bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduced-Order Modeling in a General Reservoir Simulation Setting
Authors: Tang Haoyu , Volkov Oleg , Tchelepi Hamdi A. , Durlofsky Louis J. 
Published: November 2020

Abstract
Reduced-order modeling can lead to computational savings in reservoir management applications when many related models must be simulated, as is the case, for example, in production optimization. In this study, we implement two reduced-order modeling procedures into our in-house simulator AD-GPRS (Automatic Differentiation General Purpose Research Simulator). The methods considered are a POD-Only (proper orthogonal decomposition) technique and a Gauss-Newton with approximated tensors (GNAT) procedure. Both approaches entail offline (training runs plus preprocessing) and online (runtime) computations. Typically, around 3-5 training runs are performed with these methods. POD-Only involves expensive online matrix multiplications, which greatly limit the attainable speedup. GNAT, by contrast, entails much less costly runtime computations. The methods are applied to a 2D oil-water model and to a 3D, four- component, oil-gas compositional case. These models contain 13,000 and 4800 grid blocks, respectively. Some amount of numerical experimentation is required to determine the appropriate POD-Only and GNAT parameters. We show that, using parameters that provide accurate reduced-order model results, POD-Only is actually slower than the full-order AD-GPRS simulations, but GNAT provides typical speedups of about a factor of 2-3 for the cases considered. More substantial speedup is achieved in some compositional cases for which AD-GPRS encounters numerical difficulties. Application of POD-Only and GNAT on locally refined versions of the original models is, however, found to require more computational effort than expected. This issue, which may be due to our detailed numerical treatments, should be addressed in future work.
Field-Scale Numerical Investigation of Proppant Transport among Multicluster Hydraulic Fractures
Authors: Mao Shaowen , Zhang Zhuo , Chun Troy , Wu Kan 
Published: November 2020

Summary
Plug-and-perforation (P-n-P) completion has been widely used in horizontal wells for the development of unconventional reservoirs. In the field, uneven proppant distribution among different fractures within a fracturing stage has been frequently observed in P-n-P treatments, leaving a large portion of reservoir volume understimulated. In this paper, an efficient 3D multiphase particle-in-cell (MP-PIC) method has been used to simulate proppant transport among multiple fractures (fracture near the heel, middle fracture, fracture near the toe) at the field scale. This work studies the fundamental physics of the proppant transport process and reveals the mechanisms of uneven proppant placement, giving strategies to improve the proppant placement.
Before applying the MP-PIC method to field-scale problems, we conducted indoor experiments to validate the model. The simulation results show an excellent agreement with the vertical slot experimental results. After model validation, we used the MP-PIC method to directly simulate the field process of proppant transport, involving slurry transport from the wellbore through perforation holes and finally into fractures. A base case with three fractures in a stage was first established to calculate the percentage of proppant mass distribution in each fracture. Then, we performed the sensitivity analysis of both proppant size and injection rate to investigate their effects on proppant placement.
The results reveal that all the cases tend to have a heel-biased proppant distribution among three fractures, which agrees with the field observations. There are two reasons for the heel-biased proppant distribution. First, at the very beginning of the injection, more proppants tend to flow toward the toe side because of large momentum. As more and more proppants move to the toe side, the concentration near the toe side gradually increases, which adds flow resistance to the newly injected proppants. Therefore, most newly injected proppants will go to the first fracture. The second reason comes from the fracture geometry. Because the first fracture has the largest fracture width among three fractures, it has the smallest flow resistance for proppant transport. More slurry will flow into the first fracture. Apart from giving explanations for the heel-biased distribution, we also suggest some strategies to improve the proppant distribution. The sensitivity analysis shows that the strong heel-biased proppant distribution can be mitigated by optimizing the proppant size and injection rate.
Our study for the first time conducts a field-scale numerical investigation of proppant transport in the wellbore-fracture system during P-n-P treatments. The results can provide us with more insights into the optimization of fracture design in field practice.
Dose-related biphasic effect of the Parkinson’s disease neurotoxin MPTP, on the spread, accumulation, and toxicity of α-synuclein
Authors: Haque M Emdadul , Merghani Madiha Mohieldin , Ardah Mustafa T. , Kitada Tohru 
Published: November 2020

