bluuebunny/crossref_metadata_2025 huggingface dataset:
Suicide Prevention in the Americas
Authors: Silverman Morton M. , Barnaby Loraine , Mishara Brian L. , Reidenberg Daniel J.
Published: March 2020

Abstract. The Americas encompass the entirety of the continents of North America and South America, representing 49 countries. Together, they make up most of Earth's western hemisphere. The population is over 1 billion (2006 figure), with over 65 % living in one of the three most populated countries (the United States, Brazil, and Mexico). The Americas have low-, middle-, and high-income countries. Data from this region have not been readily and consistently available. There are several English-speaking Caribbean nations and countries in South America that have not had updated information. This chapter will focus on suicide prevention within North America (United States and Canada), some countries in the Caribbean region, and some countries in South America. Guyana, Suriname, and Trinidad and Tobago have severe issues with pesticide suicide, with average rates of 44.2 (global rank 1); 27.8 (global rank 5) and 13.0 (global rank 41) per 100,000 respectively. Jamaica, however, had one of the lowest rates: 1.2 per 100,000 (global rank 166). General, regional, and country-specific prevention proposals are suggested, highlighting intersectoral, private collaboration, attention to at-risk persons, substance abuse and mental health interventions, training, and reducing access to lethal means.
Magnetic Reconnection Inside a Flux Rope Induced by Kelvin‐Helmholtz Vortices
Authors: Hwang K.‐J. , Dokgo K. , Choi E. , Burch J. L. , Sibeck D. G. , Giles B. L. , Hasegawa H. , Fu H. S. , Liu Y. , Wang Z. , Nakamura T. K. M. , Ma X. , Fear R. C. , Khotyaintsev Y. , Graham D. B. , Shi Q. Q. , Escoubet C. P. , Gershman D. J. , Paterson W. R. , Pollock C. J. , Ergun R. E. , Torbert R. B. , Dorelli J. C. , Avanov L. , Russell C. T. , Strangeway R. J.
Published: March 2020

On 5 May 2017, MMS observed a crater‐type flux rope on the dawnside tailward magnetopause with fluctuations. The boundary‐normal analysis shows that the fluctuations can be attributed to nonlinear Kelvin‐Helmholtz (KH) waves. Reconnection signatures such as flow reversals and Joule dissipation were identified at the leading and trailing edges of the flux rope. In particular, strong northward electron jets observed at the trailing edge indicated midlatitude reconnection associated with the 3‐D structure of the KH vortex. The scale size of the flux rope, together with reconnection signatures, strongly supports the interpretation that the flux rope was generated locally by KH vortex‐induced reconnection. The center of the flux rope also displayed signatures of guide‐field reconnection (out‐of‐plane electron jets, parallel electron heating, and Joule dissipation). These signatures indicate that an interface between two interlinked flux tubes was undergoing interaction, causing a local magnetic depression, resulting in an M‐shaped crater flux rope, as supported by reconstruction.
Constraining Fossil Fuel CO2 Emissions From Urban Area Using OCO‐2 Observations of Total Column CO2
Authors: Ye Xinxin , Lauvaux Thomas , Kort Eric A. , Oda Tomohiro , Feng Sha , Lin John C. , Yang Emily G. , Wu Dien
Published: March 2020

Satellite observations of the total column dry‐air CO2 (XCO2) are expected to support the quantification and monitoring of fossil fuel CO2 (ffCO2) emissions from urban areas. We evaluate the utility of the Orbiting Carbon Observatory 2 (OCO‐2) XCO2 retrievals to optimize whole‐city emissions, using a Bayesian inversion system and high‐resolution transport modeling. The uncertainties of constrained emissions related to transport model, satellite measurements, and local biospheric fluxes are quantified. For the first two uncertainty sources, we examine cities of different landscapes: “plume city” located in relatively flat terrain, represented by Riyadh and Cairo; and “basin city” located in basin terrain, represented by Los Angeles (LA). The retrieved scaling factors of emissions and their uncertainties show prominent variabilities from track to track, due to the varying meteorological conditions and relative locations of the tracks transecting plumes. To explore the performance of multiple tracks in retrieving emissions, pseudo data experiments are carried out. The estimated least numbers of tracks required to constrain the total emissions for Riyadh (<10% uncertainty), Cairo (<10%), and LA (<5%) are 8, 5, and 7, respectively. Additionally, to evaluate the impact of biospheric fluxes on derivation of the ffXCO2 enhancements, we conduct simulations for Pearl River Delta metropolitan area. Significant fractions of local XCO2 enhancements associated with local biospheric XCO2 variations are shown, which potentially lead to biased estimates of ffCO2 emissions. We demonstrate that satellite measurements can be used to improve urban ffCO2 emissions with a sufficient amount of measurements and appropriate representations of the uncertainty components.
Climatology and Detection of Overshooting Convection From 4 Years of GPM Precipitation Radar and Passive Microwave Observations
Authors: Liu Nana , Liu Chuntao , Hayden Lindsey
Published: March 2020

