bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methane emission from high latitude lakes: methane-centric lake classification and satellite-driven annual cycle of emissions
Authors: Matthews E. , Johnson Matthew S. , Genovese V. , Du J. , Bastviken D. 
Published: July 2020

AbstractMethane (CH4) is emitted from lakes by several processes: bubbles released from bottom sediments that reach the atmosphere (ebullition); spring release of CH4 trapped in bubbles in and under the ice during fall freeze (bubble release), and diffusion of CH4 from sediments to the surface. Each of these emission routes is highly variable over space and time, and episodic in the extreme, making reliable measurements difficult to carry out. However, lakes are receiving increasing interest for their important contribution to global CH4 emissions. Their area, distribution and emissions respond to interannual and longer-term climate fluctuations and close to half the world’s lake area is in high northern latitudes that are experiencing rapidly-warming temperatures and lengthening thaw periods. We report on a new spatially-explicit data set of lakes > 50°N, classified with methane-relevant criteria. The seasonality of daily CH4 fluxes is driven with satellite observations of thaw timing and duration. We found that observed thaw seasons are 10–30% shorter than those assumed in previous studies. The area of lakes is 1,095 × 103 km2 and total CH4 emission is 13.8–17.7 Tg CH4 year−1: 11.2–14.4 Tg via diffusion and ebullition and 2.6–3.3 Tg from spring release of CH4 stored in bubbles in winter lake ice. This novel suite of data and methodologies provides a unique framework to model CH4 emission from lakes under current, past and future climates.
Hybrid predictor for ground-motion intensity with machine learning and conventional ground motion prediction equation
Authors: Kubo Hisahiko , Kunugi Takashi , Suzuki Wataru , Suzuki Shingo , Aoi Shin 
Published: July 2020

AbstractThe use of strongly biased data generally leads to large distortions in a trained machine learning model. We face this problem when constructing a predictor for earthquake-generated ground-motion intensity with machine learning. The machine learning predictor constructed in this study has an underestimation problem for strong motions, although the data fit on relatively weak ground motions is good. This underestimation problem is caused by the strong bias in available ground-motion records; there are few records of strong motions in the dataset. Therefore, we propose a hybrid approach of machine learning and conventional ground-motion prediction equation. This study demonstrates that this hybrid approach machine learning technology and physical model reduces the underestimation of strong motions and leads to better prediction than either of the individual approaches applied alone.
Comparative efficacy of antitumor necrosis factor agents and tacrolimus in naïve steroid-refractory ulcerative colitis patients
Authors: Kitayama Moto , Akazawa Yuko , Yoshikawa Daisuke , Higashi Shuntaro , Morisaki Tomohito , Oda Hidetoshi , Ikeda Maho , Nakashima Yujiro , Tabuchi Maiko , Hashiguchi Keiichi , Matsushima Kayoko , Yamaguchi Naoyuki , Kondo Hisayoshi , Nakao Kazuhiko , Takeshima Fuminao 
Published: July 2020

AbstractWhile retrospective studies have compared the efficacy of anti–tumour necrosis factor (TNF) agents and tacrolimus (TAC) in ulcerative colitis (UC), information regarding first-time use of these agents is limited. The aim of our study was to investigate the short- and long-term efficacy of anti-TNF agents [adalimumab (ADA) and infliximab (IFX)] and TAC in anti-TNF agent- and TAC-naïve steroid-refractory UC patients. We evaluated 150 steroid-refractory UC patients receiving anti-TNF agents (IFX: n = 30, ADA: n = 41) or TAC (n = 79) at eight institutions in Japan. Clinical response rates at 8 weeks were 73.2% and 75.9% while remission rates were 30.1% and 25.3% in the anti-TNF and TAC groups, respectively. Logistic regression analysis showed the male sex and higher C-reactive protein to be independent factors for response to anti-TNF agents and TAC, respectively. Use of TAC was an independent factor for relapse. No differences in response to the treatment or relapse were observed between IFX and ADA. In conclusion, TAC and anti-TNF agents promoted similar short-term effects, but anti-TNF agents ensured better long-term outcomes at first-time treatment of steroid-refractory UC patients.
Molecular evidence for the involvement of cotton GhGLP2, in enhanced resistance to Verticillium and Fusarium Wilts and oxidative stress
Authors: Pei Yakun , Zhu Yutao , Jia Yujiao , Ge Xiaoyang , Li Xiancai , Li Fuguang , Hou Yuxia 
Published: July 2020

