bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence analysis of 43‐year old samples of Plantago lanceolata show that Plantain virus X is synonymous with Actinidia virus X and is widely distributed
Authors: Hammond John , Adams Ian P. , Fowkes Aimee R. , McGreig Sam , Botermans Marleen , van Oorspronk Joanieke J. A. , Westenberg Marcel , Verbeek Martin , Dullemans Annette M. , Stijger Christina C. M. M. , Blouin Arnaud G. , Massart Sebastien , De Jonghe Kris , Heyneman Maaike , Walsh John A. , Fox Adrian 
Published: November 2020

AbstractPlantain virus X was first recognized by the ICTV as a species in the genus Potexvirus in 1982. However, because no sequence was available for plantain virus X (PlVX), abolishing the species was proposed to the Flexiviridae working group of the ICTV in 2015. This initiated efforts to sequence the original isolates from Plantago lanceolata samples. Here we report the full‐genome sequencing of two original isolates of PlVX, which demonstrate that the virus is synonymous to Actinidia virus X, a species previously reported from kiwifruit (Actinidia sp.) and blackcurrant (Ribes nigrum). PlVX was previously noted to be widespread in the UK in P. lanceolata. This report additionally presents novel data on the distribution and diversity of PlVX, collected at the same site as the original UK isolates, and from three independent surveys, two in the Netherlands and one in Belgium. This study also includes two new host records for PlVX, Browallia americana and Capsicum annuum (sweet pepper), indicating the virus is more widespread and infects a broader range of hosts than previously reported. This stresses the importance of surveys of noncultivated species to gain insight into viral distribution and host range. This study also demonstrates the value of generating sequence data for isolates retained in virus collections. Additionally, it demonstrates the potential value in prepublication data sharing for giving context to virus detections such as the four independent studies here which, when combined, give greater clarity to the identity, diversity, distribution, and host range of plantain virus X.
Non‐structural carbohydrates and sugar export in grapevine leaves exposed to different light regimes
Authors: Dayer Silvina , Murcia Germán , Prieto Jorge A. , Durán Martin , Martínez Liliana , Píccoli Patricia , Perez Peña Jorge 
Published: November 2020

AbstractLight is a main environmental factor that determines leaf microclimate within the vine, as well as its photosynthesis and carbohydrate metabolism. This study aimed to examine the relationships between photosynthesis, carbohydrate metabolism, and the expression of related genes in leaves of grapevine grown under different radiation regimes. During the 2014/2015 growing season, an experiment was conducted on a Malbec vineyard (Vitis vinifera L.) in which four radiation exposure treatments were established on the leaves: (1) East, (2) West, (3) Sun, and (4) Shade (i.e., reduction in light intensity). Diurnal dynamics of photosynthesis and non‐structural carbohydrates were measured and leaf export rates were calculated. Transcript profiles of leaf sugar transporters (VvHT1, VvHT3, VvSUC27), a sucrose phosphate synthase enzyme (VvSPS), and invertases (VvGIN1, VvCWI) were also examined. We showed that East and Sun leaves had higher daily photosynthetic and export rates than West leaves, which was mainly explained by the environmental conditions (air and leaf temperature, VPDleaf‐air) and leaf water status. Shade leaves accumulated less starch and soluble sugars than exposed leaves, which correlated with a higher expression of hexose transporters and invertases. The hypotheses that these sugars in Shade leaves would play a role as signaling molecules and/or have increased sink strength and phloem unloading are discussed. These results allow us to understand the physiological and molecular behavior of leaves exposed to different radiation regimes, which can be used to design appropriate vineyard management practices.
Endogenous •NO accumulation in soybean is associated with initial stomatal response to water deficit
Authors: Casaretto Esteban , Signorelli Santiago , Gallino Juan P. , Vidal Sabina , Borsani Omar 
Published: November 2020

