bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of methylation‐driven genes related to prognosis in clear‐cell renal cell carcinoma
Authors: Wang Jia , Zhang Qiujing , Zhu Qingqing , Liu Chengxiang , Nan Xueli , Wang Fuxia , Fang Lihua , Liu Jie , Xie Chao , Fu Shuai , Song Bao 
Published: July 2019

AbstractWith the participation of the existing treatment methods, the prognosis of advanced clear‐cell renal cell carcinoma (ccRCC) is poor. More evidence indicates the presence of methylation in ccRCC cancer cells, but there is a lack of studies on methylation‐driven genes in ccRCC. We analyzed the open data of ccRCC in The Cancer Genome Atlas database to obtain ccRCC‐related methylation‐driven genes, and then carried out pathway enrichment, survival, and joint survival analyses. More important, we deeply explored the correlation between differential methylation sites and the expression of these driving genes. Finally, we screened 29 methylation‐driven genes via MethylMix, of which six were significantly associated with the survival of ccRCC patients. This study demonstrated that the effect of hypermethylation or hypomethylation on prognosis is different, and the level of methylation of key methylation sites is associated with gene expression. We identified methylation‐driven genes independently predicting prognosis in ccRCC, which offers theoretical support in bioinformatics for the study of methylation in ccRCC and a new perspective for the epigenetic study of ccRCC.
Highly efficient and reversible absorption of SO2 by hydroxyl ammonium ionic liquids at low partial pressure
Authors: Qi Yanfei , Hu Xiude , Liu Yongzhuo , Sun Deshuai , Li Runhao , Zhu Hongtang 
Published: July 2019

AbstractBLACKGROUNDThe control of sulfur dioxide (SO2) emissions is vital for the treatment of flue gases of combustion. The wet flue gas desulfurization process using limestone‐gypsum is now used widely, due to its high efficiency and reliability. However, it has the disadvantages of high cost and production of hazardous by‐products. Ionic liquids are new green organic solvents that can absorb acidic gases selectively. Hydroxyl ammonium ionic liquids with different anions were synthesized by neutralization and used to separate SO2 from simulated flue gas at low partial pressure of SO2.RESULTSThe absorption capacities of SO2 using ionic liquids were 1.02 mol/mol, 1.19 mol/mol, and 3.34 mol/mol for [TEOA][AC], [TEOA][LA] and [TEOA][CA], respectively, at the SO2 partial pressure of 4 kPa. Viscosity of ionic liquid affected the absorption process. A longer time was required to attain absorption equilibrium in the case of [TEOA][CA]. Low temperatures favoured absorption because the process was exothermic. Water in flue gas accumulated in the ionic liquids, causing a reduction in absorption of SO2. A mixture containing different ionic liquids could decrease the viscosity and achieve optimal absorption capacities. The ionic liquids could be recycled and regenerated by desorption at high temperature. A reduction of ≈2% in absorption capacities was found after four cycles of regeneration. Analysis of the absorption mechanism indicated that nitrogen atoms in the cationic part of ionic liquid molecules were the predominant site for combined chemical and physical absorption processes.CONCLUSIONHydroxyl ammonium ionic liquids exhibited excellent potential for absorption of SO2 at low partial pressure by combined chemical and physical absorption processes. © 2019 Society of Chemical Industry
A seamless and nonprotein A‐based monoclonal antibody purification platform using void‐exclusion anion exchange chromatography and electropositive multimodal chromatography enhanced by advance chromatin extraction
Authors: Liu Wenshuai , Chen Quan , Fan Xiying , Liang Yunlong , Sun Yue , Yu Jianli , Bao Zixian , Peng Xinying , Xian Mo , Nian Rui 
Published: July 2019