AbstractGermin-like proteins (GLPs) are a diverse and ubiquitous family of plant glycoproteins belonging to the cupin super family; they play considerable roles in plant responses against various abiotic and biotic stresses. Here, we provide evidence that GLP2 protein from cotton (Gossypium hirsutum) functions in plant defense responses against Verticillium dahliae, Fusarium oxysporum and oxidative stress. Purified recombinant GhGLP2 exhibits superoxide dismutase (SOD) activity and inhibits spore germination of pathogens. Virus-induced silencing of GhGLP2 in cotton results in increased susceptibility to pathogens, plants exhibited severe wilt on leaves, enhanced vascular browning and suppressed callose deposition. Transgenic Arabidopsis (Arabidopsis thaliana) plants overexpressing GhGLP2 showed significant resistance to V. dahliae and F. oxysporum, with reduced mycelia growth, increased callose deposition and cell wall lignification at infection sites on leaves. The enhanced tolerance of GhGLP2-transgenic Arabidopsis to oxidative stress was investigated by methyl viologen and ammonium persulfate treatments, along with increased H2O2 production. Further, the expression of several defense-related genes (PDF1.2, LOX2, and VSP1) or oxidative stress-related genes (RbohD, RbohF) was triggered by GhGLP2. Thus, our results confirmed the involvement of GhGLP2 in plant defense response against Verticillium and Fusarium wilt pathogens and stress conditions.
A novel method for identifying and distinguishing Cryptococcus neoformans and Cryptococcus gattii by surface-enhanced Raman scattering using positively charged silver nanoparticles
Authors: Hu Shan , Gu Feng , Chen Min , Wang Chongwen , Li Jia , Yang Jian , Wang Guangyu , Zhou Zhe , Yang Ying 
Published: July 2020

AbstractThere are approximately 1 million cryptococcal infections per year among HIV+ individuals, resulting in nearly 625,000 deaths. Cryptococcus neoformans and Cryptococcus gattii are the two most common species that cause human cryptococcosis. These two species of Cryptococcus have differences in pathogenicity, diagnosis, and treatment. Cryptococcal infections are usually difficult to identify because of their slow growth in vitro. In addition, the long detection cycle of Cryptococcus in clinical specimens makes the diagnosis of Cryptococcal infections difficult. Here, we used positively charged silver nanoparticles (AgNPs+) as a substrate to distinguish between C. neoformans and C. gattii in clinical specimens directly via surface-enhanced Raman scattering (SERS) and spectral analysis. The AgNPs+ self-assembled on the surface of the fungal cell wall via electrostatic aggregation, leading to enhanced SERS signals that were better than the standard substrate negatively charged silver nanoparticles (AgNPs). The SERS spectra could also be used as a sample database in the multivariate analysis via orthogonal partial least-squares discriminant analysis. This novel SERS detection method can clearly distinguish between the two Cryptococcus species using principal component analysis. The accuracy of the training data and test data was 100% after a tenfold crossover validation.
STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts
Authors: Kitchen S. A. , Von Kuster G. , Kuntz K. L. Vasquez , Reich H. G. , Miller W. , Griffin S. , Fogarty Nicole D. , Baums I. B. 
Published: July 2020

AbstractStandardized identification of genotypes is necessary in animals that reproduce asexually and form large clonal populations such as coral. We developed a high-resolution hybridization-based genotype array coupled with an analysis workflow and database for the most speciose genus of coral,Acropora, and their symbionts. We designed the array to co-analyze host and symbionts based on bi-allelic single nucleotide polymorphisms (SNP) markers identified from genomic data of the two CaribbeanAcroporaspecies as well as their dominant dinoflagellate symbiont,Symbiodinium ‘fitti’.SNPs were selected to resolve multi-locus genotypes of host (called genets) and symbionts (called strains), distinguish host populations and determine ancestry of coral hybrids between Caribbean acroporids. Pacific acroporids can also be genotyped using a subset of the SNP loci and additional markers enable the detection of symbionts belonging to the generaBreviolum, Cladocopium, andDurusdinium. Analytic tools to produce multi-locus genotypes of hosts based on these SNP markers were combined in a workflow called theStandardTools forAcroporidGenotyping (STAG). The STAG workflow and database are contained within a customized Galaxy environment (https://coralsnp.science.psu.edu/galaxy/), which allows for consistent identification of host genet and symbiont strains and serves as a template for the development of arrays for additional coral genera. STAG data can be used to track temporal and spatial changes of sampled genets necessary for restoration planning and can be applied to downstream genomic analyses. Using STAG, we uncover bi-directional hybridization between and population structure within Caribbean acroporids and detect a cryptic Acroporid species in the Pacific.
Molecular characterization of megaplasmids encoding the type VI secretion system in Campylobacter jejuni isolated from chicken livers and gizzards
Authors: Marasini Daya , Karki Anand B. , Bryant John M. , Sheaff Robert J. , Fakhr Mohamed K. 
Published: July 2020

