bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatiotemporal Variability and Driving Factors of Tibetan Plateau Water Use Efficiency
Authors: Lin Shan , Wang Genxu , Hu Zhaoyong , Huang Kewei , Sun Juying , Sun Xiangyang 
Published: October 2020

AbstractWater use efficiency (WUE) provides vital information about the carbon‐water coupling relationship of a terrestrial ecosystem. Understanding the spatiotemporal variability and driving factors of the Tibetan Plateau (TP) WUE can facilitate the prediction of the response of the carbon‐water process in the TP to climate change. We used a land surface model to investigate spatiotemporal changes in WUE and the responses to environmental factors, such as atmospheric CO2 concentration and climate and land use change. Our results suggest that the average annual TP WUE was 0.38 g C kg−1 H2O and that this variable tended to increase at a rate of 0.001 g C kg−1 H2O year−1 during the period of 1979–2010. Changes in atmospheric CO2 concentration caused a significant increase in the rate of WUE change (i.e., 0.00051 g C kg−1 H2O year−1); these changes were also found to most significantly contribute to WUE increase in the TP and account for approximately 51% of the WUE fluctuation. Increasing temperature was found to result in a decreasing WUE (rate: −0.00028 g C kg−1 H2O year−1). Regarding results on vegetation type, forested areas had the highest WUE (i.e., 0.88 g C kg−1 H2O) and the highest rate of WUE change (i.e., 0.004 g C kg−1 H2O year−1), whereas the lowest WUE (i.e., 0.26 g C kg−1 H2O) was found in steppe and alpine vegetation areas. Although all other vegetation types were associated with increasing WUE, there was no significant change in the WUE of steppe areas. The main factors influencing WUE fluctuation for different vegetation types were found to be atmospheric CO2 concentration and temperature change.
Influence of Geomagnetic Activity on Derivation of Temperatures From Meteor Wind Radars
Authors: Hall C. M. , Johnsen M. G. 
Published: October 2020

AbstractEchoes from meteor trails can be analyzed to derive diffusion coefficient and thereafter estimates of neutral temperatures, typically around 90 km altitude. The method entails some assumptions and, usually, use of model pressures. Even so, variations in derived temperatures have been assumed to be representative and indicators of other mesospheric processes. However, we now find that the observed variations, seen as enhancements, are very closely associated with enhancements in geomagnetic activity. Here we introduce a metric for describing geomagnetic activity (as an alternative to, e.g., the k‐index) and suggest a methodology for near‐real‐time correction of results.
The Flare Irradiance Spectral Model‐Version 2 (FISM2)
Authors: Chamberlin P. C. , Eparvier F. G. , Knoer V. , Leise H. , Pankratz A. , Snow M. , Templeman B. , Thiemann E. M. B. , Woodraska D. L. , Woods T. N. 
Published: October 2020

AbstractThe Flare Irradiance Spectral Model (FISM) is an important tool for estimating solar variability for a myriad of space weather research studies and applications, and FISM Version 2 (FISM2) recently was released. FISM2 is an empirical model of the solar ultraviolet irradiance created to fill spectral and temporal gaps in the satellite observations. FISM2 estimates solar ultraviolet irradiance variations due to the solar cycle, solar rotations, and solar flares. The major improvement provided by FISM2 is that it is based on multiple new, more accurate instruments that have now captured almost a full solar cycle and thousands of flares, drastically improving the accuracy of the modeled FISM2 solar irradiance spectra. Specifically, these new instruments are the Solar Dynamics Observatory (SDO)/Extreme Ultraviolet Variability Experiment (EVE), Solar Radiation and Climate Experiment (SORCE)/X‐ray Photometer System (XPS), and SORCE/Solar Stellar Irradiance Comparison Experiment (SOLSTICE). FISM2 is also improved to 0.1‐nm spectral bins across the same 0‐ to 190‐nm spectral range and is already being used in research to estimate space weather changes due to solar irradiance variability in planetary thermospheres and ionospheres.
Transit Time Distributions Estimation Exploiting Flow‐Weighted Time: Theory and Proof‐of‐Concept
Authors: Kim Minseok , Troch Peter A. 
Published: October 2020