A 4‐year Global Precipitation Measurement (GPM) Precipitation Feature (PF) data set is used to quantify the frequency and global distribution of overshooting convection. In this study, overshooting convection is defined as PFs with maximum 20 dBZ echo top height (MAXHT20) greater than the height of the lapse rate tropopause, derived from ERA‐Interim reanalysis data. The geographical distribution of overshooting convection exhibits a strong preference for specific land regions, such as over the central United States, Argentina, Central Africa, and Colombia. Larger areas and greater occurrence of 20 dBZ radar reflectivity at the tropopause are found in northern middle to high latitudes than in the tropics. The occurrence of 20 dBZ radar reflectivity reaching above the level of 380 K potential temperature (Z380K) in middle and high latitudes is found to be comparable to that in the tropics. Furthermore, a methodology is developed to detect overshooting convection using the GPM Microwave Imager measured brightness temperature at 183.31 ± 3 and 183.31 ± 7 GHz, and Polarization Corrected Temperature at 89 GHz. The geographical distribution of overshooting convection can be closely reproduced using the combinations of these brightness temperatures with an average Heidke skill score of 0.4 and probability of 0.38. This shows the possibility of identifying overshooting convection from microwave observations at high‐frequency channels near the water vapor absorption line centered at 183.31 GHz from other satellite missions.
The Chemistry Mechanism in the Community Earth System Model Version 2 (CESM2)
Authors: Emmons Louisa K. , Schwantes Rebecca H. , Orlando John J. , Tyndall Geoff , Kinnison Douglas , Lamarque Jean‐François , Marsh Daniel , Mills Michael J. , Tilmes Simone , Bardeen Charles , Buchholz Rebecca R. , Conley Andrew , Gettelman Andrew , Garcia Rolando , Simpson Isobel , Blake Donald R. , Meinardi Simone , Pétron Gabrielle
Published: March 2020

The Community Earth System Model version 2 (CESM2) includes a detailed representation of chemistry throughout the atmosphere in the Community Atmosphere Model with chemistry and Whole Atmosphere Community Climate Model configurations. These model configurations use the Model for Ozone and Related chemical Tracers (MOZART) family of chemical mechanisms, covering the troposphere, stratosphere, mesosphere, and lower thermosphere. The new MOZART tropospheric chemistry scheme (T1) has a number of updates over the previous version (MOZART‐4) in CESM, including improvements to the oxidation of isoprene and terpenes, organic nitrate speciation, and aromatic speciation and oxidation and thus improved representation of ozone and secondary organic aerosol precursors. An evaluation of the present‐day simulations of CESM2 being provided for Climate Model Intercomparison Project round 6 (CMIP6) is presented. These simulations, using the anthropogenic and biomass burning emissions from the inventories specified for CMIP6, as well as online calculation of emissions of biogenic compounds, lightning NO, dust, and sea salt, indicate an underestimate of anthropogenic emissions of a variety of compounds, including carbon monoxide and hydrocarbons. The simulation of surface ozone in the southeast United States is improved over previous model versions, largely due to the improved representation of reactive nitrogen and organic nitrate compounds resulting in a lower ozone production rate than in CESM1 but still overestimates observations in summer. The simulation of tropospheric ozone agrees well with ozonesonde observations in many parts of the globe. The comparison of NOxand PAN to aircraft observations indicates the model simulates the nitrogen budget well.
Riparian Lowlands in Clay Till Landscapes: Part I—Heterogeneity of Flow Paths and Water Balances
Authors: Petersen R. J. , Prinds C. , Iversen B. V. , Engesgaard P. , Jessen S. , Kjaergaard C.
Published: March 2020

Riparian lowlands act as interfaces between the streams and upland areas. This study identified and quantified local flow paths in four transects of a 26 ha Danish riparian lowland in a glacial till landscape. The riparian lowland was fed by drain water from the upland agricultural drainage catchments. Precipitation, stream stage, and drainage discharge into the riparian lowland were measured continuously, while groundwater hydraulic heads were measured in piezometer pipes twice per month. A water balance model was developed to quantify water fluxes leaving the riparian lowland area via evapotranspiration, leakage to a deeper aquifer, and via groundwater flow, drain flow, and overland flow to the adjacent stream. Overland flow originating from the tile drains was the main flow path in all four transects, and also fluxes to the stream via groundwater or lowland tile drains were significant in some subareas. The presence of a secondary tile drainage network within parts of the riparian lowland reduced overland flow and increased interaction with the riparian lowland soils. Area‐normalized fluxes varied greatly between transects, largely reflecting variations in hydraulic loading rate (ratio of water input rate to the area of the receiving riparian lowland). This, combined with the significance of groundwater flow and riparian lowland tile drain flow in some of the investigated transects, revealed a heterogeneous distribution of flow paths within the small headwater lowland. The rate of overland flow was highly correlated to the hydraulic loading rate, which in turn was dominated by the drainage discharge rate at the hillslope boundary.
Impairment of carbonic anhydrase IX ectodomain cleavage reinforces tumorigenic and metastatic phenotype of cancer cells
Authors: Kajanova Ivana , Zatovicova Miriam , Jelenska Lenka , Sedlakova Olga , Barathova Monika , Csaderova Lucia , Debreova Michaela , Lukacikova Lubomira , Grossmannova Katarina , Labudova Martina , Golias Tereza , Svastova Eliska , Ludwig Andreas , Muller Petr , Vojtesek Borivoj , Pastorek Jaromir , Pastorekova Silvia
Published: March 2020

Background

Carbonic anhydrase IX (CA IX) is a hypoxia-induced enzyme regulating tumour pH and facilitating cell migration/invasion. It is primarily expressed as a transmembrane cell-surface protein, but its ectodomain can be shed by ADAM17 to extracellular space. This study aims to elucidate the impact of CA IX shedding on cancer cells.

Methods

We generated a non-shed CA IX mutant by deletion of amino acids 393–402 from the stalk region and studied its phenotypic effects compared to full-length, shedding-competent CA IX using a range of assays based on immunodetection, confocal microscopy, in vitro real-time cell monitoring and in vivo tumour cell inoculation using xenografted NMRI and C57BL/6J female mice.