AbstractMegaplasmids in Campylobacter spp. likely play important roles in antibiotic resistance, virulence, and horizontal gene transfer. In this study, megaplasmids pCJDM202 (119 kb) and pCJDM67L (116 kb) from C. jejuni strains WP2-202 and OD2-67, respectively, were sequenced and characterized. These megaplasmids contained genes for tetracycline resistance [tet(O)], the Type IV secretion system, conjugative transfer and the Type VI secretion system (T6SS). The T6SS genes in Campylobacter plasmids encoded genes and proteins that were similar to those identified in Campylobacter chromosomal DNA. When the megaplasmid pCJDM202 from C. jejuni WP2-202 was transferred via conjugation to C. jejuni NCTC11168 Nal+, transconconjugants acquired tetracycline resistance and enhanced cytotoxicity towards red blood cells. A T6SS mutant of strain WP2-202 was generated and designated Δhcp3; the mutant was significantly impaired in its ability to lyse red blood cells and survive in defibrinated blood. The cytotoxicity of Campylobacter strains towards the human embryonic kidney cell line HEK 293 was not impacted by the T6SS. In summary, the T6SS encoded by Campylobacter megaplasmids mediates lysis of RBCs and likely contributes to survival on retail meats where blood cells are abundant.
A multilevel statistical toolkit to study animal social networks: the Animal Network Toolkit Software (ANTs) R package
Authors: Sosa Sebastian , Puga-Gonzalez Ivan , Hu Fenghe , Pansanel Jérôme , Xie Xiaohua , Sueur Cédric 
Published: July 2020

AbstractThe possible role played by individual attributes, sociodemographic characteristics and/or ecological pressures in the interaction between animals and the development of social relationships between them is of great interest in animal ecology and evolutionary biology. Social Network Analysis is an ideal tool to study these types of questions. The Animal Network Toolkit Software (ANTs) R package was specifically developed to provide all the different social network analysis techniques currently used in the study of animal social networks. This global package enables users to (1) compute global, polyadic and nodal network measures; (2) perform data randomisation: data stream and network (node and link) permutations; (3) perform statistical permutation tests for static or temporal network analyses, and (4) visualise networks. ANTs allows researchers to perform multilevel network analyses ranging from individual network measures to interaction patterns and the analysis of the overall network structure, and carry out static or temporal network analyses without switching between different R packages, thus making a substantial contribution to advances in the study of animal behaviour. ANTs outperforms existing R packages for the computation speed of network measures and permutations.
Rapid isolation of rare targets from large fluid volumes
Authors: Hedde Per Niklas , Bouzin Margaux , Abram Timothy J. , Chen Xiaoming , Toosky Melody N. , Vu Tam , Li Yiyan , Zhao Weian , Gratton Enrico 
Published: July 2020

AbstractRapidly isolating rare targets from larger, clinically relevant fluid volumes remains an unresolved problem in biomedicine and diagnosis. Here, we describe how 3D particle sorting can enrich targets at ultralow concentrations over 100-fold within minutes not possible with conventional approaches. Current clinical devices based on biochemical extraction and microfluidic solutions typically require high concentrations and/or can only process sub-milliliter volumes in time. In a proof-of-concept application, we isolated bacteria from whole blood as demanded for rapid sepsis diagnosis where minimal numbers of bacteria need to be found in a 1–10 mL blood sample. After sample encapsulation in droplets and target enrichment with the 3D particle sorter within a few minutes, downstream analyses were able to identify bacteria and test for antibiotic susceptibility, information which is critical for successful treatment of bloodstream infections.
Identification of key interactions between SARS-CoV-2 main protease and inhibitor drug candidates
Authors: Yoshino Ryunosuke , Yasuo Nobuaki , Sekijima Masakazu 
Published: July 2020

