bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Integrated Simulation Approach To Predict Permeability Impairment under Simultaneous Aggregation and Deposition of Asphaltene Particles
Authors: Su Xin , Moghanloo Rouzbeh G. , Qi Minhui , Yue Xiang-an 
Published: February 2021

Summary
Formation damage mechanisms in general lower the quality of the near wellbore, often manifested in the form of permeability reduction, and thus reducing the productivity of production wells and injectivity of injection wells. Asphaltene deposition, as one of the important causes, can trigger serious formation damage issues and significantly restrict the production capacity of oil wells. Several mechanisms acting simultaneously contribute to the complexity associated with prediction of permeability impairment owing to asphaltene deposition; thus, integration of modeling efforts for asphaltene aggregation and deposition mechanisms seems inevitable for improved predictability.
In this work, an integrated simulation approach is proposed to predict permeability impairment in porous medium. The proposed approach is novel because it integrates various mathematical models to study permeability impairment considering porosity reduction, particle aggregation, and pore connectivity loss caused by asphaltene deposition.
To improve the accuracy of simulation results, porous media is considered as a bundle (different size) of capillary tubes with dynamic interconnectivity. The total volume change of interconnected tubes will directly represent permeability reduction realized in porous media. The prediction of asphaltene deposition in porous media is improved in this paper via integration of the particle aggregation model into calculation.
The simulation results were verified by comparing with existing experimental data sets. After that, a sensitivity analysis was performed to study parameters that affect permeability impairment. The simulation results show that our permeability impairment model—considering asphaltene deposition, aggregation, and pore connectivity loss—can accurately reproduce the experimental results with fewer fitting or empirical parameters needed. The sensitivity analysis shows that longer aggregation time, higher flow velocity, and bigger precipitation concentration will lead to a faster permeability reduction.
The findings of this study can help provide better understanding of the permeability impairment caused by asphaltene deposition and pore blockage, which provides useful insights for prediction of production performance of oil wells.
The Global Adaptation Mapping Initiative (GAMI): Part 2 – Screening protocol
Authors: Fischer A. Paige , Callaghan Max , Berrang-Ford Lea , Nielsen Miriam , Sotnik Garry , Canosa Ivan Villaverde , Haddaway Neal , Biesbroek Robbert , Harper Sherilee , Minx Jan , Perez Erin Coughlan de , Reckien Diana , Aalst Maarten Van 
Published: February 2021

Abstract
Context: It is now widely accepted that the climate is changing, and that societal response will need to be rapid and comprehensive to prevent the most severe impacts. A key milestone in global climate governance is to assess progress on adaptation. To-date, however, there has been negligible robust, systematic synthesis of progress on adaptation or adaptation-relevant responses globally. Aim: The purpose of this review protocol is to outline the methods used by the Global Adaptation Mapping Initiative (GAMI) to systematically review human adaptation responses to climate-related changes that have been documented globally since 2013 in the scientific literature. The broad question underpinning this review is: Are we adapting to climate change? More specifically, we ask ‘what is the evidence relating to human adaptation-related responses that can (or are) directly reducing risk, exposure, and/or vulnerability to climate change?’ Methods: We review scientific literature 2013-2019 to identify documents empirically reporting on observed adaptation-related responses to climate change in human systems that can directly reduce risk. We exclude non-empirical (theoretical & conceptual) literature and adaptation in natural systems that occurs without human intervention. Included documents were coded across a set of questions focused on: Who is responding? What responses are documented? What is the extent of the adaptation-related response? What is the evidence that adaptation-related responses reduce risk, exposure and/or vulnerability? Once articles are coded, we conduct a quality appraisal of the coding and develop ‘evidence packages’ for regions and sectors. We supplement this systematic mapping with an expert elicitation exercise, undertaken to assess bias and validity of insights from included/coded literature vis a vis perceptions of real-world adaptation for global regions and sectors, with associated confidence assessments. Related protocols: This protocol represents Part 2 of a 5-part series outlining the phases of methods for this initiative. Part 2 outlines the methods used to conduct keyword searches and implement machine-assisted screening of documents based on inclusion and exclusion criteria. See Figures 1 and 2.
Estimating the tolerance of Brachial Plexus to hypofractionated Stereotactic Body Radiotherapy – A modelling-based approach from clinical experience.
Authors: Kapitanova Irina , Biswas Sharmi , Divekar Sabrina , Kemmerer Eric J , Rostock Robert A , Forster Kenneth M , Grimm Rachel J , Scofield Carla J , Grimm Jimm , Emami Bahman , Mahadevan Anand 
Published: February 2021

