bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a gRNA-tRNA Array of CRISPR/Cas9 in Combination with Grafting Technique to Improve Gene Editing Efficiency of Sweet Orange
Authors: Tang Xiaomei , Chen Shulin , Yu Huiwen , Zheng Xiongjie , Zhang Fei , Deng Xiuxin , Xu Qiang 
Published: August 2021

Abstract
Sweet orange is one of the most popular fruit crops worldwide. Traditional breeding approaches in sweet orange is impracticable due to the apomixis and long juvenility, making it difficult to obtain hybrids and selection of ideal genotypes. The development of targeted genome engineering technologies made it possible for the precise modification of target genes. Recently, a more efficient gene editing tool has been emerged based on the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system (Bhaya et al. 2011). The development of CRISPR/Cas9 technology is promising to accelerate the process of genetic improvement in perennial crops.
NOX2-Derived Hydrogen Peroxide Impedes the AMPK/Akt-mTOR Signaling Pathway in Parkinson's Disease in Vitro Models
Authors: Zhang Ruijie , Zhang Nana , Dong Xiaoqing , Chen Xin , Ma Jing , Gao Wei , Huang Shile , Chen Long 
Published: August 2021

Abstract
Oxidative stress is closely related to the pathogenesis of Parkinson's disease (PD), a typical neurodegenerative disease. NADPH oxidase 2 (NOX2) is involved in hydrogen peroxide (H2O2) generation. Recently, we have reported that H2O2 and PD toxins, including 6-hydroxydopamine (6-OHDA), 1-Methyl-4-phenylpyridin-1-ium (MPP+) and rotenone, induce neuronal apoptosis by inhibiting mTOR pathway. Here, we show that 6-OHDA, MPP+ or rotenone induced H2O2 generation by upregulation of NOX2 and its regulatory proteins (p22phox, p40phox, p47phox, p67phox, and Rac1), leading to apoptotic cell death in PC12 cells and primary neurons. Pretreatment with catalase, a H2O2-scavenging enzyme, significantly blocked PD toxins-evoked NOX2-derived H2O2, thereby hindering activation of AMPK, inhibition of Akt/mTOR, induction of apoptosis in neuronal cells. Similar events were also seen in the cells pretreated with Mito-TEMPO, a mitochondria-specific superoxide scavenger, implying a mitochondrial H2O2-dependent mechanism involved. Further research revealed that inhibiting NOX2 with apocynin or silencing NOX2 attenuated the effects of PD toxins on AMPK/Akt/mTOR and apoptosis in the cells. Of importance, ectopic expression of constitutively active Akt or dominant negative AMPKα, or inhibition of AMPK with compound C suppressed PD toxins-induced expression of NOX2 and its regulatory proteins, as well as consequential H2O2 and apoptosis in the cells. Taken together, these results indicate that certain PD toxins can impede the AMPK/Akt-mTOR signaling pathway leading to neuronal apoptosis by eliciting NOX2-derived H2O2. Our findings suggest that neuronal loss in PD may be prevented by regulating of NOX2, AMPK/Akt-mTOR signaling and/or administering antioxidants to ameliorate oxidative stress.
The Synergetic Effect of Sitafloxacin-Arbekacin Combination in the Mycobacteroides abscessus Complex
Authors: Watanabe Junko , Ihara Hiroaki , Takei Satomi , Nakamura Ayako , Fujimoto Yuichi , Handoh Tetsuya , Kurokawa Kana , Arai Yuta , Shibayama Kohei , Sumiyoshi Issei , Ochi Yusuke , Okabe Takahiro , Misawa Shigeki , Togo Shinsaku , Miida Takashi , Takahashi Kazuhisa 
Published: August 2021