AbstractThe number of cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (COVID-19) has reached over 114,000. SARS-CoV-2 caused a pandemic in Wuhan, China, in December 2019 and is rapidly spreading globally. It has been reported that peptide-like anti-HIV-1 drugs are effective against SARS-CoV Main protease (Mpro). Due to the close phylogenetic relationship between SARS-CoV and SARS-CoV-2, their main proteases share many structural and functional features. Thus, these drugs are also regarded as potential drug candidates targeting SARS-CoV-2 Mpro. However, the mechanism of action of SARS-CoV-2 Mpro at the atomic-level is unknown. In the present study, we revealed key interactions between SARS-CoV-2 Mpro and three drug candidates by performing pharmacophore modeling and 1 μs molecular dynamics (MD) simulations. His41, Gly143, and Glu166 formed interactions with the functional groups that were common among peptide-like inhibitors in all MD simulations. These interactions are important targets for potential drugs against SARS-CoV-2 Mpro.
Landscape of snake’ sex chromosomes evolution spanning 85 MYR reveals ancestry of sequences despite distinct evolutionary trajectories
Authors: Viana Patrik F. , Ezaz Tariq , de Bello Cioffi Marcelo , Liehr Thomas , Al-Rikabi Ahmed , Goll Leonardo G. , Rocha Anderson M. , Feldberg Eliana 
Published: July 2020

AbstractMost of snakes exhibit a ZZ/ZW sex chromosome system, with different stages of degeneration. However, undifferentiated sex chromosomes and unique Y sex-linked markers, suggest that an XY system has also evolved in ancestral lineages. Comparative cytogenetic mappings revealed that several genes share ancestry among X, Y and Z chromosomes, implying that XY and ZW may have undergone transitions during serpent’s evolution. In this study, we performed a comparative cytogenetic analysis to identify homologies of sex chromosomes across ancestral (Henophidia) and more recent (Caenophidia) snakes. Our analysis suggests that, despite ~ 85 myr of independent evolution, henophidians and caenophidians retained conserved synteny over much of their genomes. However, our findings allowed us to discover that ancestral and recent lineages of snakes do not share the same sex chromosome and followed distinct pathways for sex chromosomes evolution.
Undersized stent graft for treatment of cephalic arch stenosis in arteriovenous hemodialysis access
Authors: Huang Eric Po-Yu , Li Ming-Feng , Hsiao Chia-Chi , Chen Hsin-Yu , Wu Ping-An , Liang Huei-Lung 
Published: July 2020

AbstractCephalic arch stenosis (CAS) is a common cause of AV dialysis access failure and is notoriously difficult to treat with conventional venoplasty. Although stent graft (SG) placement has improved patency rate, they are prone to stent failure caused by edge stenosis. We investigate the effect of SG diameter relative to cephalic vein on patency rate among hemodialysis patients with dysfunctional arteriovenous access caused by CAS. We identified 22 patients with recalcitrant cephalic arch stenosis or post-venoplasty vessel rupture and received SG placement. Patients were divided into two groups based on the stent-to-vessel diameter (S/V) ratio: undersized group, < 1; and apposed group, 1–1.2. Outcomes were assessed through follow-up angiography. S/V ratio was significant smaller in the undersized patient group (p < 0.001). Placement of undersized SG demonstrated higher primary stent (p = 0.001) and access patency rates (p = 0.021) and a reduced number of post-treatment reinterventions per access year (p = 0.021). A decreased number of lateral edge stenosis was noted in undersized SG (p = 0.005). Increased S/V ratio was significantly associated with lateral edge stenosis (OR = 5.19; p = 0.027). Undersized SG is associated with higher primary stent and access patency rate, and decreased number of post-SG interventions, and are suggested in the treatment of cephalic arch stenosis.
Entropy generation in MHD Casson fluid flow with variable heat conductance and thermal conductivity over non-linear bi-directional stretching surface
Authors: Sohail Muhammad , Shah Zahir , Tassaddiq Asifa , Kumam Poom , Roy Prosun 
Published: July 2020

