bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating multiple sources of ecological data to unveil macroscale species abundance
Authors: Fukaya Keiichi , Kusumoto Buntarou , Shiono Takayuki , Fujinuma Junichi , Kubota Yasuhiro 
Published: April 2020

AbstractThe pattern of species abundance, represented by the number of individuals per species within an ecological community, is one of the fundamental characteristics of biodiversity. However, despite their obvious significance in ecology and biogeography, there is still no clear understanding of these patterns at large spatial scales. Here, we develop a hierarchical modelling approach to estimate macroscale patterns of species abundance. Using this approach, estimates of absolute abundance of 1248 woody plant species at a 10-km-grid-square resolution over East Asian islands across subtropical to temperate biomes are obtained. We provide two examples of the basic and applied use of the estimated species abundance for (1) inference of macroevolutionary processes underpinning regional biodiversity patterns and (2) quantitative community-wide assessment of a national red list. These results highlight the potential of the elucidation of macroscale species abundance that has thus far been an inaccessible but critical property of biodiversity.
Superior colliculus modulates cortical coding of somatosensory information
Authors: Gharaei Saba , Honnuraiah Suraj , Arabzadeh Ehsan , Stuart Greg J. 
Published: April 2020

AbstractThe cortex modulates activity in superior colliculus via a direct projection. What is largely unknown is whether (and if so how) the superior colliculus modulates activity in the cortex. Here, we investigate this issue and show that optogenetic activation of superior colliculus changes the input–output relationship of neurons in somatosensory cortex, enhancing responses to low amplitude whisker deflections. While there is no direct pathway from superior colliculus to somatosensory cortex, we found that activation of superior colliculus drives spiking in the posterior medial (POm) nucleus of the thalamus via a powerful monosynaptic pathway. Furthermore, POm neurons receiving input from superior colliculus provide monosynaptic excitatory input to somatosensory cortex. Silencing POm abolished the capacity of superior colliculus to modulate cortical whisker responses. Our findings indicate that the superior colliculus, which plays a key role in attention, modulates sensory processing in somatosensory cortex via a powerful di-synaptic pathway through the thalamus.
Pooled CRISPRi screening of the cyanobacterium Synechocystis sp PCC 6803 for enhanced industrial phenotypes
Authors: Yao Lun , Shabestary Kiyan , Björk Sara M. , Asplund-Samuelsson Johannes , Joensson Haakan N. , Jahn Michael , Hudson Elton P. 
Published: April 2020

AbstractCyanobacteria are model organisms for photosynthesis and are attractive for biotechnology applications. To aid investigation of genotype-phenotype relationships in cyanobacteria, we develop an inducible CRISPRi gene repression library in Synechocystis sp. PCC 6803, where we aim to target all genes for repression. We track the growth of all library members in multiple conditions and estimate gene fitness. The library reveals several clones with increased growth rates, and these have a common upregulation of genes related to cyclic electron flow. We challenge the library with 0.1 M L-lactate and find that repression of peroxiredoxin bcp2 increases growth rate by 49%. Transforming the library into an L-lactate-secreting Synechocystis strain and sorting top lactate producers enriches clones with sgRNAs targeting nutrient assimilation, central carbon metabolism, and cyclic electron flow. In many examples, productivity can be enhanced by repression of essential genes, which are difficult to access by transposon insertion.
Approaching the activity limit of CoSe2 for oxygen evolution via Fe doping and Co vacancy
Authors: Dou Yuhai , He Chun-Ting , Zhang Lei , Yin Huajie , Al-Mamun Mohammad , Ma Jianmin , Zhao Huijun 
Published: April 2020

