRISPR/Cas9-mediated generation of a tyrosine hydroxylase reporter iPSC line for live imaging and isolation of dopaminergic neurons
Authors: Calatayud Carles , Carola Giulia , Fernández-Carasa Irene , Valtorta Marco , Jiménez-Delgado Senda , Díaz Mònica , Soriano-Fradera Jordi , Cappelletti Graziella , García-Sancho Javier , Raya Ángel , Consiglio Antonella
Published: May 2019

Patient-specific induced pluripotent stem cells (iPSCs) are a powerful tool to investigate the molecular mechanisms underlying Parkinson’s disease (PD), and might provide novel platforms for systematic drug screening. Several strategies have been developed to generate iPSC-derived tyrosine hydroxylase (TH)-positive dopaminergic neurons (DAn), the clinically relevant cell type in PD; however, they often result in mixed neuronal cultures containing only a small proportion of TH-positive DAn. To overcome this limitation, we used CRISPR/Cas9-based editing to generate a human iPSC line expressing a fluorescent protein (mOrange) knocked-in at the last exon of the TH locus. After differentiation of the TH-mOrange reporter iPSC line, we confirmed that mOrange expression faithfully mimicked endogenous TH expression in iPSC-derived DAn. We also employed calcium imaging techniques to determine the intrinsic functional differences between dopaminergic and non-dopaminergic ventral midbrain neurons. Crucially, the brightness of mOrange allowed direct visualization of TH-expressing cells in heterogeneous cultures, and enabled us to isolate live mOrange-positive cells through fluorescence-activated cell sorting, for further differentiation. This technique, coupled to refined imaging and data processing tools, could advance the investigation of PD pathogenesis and might offer a platform to test potential new therapeutics for PD and other neurodegenerative diseases.
Amelioration of obesity-related biomarkers by Lactobacillus sakei CJLS03 in a high-fat diet-induced obese murine model
Authors: Ji Yosep , Park Soyoung , Chung Youngmee , Kim Bobae , Park Haryung , Huang Eunchong , Jeong Dahye , Jung Hoe-Yune , Kim Bongjoon , Hyun Chang-Kee , Holzapfel Wilhelm H.
Published: May 2019

Recent progresses in clinical diagnostic analyses have demonstrated the decisive influence of host gut microbiota on the status of metabolic disorders. Short chain fatty acids (SCFAs) produced by gut microbiota, in particular, are considered as a key biomarker, both of communication between gut microbiota and the host, and of impact on host metabolic homeostasis. Microbiota modulation and concomitant anti-obesity effects of probiotics have been reported by different researchers. However, the underlying modulatory functions of probiotics on gut microbiota towards host metabolic homeostasis are still not fully understood. In this study, the impact of Lactobacillus sakei CJLS03 (isolated from Korean kimchi) on obesity-related biomarkers was investigated using a diet-induced obese mouse model. Body weight increase, SCFAs, the gut microbiota and various obesity-associated biomarkers were significantly and beneficially influenced by L. sakei CJLS03 administration compared to the control groups. Analytical data on faecal samples support the role of the colonic microbial population in SCFA production. The composition of the latter may be influenced by modulation of the distal gastro-intestinal microbiota by putative probiotics such as L. sakei CJLS03.
Intrinsic coating morphology modulates acute drug transfer in drug-coated balloon therapy
Authors: Chang Gary H. , Azar Dara A. , Lyle Chimera , Chitalia Vipul C. , Shazly Tarek , Kolachalama Vijaya B.
Published: May 2019

The hallmark of drug-coated balloon (DCB) therapy for the treatment of peripheral vascular disease is that it allows for reopening of the narrowed lumen and local drug delivery without the need for a permanent indwelling metal implant such as a stent. Current DCB designs rely on transferring drugs such as paclitaxel to the arterial vessel using a variety of biocompatible excipients coated on the balloons. Inherent procedural challenges, along with limited understanding of the interactions between the coating and the artery, interactions between the coating and the balloon as well as site-specific differences, have led to DCB designs with poor drug delivery efficiency. Our study is focused on two clinically significant DCB excipients, urea and shellac, and uses uniaxial mechanical testing, scanning electron microscopy (SEM), and biophysical modeling based on classic Hertz theory to elucidate how coating microstructure governs the transmission of forces at the coating-artery interface. SEM revealed shellac-based coatings to contain spherical-shaped microstructural elements whereas urea-based coatings contained conical-shaped microstructural elements. Our model based on Hertz theory showed that the interactions between these intrinsic coating elements with the arterial wall were fundamentally different, even when the same external force was applied by the balloon on the arterial wall. Using two orthogonal cell-based assays, our study also found differential viability when endothelial cells were exposed to titrated concentrations of urea and shellac, further highlighting the need to maximize coating transfer efficiency in the context of DCB therapies. Our results underscore the significance of the excipient in DCB design and suggest that coating microstructure modulates acute drug transfer during device deployment.
Shade tolerance in Swarnaprabha rice is associated with higher rate of panicle emergence and positively regulated by genes of ethylene and cytokinin pathway
Authors: Panigrahy Madhusmita , Ranga Aman , Das Jyotirmayee , Panigrahi Kishore C. S.
Published: May 2019