Abstract
Background: 1-methyl, 4-phenyl, 1,2,3,6 tetrahydropyridine (MPTP), a mitochondrial neurotoxin, has been used previously to generate a PD mouse model. However, MPTP does not induce Lewy bodies or α-syn aggregation in mice. In the present study, we evaluated the effect of different doses of MPTP (10 mg/kg.b.wt and/or 25 mg/kg.b.wt) on the spread, accumulation, and toxicity of endogenous α-syn in mice administered an intrastriatal injection of human α-syn PFFMethods: We inoculated human WT α-syn PFF in mouse striatum. At 6 weeks post PFF injection, we challenged the animal with two different doses of MPTP (10 mg/kg.b.wt and 25 mg/kg.b.wt) once daily for five consecutive days. At 2 weeks from the start of the MPTP regimen, we collected the mice brain and performed immunohistochemical analysis, and Rotarod test to assess motor coordination and muscle strength before and after MPTP injection.Results: A single injection of human WT α-syn PFF in the mice striatum induced the propagation of α-syn, occurring as phosphorylated α-synuclein (pS129), towards the SNpc, within a very short time. Injection of a low dose of MPTP (10 mg/kg.b.wt) at 6 weeks post α-syn PFF inoculation further enhanced the spread, whereas a high dose of MPTP (25 mg/kg.b.wt.) reduced the spread. Majority of the accumulated α-syn were proteinase K resistant, as recognized using a conformation-specific α-syn antibody. Injection of α-syn PFF alone caused 12% DA neuronal loss while α-syn PFF + a low dose of MPTP caused 33% loss, compared to the control mice injected with saline. Interestingly, a low dose of MPTP alone did not cause any significant DA cell death compared to saline treatment. Animals that received α-syn PFF and a high dose of MPTP showed massive activation of glial cells and decreased spread of α-syn, majority of which were detected in the nucleus. Conclusion: Our results suggest that a combination of human WT α-syn PFF and a low dose of MPTP increases the pathological conversion and propagation of endogenous α-syn, and neurodegeneration, within a very short time. Our model can be used to study the mechanisms of α-syn propagation and screen for potential drugs against PD.
Human Injury causing Road Traffic Accident at Debre Markos Town
Authors: Tilaye Wubetie Habtamu 
Published: November 2020

Abstract
Objective: A Road traffic accident (RTA) is when in a road Vehicle collides with another Vehicle, pedestrian, animal or geographical or architectural obstacle. The RTAs can result in human injury, property damage and death. RTA result in the deaths of 1.2 million people worldwide each year and injuries about 4 times this number. The objective of this study is to identify the main causing-factors that contribute to road traffic accidents involving human injuries. Literature suggested factors considered for analysis are: Driver's Age, Driver’s Education status, Driver's experience, Vehicle type, Driver Vehicle Ownership, Vehicle year of service, Road type, Road division, Road condition, Problem with car, Weather condition, and accident time (day or night). Results: Among the candidate variables, Pearson Chi-Square method identified weather condition, driver’s experience, Vehicle year of service; Road division, Driver Vehicle Ownership, and accident time (day or night ) as significantly associated variables. Furthermore, percentage is used to describe the magnitude of associated variable. The result from Poisson regression analyses revealed that low driver experience, high Vehicle year of service (old cars), and Road division (one way road) are the significant contributing factors for increment of human injuries accidents.
Performance of Xpert® MTB/RIF in diagnosing tuberculous pleuritis using thoracoscopic pleural biopsy
Authors: Li Chengjun , Liu Chang , Sun Bingqi , Zhang Wei , Wang Yang , Sun Jiao , Ma Fang , Chen Yu 
Published: November 2020