Abstract
Background
Mycobacteroides abscessus (M. abscessus) is the most commonly isolated rapidly growing mycobacteria (RGM) and is one of the most antibiotic-resistant RGM with rapid progression, therefore, treatment of M. abscessus is still challenging. The genus mycobacterium has long been known to have both rough and smooth colony phenotypes. Rough morphotypes generally are more virulent than smooth morphotypes. Recently, the efficacy of sitafloxacin, new fluoroquinolone (FQ), containing regimens against M. abscessus complex have been reported. We here presented a new combination treatment with sitafloxacin that targeted rough morphotypes of M. abscessus, causing aggressive infections.
Results
Thirty-four clinical strains of M. abscessus were isolated from various clinical samples at the Juntendo university hospital from 2011 to 2020. The susceptibility to a combination of sitafloxacin and antimicrobial agents was compared to that of the antimicrobial agents alone. Ten isolates (90.9%) of M. abscessus subsp. abscessus were susceptible to both sitafloxacin and arbekacin when the combination is administered; while, 11 isolates (50.0%) of M. abscessus subsp. massiliense were susceptible. Synergistic effects against M. abscessus complex were shown in 8 strains (23.5%) treated with sitafloxacin-amikacin combination, 9 (26.5%) and 19 (55.9%) of sitafloxacin-imipenem combination, and sitafloxacin-arbekacin combination, respectively. Sitafloxacin-arbekacin combination also exhibited synergistic effects against 10 strains (45.5%) of M. abscessus subsp. massiliense and 8 stains (72.7%) of M. abscessus subsp. abscessus, a highly resistant subspecies of M. abscessus. The sitafloxacin-arbekacin combination revealed more synergistic effects in rough morphotypes of M. abscessus complex (p = 0.008).
Conclusion
We demonstrated the synergistic effect of the sitafloxacin-arbekacin combination against M. abscessus complex. Further, this combination regimen might be more effective against M. abscessus subsp. abscessus or rough morphotypes of M. abscessus complex.
Vehicle Driving State Estimation Using an Improved Adaptive Unscented Kalman Filter
Authors: Pang Hui , Wang Peng , Xu Zijun , Wang Gang 
Published: August 2021

Abstract
This paper proposes an improved adaptive unscented Kalman filter (iAUKF)-based vehicle driving state estimation method. A three-degree-of-freedom vehicle dynamics model is first established, then the varying principles of estimation errors for vehicle driving states using constant process and measurement noises in the standard unscented Kalman filter (UKF) are compared and analyzed. Next, a new type of normalized innovation square-based adaptive noise covariance adjustment strategy is designed and incorporated into the UKF to derive our expected vehicle driving state estimation method. Finally, a comparative simulation investigation using CarSim and MATLAB/Simulink is conducted to validate the effectiveness of the proposed method, and the results show that our proposed iAUKF-based estimation method has higher accuracy and stronger robustness against the standard UKF algorithm.
The P2Y12 Receptor Antagonist Ticagrelor Ameliorates Pulmonary Hypertension
Authors: li nannan , yin jie , shi yugen , sun li , zhang qingshan , bao shuai , zhang juan , li youlei , wang miaomiao , zhang yanwei , cai weidong , zhang hongxing , li yan , yan suhua , you shuling , Li Xiaolu 
Published: August 2021

Abstract
Background: Pulmonary arterial hypertension (PAH) is a disease that the pulmonary artery is abnormally elevated. P2Y12 is an adenosine diphosphate (ADP) receptor and it act as the target of thienopyridine antiplatelet drugs by controlling vascular remodeling. Inhibition of P2Y12 receptor in the process of PAH was explored in this study.Methods: The PAH model was established in Sprague-Dawley rats by single subcutaneous injection of 60 mg/kg monocrotaline (MCT). The ticagrelor solution (a selective P2Y12R inhibitor) was intraperitoneally injected into rats at a dose of 14 mg/kg from the time of MCT injection to day 28.Results: In the lung tissues of PAH rats, the marked P2Y12R was detected. Treatment with ticagrelor greatly decreased P2Y12R level and efficiently abolished the upregulation of α-SMA as demonstrated by Western blot and RT-PCR. The wall thickness and occlusion score of the pulmonary arterioles showed that blockade of P2Y12R could relieve lung remodeling caused by PAH. The haemodynamic changes at 4 weeks determined that P2Y12R inhibition affected RV pressure and right heart hypertrophy.Conclusions: P2Y12R might be involved in the pathogenesis of PAH. Blockade of P2Y12R has potential in treating PAH.
Rapid Response System Improves Sepsis Bundle Compliances &amp; Survival in Hospital Wards for 10 Years
Authors: Choi Sunhui , Son Jeongsuk , Huh Jin Won , Lim Chae-Man , Oh Dong Kyu , Hong Sang-Bum 
Published: August 2021