AbstractDrought is the main cause of productivity losses in soybean plants, triggering physiological and biochemical responses, stomatal closure being essential to prevent water losses and thus mitigate the negative effects of drought. Abscisic acid (ABA) is the main molecule involved in stomatal closure under drought conditions along with nitric oxide (•NO). However, the role of •NO in this process is not yet fully understood and contrasting findings about its role have been reported. Most of the assays in the literature have been carried out under in vitro conditions using •NO donors or scavengers, but little is known about the effects of endogenously produced •NO under drought conditions. This study is aimed to determine the pattern of endogenous •NO accumulation from the establishment of water stress and how this relates to stomatal closure and other biochemical and physiological responses. The analysis of soybean plant responses to drought revealed no correlation between whole‐leaf •NO accumulation and typical water‐deficit stress markers. Moreover, •NO accumulation did not explain oxidative damage induced by drought. However, endogenous •NO content correlated with the early stomatal closure. Analysis of stomatal behavior and endogenous •NO content in guard cells through epidermal peel technique showed a stomatal population with high variation in stomatal opening and •NO content under the initial stages of water stress, even when ABA responses are activated. Our data suggest that upon early stress perception, soybean plants respond by accumulating •NO in the guard cells to inhibit stomatal closure, potentially through the inhibition of ABA responses.
Modulation of cell cycle progression and chromatin dynamic as tolerance mechanisms to salinity and drought stress in maize
Authors: Kamal Khaled Y. , Khodaeiaminjan Mortaza , Yahya Galal , El‐Tantawy Ahmed A. , Abdel El‐Moneim Diaa , El‐Esawi Mohamed A. , Abd‐Elaziz Mohamed A. A. , Nassrallah Amr A. 
Published: November 2020

AbstractSalinity and drought are the major abiotic stresses that disturb several aspects of maize plants growth at the cellular level, one of these aspects is cell cycle machinery. In our study, we dissected the molecular alterations and downstream effectors of salinity and drought stress on cell cycle regulation and chromatin remodeling. Effects of salinity and drought stress were determined on maize seedlings using 200 mM NaCl (induced salinity stress), and 250 mM mannitol (induced drought stress) treatments, then cell cycle progression and chromatin remodeling dynamics were investigated. Seedlings displayed severe growth defects, including inhibition of root growth. Interestingly, stress treatments induced cell cycle arrest in S‐phase with extensive depletion of cyclins B1 and A1. Further investigation of gene expression profiles of cell cycle regulators showed the downregulation of the CDKA, CDKB, CYCA, and CYCB. These results reveal the direct link between salinity and drought stress and cell cycle deregulation leading to a low cell proliferation rate. Moreover, abiotic stress alters chromatin remodeling dynamic in a way that directs the cell cycle arrest. We observed low DNA methylation patterns accompanied by dynamic histone modifications that favor chromatin decondensation. Also, the high expression of DNA topoisomerase 2, 6 family was detected as consequence of DNA damage. In conclusion, in response to salinity and drought stress, maize seedlings exhibit modulation of cell cycle progression, resulting in the cell cycle arrest through chromatin remodeling.
Minimizing hazard impacts of soil salinity and water stress on wheat plants by soil application of vermicompost and biochar
Authors: Hafez Emad M. , Omara Alaa El Dein , Alhumaydhi Fahad A. , El‐Esawi Mohamed A. 
Published: November 2020

AbstractSoil water and nutrient status are two of the most important factors for plant development and crop yield. Vermicompost and biochar are supposed to amend soil attributes and increase the productivity. However, little is known about their mixture application on soil quality and nutrient uptake under natural conditions. The aim of this investigation was to understand the impact of soil amendments (control, vermicompost, biochar, and vermicompost + biochar) on yield, soil quality, physiological and biochemical attributes, as well as nutrient uptake of wheat plants grown at different irrigation water treatments (50%, 75%, and 100% of field capacity [FC]) in saline sodic soil. Vermicompost improved wheat growth and yield. Biochar‐treated plants had higher growth performance and yield than control plants in all traits and than vermicompost in some cases, thus confirming its potential for enhancing soil quality and increasing nutrient uptake, which stimulates soil chemical properties. When vermicompost was added in combination with biochar, further enhancement in the growth and yield was recorded, highlighting the beneficial effect of vermicompost on plant yield. Vermicompost–biochar mixture application followed by biochar as a singular application caused significant improvements in relative water content, chlorophyll content, stomatal conductance, cytotoxicity, leaf K+ content with respect to nutrient uptake (N, P, and K), while reducing oxidative stress (i.e., activities of catalase [CAT] and ascorbate peroxidase [APX], and expression levels of CAT, APX, and Mn‐SOD genes), leaf Na+ content, and proline content. This resulted in increases in yield‐related traits and productivity owing to the enhancement in soil chemical characteristics and soil moisture content. Grain yield and nutrient uptake attained the highest values at 75% FC in wheat plants treated by the combination of vermicompost and biochar. In summary, this investigation revealed that the synergistic effect of vermicompost and biochar can not only enhance crop production but also eliminates the detrimental effects of soil salinity and water stress.
Beta–Negative Binomial Auto-Regressions for Modelling Integer-Valued Time Series with Extreme Observations
Authors: Gorgi Paolo 
Published: November 2020