AbstractElectronic structure engineering lies at the heart of efficient catalyst design. Most previous studies, however, utilize only one technique to modulate the electronic structure, and therefore optimal electronic states are hard to be achieved. In this work, we incorporate both Fe dopants and Co vacancies into atomically thin CoSe2 nanobelts for /coxygen evolution catalysis, and the resulted CoSe2-DFe–VCo exhibits much higher catalytic activity than other defect-activated CoSe2 and previously reported FeCo compounds. Deep characterizations and theoretical calculations identify the most active center of Co2 site that is adjacent to the VCo-nearest surface Fe site. Fe doping and Co vacancy synergistically tune the electronic states of Co2 to a near-optimal value, resulting in greatly decreased binding energy of OH* (ΔEOH) without changing ΔEO, and consequently lowering the catalytic overpotential. The proper combination of multiple defect structures is promising to unlock the catalytic power of different catalysts for various electrochemical reactions.
Plasmapause surface wave oscillates the magnetosphere and diffuse aurora
Authors: He Fei , Guo Rui-Long , Dunn William R. , Yao Zhong-Hua , Zhang Hua-Sen , Hao Yi-Xin , Shi Quan-Qi , Rong Zhao-Jin , Liu Jiang , Tian An-Min , Zhang Xiao-Xin , Wei Yong , Zhang Yong-Liang , Zong Qiu-Gang , Pu Zu-Yin , Wan Wei-Xing 
Published: April 2020

AbstractEnergy circulation in geospace lies at the heart of space weather research. In the inner magnetosphere, the steep plasmapause boundary separates the cold dense plasmasphere, which corotates with the planet, from the hot ring current/plasma sheet outside. Theoretical studies suggested that plasmapause surface waves related to the sharp inhomogeneity exist and act as a source of geomagnetic pulsations, but direct evidence of the waves and their role in magnetospheric dynamics have not yet been detected. Here, we show direct observations of a plasmapause surface wave and its impacts during a geomagnetic storm using multi-satellite and ground-based measurements. The wave oscillates the plasmapause in the afternoon-dusk sector, triggers sawtooth auroral displays, and drives outward-propagating ultra-low frequency waves. We also show that the surface-wave-driven sawtooth auroras occurred in more than 90% of geomagnetic storms during 2014–2018, indicating that they are a systematic and crucial process in driving space energy dissipation.
Increasing ambient temperature progressively disassembles Arabidopsis phytochrome B from individual photobodies with distinct thermostabilities
Authors: Hahm Joseph , Kim Keunhwa , Qiu Yongjian , Chen Meng 
Published: April 2020

AbstractWarm temperature is postulated to induce plant thermomorphogenesis through a signaling mechanism similar to shade, as both destabilize the active form of the photoreceptor and thermosensor phytochrome B (phyB). At the cellular level, shade antagonizes phyB signaling by triggering phyB disassembly from photobodies. Here we report temperature-dependent photobody localization of fluorescent protein-tagged phyB (phyB-FP) in the epidermal cells of Arabidopsis hypocotyl and cotyledon. Our results demonstrate that warm temperature elicits different photobody dynamics than those by shade. Increases in temperature from 12 °C to 27 °C incrementally reduce photobody number by stimulating phyB-FP disassembly from selective thermo-unstable photobodies. The thermostability of photobodies relies on phyB’s photosensory module. Surprisingly, elevated temperatures inflict opposite effects on phyB’s functions in the hypocotyl and cotyledon despite inducing similar photobody dynamics, indicative of tissue/organ-specific temperature signaling circuitry either downstream of photobody dynamics or independent of phyB. Our results thus provide direct cell biology evidence supporting an early temperature signaling mechanism via dynamic assembly/disassembly of individual photobodies possessing distinct thermostabilities.
Comprehensive sequence-to-function mapping of cofactor-dependent RNA catalysis in the glmS ribozyme
Authors: Andreasson Johan O. L. , Savinov Andrew , Block Steven M. , Greenleaf William J. 
Published: April 2020

AbstractMassively parallel, quantitative measurements of biomolecular activity across sequence space can greatly expand our understanding of RNA sequence-function relationships. We report the development of an RNA-array assay to perform such measurements and its application to a model RNA: the core glmS ribozyme riboswitch, which performs a ligand-dependent self-cleavage reaction. We measure the cleavage rates for all possible single and double mutants of this ribozyme across a series of ligand concentrations, determining kcat and KM values for active variants. These systematic measurements suggest that evolutionary conservation in the consensus sequence is driven by maintenance of the cleavage rate. Analysis of double-mutant rates and associated mutational interactions produces a structural and functional mapping of the ribozyme sequence, revealing the catalytic consequences of specific tertiary interactions, and allowing us to infer structural rearrangements that permit certain sequence variants to maintain activity.
Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs
Authors: Mondeel Thierry D. G. A. , Ivanov Oleksandr , Westerhoff Hans V. , Liebermeister Wolfram , Barberis Matteo 
Published: April 2020