Results

We demonstrated that the impairment of shedding does not alter the ability of CA IX to bind ADAM17, internalise, form oligomers and regulate pH, but induces cancer-promoting changes in extracellular proteome. Moreover, it affects intrinsic properties of cells expressing the non-shed variant, in terms of their increased ability to migrate, generate primary tumours and form metastatic lesions in lungs.

Conclusions

Our results show that the ectodomain shedding controls pro-tumorigenic and pro-metastatic roles of the cell-associated CA IX and suggest that this phenomenon should be considered when developing CA IX-targeted therapeutic strategies.
Prognostic and clinical impact of PD-L2 and PD-L1 expression in a cohort of 437 oesophageal cancers
Authors: Okadome Kazuo , Baba Yoshifumi , Nomoto Daichi , Yagi Taisuke , Kalikawe Rebecca , Harada Kazuto , Hiyoshi Yukiharu , Nagai Yohei , Ishimoto Takatsugu , Iwatsuki Masaaki , Iwagami Shiro , Miyamoto Yuji , Yoshida Naoya , Watanabe Masayuki , Komohara Yoshihiro , Shono Takashi , Sasaki Yutaka , Baba Hideo
Published: March 2020

Background

The PD-1/PD-L1 pathway plays critical roles in tumour immunology, and serves as an immune-based therapeutic target. Less is known regarding PD-L2, another ligand of PD-1, and its relation to clinical outcome in human cancers.

Methods

We used a database of 437 surgically and 100 endoscopically resected oesophageal cancers (squamous cell carcinoma, n = 483; adenocarcinoma, n = 36; others, n = 18) to evaluate PD-L2 and PD-L1 expression by immunohistochemistry.

Results

Compared with PD-L2-negative cases (n = 366, 83.8%), PD-L2-positive cases (n = 71, 16.2%) had worse overall survival (P = 0.011, log-rank test). There was not a significant correlation between PD-L2 and PD-L1 expression. Multiplex immunofluorescence revealed that there was variability in the expression pattern of PD-L2 and PD-L1. In early-stage tumours, PD-L2 expression was more frequently observed compared with PD-L1.

Conclusions

PD-L2 as well as PD-L1 were associated with an unfavourable prognosis in oesophageal cancer, supporting the role of PD-L2 as a prognostic biomarker. Considering that PD-L2 and PD-L1 had different features in terms of expression timing and responses to chemotherapeutic drugs, evaluation of both PD-L2 and PD-L1 expression may be clinically important.
Human activity recognition using magnetic induction-based motion signals and deep recurrent neural networks
Authors: Golestani Negar , Moghaddam Mahta
Published: March 2020

Recognizing human physical activities using wireless sensor networks has attracted significant research interest due to its broad range of applications, such as healthcare, rehabilitation, athletics, and senior monitoring. There are critical challenges inherent in designing a sensor-based activity recognition system operating in and around a lossy medium such as the human body to gain a trade-off among power consumption, cost, computational complexity, and accuracy. We introduce an innovative wireless system based on magnetic induction for human activity recognition to tackle these challenges and constraints. The magnetic induction system is integrated with machine learning techniques to detect a wide range of human motions. This approach is successfully evaluated using synthesized datasets, laboratory measurements, and deep recurrent neural networks.
δ and φ back-donation in AnIV metallacycles
Authors: Kelley Morgan P. , Popov Ivan A. , Jung Julie , Batista Enrique R. , Yang Ping
Published: March 2020

In all known examples of metal–ligand (M–L) δ and φ bonds, the metal orbitals are aligned to the ligand orbitals in a “head-to-head” or “side-to-head” fashion. Here, we report two fundamentally new types of M–L δ and φ interactions; “head-to-side” δ and “side-to-side” φ back-bonding, found in complexes of metallacyclopropenes and metallacyclocumulenes of actinides (Pa–Pu) that makes them distinct from their corresponding Group 4 analogues. In addition to the known Th and U complexes, our calculations include complexes of Pa, Np, and Pu. In contrast with conventional An–C bond decreasing, due to the actinide contraction, the An–C distance increases from Pa to Pu. We demonstrate that the direct L–An σ and π donations combined with the An–L δ or φ back-donations are crucial in explaining this non-classical trend of the An–L bond lengths in both series, underscoring the significance of these δ/φ back-donation interactions, and their importance for complexes of Pa and U in particular.
Housing temperature influences exercise training adaptations in mice
Authors: Raun Steffen H. , Henriquez-Olguín Carlos , Karavaeva Iuliia , Ali Mona , Møller Lisbeth L. V. , Kot Witold , Castro-Mejía Josué L. , Nielsen Dennis Sandris , Gerhart-Hines Zachary , Richter Erik A. , Sylow Lykke
Published: March 2020

Exercise training is a powerful means to combat metabolic diseases. Mice are extensively used to investigate the benefits of exercise, but mild cold stress induced by ambient housing temperatures may confound translation to humans. Thermoneutral housing is a strategy to make mice more metabolically similar to humans but its effects on exercise adaptations are unknown. Here we show that thermoneutral housing blunts exercise-induced improvements in insulin action in muscle and adipose tissue and reduces the effects of training on energy expenditure, body composition, and muscle and adipose tissue protein expressions. Thus, many reported effects of exercise training in mice are likely secondary to metabolic stress of ambient housing temperature, making it challenging to translate to humans. We conclude that adaptations to exercise training in mice critically depend upon housing temperature. Our findings underscore housing temperature as a critical parameter in the design and interpretation of murine exercise training studies.
c-di-GMP modulates type IV MSHA pilus retraction and surface attachment in Vibrio cholerae
Authors: Floyd Kyle A. , Lee Calvin K. , Xian Wujing , Nametalla Mahmoud , Valentine Aneesa , Crair Benjamin , Zhu Shiwei , Hughes Hannah Q. , Chlebek Jennifer L. , Wu Daniel C. , Hwan Park Jin , Farhat Ali M. , Lomba Charles J. , Ellison Courtney K. , Brun Yves V. , Campos-Gomez Javier , Dalia Ankur B. , Liu Jun , Biais Nicolas , Wong Gerard C. L. , Yildiz Fitnat H.
Published: March 2020