SummaryThe paper introduces a general class of heavy-tailed auto-regressions for modelling integer-valued time series with outliers. The specification proposed is based on a heavy-tailed mixture of negative binomial distributions that features an observation-driven dynamic equation for the conditional expectation. The existence of a stationary and ergodic solution for the class of auto-regressive processes is shown under general conditions. The estimation of the model can be easily performed by maximum likelihood given the closed form of the likelihood function. The strong consistency and the asymptotic normality of the estimator are formally derived. Two examples of specifications illustrate the flexibility of the approach and the relevance of the theoretical results. In particular, a linear dynamic equation and a score-driven equation for the conditional expectation are studied. The score-driven specification is shown to be particularly appealing as it delivers a robust filtering method that attenuates the effect of outliers. Empirical applications to the series of narcotics trafficking reports in Sydney and the euro–pound sterling exchange rate illustrate the effectiveness of the method in handling extreme observations.
Functional Ensemble Survival Tree: Dynamic Prediction of Alzheimer’s Disease Progression Accommodating Multiple Time-Varying Covariates
Authors: Jiang Shu , Xie Yijun , Colditz Graham A. 
Published: November 2020

Abstract
With the exponential growth in data collection, multiple time-varying biomarkers are commonly encountered in clinical studies, along with a rich set of baseline covariates. This paper is motivated by addressing a critical issue in the field of Alzheimer’s disease (AD) in which we aim to predict the time for AD conversion in people with mild cognitive impairment to inform prevention and early treatment decisions. Conventional joint models of biomarker trajectory with time-to-event data rely heavily on model assumptions and may not be applicable when the number of covariates is large. This motivated us to consider a functional ensemble survival tree framework to characterize the joint effects of both functional and baseline covariates in predicting disease progression. The proposed framework incorporates multivariate functional principal component analysis to characterize the changing patterns of multiple time-varying neurocognitive biomarker trajectories and then nest these features within an ensemble survival tree in predicting the progression of AD. We provide a fast implementation of the algorithm that accommodates personalized dynamic prediction that can be updated as new observations are gathered to reflect the patient’s latest prognosis. The algorithm is empirically shown to perform well in simulation studies and is illustrated through the analysis of data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) (http://adni.loni.usc.edu/). We provide implementation of our proposed method in an R package funest.
Single‐center experience with use of letermovir for treatment of CMV infection in stem cell transplant recipients
Authors: Kachur Ekaterina , Roshdy Danya , Hamadeh Issam , Dodd Brandy , Shahid Zainab 
Published: November 2020