Abstract

Background
Hospitalized patients can develop septic shock at any time. Therefore, it is important to identify septic patients in hospital wards and rapidly perform the optimal treatment. Although the sepsis bundle has already been reported to improve survival rates, the controversy over evidence of the effect of in-hospital sepsis continues to exist. We aimed to estimate the outcomes and bundle compliance of patients with septic shock in hospital wards managed through the rapid response system (RRS).
Methods
Retrospective cohort study of 976 patients with septic shock managed through the RRS at an academic, tertiary care hospital in South Korea from 2008 to 2017.
Results
Of the 976 enrolled patients, the compliance of each sepsis bundle was high (80.8–100.0%), but the overall success rate of the bundle was low (58.3%). The compliance rate for achieving the overall sepsis bundle increased from 26.5–70.0%, and the 28-day mortality continuously decreased from 50–32.1% over 10 years. We analyzed the two groups according to whether they completed the overall sepsis bundle or not. Of the 976 enrolled patients, 569 (58.3%) sepsis bundles were completed, whereas 407 (41.7%) were incomplete. The complete bundle group showed lower 28-day mortality than the incomplete bundle group (37.1% vs. 53.6%, p < 0.001). In the multivariate multiple logistic regression model, the 28-day mortality was significantly associated with the complete bundle (adjusted odds ratio (OR), 0.58; 95% confidence intervals (CI), 0.39–0.87; p = 0.008). Obtention of blood cultures (adjusted OR, 0.45; 95% CI, 0.33–0.63; p < 0.001) and lactate remeasurement (adjusted OR, 0.69; 95% CI, 0.50–0.95; p = 0.024) in each component of the sepsis bundle were associated with the 28-day mortality.
Conclusions
The rapid response system provides improving sepsis bundle compliances and survival in patients with septic shock in hospital wards.
Climate Change will Increase Ozone Levels and unravel Air Quality Regulations
Authors: Adler David , Bento Antonio , Miller Noah , Severnini Edson 
Published: August 2021

Abstract
Using daily data for the United States over the period 1980-2019, we estimate the impacts of temperature on ambient ozone concentrations, accounting for adaptation to climatic change. We find that even with adaptation, rises in temperature will steeply increase ozone levels by over 9 ppb on days above 25◦C. By mid-century, we calculate that 189 additional counties will be violating the air quality standards, with 33 million more residents exposed to unhealthy levels of ozone. Climate change will thus likely increase the costs of compliance with existing ambient ozone standards. In light of a recent EPA ruling that would effectively remove co-benefits of ozone precursor reductions from the cost-benefit analysis of those standards, they will be in peril, further threatening public health.
Native gold enrichment process during growth of chalcopyrite-lined conduits within a modern hydrothermal chimney (Manus Basin, PNG)
Authors: Hu Si-Yu , Barnes Stephen J. , Pagès Anais , Verrall Michael , Parr Joanna , Quadir Zakaria , Schoneveld Louise , Binns Ray 
Published: August 2021

Abstract
Seafloor hydrothermal chimneys from back-arc basins are important hosts for metals such as Cu, Zn, Pb, Ag, and Au. Although the general growth history of chimneys has been well documented, recent studies have revealed that the fine-scale mineralogy can be highly complex and reflects variable physicochemical conditions of formation. This study utilized a novel combination of scanning electron microscopy (SEM)-based electron backscattered diffraction (EBSD) and synchrotron X-ray fluorescence microscopy (SXFM) to uncover the detailed growth processes of multiple chalcopyrite-lined conduits within a modern chalcopyrite-sphalerite chimney from Manus Basin and to assess the controls on native gold precipitation. On the basis of previous studies, the chimney conduit was thought to develop from an initial sulfate-dominated wall, which was subsequently dissolved and replaced by sphalerite and chalcopyrite during gradual mixing of hydrothermal fluids and seawater. During this process, sphalerite was epitaxially overgrown by chalcopyrite. Accretionary growth of chalcopyrite onto this early formed substrate thickened the chimney walls by bi-directional growth inward and outward from the original tube wall, also enclosing the outgrown pyrite cluster. A group of similar conduits with slightly different mineral assemblages continued to form in the vicinity of the main conduit during the further fluid mixing process. Four types of distinct native gold-sulfide/sulfosalt associations were developed during the varying mixing of hydrothermal fluids and seawater. Previously unobserved chains of gold nanoparticles occur at the boundary of early sphalerite and chalcopyrite, distinct from gold observed in massive sphalerite as identified in other studies. These observations provide baseline data in a well-preserved modern system for studies of enrichment mechanisms of native gold in hydrothermal chimneys. Furthermore, native gold is relatively rarely observed in chalcopyrite-lined conduit walls. Our observations imply that: (1) native gold is closely associated with various sulfides/sulfosalts in chalcopyrite-lined conduit walls rather than limited to the association with tennantite, Bi-rich minerals, and bornite as reported previously; and (2) the broad spectrum of gold occurrence in chalcopyrite-line conduits is likely to be determined by the various mixing process between hot hydrothermal fluids with surrounding fluids or seawater. Quantitative modeling of fluid mixing processes is recommended in the future to probe the precise gold deposition stages to efficiently locate gold in modern hydrothermal chimneys.
Phosphate removal by Ion exchange in batch mode
Authors: Bektaş T. E. , Uğurluoğlu B. Kıvanç , Tan B. 
Published: August 2021