Biofilm formation by Vibrio cholerae facilitates environmental persistence, and hyperinfectivity within the host. Biofilm formation is regulated by 3’,5’-cyclic diguanylate (c-di-GMP) and requires production of the type IV mannose-sensitive hemagglutinin (MSHA) pilus. Here, we show that the MSHA pilus is a dynamic extendable and retractable system, and its activity is directly controlled by c-di-GMP. The interaction between c-di-GMP and the ATPase MshE promotes pilus extension, whereas low levels of c-di-GMP correlate with enhanced retraction. Loss of retraction facilitated by the ATPase PilT increases near-surface roaming motility, and impairs initial surface attachment. However, prolonged retraction upon surface attachment results in reduced MSHA-mediated surface anchoring and increased levels of detachment. Our results indicate that c-di-GMP directly controls MshE activity, thus regulating MSHA pilus extension and retraction dynamics, and modulating V. cholerae surface attachment and colonization.
Somatodendritic consistency check for temporal feature segmentation
Authors: Asabuki Toshitake , Fukai Tomoki
Published: March 2020

The brain identifies potentially salient features within continuous information streams to process hierarchical temporal events. This requires the compression of information streams, for which effective computational principles are yet to be explored. Backpropagating action potentials can induce synaptic plasticity in the dendrites of cortical pyramidal neurons. By analogy with this effect, we model a self-supervising process that increases the similarity between dendritic and somatic activities where the somatic activity is normalized by a running average. We further show that a family of networks composed of the two-compartment neurons performs a surprisingly wide variety of complex unsupervised learning tasks, including chunking of temporal sequences and the source separation of mixed correlated signals. Common methods applicable to these temporal feature analyses were previously unknown. Our results suggest the powerful ability of neural networks with dendrites to analyze temporal features. This simple neuron model may also be potentially useful in neural engineering applications.
Water and health interlinkages of the sustainable development goals in remote Indigenous Australia
Authors: Hall Nina Lansbury , Creamer Sandra , Anders Wendy , Slatyer Anthony , Hill Peter S.
Published: March 2020

Australia has committed to the 17 Sustainable Development Goals (SDGs) goals under the UN’s 2030 Agenda. However, these goals may not be fully achieved in Australia under current policy settings. Australia reports success in achieving the goal for quality and access to safe drinking water and sanitation (SDG 6), though for Australians living in remote Indigenous communities, the experience is very different. Furthermore, the burden of disease is higher in remote communities (SDG 3). Many of these diseases are waterborne or hygiene-related, including prevalence in some remote Indigenous communities of endemic trachoma eye infection, preventable through access to functioning water services and available soap. This research provides a case for identifying, then understanding the interlinkages between SDGs 3, 6, and others locally, as well as nationally. This will enable governments to enact policies for long-term sustainable solutions for remotely-located and marginalised peoples in Australia in line with Agenda 2030 commitments.
Neurotrophic effects of GM1 ganglioside, NGF, and FGF2 on canine dorsal root ganglia neurons in vitro
Authors: Schwarz S. , Lehmbecker A. , Tongtako W. , Hahn K. , Wang Y. , Felmy F. , Zdora I. , Brogden G. , Branitzki-Heinemann K. , von Köckritz-Blickwede M. , Baumgärtner W. , Gerhauser I.
Published: March 2020

Dogs share many chronic morbidities with humans and thus represent a powerful model for translational research. In comparison to rodents, the canine ganglioside metabolism more closely resembles the human one. Gangliosides are components of the cell plasma membrane playing a role in neuronal development, intercellular communication and cellular differentiation. The present in vitro study aimed to characterize structural and functional changes induced by GM1 ganglioside (GM1) in canine dorsal root ganglia (DRG) neurons and interactions of GM1 with nerve growth factor (NGF) and fibroblast growth factor (FGF2) using immunofluorescence for several cellular proteins including neurofilaments, synaptophysin, and cleaved caspase 3, transmission electron microscopy, and electrophysiology. GM1 supplementation resulted in increased neurite outgrowth and neuronal survival. This was also observed in DRG neurons challenged with hypoxia mimicking neurodegenerative conditions due to disruptions of energy homeostasis. Immunofluorescence indicated an impact of GM1 on neurofilament phosphorylation, axonal transport, and synaptogenesis. An increased number of multivesicular bodies in GM1 treated neurons suggested metabolic changes. Electrophysiological changes induced by GM1 indicated an increased neuronal excitability. Summarized, GM1 has neurotrophic and neuroprotective effects on canine DRG neurons and induces functional changes. However, further studies are needed to clarify the therapeutic value of gangliosides in neurodegenerative diseases.
Iron phthalocyanine-sensitized magnetic catalysts for BPA photodegradation
Authors: Neamtu Mariana , Nadejde Claudia , Brinza Loredana , Dragos Oana , Gherghel Daniela , Paul Andrea
Published: March 2020