AbstractThe approval of letermovir provided a new option for cytomegalovirus (CMV) prophylaxis in CMV seropositive allogeneic hematopoietic stem cell transplantation (allo‐HSCT) recipients. Data are limited on the use of letermovir for the treatment of CMV infection. We performed a single‐center retrospective review of allo‐HSCT recipients who received letermovir off‐label for treatment of CMV infection (CMV DNAemia and CMV disease) from November 2017 until November 2019. Fifteen patients were included, 14 of which received letermovir for treatment of CMV DNAemia. The median duration from transplant to CMV DNAemia was 41 days and median duration of letermovir therapy was 53 days (IQR, 43‐59). Median time to first undetectable CMV viral load from the start of letermovir was 16 days (IQR, 13‐21). No significant correlation was noted between the time to CMV DNA clearance and either CMV DNA at the time of starting letermovir (r = −.12, 95% CI: −0.63‐0.46; P = .69) or CMV DNA peak (r = .04, 95% CI: −0.51‐0.58, P = .87). Three patients had late reactivation of CMV after completion of letermovir (20%) after 87 days (IQR, 68‐103) of therapy cessation. Clinical failure or treatment intolerance occurred in two patients (14%). One patient failed to achieve an undetectable viral load. In another patient, letermovir was discontinued due to documented therapy‐related thrombocytopenia. Our analysis suggests that letermovir might have a potential role for the treatment of CMV infection in select patients with contraindication or intolerance to more validated therapies.
Prevalence and associated risk factors of Helicobacter pylori infection in the Wuwei cohort of north‐western China
Authors: Zhang Fuhua , Pu Ke , Wu Zhengqi , Zhang Zhiyi , Liu Xin , Chen Zhaofeng , Ye Yuwei , Wang Yuping , Zheng Ya , Zhang Jinhua , An Feng , Zhao Shijun , Hu Xiaobin , Li Youpeng , Li Qiang , Liu Min , Lu Hong , Zhang Hongling , Zhao Yue , Yuan Hao , Ding Xiangping , Shu Xiaochuang , Ren Qian , Gou Xi , Hu Zenan , Wang Jun , Wang Yuling , Guan Quanlin , Guo Qinghong , Ji Rui , Zhou Yongning 
Published: November 2020

AbstractObjectivesTo evaluate the prevalence of Helicobacter pylori infection and risk factors and to serotype the strains in Wuwei, located in north‐western China, which has a high incidence of gastric cancer.MethodsHelicobacter pylori infection was analysed in 21 291 adults by 14C‐urea breath test, and H. pylori antibody were detected in 9183 serum samples by latex immunoturbidimetric method. The correlation of H. pylori infection with demographic–economic, lifestyle factors and medical history among the participants was determined by questionnaire. The antibodies against H. pylori urease, VacA and CagA in serum were determined by dot immunobinding assay.ResultsThe infection rate of H. pylori was 53.0%, and 90.1% of strains were type I strains. The H. pylori infection rate was higher among farmers (OR = 1.34, 95% CI: 1.19–1.50) and individuals who had a junior high school or higher education level (OR = 1.10, 95% CI: 1.06–1.15), and was lower in older individuals (OR = 0.86, 95% CI: 0.83–0.90), individuals with high income (OR = 0.93, 95% CI: 0.90–0.95), individuals with a habit of eating quickly (OR = 0.93, 95% CI: 0.87–0.99) and individuals who consumed more fruit and vegetables (OR = 0.90, 95% CI: 0.85–0.95). Individuals with history of cholecystitis/cholecystolithiasis, hypertension and asthma were negatively correlated with H. pylori infection (P < 0.05).ConclusionThe prevalence of H. pylori infection is high in Wuwei. The major prevalent strain is type I strain. Age, education, occupation, household income, consumption of fruit and vegetables, and habit of eating quickly are independent risk factors for H. pylori infection, which is also associated with individuals with a history of extragastric diseases.
Development of ecosystem‐based flood mitigation approach – investigations by experiments and numerical simulation
Authors: Tariq Kamran , Pasha Ghufran Ahmed , Tanaka Norio , Ghani Usman , Ahmed Afzal 
Published: November 2020

AbstractThe purpose of this research was to understand how to minimise the destructive effects of floods by establishing a bio‐shield of natural vegetation. Experiments were conducted in a water flume to determine the flow properties under different vegetation conditions whereas; volume of fluid (VOF) multiphase approach with a standard k‐ɛ turbulence model was developed for a simulation. The study involved comparative analysis of flow structures and loss of energy in a single patch of finite length, layered (single or double layer with gaps) and continuous (full width) vegetation models. The results showed that, for a single patch, the increase in vegetation density and aspect ratio increased the backwater rise in front of vegetation, reduced velocity and enhanced energy dissipation. Furthermore, in the case of horizontally layered vegetation models (single and double horizontal layers), the loss of energy was higher in double horizontally layered vegetation layouts. Gaps between vegetation patches of a single horizontally layered vegetation model possessed high flow velocity, which was countered by providing a second horizontal layer of vegetation with an alternate gap. The findings from this research are critical in designing optimum vegetation layouts for flood mitigation.
Effect of waste landfill site on surface and ground water drinking quality
Authors: Amano Kofi Owusu Ansah , Danso‐Boateng Eric , Adom Ebenezer , Kwame Nkansah Desmond , Amoamah Ernest Sintim , Appiah‐Danquah Emmanuel 
Published: November 2020