AbstractSome biological networks exhibit oscillations in their components to convert stimuli to time-dependent responses. The eukaryotic cell cycle is such a case, being governed by waves of cyclin-dependent kinase (cyclin/Cdk) activities that rise and fall with specific timing and guarantee its timely occurrence. Disruption of cyclin/Cdk oscillations could result in dysfunction through reduced cell division. Therefore, it is of interest to capture properties of network designs that exhibit robust oscillations. Here we show that a minimal yeast cell cycle network is able to oscillate autonomously, and that cyclin/Cdk-mediated positive feedback loops (PFLs) and Clb3-centered regulations sustain cyclin/Cdk oscillations, in known and hypothetical network designs. We propose that Clb3-mediated coordination of cyclin/Cdk waves reconciles checkpoint and oscillatory cell cycle models. Considering the evolutionary conservation of the cyclin/Cdk network across eukaryotes, we hypothesize that functional (“healthy”) phenotypes require the capacity to oscillate autonomously whereas dysfunctional (potentially “diseased”) phenotypes may lack this capacity.
Effective Removal of Levofloxacin from Pharmaceutical Wastewater Using Synthesized Zinc Oxid, Graphen Oxid Nanoparticles Compared with their Combination
Authors: El-Maraghy Christine M. , El-Borady Ola M. , El-Naem Omnia A. 
Published: April 2020

AbstractThe presence of antibiotic traces in the aquatic system due to the inefficient treatment of the pharmaceutical wastewater represented threats, such as bioaccumulation and antibiotic-resistance, to the environment and human health. Accordingly, for the first time, the current work utilized the photocatalytic degradation and the adsorption approach for Levofloxacin (LEVO) in pharmaceutical wastewater using new designed nano aspects. Therefore, spherical Zinc oxide nanoparticles (ZnONP) sized 17 nm and ultrathin sheet-like structure graphene oxide nanosheets (GONS) with layer thickness ~5 nm were fabricated separately or in a combination between them then characterized via Transmission Electron Microscope (TEM), Scanning Electron Microscope (SEM), X-Ray Diffraction (XRD), Fourier Transforms Infrared Spectroscopy (FTIR), absorption spectra (UV-Vis) and Brunauer-Emmett-Teller (BET). Additionally, several parameters were investigated to evaluate the potential of the removal process, such as pH, the exposure time to UV radiation, the type and concentration of the nanoparticles (NPs) and the initial concentration of the drug using a mixed fractional factorial design. The most effective parameter for LEVO removal was the NPs type followed by the initial drug concentration. Furthermore, an RP-HPLC/UV method was developed and validated for measuring the percentage of removal for LEVO drug. The highest percentage removal for both 50 and 400 µg mL−1 LEVO was 99.2% and 99.6%, respectively, which was achieved using ZnONP/GONS combination at pH 9 ± 0.05 and UV light exposure time 120 min. In addition, the negative antibacterial activity of the treated wastewater sample confirmed the drug removal. The established protocol was successfully applied on wastewater samples collected from a pharmaceutical company that encouraged researchers to mainstream this design to be applied on other pharmaceutical wastewater drugs.
Hierarchical Cluster and Region of Interest Analyses Based on Mass Spectrometry Imaging of Human Brain Tumours
Authors: Hiratsuka Takuya , Arakawa Yoshiki , Yajima Yuka , Kakimoto Yu , Shima Keisuke , Yamazaki Yuzo , Ikegami Masahiro , Yamamoto Takushi , Fujiwake Hideshi , Fujimoto Koichi , Yamada Norishige , Tsuruyama Tatsuaki 
Published: April 2020