AbstractTime‐variable transit time distributions (TTDs) have been utilized as a tool to understand how catchments transmit water. However, most of the existing TTD estimation methods require to impose certain structures on those TTDs a priori, which could lead to misinterpreting data. We present a data‐based method to estimate time‐variable TTDs without imposing their structure a priori. The core of the method is the use of a revised flow‐weighted time, where TTDs do not reflect variable external forcings directly. The functional forms of the TTDs are much simpler in flow‐weighted time, compared to those in calendar time, and this allows for easier estimation of TTDs. Dynamic (state‐dependent) multiple linear regression methods were applied to estimate the time‐variable TTDs in flow‐weighted time, which can eventually be transformed back to calendar time. The method performs well in a proof‐of‐concept demonstration with synthetic data sets. We also discuss potential generalizations of the proposed method.
Transition From Viscous Fingering to Capillary Fingering: Application of GPU‐Based Fully Implicit Dynamic Pore Network Modeling
Authors: An Senyou , Erfani Hamidreza , Godinez‐Brizuela Omar E. , Niasar Vahid 
Published: October 2020

AbstractImmiscible two‐phase flow through porous materials exhibits different invasion patterns controlled by dynamic conditions, competition between the viscous and capillary forces, and the contrast between the fluids viscosities. Two distinct invasion patterns are viscous and capillary fingering. While the first one happens under unfavorable viscosity ratios at high injection rates, the second one happens when the viscous forces are very small compared to the capillary forces. Depending on whether the invasion is under the capillary fingering or viscous fingering regime, the remaining oil saturation and the effective permeability of the fluids can significantly change. The contribution of the present work has two key aspects: (a) It addresses how the remaining saturation changes at different flow rates (i.e., capillary numbers) for different unfavorable viscosity ratios in a three‐dimensional system; (b) it presents a new dynamic pore network model using the fully implicit scheme which has been enhanced by the graphic processing unit (GPU) parallel computing. Additionally, the model has been carefully validated against micromodel experiments in both time and space, which to our best knowledge has not been reported in such detail in the literature. The results of the validated 3‐D dynamic pore network model demonstrate the remaining saturation at the breakthrough time as a nonmonotonic trend with the imposed capillary number.
Practical guide for managing large-scale human genome data in research
Authors: Tanjo Tomoya , Kawai Yosuke , Tokunaga Katsushi , Ogasawara Osamu , Nagasaki Masao 
Published: October 2020

AbstractStudies in human genetics deal with a plethora of human genome sequencing data that are generated from specimens as well as available on public domains. With the development of various bioinformatics applications, maintaining the productivity of research, managing human genome data, and analyzing downstream data is essential. This review aims to guide struggling researchers to process and analyze these large-scale genomic data to extract relevant information for improved downstream analyses. Here, we discuss worldwide human genome projects that could be integrated into any data for improved analysis. Obtaining human whole-genome sequencing data from both data stores and processes is costly; therefore, we focus on the development of data format and software that manipulate whole-genome sequencing. Once the sequencing is complete and its format and data processing tools are selected, a computational platform is required. For the platform, we describe a multi-cloud strategy that balances between cost, performance, and customizability. A good quality published research relies on data reproducibility to ensure quality results, reusability for applications to other datasets, as well as scalability for the future increase of datasets. To solve these, we describe several key technologies developed in computer science, including workflow engine. We also discuss the ethical guidelines inevitable for human genomic data analysis that differ from model organisms. Finally, the future ideal perspective of data processing and analysis is summarized.
Advances in targeted therapy mainly based on signal pathways for nasopharyngeal carcinoma
Authors: Kang Yuanbo , He Weihan , Ren Caiping , Qiao Jincheng , Guo Qiuyong , Hu Jingyu , Xu Hongjuan , Jiang Xingjun , Wang Lei 
Published: October 2020

AbstractNasopharyngeal carcinoma (NPC) is a malignant epithelial carcinoma of the head and neck region which mainly distributes in southern China and Southeast Asia and has a crucial association with the Epstein–Barr virus. Based on epidemiological data, both incidence and mortality of NPC have significantly declined in recent decades grounded on the improvement of living standard and medical level in an endemic region, in particular, with the clinical use of individualized chemotherapy and intensity-modulated radiotherapy (IMRT) which profoundly contributes to the cure rate of NPC patients. To tackle the challenges including local recurrence and distant metastasis in the current NPC treatment, we discussed the implication of using targeted therapy against critical molecules in various signal pathways, and how they synergize with chemoradiotherapy in the NPC treatment. Combination treatment including targeted therapy and IMRT or concurrent chemoradiotherapy is presumably to be future options, which may reduce radiation or chemotherapy toxicities and open new avenues for the improvement of the expected functional outcome for patients with advanced NPC.
Host specificity of microbiome assembly and its fitness effects in phytoplankton
Authors: Jackrel Sara L , Yang Jinny W , Schmidt Kathryn C , Denef Vincent J 
Published: October 2020