The catalytic behavior of iron phthalocyanine (FePc)-sensitized magnetic nanocatalysts was evaluated for their application in the oxidative treatment of Bisphenol A (BPA) under mild environmental conditions. Two types of FePc (Fe(II)Pc and Fe(III)Pc), which are highly photosensitive compounds, were immobilized on the surface of functionalized magnetite. The nanomaterials were characterized by high resolution transmission electron microscopy (HR-TEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and thermogravimetric analyses (TGA). The generation of singlet oxygen by nanomaterials was also investigated. In the presence of UVA light exposure (365 nm) and 15 mM H2O2, the M@Fe(III)Pc photocatalyst gave the best results; for a catalyst concentration of 2.0 g L − 1, around 60% BPA was removed after 120 min of reaction. These experimental conditions were further tested under natural solar light exposure, for which also M@Fe(III)Pc exhibited enhanced oxidative catalytic activity, being able to remove 83% of BPA in solution. The water samples were less cytotoxic after treatment, this being confirmed by the MCF-7 cell viability assay.
Author Correction: Influence of pure fluorides and stannous ions on the initial bacterial colonization in situ
Authors: Kirsch Jasmin , Hannig Matthias , Winkel Pia , Basche Sabine , Leis Birgit , Pütz Norbert , Kensche Anna , Hannig Christian
Published: March 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Field evaluation of sex pheromones and binding specificity of pheromone binding protein 4 in Tryporyza intacta (Lepidoptera: Crambidae)
Authors: Hu Yuwei , Liu Yuying , Bi Jie , Chen Ya , Zheng Ya , Mao Yongkai , Mao Yuling , Xu Hanliang , Guan Chuxiong , Chen Yan , Ai Hui
Published: March 2020

The recognition of chemical signal including volatile odorants and pheromones is very important in the olfactory physiological behaviors of insects, such as avoiding predators, seeking food and mating partners. The sugarcane borer, Tryporyza intacta is the most harmful insect in sugarcane region in Southeast Asia and Southern China, however, the study of their molecular biology and physiology was limited. Here we demonstrated that the sex pheromone (E11-16:Ald: Z11-16:Ald = 7:3) were most effective to T. intacta. In addition, compared the traditional rubber lure, a new microsphere formulation lure can optimize the trapping effect and might be widely used in the sugarcane growing area. To obtain a better understanding of the olfactory molecular mechanism of pheromone-based mate recognition system, we have cloned the full-length gene of the TintPBP4 and expressed in Escherichia coli. Our phylogenetic analysis highlighted that the TintPBP4 was highly conserved among diverse species of Lepidoptera. Furthermore, the results of QRT-PCR demonstrated that TintPBP4 transcripts were abundantly expressed in the antennae of T. intacta, especially in the male adults. The fluorescence binding experiments showed the TintPBP4 exhibited strong binding capacities to the sex pheromone components. These results will not only provide more understanding for the functional analysis of olfactory proteins from T. intacta, but also assist in the exploitation and development of sex pheromones in the integrated biological control of this pest.
Rapid Learning of Earthquake Felt Area and Intensity Distribution with Real-time Search Engine Queries
Authors: Zhu Hengshu , Sun Ying , Zhao Wenjia , Zhuang Fuzhen , Wang Baoshan , Xiong Hui
Published: March 2020

Immediately after a destructive earthquake, the real-time seismological community has a major focus on rapidly estimating the felt area and the extent of ground shaking. This estimate provides critical guidance for government emergency response teams to conduct orderly rescue and recovery operations in the damaged areas. While considerable efforts have been made in this direction, it still remains a realistic challenge for gathering macro-seismic data in a timely, accurate and cost-effective manner. To this end, we introduce a new direction to improve the information acquisition through monitoring the real-time information-seeking behaviors in the search engine queries, which are submitted by tens of millions of users after earthquakes. Specifically, we provide a very efficient, robust and machine-learning-assisted method for mapping the user-reported ground shaking distribution through the large-scale analysis of real-time search queries from a dominant search engine in China. In our approach, each query is regarded as a “crowd sensor” with a certain weight of confidence to proactively report the shaking location and extent. By fitting the epicenters of earthquakes occurred in mainland China from 2014 to 2018 with well-designed machine learning models, we can efficiently learn the realistic weight of confidence for each search query and sketch the felt areas and intensity distributions for most of the earthquakes. Indeed, this approach paves the way for using real-time search engine queries to efficiently map earthquake felt area in the regions with a relatively large population of search engine users.
Expectancy effects in the EEG during joint and spontaneous word-by-word sentence production in German
Authors: Goregliad Fjaellingsdal Tatiana , Schwenke Diana , Scherbaum Stefan , Kuhlen Anna K. , Bögels Sara , Meekes Joost , Bleichner Martin G.
Published: March 2020

Our aim in the present study is to measure neural correlates during spontaneous interactive sentence production. We present a novel approach using the word-by-word technique from improvisational theatre, in which two speakers jointly produce one sentence. This paradigm allows the assessment of behavioural aspects, such as turn-times, and electrophysiological responses, such as event-related-potentials (ERPs). Twenty-five participants constructed a cued but spontaneous four-word German sentence together with a confederate, taking turns for each word of the sentence. In 30% of the trials, the confederate uttered an unexpected gender-marked article. To complete the sentence in a meaningful way, the participant had to detect the violation and retrieve and utter a new fitting response. We found significant increases in response times after unexpected words and – despite allowing unscripted language production and naturally varying speech material – successfully detected significant N400 and P600 ERP effects for the unexpected word. The N400 EEG activity further significantly predicted the response time of the subsequent turn. Our results show that combining behavioural and neuroscientific measures of verbal interactions while retaining sufficient experimental control is possible, and that this combination provides promising insights into the mechanisms of spontaneous spoken dialogue.
Symbiotic nitrogen fixation and endophytic bacterial community structure in Bt-transgenic chickpea (Cicer arietinum L)
Authors: Alok Das , Annapragada Harika , Singh Shilpa , Murugesan Senthilkumar , Singh Narendra Pratap
Published: March 2020