AbstractImaging mass spectrometry (IMS) has been rarely used to examine specimens of human brain tumours. In the current study, high quality brain tumour samples were selected by tissue observation. Further, IMS analysis was combined with a new hierarchical cluster analysis (IMS-HCA) and region of interest analysis (IMS-ROI). IMS-HCA was successful in creating groups consisting of similar signal distribution images of glial fibrillary acidic protein (GFAP) and related multiple proteins in primary brain tumours. This clustering data suggested the relation of GFAP and these identified proteins in the brain tumorigenesis. Also, high levels of histone proteins, haemoglobin subunit α, tubulins, and GFAP were identified in a metastatic brain tumour using IMS-ROI. Our results show that IMS-HCA and IMS-ROI are promising techniques for identifying biomarkers using brain tumour samples.
Streamlined selection of cancer antigens for vaccine development through integrative multi-omics and high-content cell imaging
Authors: Han Ki-Cheol , Park Daechan , Ju Shinyeong , Lee Young Eun , Heo Sun-Hee , Kim Young-Ae , Lee Ji Eun , Lee Yuna , Park Kyong Hwa , Park Se-Ho , Lee Hee Jin , Lee Cheolju , Jang Mihue 
Published: April 2020

AbstractIdentification of tumor antigens that induce cytotoxic T lymphocytes (CTLs) is crucial for cancer-vaccine development. Despite their predictive ability, current algorithmic approaches and human leukocyte antigen (HLA)-peptidomic analysis allow limited selectivity. Here, we optimized a method to rapidly screen and identify highly immunogenic epitopes that trigger CTL responses. We used a combined application of this method involving immune-specific signature analysis and HLA-associated peptidomics using samples from six patients with triple-negative breast cancer (TNBC) in order to select immunogenic HLA epitopes forin vitrotesting. Additionally, we applied high-throughput imaging at the single-cell level in order to confirm the immunoreactivity of the selected peptides. The results indicated that this method enabled identification of promising CTL peptides capable of inducing antitumor immunity. This platform combining high-resolution computational analysis, HLA-peptidomics, and high-throughput immunogenicity testing allowed rapid and robust identification of highly immunogenic epitopes and represents a powerful technique for cancer-vaccine development.
Soil CO2 emission in response to organic amendments, temperature, and rainfall
Authors: Ray Ram L. , Griffin Richard W. , Fares Ali , Elhassan Almoutaz , Awal Ripendra , Woldesenbet Selamawit , Risch Eric 
Published: April 2020

AbstractVegetated land surfaces play an important role in determining the fate of carbon in the global carbon cycle. However, our understanding of the terrestrial biosphere on a global scale is subject to considerable uncertainty, especially concerning the impacts of climatic variables on the carbon cycle. Soil is a source and also a sink of CO2 exchange and helps in carbon sequestration. Agricultural management practices influence soil water dynamics, as well as carbon cycling by changing soil CO2 emission and uptake rates. The rate of soil CO2 emission varies for different crops and different organic amendments. The major goal of this study was to assess the impacts of the type and rate of organic amendment on soil CO2 emission in a collard greens crop grown in the southeast Texas environment. Thirty-six plots were developed to grow collard greens on Prairie View A&M University’s Research Farm. Three types of organic amendments (Chicken manure, Dairy manure, and Milorganite), at four levels of application (0, 168, 336, and 672 kg N/ha) were used and replicated three times. Each organic amendment type was applied to nine randomly selected plots. Three random plots were used as a control in each row. We measured daily soil CO2 emission for the first two weeks and every other day in a week during the experiment. We evaluated the effects of organic amendments and the application rates on soil CO2 emission for collard greens during two growing seasons. The results showed higher the application rates for each organic amendment, higher the CO2 emissions from the soil. The results also showed higher cumulative CO2 emissions for the soils amended with chicken manure and milorganite, but lowest for the soils amended with dairy manure. This field experiment and analyses help better understand the temporal and spatial variations of soil CO2 emission, and also help to develop best management practices to maximize carbon sequestration and to minimize soil CO2 emissions during the growth periods of collard greens under changing temperatures using different organic amendments, and application rates.
Digital DNA microarray generation on glass substrates
Authors: Wöhrle Johannes , Krämer Stefan D. , Meyer Philipp A. , Rath Christin , Hügle Matthias , Urban Gerald A. , Roth Günter 
Published: April 2020