AbstractBACKGROUNDDownstream production of monoclonal antibodies (mAbs) involves several complex unit operations, directly affecting whether they can be used in clinical practice. Protein A affinity chromatography is considered the de facto standard due to its ability to selectively capture antibodies from cell culture supernatant (CCS). Recent studies on various associations of host cell contaminants have shown that downstream purification can be enhanced substantially with advance chromatin removal, facilitating the development of more promising nonaffinity purification platforms.RESULTSIn this study, void‐exclusion anion exchange chromatography (VEAX) was systematically characterized for its potential use as an initial antibody separation and recovery step. Void exclusion refers to a new chromatographic mode, which is different from the traditional bind‐elute and flow‐through operations. The new separation method is based on the size of the molecules as well as their surface charges. This process causes the initial immunoglobulin G (IgG) separation to become independent of sample composition (especially for pH and conductivity), eliminating the need to equilibrate the sample. Electropositive multimodal chromatography was then seamlessly incorporated with direct protein loading for further antibody polishing. With the aid of advanced chromatin removal, the two‐step purification platform achieved production of an antibody with <1 ppb DNA, <1 ppm HCP and <0.05% high‐molecular‐weight aggregates with IgG recovery of 90.4%.CONCLUSIONThis outcome provides a highly promising nonaffinity purification process and a competitive alternative for the current protein A‐dominated antibody processing strategy. © 2019 Society of Chemical Industry
Nitrogen‐doped graphene prepared by thermal annealing of fluorinated graphene oxide as supercapacitor electrode
Authors: Jiang Fei , Zhang Jixiang , Li Nian , Liu Cui , Zhou Yongqiang , Yu Xinling , Sun Lidong , Song Yanping , Zhang Shudong , Wang Zhenyang 
Published: July 2019

AbstractBACKGROUNDNitrogen doping significantly improves the electrochemical properties of graphene. Here, a new and effective methodology of preparing nitrogen‐doped graphene (NG) by thermal annealing of fluorinated graphene oxide (FGO) under the atmosphere of ammonia, is reported, in which ammonia is the reductant for FGO reduction and also the nitrogen source for nitrogen doping. This method can achieve higher nitrogen doping content than conventional approaches.RESULTSFGO prepared from fluorinated graphite polymer (CF) is directly used as a precursor to synthesize NG. Four samples with the same reaction time and different annealing temperatures are compared, and the highest nitrogen content of the NG reaches 12.45 at% at the reaction condition of 800 °C and 3 h. The synthesized NG samples are examined as a supercapacitor electrode material, displaying excellent performance due to the high nitrogen doping and a large number of active sites.CONCLUSIONWith the increase of annealing temperature, the nitrogen content of different NG samples first increases and then decreases. The specific capacitance of NG electrode material also shows the same trend as the nitrogen content. The highest specific capacitance in three‐electrode configuration attains 225.2 F g−1 at a current density of 1 A g−1. The electrode maintains a 90% capacitance after 5000 cycles, showing good cycle stability. This synthetic method provides a new approach for the preparation of NG with high nitrogen doping as supercapacitor electrode materials. © 2019 Society of Chemical Industry
Cold oxygen plasma induces changes on the surface of carbon materials enhancing methanogenesis and N2O reduction in anaerobic sludge incubations
Authors: De Velasco‐Maldonado Paola S , Pat‐Espadas Aurora M , Cházaro‐Ruíz Luis F , Cervantes Francisco J , Hernández‐Montoya Virginia 
Published: July 2019

AbstractBACKGROUNDConductive materials, such as activated carbon (AC), graphene and biochar, have recently been applied for enhancing methane (CH4) production in anaerobic digesters. However, few efforts have been made to develop engineered conductive materials for these purposes. The aim of this work was to synthesize carbon materials from pecan nut shells and peach stones to apply them in anaerobic sludge incubations for enhancing the methanogenic activity, as well as the reduction of nitrous oxide (N2O).RESULTAddition of conductive materials increased up to six‐fold the maximum CH4 production rate. Moreover, oxidation of these carbon materials with cold oxygen plasma enriched their surface with redox functional groups (e.g. quinones), so that their application further increased the methanogenic production rate up to 11‐fold as compared to controls lacking conductive materials. Furthermore, the reduction rate of N2O was increased several orders of magnitude in the presence of synthesized carbon materials, which constitutes the first demonstration that conductive materials can significantly increase the reduction rate of this greenhouse gas.CONCLUSIONResults indicate that there is great potential to develop engineered conductive materials to enhance both the production of CH4 and the reduction of N2O from wastewater treatment plants (WWTP), which may contribute to achieve more efficient processes. © 2019 Society of Chemical Industry
Investigation of a large waterborne acute gastroenteritis outbreak caused by group B rotavirus in Maharashtra state, India
Authors: Joshi Madhuri S. , Lole Kavita S. , Barve Uday S. , Salve Dawal S. , Ganorkar Nital N. , Chavan Nutan A. , Shinde Manohar S. , Gopalkrishna Varanasi 
Published: July 2019