This study identifies characteristics of seedling, mature plant phenotypes, changes at genetic and genomic level associated with Swarnaprabha (SP) rice grown under prolonged shade and compared with Nagina 22 (N22). Coleoptile length under low red/far-red was intermediate between that in dark and red light in a 7-days growth frame. Whereas, highest rootlet number was discriminating in seedlings grown for 28 days in hydroponics. In shade, SP and N22 both showed several tolerant mature plant phenotypes, except the panicle length, yield per plant and % grain filling, which were higher in SP. Percentage decrease in yield / plant in shade showed significant positive correlation with increase in NDVI, decrease in panicle length and % grain filling (p ≤ 0.01). Rate of panicle emergence in shade was higher in SP than N22. Expression patterns of PHYTOCHROME INTERACTING FACTOR LIKE-13 and PHYTOCHROME B were contrasting in SP and N22 seedlings under continuous red or red/far-red. Microarray analysis revealed the up-regulation of most of the ethylene and cytokinin pathway genes in shade grown panicles of SP. Significant up-regulation of ETHYLENE RESPONSE ELEMENT BINDING PROTEIN-2, MOTHER OF FLOWERING TIME 1, and SHORT PANICLE1 genes in shade grown panicles of SP could explain its sustainable higher yield in shade.
Conformational Change of Amyloid-β 40 in Association with Binding to GM1-Glycan Cluster
Authors: Tachi Yuhei , Okamoto Yuko , Okumura Hisashi
Published: May 2019

Aggregates of amyloid-β(Aβ) peptide are well known to be the causative substance of Alzheimer’s disease (AD). Recent studies showed that monosialotetrahexosylganglioside (GM1) clusters induce the pathological aggregation of Aβpeptide responsible for the onset and development of AD. However, the effect of GM1-glycan cluster on Aβconformations has yet to be clarified. Interactions between Aβpeptide and GM1-glycan cluster is important for the earliest stage of the toxic aggregation on GM1 cluster. Here, we performed all-atom molecular dynamics (MD) simulations of Aβ40 on a recently developed artificial GM1-glycan cluster. The artificial GM1-glycan cluster facilitates the characterization of interactions between Aβ40 and multiple GM1-glycans. We succeeded in observing the binding of Aβ40 to the GM1-glycan cluster in all of our MD simulations. Results obtained from these MD simulations indicate the importance of HHQ (13-15) segment of Aβ40 for the GM1-glycan cluster recognition. This result is consistent with previous experimental studies regarding the glycan recognition of Aβpeptide. The recognition mechanism of HHQ (13-15) segment is mainly explained by non-specific stacking interactions between side-chains of histidine and rings of sugar residues, in which the HHQ regime forms coil and bend structures. Moreover, we found that Aβ40 exhibits helix structures at C-terminal side on the GM1-glycan cluster. The helix formation is the initial stage of the pathological aggregation at ceramide moieties of GM1 cluster. The binding of Lys28 to Neu triggers the helix formation at C-terminus side because the formation of a salt bridge between Lys28 and Neu leads to change of intrachain interactions of Aβ40. Our findings suggest that the pathological helix formation of Aβ40 is initiated at GM1-glycan moieties rather than lipid ceramide moieties.
In silico structural elucidation of RNA-dependent RNA polymerase towards the identification of potential Crimean-Congo Hemorrhagic Fever Virus inhibitors
Authors: Mirza Muhammad Usman , Vanmeert Michiel , Froeyen Matheus , Ali Amjad , Rafique Shazia , Idrees Muhammad
Published: May 2019

The Crimean-Congo Hemorrhagic Fever virus (CCHFV) is a segmented negative single-stranded RNA virus (−ssRNA) which causes severe hemorrhagic fever in humans with a mortality rate of ~50%. To date, no vaccine has been approved. Treatment is limited to supportive care with few investigational drugs in practice. Previous studies have identified viral RNA dependent RNA Polymerase (RdRp) as a potential drug target due to its significant role in viral replication and transcription. Since no crystal structure is available yet, we report the structural elucidation of CCHFV-RdRp by in-depth homology modeling. Even with low sequence identity, the generated model suggests a similar overall structure as previously reported RdRps. More specifically, the model suggests the presence of structural/functional conserved RdRp motifs for polymerase function, the configuration of uniform spatial arrangement of core RdRp sub-domains, and predicted positively charged entry/exit tunnels, as seen in sNSV polymerases. Extensive pharmacophore modeling based on per-residue energy contribution with investigational drugs allowed the concise mapping of pharmacophoric features and identified potential hits. The combination of pharmacophoric features with interaction energy analysis revealed functionally important residues in the conserved motifs together with in silico predicted common inhibitory binding modes with highly potent reference compounds.