Abstract
Background: Etiological diagnosis of tuberculous pleuritis is challenging, owing to a paucity of Mycobacterium tuberculosis (MTB) in the affected region. Moreover, currently available methods, such as the detection of acid-fast bacilli and microbiological culture, are not always conducive to timely diagnosis and treatment. In this study, we evaluated the performance of Xpert® MTB/RIF assay (hereinafter referred to as “Xpert”) in detecting MTB in difficult-to-diagnose patients using suspensions of pleural biopsy tissue specimens obtained under direct thoracoscopic guidance.Methods: One hundred and sixty patients with an unexplained pleural effusion were included from the Shenyang Tenth People’s Hospital and Shenyang Chest Hospital, China, between 2017 and 2018. The included patients underwent thoracoscopy under local anesthesia, with an intercostal incision of approximately 1.0 cm for biopsy. The biopsy specimens were used for pathological and etiological examinations. The Xpert test was evaluated for its sensitivity and specificity, as well as positive and negative predictive values (PPV and NPV, respectively), against data obtained using standards: the BACTEC™ MGIT™ 960 liquid culture system and a composite reference standard (CRS).Results: The sensitivity and specificity of Xpert were 68.8% and 64.6%, respectively, against the MGIT 960 culture data. The PPV and NPV of Xpert were 56.4% and 75.6%, respectively. The sensitivity of Xpert was 69.0% against the CRS data, which was significantly higher than that of MGIT 960 culture (56.6%). The PPV and NPV of Xpert against the CRS data were 100.0% and 57.3%, respectively.Conclusions: Xpert is a good rule-in test but has limited value as a rule-out test for the diagnosis of tuberculosis pleuritis.
QTL Mapping of Agronomic and Economic Traits for Four F2 Populations in Upland Cotton
Authors: Li Hongge , Pan Zhaoe , He Shoupu , Jia Yinhua , Geng Xiaoli , Chen Baojun , Wang Liru , Pang Baoyin , Du Xiongming 
Published: November 2020

Abstract
Background: Upland cotton (Gossypium hirsutum) accounts for more than 90% of annual world cotton output due to its high yield potential. However, yield traits and fiber quality traits exhibit negative correlations in most cases. Here, we constructed four F2 populations, using two normal lines and two introgression lines, for simultaneously detection the genetic basis underlying complex traits such as yield and fiber quality in upland cotton. Subsequently, the phenotyping of 8 agronomic and economic traits along with quantitative trait loci (QTL) mapping was implemented. Results: Extensive phenotype variations and transgressive segregation were found across segregation populations. Four genetic maps were constructed with the length of 585.97cM, 752.45cM, 752.45cM and 1 163.66cM. A total of 50 QTLs were identified across four populations (7 for plant height, 27 for fiber quality traits and 16 for yield traits). The same QTLs were identified from different populations such as qBW4 and qBW2 which were linked to common markers. A QTL cluster was characterized in D09 of population 4Su which contained 8 QTLs for 6 different traits. Conclusions: These findings will provide insight into the genetic basis of simultaneous improvement of yield and fiber quality in upland cotton breeding.
Evaluating the Impact of Social Deprivation on Press Ganey® Outpatient Medical Practice Survey Scores
Authors: Stephens Andrew R , Potter Jared W , Tyser Andrew R , Kazmers Nikolas H 
Published: November 2020