AbstractDrinking water quality of surface and underground water within 1.34 km from a waste landfill site in Kumasi, Ghana was investigated. Physico‐chemical properties and heavy metal concentrations were analysed to determine water quality and pollution indices. It was found that turbidity of 83% of hand dug wells, 50% of the streams and 33% of boreholes were higher than World Health Organisation (WHO) standards for drinking water. Water quality index (WQI) showed that 25% of the water sources are of excellent quality, while 50%, 15% and 5% are good quality, poor quality, very poor quality and unsuitable for drinking, respectively. Heavy metal pollution index (HPI) indicated that the water sources were above the critical limit for drinking water (HPI > 100). Principal component analysis (PCA) revealed 75.30% and 70.88% of the total variance for the physico‐chemical parameters and heavy metals, respectively. The findings concluded that cadmium concentrations in all the water sources were extremely higher (0.0122–0.1090 mg/L) than WHO limit (0.003 mg/L), rendering them unwholesome for consumption.
Application of algae to free surface wetlands for effluent reuse
Authors: Yehia Shereen , El‐Saadi Aiman , Galal Mona M. 
Published: November 2020

AbstractThe main goal of this study is to assess the role of Algae in the treatment of wastewater and its capability to improve the performance of the free surface wetland as a green solution. It offers a non‐conventional water resource that participate in solving the water scarcity issue in Egypt. This study was carried out in Lake Manzala Water Research Station which is located at the tail end of Bahr El Baqar Drain in Northern Delta in ‏Egypt. A pilot scale wetland consisting of four parallel basins under natural climatic conditions were used for the experiment. The first cell was cultivated with Reeds (traditional plant used in wetlands), while the algae were cultivated in the three other basins. Three different microalgae and algae species (Chlorella, Spirulina and Azolla) were experimented and compared to assess for the finest removal efficiency for different contaminants as BOD, COD, TN, TP, TC, FC and heavy metals. A tailor‐made module was developed with Excel Visual Basic Application programming language to compare the efficiencies of the different treatment systems. Results showed that BOD and COD best removal results were reached by Chlorella with 88% and 84% removal efficiencies respectively. Results also showed that Azolla is the most efficient treatment media for drainage water containing high concentrations of TN while Spirulina was found to be the most efficient in extracting the heavy metals such as Aluminum (Al), Iron (Fe) and Manganese (Mn).
Assessment of Interacting Corrosion Defects in Thin-Walled Pipes
Authors: Soliman Ahmed A. , Megahed Mohammad M. , Saleh Ch. A. , Shazly Mostafa 
Published: November 2020

AbstractCorrosion in pipes is usually found in the form of closely spaced defects, which eventually reduce the pipe pressure carrying capacity and piping planned useful life. Codes and standards have been developed to evaluate the effect of such form of metal loss on the piping pressure carrying capacities. However, predictions of such codes are usually conservative, and hence, there is a need to assess their degree of conservatism. The present paper utilizes nonlinear finite element analysis (FEA) in estimating pressure carrying capacities of defective pipes, and hence provides an evaluation of codes degree of conservatism. Shell elements with reduced thickness at the corrosion defect are adopted and their accuracy is assessed by comparison with those of solid elements as well as experimental test results. The influence of defects interaction is investigated by considering two neighboring defects in an inclined direction to each other. The influence of inclination angle, inclined proximity distance between the two defects, and the defect depth to wall thickness ratio are investigated. Comparisons were made with predictions of codes of practice in all cases. Code predictions were found to be conservative compared to FEA results. Furthermore, the interaction rule embedded in the codes for checking for interaction leads to inaccurate predictions for closely spaced defects as it does not include the effect of defect depth.