AbstractIn this work we show how DNA microarrays can be produced batch wise on standard microscope slides in a fast, easy, reliable and cost-efficient way. Contrary to classical microarray generation, the microarrays are generated via digital solid phase PCR. We have developed a cavity-chip system made of a PDMS/aluminum composite which allows such a solid phase PCR in a scalable and easy to handle manner. For the proof of concept, a DNA pool composed of two different DNA species was used to show that digital PCR is possible in our chips. In addition, we demonstrate that DNA microarray generation can be realized with different laboratory equipment (slide cycler, manually in water baths and with an automated cartridge system). We generated multiple microarrays and analyzed over 13,000 different monoclonal DNA spots to show that there is no significant difference between the used equipment. To show the scalability of our system we also varied the size and number of the cavities located in the array region up to more than 30,000 cavities with a volume of less than 60 pL per cavity. With this method, we present a revolutionary tool for novel DNA microarrays. Together with new established label-free measurement systems, our technology has the potential to give DNA microarray applications a new boost.
Therapeutic outcomes of non-grafted and platelet concentrations-grafted transcrestal maxillary sinus elevation (TSFE): a systematic review and meta-analysis
Authors: Guo Tianqi , Gulati Karan , Shen Ziyun , Han Pingping , Fan Zhen 
Published: April 2020

AbstractTo evaluate and compare the stability, quantity and quality of bone augmentation at maxillary sinus elevation sites by non-grafted transcrestal sinus floor elevation (TSFE) and platelet concentration grafted transcrestal sinus floor elevation (PC-TSFE). A complete literature search was performed up to April 2019. Clinical controlled trials, retrospective cohort studies, and prospective cohort studies were selected based on inclusion criteria. The clinical outcomes were implant survival rate (ISR), marginal/crestal bone loss (MBL/CBL) and endo-sinus bone gain (ESBG). Meta‐analysis was conducted on these 1-year based values. Furthermore, another meta-analysis on 1-year ISR value was conducted among studies with different residual bone heights (RBH) within the non-grafted TSFE group. A total of 18 studies were included: 13 in TSFE group and 5 in PC-TSFE group. No significant differences were displayed between the 1-year ISR of TSFE (97%, 95%CI = 0.96–0.99) and PC-TSFE group (99%, 95%CI = 0.97–1.00). Among the various studies with different RBH within TSFE group, no significant differences in 1-year ISR were displayed. The 1-year MBL/CBL value of PC-TSFE group (0.73 mm, 95%CI = 0.43–1.13 mm) did not show significant difference as compared to TSFE group (0.60 mm, 95%CI = 0.10–1.10 mm). Furthermore, no significant enhancement was observed on 1-year ESBG value on PC-TSFE group (3.51 mm, 95%CI = 2.31–4.71 mm) in comparison with the TSFE group (2.87 mm, 95%CI = 2.18m–3.55 mm). Grafting platelet concentrations around dental implants at TSFE sites did not significantly enhance the adjacent bone regeneration. Moreover, TSFE was shown to be a reliable therapeutic option for implant sites that need simultaneous maxillary sinus augmentation, even under limited RBH.
Rumor spreading model considering rumor credibility, correlation and crowd classification based on personality
Authors: Chen Xuelong , Wang Nan 
Published: April 2020

AbstractThe study of rumor spreading or rumor controlling is important and necessary because rumors can cause serious negative effects on society. The process of rumor spreading is influenced by many factors. In this paper, we suggest that people with different personalities will behave differently after hearing rumors. Thus, we divide the population into two types: radical people and steady people. Furthermore, we suggest that the credibility of rumors and the correlation between rumors and people’s lives are important factors that will influence the spread of rumors. Based on these considerations, we propose the SEIsIrR model. We establish differential equations to describe the dynamics of the rumor spreading process in homogeneous and heterogeneous networks. Using the Jacobian matrix and next generation matrix, we obtain the spreading threshold of the SEIsIrR model and discuss the relationship of the spreading threshold between homogeneous networks and heterogeneous networks. We employ a real rumor dataset obtained from Twitter to verify the SEIsIrR model and perform numerical simulations in Watts-Strogatz (WS) networks and Barabasi-Albert (BA) networks to verify the obtained spreading thresholds and discuss the impacts of these factors on the rumor spreading process and the differences in the rumor spreading processes between WS networks and BA networks. The simulation results show that these factors influence the speed and range of rumor spreading.