AbstractAn acute gastroenteritis outbreak at Devli Karad village, Maharashtra, India with an attack rate of 22.6% affected mainly adolescent and adult population. The viral investigations conducted on fecal specimens of patients hospitalized indicated the presence of rotavirus B (RVB) using RNA polyacrylamide gel electrophoresis and reverse transcription polymerase chain reaction. The samples collected from the source of drinking water also showed the presence of the only RVB. Absence of other viral agents and identification of RVB of genotype G2 as the etiological agent of the acute gastroenteritis outbreak highlights, the necessity of monitoring RVB, the viral agent known for its large outbreak potential.
Patient care effectiveness and financial outcomes of hospital physician contracting emphasis
Authors: Mishra Saurabh , Salzarulo Peter A. , Modi Sachin B. 
Published: July 2019

AbstractThis study investigates the influence of hospitals' physician contracting emphasis on patient care effectiveness and financial outcomes. It utilizes secondary data for a comprehensive set of hospitals in the United States over a 21‐year period (1996–2016). Analysis confirms that hospitals with a greater emphasis on physician contracting have higher operating margins but also tend to have longer patient length of stay—indicating lower patient care effectiveness. Lower patient care effectiveness, in turn, is observed to attenuate some of the financial gains from physician contracting. Further, post hoc analysis with other measures of patient care, including experiential quality, conformance quality, readmissions, and mortality provide additional insights into the effect of physician contracting on patient care. Theory and results also highlight teaching intensity and capacity utilization of hospitals as key boundary conditions in these relationships, revealing a complex set of findings related to these variables. Together, the findings yield practical insights for hospital managers regarding their operations strategy.
Delayed primary retention suture for inset of vascularized submental lymph node flap for lower extremity lymphedema
Authors: Koide Satomi , Lin Chia‐Yu , Cheng Ming‐Huei 
Published: July 2019

AbstractBackgroundVascularized lymph node transfer (VLNT) has become one of the effective surgical treatments for extremity lymphedema. This study was to evaluate the re‐exploration and total complication rates of VLNT for lower extremity lymphedema between two different flap inset techniques.MethodsSixty‐nine patients who underwent 74 submental VLNT transfers between 2008 and 2018 were retrospectively studied. Fifty‐six flaps were inset using a new delayed primary retention suture (DPRS) technique and other 18 flaps using conventional interrupted sutures as the non‐DPRS group.ResultsThe overall flap success rate was 100%. The DPRS group was released at a mean of 1.7  ± 0.7 times and took a mean of 10.3 ± 3.3 days for wound closure. There were no statistical differences in demographics, mean symptom duration, and mean Cheng's Lymphedema Grading between two groups. Mean frequency of cellulitis of 2.5 ± 1.5 times/year in non‐DPRS group was significantly greater than 1.4 ± 1.6 times/year in DPRS group (P = .01). The re‐exploration and total complication rates were 5.4% and 7.1% in DPRS group, and 27.8% and 33.3% in non‐DPRS group, respectively (P = .02 and .02, respectively).ConclusionsThe DPRS technique is a safe, simple, and reliable method for insetting the submental VLNT, which statistically decreased the re‐exploration and total complication rates.
A high‐throughput screening method for determination of multi‐antibiotics in animal feed
Authors: Qian Mingrong , Zhang Xiaoming , Zhao Huiyu , Ji Xiaofeng , Li Xiaodan , Wang Jianmei , Wu Huizhen , Xu Jie , Li Zuguang 
Published: July 2019