Abstract
Insights into symbiosis between eukaryotic hosts and their microbiomes have shifted paradigms on what determines host fitness, ecology, and behavior. Questions remain regarding the roles of host versus environment in shaping microbiomes, and how microbiome composition affects host fitness. Using a model system in ecology, phytoplankton, we tested whether microbiomes are host-specific, confer fitness benefits that are host-specific, and remain conserved in time in their composition and fitness effects. We used an experimental approach in which hosts were cleaned of bacteria and then exposed to bacterial communities from natural environments to permit recruitment of microbiomes. We found that phytoplankton microbiomes consisted of a subset of taxa recruited from these natural environments. Microbiome recruitment was host-specific, with host species explaining more variation in microbiome composition than environment. While microbiome composition shifted and then stabilized over time, host specificity remained for dozens of generations. Microbiomes increased host fitness, but these fitness effects were host-specific for only two of the five species. The shifts in microbiome composition over time amplified fitness benefits to the hosts. Overall, this work solidifies the importance of host factors in shaping microbiomes and elucidates the temporal dynamics of microbiome compositional and fitness effects.
HCF-1 promotes cell cycle progression by regulating the expression of CDC42
Authors: Xiang Pan , Li Fei , Ma Zhihua , Yue Jiping , Lu Cailing , You Yuangang , Hou Lin , Yin Bin , Qiang Boqin , Shu Pengcheng , Peng Xiaozhong 
Published: October 2020

AbstractThe eukaryotic cell cycle involves a highly orchestrated series of events in which the cellular genome is replicated during a synthesis (S) phase and each of the two resulting copies are segregated properly during mitosis (M). Host cell factor-1 (HCF-1) is a transcriptional co-regulator that is essential for and has been implicated in basic cellular processes, such as transcriptional regulation and cell cycle progression. Although a series of HCF-1 transcriptional targets have been identified, few functional clues have been provided, especially for chromosome segregation. Our results showed that HCF-1 activated CDC42 expression by binding to the −881 to −575 region upstream of the CDC42 transcription start site, and the regulation of CDC42 expression by HCF-1 was correlated with cell cycle progression. The overexpression of a spontaneously cycling and constitutively active CDC42 mutant (CDC42F28L) rescued G1 phase delay and multinucleate defects in mitosis upon the loss of HCF-1. Therefore, these results establish that HCF-1 ensures proper cell cycle progression by regulating the expression of CDC42, which indicates a possible mechanism of cell cycle coordination and the regulation mode of typical Rho GTPases.
MEPE loss-of-function variant associates with decreased bone mineral density and increased fracture risk
Authors: Surakka Ida , Fritsche Lars G. , Zhou Wei , Backman Joshua , Kosmicki Jack A. , Lu Haocheng , Brumpton Ben , Nielsen Jonas B. , Gabrielsen Maiken E. , Skogholt Anne Heidi , Wolford Brooke , Graham Sarah E. , Chen Y. Eugene , Lee Seunggeun , Kang Hyun Min , Langhammer Arnulf , Forsmo Siri , Åsvold Bjørn O. , Styrkarsdottir Unnur , Holm Hilma , Gudbjartsson Daniel , Stefansson Kari , Baras Aris ,   Regeneron Genetics Center, Bai Xiaodong , Balasubramanian Suganthi , Barnard Leland , Blumenfeld Andrew , Cantor Michael , Coppola Giovanni , Economides Aris , Eom Gisu , Habegger Lukas , Hahn Young , Hawes Alicia , Jones Marcus B. , Khalid Shareef , Lotta Luca A. , Maxwell Evan K. , Mitnaul Lyndon J. , Overton John D. , Reid Jeffrey G. , Ferreira Manuel Allen Revez , Salerno William , Sharma Deepika , Shuldiner Alan , Staples Jeffrey C. , Yadav Ashish , Abecasis Goncalo R. , Hveem Kristian , Willer Cristen J. 
Published: October 2020