AbstractWater with phosphate concentrations above 2 μM may adversely affect aquatic life and human health. In this study, the parameters affecting phosphate removal from aqueous solutions by ion exchange were investigated – contact time and temperature, initial pH, initial phosphate concentration and resin dosage, and the presence of other ions. The best phosphate removal (99%) from 100 mg-P/L initial solution was observed at pH 10 and 25 °C after 3 hours of contact time. No negative phosphate removal results were obtained from phosphate solutions containing sulfate, nitrate and ammonium ions; i.e., resembling real wastewater. Desorption (with NaOH or NaCl) and recovery (with CaO) studies of phosphate sorbed by resin were also carried out, as well as thermodynamic investigations. The proportional desorbability of phosphate from the resin with NaCl was 85.6%. The recovery efficiency of phosphate was 79.4%. The sorption process was spontaneous and endothermic. The ion exchange mechanism was determined using different internal and external diffusion models. The mechanism controlling the removal of phosphate from aqueous solution is both internal and external diffusion. Application of the Langmuir and Freundlich isotherm models showed that the experimental results fit well with the Freundlich model.
Temporal variations of de facto wastewater reuse and disinfection by-products in public water systems in the Shenandoah River watershed, USA
Authors: Weisman Richard J. , Barber Larry B. , Faunce Kaycee E. , Rapp Jennifer L. , Ferreira Celso M. 
Published: August 2021

Abstract
Temporal variations of de facto wastewater reuse are relevant to public drinking water systems (PWSs) that obtain water from surface sources. Variations in wastewater discharge flows, streamflow, de facto reuse, and disinfection by-products (DBPs – trihalomethane-4 [THM4] and haloacetic acid-5 [HAA5]) over an 18-year period were examined at 11 PWSs in the Shenandoah River watershed, using more than 25,000 data records, in gaged and ungaged reaches. The relationship of de facto reuse with DBPs by year and quarter at the PWSs was examined. A linear relationship was found between THM4 and de facto reuse on an annual average basis (p = 0.050), as well as in quarters 3 (July – September) (p = 0.032) and 4 (October – December) (p = 0.031). Using a t-test (p &lt; 0.05), the study also showed that there were significant differences in DBP levels for PWSs relative to 1% de facto reuse. This was found for THM4 based on annual average and quarter 1 (January – March) data, and for HAA5 based on quarter 3 data during the period of record.
Evaluation of irrigation scheduling and yield response for wheat cultivars using the AquaCrop model in an arid climate
Authors: Amiri E. , Bahrani A. , Irmak S. , Mohammadiyan Roshan N. 
Published: August 2021

Abstract
Yield, soil water balance components and evapotranspiration-based water productivity (WPET) of three winter wheat cultivars were investigated using the AquaCrop model under arid conditions in Shiraz, Iran, for two consecutive years. The irrigation treatments were non-stressed (I1) and post-anthesis water stress (I2) with three wheat cultivars. Evaluation of the model was performed using the coefficient of root mean squared error (RMSE), normalized RMSE and R2. The AquaCrop model performed well in simulating grain yield and final biomass production with R2 &gt; 0.90, and RMSE and normalized RMSE values less than 10. The I1 treatment resulted in higher grain yield and biomass productivity than the I2 treatment. The I2 irrigation resulted in yield reduction of 21 and 24% in the 2006–2007 and 2007–2008 growing seasons, respectively, as compared with I2. Using the measured grain yield and AquaCrop-simulated water balance, the amount of WPET was found to vary from 0.68 to 0.95 kg m−3. The AquaCrop model was able to predict winter wheat biomass and yield production with a good accuracy in the arid conditions of this study and its ability to simulate these variables for different wheat cultivars' was especially notable. The AquaCrop model can be used to explore management scenarios to improve wheat water management in the study region.
Modeling and optimization of a continuous electrocoagulation process using an artificial intelligence approach
Authors: Graça Nuno S. , Ribeiro Ana M. , Rodrigues Alírio E. 
Published: August 2021