Abstract
Background: Social deprivation has been shown to affect access to health care services, and influences outcomes for a variety of physical and psychological conditions. However, the impact on patient satisfaction remains less clear. The objective of this study was to determine if social deprivation is an independent predictor of patient satisfaction, as measured by the Press Ganey® Outpatient Medical Practice Survey (PGOMPS). Methods: We retrospectively reviewed unique new adult patient (≥18 years of age) seen at a tertiary academic hospital and rural/urban outreach hospitals/clinics between January 2014 and December 2017. Satisfaction was defined a priori as achieving a score above the 33rd percentile. The 2015 Area Deprivation Index (ADI) was used to determine social deprivation (lower score signifies less social deprivation). Univariate and multivariable binary logistic regression were used to determine the impact of ADI on PGOMPS total and provider sub-scores while controlling for variables previously shown to impact scores (wait time, patient age, sex, race, specialty type, provider type, and insurance status).Results: Univariate analysis of PGOMPS total scores revealed a 4% decrease in odds of patient satisfaction per decile increase in ADI (p < 0.001). Patients within the most deprived quartile were significantly less likely to report satisfaction compared to the least deprived quartile (OR 0.79, p < 0.001). Multivariable analysis revealed that the odds of achieving satisfaction decreased 2% for each decile increase in ADI on the Total Score (p < 0.001), independent of other variables previously shown to impact scores. For PGOMPS Provider Sub-Score, univariate analysis showed that patients in the lowest ADI quartile were significantly less likely be satisfied, as compared to the least deprived quartile (OR 0.77; 95% CI 0.70 to 0.86; p < 0.001). A 5% decrease in a patient being satisfied was observed for each decile increase in ADI (OR 0.95; 95% CI 0.94 to 0.96; p < 0.001). Conclusions: Social deprivation was an independent predictor of outpatient visit dissatisfaction, as measured by the Press Ganey® Outpatient Medical Practice Survey. These results necessitate consideration when developing health care delivery policies that serve to minimize inequalities between patients of differing socioeconomic groups.
Sharing genomic data from clinical testing with researchers: public survey of expectations of clinical genomic data management in Queensland, Australia.
Authors: Vidgen Miranda Emily , Kaladharan Sid , Malacova Eva , Hurst Cameron , Waddell Nicola 
Published: November 2020

Abstract
Background: There has been considerable investment and strategic planning to introduce genomic testing into Australia’s public health system. As more patients’ genomic data is being held by the public health system, there will be increased requests from researchers to access this data. It is important that public policy reflects public expectations for how genomic data that is generated from clinical tests is used. To inform public policy and discussions around genomic data sharing, we sought public opinions on using genomic data contained in medical records for research purposes in the Australian state of Queensland.Methods: A total of 1,494 participants completed an online questionnaire between February and May 2019. Participants were adults living in Australia. The questionnaire explored participant preferences for sharing genomic data or biological samples with researchers, and concerns about genomic data sharing.Results: Most participants wanted to be given the choice to have their genomic data from medical records used in research. Their expectations on whether and how often they needed to be approached for permission on using their genomic data, depended on whether the data was identifiable or anonymous. Their willingness to sharing data for research purposes depended on the type of information being shared, what type of research would be undertaken and who would be doing the research. Participants were most concerned with genomics data sharing that could lead to discrimination (insurance and employment), data being used for marketing, data security, or commercial use.Conclusions: Most participants were willing to share their genomic data from medical records with researchers, as long as permission for use was sought. However, the existing policies related to this process in Queensland do not reflect participant expectations for how this is achieved, particularly with anonymous genomics data. This inconsistency may be addressed by process changes, such as inclusion of research in addition to clinical consent or general research data consent programs.
Identification, Evolution, Expression, and Docking Studies of Fatty Acid Desaturase Genes in Wheat (Triticum aestivum L.)
Authors: Hajiahmadi Zahra , Abedi Amin , Wei Hui , Sun Weibo , Ruan Honghua , Zhuge Qiang , Movahedi Ali 
Published: November 2020