AbstractA major challenge in genetic association studies is that most associated variants fall in the non-coding part of the human genome. We searched for variants associated with bone mineral density (BMD) after enriching the discovery cohort for loss-of-function (LoF) mutations by sequencing a subset of the Nord-Trøndelag Health Study, followed by imputation in the remaining sample (N = 19,705), and identified ten known BMD loci. However, one previously unreported variant, LoF mutation in MEPE, p.(Lys70IlefsTer26, minor allele frequency [MAF] = 0.8%), was associated with decreased ultradistal forearm BMD (P-value = 2.1 × 10−18), and increased osteoporosis (P-value = 4.2 × 10−5) and fracture risk (P-value = 1.6 × 10−5). The MEPE LoF association with BMD and fractures was further evaluated in 279,435 UK (MAF = 0.05%, heel bone estimated BMD P-value = 1.2 × 10−16, any fracture P-value = 0.05) and 375,984 Icelandic samples (MAF = 0.03%, arm BMD P-value = 0.12, forearm fracture P-value = 0.005). Screening for the MEPE LoF mutations before adulthood could potentially prevent osteoporosis and fractures due to the lifelong effect on BMD observed in the study. A key implication for precision medicine is that high-impact functional variants missing from the publicly available cosmopolitan panels could be clinically more relevant than polygenic risk scores.
Sources and upstream pathways of the densest overflow water in the Nordic Seas
Authors: Huang Jie , Pickart Robert S. , Huang Rui Xin , Lin Peigen , Brakstad Ailin , Xu Fanghua 
Published: October 2020

AbstractOverflow water from the Nordic Seas comprises the deepest limb of the Atlantic Meridional Overturning Circulation, yet questions remain as to where it is ventilated and how it reaches the Greenland-Scotland Ridge. Here we use historical hydrographic data from 2005-2015, together with satellite altimeter data, to elucidate the source regions of the Denmark Strait and Faroe Bank Channel overflows and the pathways feeding these respective sills. A recently-developed metric is used to calculate how similar two water parcels are, based on potential density and potential spicity. This reveals that the interior of the Greenland Sea gyre is the primary wintertime source of the densest portion of both overflows. After subducting, the water progresses southward along several ridge systems towards the Greenland-Scotland Ridge. Kinematic evidence supports the inferred pathways. Extending the calculation back to the 1980s reveals that the ventilation occurred previously along the periphery of the Greenland Sea gyre.
Seasonal modulation of phytoplankton biomass in the Southern Ocean
Authors: Arteaga Lionel A. , Boss Emmanuel , Behrenfeld Michael J. , Westberry Toby K. , Sarmiento Jorge L. 
Published: October 2020

AbstractOver the last ten years, satellite and geographically constrained in situ observations largely focused on the northern hemisphere have suggested that annual phytoplankton biomass cycles cannot be fully understood from environmental properties controlling phytoplankton division rates (e.g., nutrients and light), as they omit the role of ecological and environmental loss processes (e.g., grazing, viruses, sinking). Here, we use multi-year observations from a very large array of robotic drifting floats in the Southern Ocean to determine key factors governing phytoplankton biomass dynamics over the annual cycle. Our analysis reveals seasonal phytoplankton accumulation (‘blooming’) events occurring during periods of declining modeled division rates, an observation that highlights the importance of loss processes in dictating the evolution of the seasonal cycle in biomass. In the open Southern Ocean, the spring bloom magnitude is found to be greatest in areas with high dissolved iron concentrations, consistent with iron being a well-established primary limiting nutrient in this region. Under ice observations show that biomass starts increasing in early winter, well before sea ice begins to retreat. The average theoretical sensitivity of the Southern Ocean to potential changes in seasonal nutrient and light availability suggests that a 10% change in phytoplankton division rate may be associated with a 50% reduction in mean bloom magnitude and annual primary productivity, assuming simple changes in the seasonal magnitude of phytoplankton division rates. Overall, our results highlight the importance of quantifying and accounting for both division and loss processes when modeling future changes in phytoplankton biomass cycles.
Sensing of autoinducer-2 by functionally distinct receptors in prokaryotes
Authors: Zhang Lei , Li Shuyu , Liu Xiaozhen , Wang Zhuo , Jiang Mei , Wang Ruiying , Xie Laigong , Liu Qinmeng , Xie Xiaorong , Shang Daohan , Li Mengyun , Wei Zhiyan , Wang Yao , Fan Chengpeng , Luo Zhao-Qing , Shen Xihui 
Published: October 2020