Abstract
An artificial neural network (ANN) with the topology 8-94-85-2 (input – hidden layer 1 - hidden layer 2 - output) was used to model the operation of the continuous electrocoagulation (CEC) process for the removal of fluoride from water. After the ANN training, the sum of the squared errors (MSE) and the determination coefficient (R2) of the testing set model predictions were 0.0088 and 0.999, respectively, showing a good generalization and the model's predictive capacity. The optimization of the process cost using the genetic algorithm (GA) showed that the optimal conditions are highly dependent on the feed concentration and the fluoride removal requirements. For 5 L of water containing 10 mg/L of fluoride, the optimal conditions to reduce the fluoride concentration below the permissible limit (1.5 mg/L) are 88.3 mA of current intensity, a flow rate of 73.6 mL/min, and the use of a series monopolar (SM) electrode configuration, corresponding to a fluoride removal of 85% and an operating cost of 0.05 €/L.
Value composition and quantitative calculation of economic value produced by river ecological base flow
Authors: Yue Siyu , Li Huaien , Cheng Bo 
Published: August 2021

Abstract
The definition of the economic value (EV) produced by river ecological base flow (REBF) is the role of REBF in avoiding river shrink or dry up and maintaining ecosystem health and natural process of river. Scientific and accurate establishment of quantitative method for calculating the EV produced by REBF is helpful for humans to understand the benefits of REBF protection directly and optimize the allocation of water resources by means of economics. Based on the characteristics of non-consumable and multi-values of REBF, we first identified its value composition by referring to the EV classification of river. Next, we established calculation methods for each sub-value using evaluation techniques of resources and environment economics. Finally, on the basis of calculation results of sub-values and the relationship of sub-values, we determined the maximum EV supported by each kind of water requirements of REBF, and summed up all independent parts to obtain the total EV. This method can remove repeated calculations in the process of assessing the EV produced by REBF. Our results indicated that the minimum total EV produced by REBF in the Shaanxi section of the Wei River was 4.54 billion yuan in 2017, which is close to previous studies. The new method developed here should provide a better theoretical support for quantitative research of the EV produced by REBF and scientific management of limited water resources coming from river.
Recent Development of Bioinformatics Tools for microRNA Target Prediction
Authors: Khatun Mst Shamima , Alam Md Ashad , Shoombuatong Watshara , Mollah Md Nurul Haque , Kurata Hiroyuki , Hasan Md Mehedi 
Published: August 2021

Abstract:MicroRNAs (miRNAs) are central players that regulate the post-transcriptional processes of gene expression. Binding of miRNAs to target mRNAs can repress their translation by inducing the degradation or by inhibiting the translation of the target mRNAs. High-throughput experimental approaches for miRNA target identification are costly and time-consuming, depending on various factors. It is vitally important to develop bioinformatics methods for accurately predicting miRNA targets. With the increase of RNA sequences in the post-genomic era, bioinformatics methods are being developed for miRNA studies especially for miRNA target prediction. This review summarizes the current development of state-of-the-art bioinformatics tools for miRNA target prediction, points out the progress and limitations of the available miRNA databases, and their working principles. Finally, we discuss the caveat and perspectives of the next-generation algorithms for the prediction of miRNA targets.
Liposomes-based Nanoplatform Enlarges Ultrasound-related Diagnostic and Therapeutic Precision
Authors: Zhang Ying , Fowlkes Brian 
Published: August 2021

:
Ultrasound (US) is recognized in the medical field as a safe and effective imaging
modality due to its lack of ionizing radiation, non-invasive approach, and real-time
monitoring capability. Accompanying recent progress in nanomedicine, US has been
providing hope of theranostic capability not only for imaging-based diagnosis but also for
US-based therapy by taking advantage of the bioeffects induced by US. Cavitation, sonoporation,
thermal effects, and other cascade effects stimulated by acoustic energy conversion
have contributed to medical problem-solving in the past decades, although to varying
degrees of efficacy in comparison to other methods. Recently, the usage of liposomesbased
nanoplatform fuels the development of nanomedicine and provides novel clinical
strategies for antitumor, thrombolysis, and controlled drug release. The merging of novel
liposome-based nanoplatforms and US-induced reactions has promise for a new blueprint
for future medicine. In the present review article, the value of liposome-based nanoplatforms
in US-related diagnosis and therapy will be discussed and summarized along with
potential future directions for further investigations.