AbstractThis consideration highlights the belongings of momentum, entropy generation, species and thermal dissemination on boundary layer flow (BLF) of Casson liquid over a linearly elongating surface considering radiation and Joule heating effects significant. Transportation of thermal and species are offered by using the temperature-dependent models of thermal conductivity and mass diffusion coefficient. Arising problem appear in the form of nonlinear partial differential equations (NPDEs) against the conservation laws of mass, momentum, thermal and species transportation. Appropriate renovation transfigures the demonstrated problem into ordinary differential equations. Numerical solutions of renovated boundary layer ordinary differential equations (ODEs) are attained by a proficient and reliable technique namely optimal homotopy analysis method (OHAM). A graphical and tabular interpretation is given for convergence of analytic solutions through error table and flow behavior of convoluted physical parameters on calculated solutions are presented and explicated in this examination. Reliability and effectiveness of the anticipated algorithm is established by comparing the results of present contemplation as a limiting case of available work, and it is found to be in excellent settlement. Decline in fluid velocity and enhancement in thermal and species transportation is recorded against the fluctuating values of Hartman number. Also reverse comportment of Prandtl number and radiation parameter is portrayed. Moreover, it is conveyed that supplementing values of the magnetic parameter condenses the fluid velocity and upsurges the thermal and concentration distributions. Negative impact of elevating Joule heating phenomenon is noted on the molecular stability of the system via Brinkman number $$\left( {Br} \right).$$Br. Furthermore, the system’s stability at a molecular level is controlled by diminishing values of radiation $$\left( R \right),$$R, temperature difference $$\left( { \in_{1} } \right),$$∈1, concentration difference $$\left( { \in_{2} } \right),$$∈2, diffusion parameters $$\left( { \in_{3} } \right)$$∈3 and Brinkman number $$\left( {Br} \right).$$Br.
Deciphering the coagulation profile through the dynamics of thrombin activity
Authors: de Laat-Kremers Romy M. W. , Yan Qiuting , Ninivaggi Marisa , de Maat Moniek , de Laat Bas 
Published: July 2020

AbstractThrombosis has proven to be extremely difficult to predict. Measuring the generation of thrombin is a very sensitive method to detect changes in the hemostatic system. We developed a method based on the generation of thrombin to further fingerprint hemostasis, which we have named thrombin dynamics. Via this method we are able to exactly measure the prothrombin conversion and thrombin inactivation, and any change in the coagulation cascade will be reflected in these two processes. In the current study we analyzed the importance of the members of the prothrombin complex on the dynamics of thrombin activation and inactivation. We show that prothrombin conversion is predominantly influenced by factor X and antithrombin, which will provide essential insights in complex thrombosis-related diseases, such as liver cirrhosis and kidney failure.
Effects of the brown algae Sargassum horneri and Saccharina japonica on survival, growth and resistance of small sea urchins Strongylocentrotus intermedius
Authors: Hu Fangyuan , Yang Mingfang , Ding Peng , Zhang Xu , Chen Zhouling , Ding Jingyun , Chi Xiaomei , Luo Jia , Zhao Chong , Chang Yaqing 
Published: July 2020

AbstractMass mortality of the long line culture of the sea urchin Strongylocentrotus intermedius in summer, which is greatly associated with their disease, energy storage and resistant abilities, is the most serious problem for the development of the aquaculture. Here, a feeding experiment was conducted for ~ 9 weeks to investigate the survival, growth and gonadal development of small S. intermedius (~ 3 cm) fed either brown algae Sargassum horneri or Saccharina japonica. Subsequently, we assessed their resistant abilities via observing the behaviors of righting, tube feet extension and Aristotle's lantern reflex at both moderately elevated and acutely changed water temperatures. Sea urchins fed S. horneri showed significantly fewer diseased individuals and slower gonadal development than those fed S. japonica. Consistently, significantly greater Aristotle's lantern reflex occurred in sea urchins fed S. horneri at moderately elevated temperatures. These findings suggest that S. horneri has direct application potential as food for the long line culture of S. intermedius in summer because of the advantage in health, energy storage (avoid the energy loss caused by gonadal development at small body sizes) and resistance abilities. In comparison, sea urchins fed S. japonica outperformed those fed S. horneri for all experimental behaviors under the acutely changed water temperatures. These findings clearly suggest that S. intermedius fed S. japonica is more suitable for the areas with cold water mass in summer, because it can effectively avoid or reduce the negative impacts of acute changes of water temperature on sea urchins. The present study provides valuable information into the management of the long line culture of S. intermedius in summer.