AbstractAutoinducer-2 (AI-2) is a quorum sensing signal that mediates communication within and between many bacterial species. However, its known receptors (LuxP and LsrB families) are not found in all the bacteria capable of responding to this signaling molecule. Here, we identify a third type of AI-2 receptor, consisting of a dCACHE domain. AI-2 binds to the dCACHE domain of chemoreceptors PctA and TlpQ of Pseudomonas aeruginosa, thus inducing chemotaxis and biofilm formation. Boron-free AI-2 is the preferred ligand for PctA and TlpQ. AI-2 also binds to the dCACHE domains of histidine kinase KinD from Bacillus subtilis and diguanylate cyclase rpHK1S-Z16 from Rhodopseudomonas palustris, enhancing their enzymatic activities. dCACHE domains (especially those belonging to a subfamily that includes the AI-2 receptors identified in the present work) are present in a large number of bacterial and archaeal proteins. Our results support the idea that AI-2 serves as a widely used signaling molecule in the coordination of cell behavior among prokaryotic species.
Increased power from conditional bacterial genome-wide association identifies macrolide resistance mutations in Neisseria gonorrhoeae
Authors: Ma Kevin C. , Mortimer Tatum D. , Duckett Marissa A. , Hicks Allison L. , Wheeler Nicole E. , Sánchez-Busó Leonor , Grad Yonatan H. 
Published: October 2020

AbstractThe emergence of resistance to azithromycin complicates treatment of Neisseria gonorrhoeae, the etiologic agent of gonorrhea. Substantial azithromycin resistance remains unexplained after accounting for known resistance mutations. Bacterial genome-wide association studies (GWAS) can identify novel resistance genes but must control for genetic confounders while maintaining power. Here, we show that compared to single-locus GWAS, conducting GWAS conditioned on known resistance mutations reduces the number of false positives and identifies a G70D mutation in the RplD 50S ribosomal protein L4 as significantly associated with increased azithromycin resistance (p-value = 1.08 × 10−11). We experimentally confirm our GWAS results and demonstrate that RplD G70D and other macrolide binding site mutations are prevalent (present in 5.42% of 4850 isolates) and widespread (identified in 21/65 countries across two decades). Overall, our findings demonstrate the utility of conditional associations for improving the performance of microbial GWAS and advance our understanding of the genetic basis of macrolide resistance.
The Egyptian Collaborative Cardiac Genomics (ECCO-GEN) Project: defining a healthy volunteer cohort
Authors: Aguib Yasmine , Allouba Mona , Afify Alaa , Halawa Sarah , El-Khatib Mohamed , Sous Marina , Galal Aya , Abdelrahman Eslam , Shehata Nairouz , El Sawy Amr , Elmaghawry Mohamed , Anwer Shehab , Kamel Omnia , El Mozy Wesam , Khedr Hadir , Kharabish Ahmed , Thabet Nagwa , Theotokis Pantazis I. , Buchan Rachel , Govind Risha , Whiffin Nicola , Walsh Roddy , Aguib Heba , Elguindy Ahmed , O’Regan Declan P. , Cook Stuart A. , Barton Paul J. , Ware James S. , Yacoub Magdi 
Published: October 2020

AbstractThe integration of comprehensive genomic and phenotypic data from diverse ethnic populations offers unprecedented opportunities toward advancements in precision medicine and novel diagnostic technologies. Current reference genomic databases are not representative of the global human population, making variant interpretation challenging, especially in underrepresented populations, such as the North African population. To address this, the Egyptian Collaborative Cardiac Genomics (ECCO-GEN) Project launched a study comprising 1000 individuals free of cardiovascular disease (CVD). Here, we present the first 391 Egyptian healthy volunteers recruited to establish a pilot phenotyped control cohort. All individuals underwent detailed clinical investigation, including cardiac magnetic resonance imaging (MRI), and were sequenced using a targeted panel of 174 genes with reported roles in inherited cardiac conditions. We identified 1262 variants in 27 cardiomyopathy genes of which 15.1% were not captured in current global and regional genetic reference databases (here: gnomAD and Great Middle Eastern Variome). The ECCO-GEN project aims at defining the genetic landscape of an understudied population and providing individual-level genetic and phenotypic data to support future studies in CVD and population genetics.