Symbiotic nitrogen fixation (SNF) of transgenic grain legumes might be influenced either by the site of transgene integration into the host genome or due to constitutive expression of transgenes and antibiotic-resistant marker genes. The present investigation confirmed proper nodulation of five tested Bt-chickpea events (IPCa2, IPCa4, IPCT3, IPCT10, and IPCT13) by native Mesorhizobium under field environment. Quantitative variations for nodulation traits among Bt-chickpea were determined and IPCT3 was found superior for nodule number and nodule biomass. Diversity, as well as richness indices, confirmed the changes in bacterial community structure of root and root-nodules from Bt-chickpea events IPCa2 and IPCT10. Especially, Gram-positive bacteria belonging to Firmicutes and Actinobacteria were selectively eliminated from root colonization of IPCa2. Richness indices (CHAO1 and ACE) of the root-associated bacterial community of IPCa2 was 13–14 times lesser than that of parent cv DCP92-3. Root nodule associated bacterial community of IPCT10 was unique with high diversity and richness, similar to the roots of non-Bt and Bt-chickpea. It indicated that the root nodules of IPCT10 might have lost their peculiar characteristics and recorded poor colonization of Mesorhizobium with a low relative abundance of 0.27. The impact of Bt-transgene on bacterial community structure and nodulation traits should be analyzed across the years and locations to understand and stabilize symbiotic efficiency for ecosystem sustainability.
Impact of air pollution on breast cancer incidence and mortality: a nationwide analysis in South Korea
Authors: Hwang Jeongeun , Bae Hyunjin , Choi Seunghyun , Yi Hahn , Ko Beomseok , Kim Namkug
Published: March 2020

Breast cancer is one of the major female health problems worldwide. Although there is growing evidence indicating that air pollution increases the risk of breast cancer, there is still inconsistency among previous studies. Unlike the previous studies those had case-control or cohort study designs, we performed a nationwide, whole-population census study. In all 252 administrative districts in South Korea, the associations between ambient NO2 and particulate matter 10 (PM10) concentration, and age-adjusted breast cancer mortality rate in females (from 2005 to 2016, Nmortality = 23,565), and incidence rate (from 2004 to 2013, Nincidence = 133,373) were investigated via multivariable beta regression. Population density, altitude, rate of higher education, smoking rate, obesity rate, parity, unemployment rate, breastfeeding rate, oral contraceptive usage rate, and Gross Regional Domestic Product per capita were considered as potential confounders. Ambient air pollutant concentrations were positively and significantly associated with the breast cancer incidence rate: per 100 ppb CO increase, Odds Ratio OR = 1.08 (95% Confidence Interval CI = 1.06–1.10), per 10 ppb NO2, OR = 1.14 (95% CI = 1.12–1.16), per 1 ppb SO2, OR = 1.04 (95% CI = 1.02–1.05), per 10 µg/m3 PM10, OR = 1.13 (95% CI = 1.09–1.17). However, no significant association between the air pollutants and the breast cancer mortality rate was observed except for PM10: per 10 µg/m3 PM10, OR = 1.05 (95% CI = 1.01–1.09).
The Spectrum-STI Groups model: syphilis prevalence trends across high-risk and lower-risk populations in Yunnan, China
Authors: Korenromp Eline L. , Zhang Wanyue , Zhang Xiujie , Ma Yanling , Jia Manhong , Luo Hongbin , Guo Yan , Zhang Xiaobin , Gong Xiangdong , Chen Fangfang , Li Jing , Nishijima Takeshi , Chen Zhongdan , Taylor Melanie M. , Hecht Kendall , Mahiané Guy , Rowley Jane , Chen Xiang-Sheng
Published: March 2020

The Spectrum-STI model, structured by sub-groups within a population, was used in a workshop in Yunnan, China, to estimate provincial trends in active syphilis in 15 to 49-year-old adults. Syphilis prevalence data from female sex workers (FSW), men who have sex with men (MSM), and lower-risk women and men in Yunnan were identified through literature searches and local experts. Sources included antenatal care clinic screening, blood donor screening, HIV/STI bio-behavioural surveys, sentinel surveillance, and epidemiology studies. The 2017 provincial syphilis prevalence estimates were 0.26% (95% confidence interval 0.17–0.34%) in women and 0.28% (0.20–0.36%) in men. Estimated prevalence was 6.8-fold higher in FSW (1.69% (0.68–3.97%) than in lower-risk women (0.25% (0.18–0.35%)), and 22.7-fold higher in MSM (5.35% (2.74–12.47%) than in lower-risk men (0.24% (0.17–0.31%). For all populations, the 2017 estimates were below the 2005 estimates, but differences were not significant. In 2017 FSW and MSM together accounted for 9.3% of prevalent cases. These estimates suggest Yunnan’s STI programs have kept the overall prevalence of syphilis low, but prevalence remains high in FSW and MSM. Strengthening efforts targeting FSW and MSM, and identification of other risk populations e.g. among heterosexual men, are critical to reduce syphilis.
Biotic and Abiotic Contribution to Diurnal Soil CO2 Fluxes from Saline/Alkaline Soils
Authors: Wang Zhong-Yuan , Xie Jiang-Bo , Wang Yu-Gang , Li Yan
Published: March 2020