AbstractA high‐throughput method based on ultrasonic‐assisted extraction, 96‐well plate thin‐film microextraction was established to determinate 18 antibiotics in animal feed. In this method, the extraction was implemented by ultrasonic‐assisted extraction for 30 min with disodium ethylenediaminetetraacetic acid‐McIlvaine buffer (pH 5) containing 6% sodium chloride w/v, purified by thin‐film microextraction and combined with 96‐well plate system to improve the efficiency. Optimization of thin‐film microextraction conditions was performed by methods of single factor and response surface, and finalized as: condition time: 20 min; adsorption time: 55 min; washing time: 5 s with water; desorption time: 30 min with acetonitrile/water (8:2, v/v) containing 0.1% formic acid v/v. Evaluation of different extractive phases showed that polystyrene‐divinylbenzene‐polyacrylonitrile was the optimum coating. The analysis was performed by ultra‐high performance liquid chromatography with tandem mass spectrometry. Recovery, inter‐ and intraday precision, linearity, limit of detection, and quantitation were evaluated. The average recoveries of 18 antibiotics were 66.6–93.5% at three spiked levels, intraday precision was 1–8.4%, and interday precision was 3.0–16.4%. The linearity was good for r2 > 0.99. Limits of detection and quantification were found in the range of 1–14 and 4–48 µg/kg, respectively.
Adaptation and sustainability of water management for rice agriculture in temperate regions: The Italian case‐study
Authors: Zampieri Matteo , Ceglar Andrej , Manfron Giacinto , Toreti Andrea , Duveiller Gregory , Romani Marco , Rocca Cesare , Scoccimarro Enrico , Podrascanin Zorita , Djurdjevic Vladimir 
Published: July 2019

AbstractWe review, analyse, and discuss the recent evolution and the future sustainability of rice paddy fields in Italy—the largest European producer—using outcomes from available literature and new analysis of agricultural statistics from local authorities, land‐use and surface temperature data from remote sensing, hydrological and climate data from observations, and numerical models. We show that Italy can be considered a good representative for rice cultivation in temperate regions that are not freshwater‐limited. However, this situation is changing. We report strong evidence linking the largest European reduction of seasonal surface water that have gradually occurred since 2000 over the rice cultivation area of Northern Italy, to the change in paddy management from traditional continuous flooding to a less greenhouse‐gases‐emitting practice, that is, dry‐seeding with postponed flooding. This change was accompanied by several improvements in agro‐practices and crop varieties. Concurrently, regional climate rapidly shifted towards sunnier weather conditions that partly contributed to higher rice yields and stability, decoupling yields from inter‐annual climate variability, but also reducing water availability. In Northern Italy, a complete shift of rice cultivation towards dry‐seeding is not compatible with seasonal water availability, and a number of drawbacks, with respect to the traditional wet seeding, are also identified from literature review. Therefore, in the context of near‐term climate change, sustainable rice cultivation in the middle latitudes seems achievable (without limiting production and/or increasing volatility) by balancing traditional and dry‐seeding.
Reproducibility crisis, the scientific method, and the quality of published studies: Untangling the knot
Authors: França Thiago F. A. , Monserrat José Maria 
Published: July 2019

Key points
Although there is no unique scientific method, there are general requirements that reports of empirical evidence must fulfil in order to be useful.
Enforcing general requirements can improve the quality of published studies without promoting a narrowly defined scientific method that would limit the scope of science.
The reproducibility movement advises against using novelty as the main requirement for publication and promotes the enforcement of transparent reporting and rigorous peer review.
Novelty is important for science but must not be the sole requirement for publication decisions as this can lead to publication bias and seriously distort the scientific literature.
While the scientific community remains responsible for thoroughly evaluating published papers, strengthening the peer review process will help to improve transparency and replicability.
Suppression of Lysophosphatidylcholine‐Induced Human Aortic Smooth Muscle Cell Calcification by Protein Kinase A Inhibition
Authors: Toita Riki , Asai Daisuke , Otani Kentaro , Kawano Takahito , Murata Masaharu , Kang Jeong‐Hun 
Published: July 2019