Abstract
Backgrounds: Fatty acid desaturases (FADs) introduce a double bond into the fatty acids acyl chain resulting in unsaturated fatty acids that have essential roles in plant development and response to biotic and abiotic stresses. Wheat germ oil, one of the important by-products of wheat, can be a good alternative for edible oils with clinical advantages due to the high amount of unsaturated fatty acids. Therefore, we performed a genome-wide analysis of the wheat FAD gene family (TaFADs).Results: 68 FAD genes were identified from the wheat genome. Based on the phylogenetic analysis, wheat FADs clustered into five subfamilies, including FAB2, FAD2/FAD6, FAD4, DES/SLD, and FAD3/FAD7/FAD8. The TaFADs were distributed on chromosomes 2A-7B with 0 to 10 introns. The Ka/Ks ratio was less than one for most of the duplicated pair genes revealed that the function of the genes had been maintained during the evolution. Several cis-acting elements related to hormones and stresses in the TaFADs promoters indicated the role of these genes in plant development and responses to environmental stresses. Likewise, 72 SSRs and 91 miRNAs in 36 and 47 TaFADs have been identified. According to RNA-seq data analysis, the highest expression in all developmental stages and tissues was related to TaFAB2.5, TaFAB2.12, TaFAB2.15, TaFAB2.17, TaFAB2.20, TaFAD2.1, TaFAD2.6, and TaFAD2.8 genes while the highest expression in response to temperature stress was related to TaFAD2.6, TaFAD2.8, TaFAB2.15, TaFAB2.17, and TaFAB2.20. Furthermore, docking simulations revealed several residues in the active site of TaFAD2.6 and TaFAD2.8 in close contact with the docked oleic acid that could be useful in future site-directed mutagenesis studies to increase the catalytic efficiency of them and subsequently improve agronomic quality and tolerance of wheat against environmental stresses. Conclusions: This study provides comprehensive information that can lead to the detection of candidate genes for wheat genetic modification.
Per-Fraction Positional and Dosimetric Performance of Prone Breast Tangential Radiotherapy on Halcyon™ Linear Accelerator Assessed with Daily Rapid Kilo-voltage Cone Beam Computed Tomography: A Single-Institution Pilot Study
Authors: Yoon Suk Whan , Taunk Neil K , Freedman Gary M , Hubley Emily , O'Reilly Shannon , Teo Boon-Keng K , Anamalayil Shibu , Dong Lei , Kennedy Christopher , Zou Wei , Metz James M , Li Taoran 
Published: November 2020

Abstract
Background: This study investigates daily breast geometry and delivered dose to prone-positioned patients undergoing tangential whole breast radiation therapy (WBRT) on an O-ring linear accelerator with 6X flattening filter free mode (6X-FFF), planned with electronic compensation (ECOMP) method. Most practices rely on skin marks or daily planar image matching for prone breast WBRT. This system provides low dose daily CBCT, which was used to study daily robustness of delivered dose parameters for prone-positioned WBRT.Methods: Eight patients treated with 16-fraction prone-breast WBRT were retrospectively studied. Planning CTs were deformed to daily CBCT to generate daily synthetic CTs, on which delivered dose distributions were calculated. A total of 8x16=128 synthetic CTs were generated. Consensus ASTRO definition was used to contour Breast PTV Eval for each daily deformed CT. Breast PTV Eval coverage (V90%) and hotspot (V105% and Dmax) were monitored daily to compare prescription dose with daily delivered dose. Various predictors including patient weight, breast width diameter (BWD), and Dice similarity coefficient (DSC) were fit into an analysis of covariance model predicting V90% and V105% deviation from prescribed (ΔV90%, ΔV105%). Statistical significance is indicated with asterisks (* for p<0.05; ** for p<0.001).Results: Daily delivered Breast PTV Eval V90% was moderately smaller than prescribed (median ΔV90%=-0.1%*), while V105% was much larger (median ΔV105%=+10.1%** or +92.4cc**). Patient’s weight loss correlated with significantly increased ΔV105% (+4.6% / -1% weight., R2=0.4**) and moderately decreased ΔV90% (-0.071%/-1% wt., R2=0.2**). Comprehensive ANCOVA models indicated three factors affect ΔV90% and ΔV105% the most: (1) BWD decrease (-0.09%* and +10%**/-1cm respectively), (2) PTV Eval volume decrease (-0.4%** and +9%**/-100cc), and for ΔV105% only, (3) the extent of breast deformation (+10%**/-0.01 DSC). Breast PTV Eval volume also decreased with time (-2.21*cc/fx), possibly indicating seroma resolution and increase in V105% over time.Conclusions: Daily CBCT revealed key delivered dose parameters vary significantly for patients undergoing tangential prone breast WBRT planned with ECOMP using 6X-FFF. Patient weight, BWD, and breast shape deformation could be used to predict dosimetric variations from prescribed. Preliminary findings suggest an adaptive plan based on daily CBCT could reduce excessive dose to the breast.