As the second largest carbon flux in terrestrial ecosystems, the soil CO2 flux is closely related to the atmospheric CO2 concentration. The soil CO2 flux is the sum of biotic respiration and abiotic geochemical CO2 exchange; however, little is known about abiotic CO2 fluxes in arid areas. To investigate the relative contribution of abiotic and biotic soil CO2 fluxes over a diurnal course, the abiotic CO2 flux was distinguished by autoclaving sterilization in both saline and alkaline soils at an arid site in northwestern China. The results demonstrated that: (1) Over the diurnal course, the abiotic CO2 was a significant component of the soil CO2 flux in both saline and alkaline soil, which accounted for more than 56% of the diurnal soil CO2 flux. (2) There was a dramatic difference in the temperature response between biotic and abiotic CO2 fluxes: the response curves of biotic respiration were exponential in the saline soil and quadratic in the alkaline soil, while the abiotic CO2 flux was linearly correlated with soil temperature. They were of similar magnitude but with opposite signs: resulting in almost neutral carbon emissions on daily average. (3) Due to this covering up effect of the abiotic CO2 flux, biotic respiration was severely underestimated (directly measured soil CO2 flux was only one-seventh of the biotic CO2 flux in saline soil, and even an order of magnitude lower in alkaline soil). In addition, the soil CO2 flux masked the temperature-inhibition of biotic respiration in the alkaline soil, and veiled the differences in soil biological respiration between the saline and alkaline soils. Hence, the soil CO2 flux may not be an ideal representative of soil respiration in arid soil. Our study calls for a reappraisal of the definition of the soil CO2 flux and its temperature dependence in arid or saline/alkaline land. Further investigations of abiotic CO2 fluxes are needed to improve our understanding of arid land responses to global warming and to assist in identifying the underlying abiotic mechanisms.
Implication of the gut microbiome composition of type 2 diabetic patients from northern China
Authors: Li Qian , Chang Yujun , Zhang Ke , Chen Hao , Tao Shiheng , Zhang Zhi
Published: March 2020

Emerging evidence has suggested the association of the gut microbiome with some human diseases, including type 2 diabetes (T2D). In this study, we analyzed the gut microbiota from a cohort of healthy and diabetic Chinese individuals from Northern China. Pyrosequencing of the V4V5 region of 16S rRNA genes revealed a significant decrease in the gut microbiota diversity of diabetic patients as compared to healthy individuals. Butyrate-producing bacteria such as Bifidobacterium and Akkermansia were significantly decreased in diabetic patients. Furthermore, the abundance of Dorea was significantly increased in T2D individuals and negatively correlated with the abundance of butyrate-producing bacteria. The increase of Dorea could play a role in the development of T2D and has been previously overlooked. Importantly, functional analysis of the gut microbiome revealed for the first time that increased levels of butyrate production via transferases and the degradation of several amino acids due to gut microbial metabolism have strong correlations with T2D in Northern China. Moreover, the potential of gut microbiota-based classifiers to identify individuals with a high risk for T2D has been demonstrated in this study. Taken together, our findings have revealed a previously unappreciated association of the gut microbiome with T2D and have also suggested that changes in gut microbiota may be used to identify individuals at high risk for T2D.
Assessment of unconventional antimicrobial compounds for the control of ‘Candidatus Liberibacter asiaticus’, the causative agent of citrus greening disease
Authors: Gardner Christopher L. , da Silva Danilo R. , Pagliai Fernando A. , Pan Lei , Padgett-Pagliai Kaylie A. , Blaustein Ryan A. , Merli Marcelo L. , Zhang Dan , Pereira Cécile , Teplitski Max , Chaparro Jose X. , Folimonova Svetlana Y. , Conesa Ana , Gezan Salvador , Lorca Graciela L. , Gonzalez Claudio F.
Published: March 2020

In this study, newly identified small molecules were examined for efficacy against ‘Candidatus Liberibacter asiaticus’ in commercial groves of sweet orange (Citrus sinensis) and white grapefruit (Citrus paradisi) trees. We used benzbromarone and/or tolfenamic acid delivered by trunk injection. We evaluated safety and efficacy parameters by performing RNAseq of the citrus host responses, 16S rRNA gene sequencing to characterize citrus-associated microbial communities during treatment, and qRT-PCR as an indirect determination of ‘Ca. L. asiaticus’ viability. Analyses of the C. sinensis transcriptome indicated that each treatment consistently induced genes associated with normal metabolism and growth, without compromising tree viability or negatively affecting the indigenous citrus-associated microbiota. It was found that treatment-associated reduction in ‘Ca. L. asiaticus’ was positively correlated with the proliferation of several core taxa related with citrus health. No symptoms of phytotoxicity were observed in any of the treated trees. Trials were also performed in commercial groves to examine the effect of each treatment on fruit productivity, juice quality and efficacy against ‘Ca. L. asiaticus’. Increased fruit production (15%) was observed in C. paradisi following twelve months of treatment with benzbromarone and tolfenamic acid. These results were positively correlated with decreased ‘Ca. L. asiaticus’ transcriptional activity in root samples.
microRNA and Metabolite Signatures Linked to Early Consequences of Lethal Radiation
Authors: Chakraborty Nabarun , Gautam Aarti , Holmes-Hampton Gregory P. , Kumar Vidya P. , Biswas Shukla , Kumar Raina , Hamad Dana , Dimitrov George , Olabisi Ayodele O. , Hammamieh Rasha , Ghosh Sanchita P.
Published: March 2020