AbstractLysophosphatidylcholine (lysoPtdCho) is produced mainly by the phospholipase A2‐dependent hydrolysis of phosphatidylcholine (PtdCho) and can induce inflammatory activation and osteogenic gene expression in vascular smooth muscle cells. However, the mechanisms mediating these processes have not been fully elucidated. In this study, we investigated whether inhibition of protein kinase A (PKA) signaling suppressed lysoPtdCho‐induced calcification of human aortic smooth muscle cells (HASMC). Calcium levels and alkaline phosphatase activity were significantly increased in HASMC treated with lysoPtdCho, but not PtdCho, compared with those in phosphate‐buffered saline‐treated HASMC. However, the addition of a PKA inhibitor (H‐89) or PKA siRNA blocked lysoPtdCho‐induced HASMC calcification. These results showed that lysoPtdCho could activate PKA‐mediated HASMC calcification and that PKA may be a therapeutic target for lysoPtdCho‐mediated vascular smooth muscle cell calcification.
Correcting citizen‐science air temperature measurements across the Netherlands for short wave radiation bias
Authors: Cornes Richard C. , Dirksen Marieke , Sluiter Raymond 
Published: July 2019

AbstractCitizen‐science thermometer measurements have the potential to provide information about surface air temperature fields on scales smaller than is typically quantified by the official monitoring network. As such, national meteorological services are becoming increasingly interested in these measurements as a possible source of data for use in weather monitoring or forecasting. However, in order for the information to be used, biases in the data need to be assessed. The most important source of bias is the potential overheating of the thermometer due to inadequate shielding or exposure. Previous research has indicated that information about the nature of the instrument and its exposure is important for correcting this bias. However, in the majority of cases this information is unavailable for amateur stations. In this paper a statistical correction for short wave radiation bias is developed for the air temperature data recorded at 159 Weather Observations Website (WOW) stations across the Netherlands during the period 2015–2016. Generalized additive mixed modelling (GAMM) is used to quantify and correct for short wave radiation bias in the hourly measurements using a background temperature field generated from the official 34 automatic weather stations along with satellite‐derived short wave radiation estimates. It is demonstrated that the corrected WOW data add local detail to the hourly temperature field, which may provide a useful source of data to supplement official measurements.
Nonrigid registration for tracking incompressible soft tissues with sliding motion
Authors: Ai Danni , Liu Dingkun , Wang Yifan , Fu Tianyu , Huang Yong , Jiang Yurong , Song Hong , Wang Yongtian , Liang Ping , Yang Jian 
Published: July 2019

PurposeRespiration causes the deformation and sliding motion of the soft tissues, and affects the accuracy of the assessment of minimally invasive abdominal surgery. Nonrigid registration is used to eliminate the effects of respiration for the assessment. Because the soft tissues with high water content are volume preserving during deformation, incompressibility has to be considered when tracking soft tissues for nonrigid registration. The purpose of the study was to develop an incompressible nonrigid registration for tracking deformable soft tissues with sliding motion.MethodsThe nonrigid registration framework proposed in the present study includes two main steps: (a) The solution in the subspace of diffeomorphisms is searched and encoded to stationary velocity field in the log domain. (b) The divergence‐free component and harmonic remainder are extracted by Fourier‐based Helmholtz‐Hodge decomposition (FHHD) and further integrated by an adaptive weight to simultaneously retain the incompressibility of deformation and compensate the sliding motion. The method was evaluated on 11 groups of synthetic datasets and five groups of clinical images. Registration accuracy is evaluated by using four quantitative measures, including mean surface distance (MSD), Hausdorff distance (HD), mean corresponding distance (MCD), and Dice similarity coefficient (DSC). Incompressibility is evaluated by using two quantitative measures, including relative volume change (RVC) and Jacobian determinant (J).ResultsCompared with three state‐of‐the‐art nonrigid registration methods, the proposed method shows an advantage in handling the incompressible deformation of images with large sliding motion. The lowest (MSD, 0.631 mm), (HD, 6.000 mm), and (MCD, 3.555 mm) and the highest (DSC, 0.970) are obtained proving the high registration accuracy with sliding motion compensation of the proposed method. The (RVC, 0.006) and Jacobian determinant (J, 1.008 ± 0.070) are nearly close to 0 and 1, respectively, showing the strong incompressibility of the proposed method. The proposed method improves registration accuracy in nearly all cases, which maintains the incompressibility of tissue transformation while simultaneously compensating the sliding motion on clinical datasets.ConclusionsThe proposed method improves the registration accuracy of incompressible tissues when dealing with large sliding motion, and thus has the potential to improve current minimally invasive abdominal surgery.