Lethal total body irradiation (TBI) triggers multifactorial health issues in a potentially short time frame. Hence, early signatures of TBI would be of great clinical value. Our study aimed to interrogate microRNA (miRNA) and metabolites, two biomolecules available in blood serum, in order to comprehend the immediate impacts of TBI. Mice were exposed to a lethal dose (9.75 Gy) of Cobalt-60 gamma radiation and euthanized at four time points, namely, days 1, 3, 7 and 9 post-TBI. Serum miRNA libraries were sequenced using the Illumina small RNA sequencing protocol, and metabolites were screened using a mass spectrometer. The degree of early impacts of irradiation was underscored by the large number of miRNAs and metabolites that became significantly expressed during the Early phase (day 0 and 1 post-TBI). Radiation-induced inflammatory markers for bone marrow aplasia and pro-sepsis markers showed early elevation with longitudinal increment. Functional analysis integrating miRNA-protein-metabolites revealed inflammation as the overarching host response to lethal TBI. Early activation of the network linked to the synthesis of reactive oxygen species was associated with the escalated regulation of the fatty acid metabolism network. In conclusion, we assembled a list of time-informed critical markers and mechanisms of significant translational potential in the context of a radiation exposure event.
Whole-genome sequencing of Burkholderia pseudomallei from an urban melioidosis hot spot reveals a fine-scale population structure and localised spatial clustering in the environment
Authors: Rachlin Audrey , Mayo Mark , Webb Jessica R. , Kleinecke Mariana , Rigas Vanessa , Harrington Glenda , Currie Bart J. , Kaestli Mirjam
Published: March 2020

Melioidosis is a severe disease caused by the environmental bacterium Burkholderia pseudomallei that affects both humans and animals throughout northern Australia, Southeast Asia and increasingly globally. While there is a considerable degree of genetic diversity amongst isolates, B. pseudomallei has a robust global biogeographic structure and genetic populations are spatially clustered in the environment. We examined the distribution and local spread of B. pseudomallei in Darwin, Northern Territory, Australia, which has the highest recorded urban incidence of melioidosis globally. We sampled soil and land runoff throughout the city centre and performed whole-genome sequencing (WGS) on B. pseudomallei isolates. By combining phylogenetic analyses, Bayesian clustering and spatial hot spot analysis our results demonstrate that some sequence types (STs) are widespread in the urban Darwin environment, while others are highly spatially clustered over a small geographic scale. This clustering matches the spatial distribution of clinical cases for one ST. Results also demonstrate a greater overall isolate diversity recovered from drains compared to park soils, further supporting the role drains may play in dispersal of B. pseudomallei STs in the environment. Collectively, knowledge gained from this study will allow for better understanding of B. pseudomallei phylogeography and melioidosis source attribution, particularly on a local level.
Semi-CAM: A semi-supervised deconvolution method for bulk transcriptomic data with partial marker gene information
Authors: Dong Li , Kollipara Avinash , Darville Toni , Zou Fei , Zheng Xiaojing
Published: March 2020

Deconvolution of bulk transcriptomics data from mixed cell populations is vital to identify the cellular mechanism of complex diseases. Existing deconvolution approaches can be divided into two major groups: supervised and unsupervised methods. Supervised deconvolution methods use cell type-specific prior information including cell proportions, reference cell type-specific gene signatures, or marker genes for each cell type, which may not be available in practice. Unsupervised methods, such as non-negative matrix factorization (NMF) and Convex Analysis of Mixtures (CAM), in contrast, completely disregard prior information and thus are not efficient for data with partial cell type-specific information. In this paper, we propose a semi-supervised deconvolution method, semi-CAM, that extends CAM by utilizing marker information from partial cell types. Analysis of simulation and two benchmark data have demonstrated that semi-CAM outperforms CAM by yielding more accurate cell proportion estimations when markers from partial/all cell types are available. In addition, when markers from all cell types are available, semi-CAM achieves better or similar accuracy compared to the supervised method using signature genes, CIBERSORT, and the marker-based supervised methods semi-NMF and DSA. Furthermore, analysis of human chlamydia-infection data with bulk expression profiles from six cell types and prior marker information of only three cell types suggests that semi-CAM achieves more accurate cell proportion estimations than CAM.
Perioperative symptomatic venous thromboembolism after immediate chemoprophylaxis in patients with pelvic and lower-extremity fractures
Authors: Lee Jin Kyu , Koo Ja Wook , Jeong Soo-Young , Choi Sihoon , Park Ki-Chul , Hwang Kyu-Tae
Published: March 2020

The purpose of this study was to investigate the incidence of symptomatic venous thromboembolism (VTE) after chemoprophylaxis in patients with pelvic and lower-extremity fractures, and to identify risk factors for VTEs in this subgroup of patients. To detect VTE, multi-detector computed tomography (CT) angiography was performed. Of 363 patients assessed, the incidence of symptomatic VTE was 12.4% (45 patients), and the incidence of symptomatic PE was 5.2% (19 patients). For the risk-factor analysis, a higher Charlson comorbidity index (p = 0.037), and a history of external fixator application (p = 0.007) were associated with increased VTE risk. Among patients who had VTE, male sex (p = 0.017), and above-the-knee fractures (p = 0.035) were associated with increased pulmonary embolism (PE) risk. In conclusions, the incidence of VTE in post-traumatic patients is not low after chemoprophylaxis. Risk factors for VTE and PE are different among patients with pelvic and lower-extremity fractures.