Abstract
Background: Brachial plexopathy (BP) is a potentially serious complication from stereotactic body radiation therapy (SBRT) that has not been widely studied. Therefore, we compared datasets from two different institutions and generated a brachial plexus dose-response model, to quantify what dose constraints would be needed to minimize the effect on normal tissue while still enabling potent therapy for the tumor.Methods: Two published SBRT datasets were pooled and modeled from patients at Indiana University and the Richard L. Roudebush Veterans Administration Medical Center from 1998 to 2007, as well as the Karolinska Institute from 2008 to 2013. All patients in both studies were treated with SBRT for apically located lung tumors localized superior to the aortic arch. Toxicities were graded according to Common Terminology Criteria for Adverse Events (CTCAE) and a probit dose response model was created with maximum likelihood parameter fitting.Results: This analysis includes a total of 89 brachial plexus Dmax values from both institutions. Among the 14 patients who developed BP, the most common complications were grade 2, comprising 7 patients. The median follow-up was 30 months (range 6.1-72.2) in the Karolinska dataset, and Indiana had a median of 13 months (range 1-71). Both studies had a median range of 3 fractions, but in the Indiana dataset 9 patients were treated in 4 fractions and the paper did not differentiate which ones were which, so our analysis is considered to be in 3-4 fractions, which is one of the main limitations. The probit model showed that the risk of BP with Dmax of 26 Gy in 3-4 fractions is 10%, and 50% with Dmax of 70 Gy in 3 -4 fractions.Conclusions: This analysis is only a preliminary result because more details are needed, and more comprehensive datasets are needed from a much broader cross-section of clinical practices. When more institutions join the QUANTEC and HyTEC methodology of reporting sufficient details to enable data pooling, our field will finally reach an improved understanding of human dose tolerance.
Medium-chain fatty acids accelerate the incorporation of eicosapentaenoic acid into lung tissue
Authors: Beermann Christopher , Fussbroich Daniela , Schubert Ralf 
Published: February 2021

Abstract
Long-chain polyunsaturated fatty acids (LCPUFAs) are reported to resolve chronic inflammation in asthma and other lung diseases. This study aimed to accelerate the incorporation of eicosapentaenoic acid (EPA) into lung tissue through the coapplication of medium-chain fatty acids (MCFAs) which enhance the fat-metabolic rate. Female C57BL/6 mice were supplemented with either 1363,6 mg EPA or 1363,6 mg EPA and MCFAs at 30% of the total fat per kg body weight per day for 28 days (each group size: n=21). The resorption of EPA into the peripheral blood and lung tissue was monitored over 63 days including the wash-out phase. In the peripheral blood plasma and clots the supplementation with EPA always led to higher EPA concentrations than the administration of EPA with MCFAs pointing to a preferred EPA incorporation into tissues induced by MCFAs (EPA in plasma at day 26: EPA 12.33 wt% ± 1.41; EPA and MCFAs 3.91 wt% ± 0.32; Δ 8.42; p< 0.001; EPA in clots at day 26: EPA 16.44 wt% ± 1.82; EPA and MCFAs 4.47 wt% ± 1.26; Δ 11.97; p< 0.001). In the lung tissue the EPA-incorporation at day 26 was increased by MCFAs compared to the EPA-administration alone (EPA in lung tissue at day 26: EPA 1.28 wt% ± 0.18; EPA and MCFAs 1.83 wt% ± 0.17; Δ 0.55; p< 0.01). The present study recommends the use of dietary LCPUFA supplementation with MCFAs to support their incorporation into lung tissues.
Glucagon-like peptide-2 receptor is a receptor for tick-borne encephalitis virus to infect nerve cells
Authors: Chen Xinwen , Yang Qi , Chen Jizheng , Pei Rongjuan , Wang Yun , Yang Min , Tang Jielin , Zhou Yuan , Zhao He , Chen Jiekai , He Jun , Xiong Xiaoli , Shi Pei-Yong 
Published: February 2021

Abstract
Tick-borne encephalitis virus (TBEV) is a tick-borne flavivirus that causes severe encephalitis disease1,2. Host proteins required for TBEV entry remain largely unknown3. Here we performed a genome-wide CRISPR-Cas9 knockout screen and identified G-protein-coupled receptor glucagon-like peptide-2 receptor (GLP2R) as a receptor for TBEV to infect nerve cells. Knockdown or knockout of GLP2R reduced TBEV infection of different nerve cells; trans supply of GLP2R restored viral infection. GLP2R directly binds to viral envelope domain III through its extracellular loop 1 (ECL1). TBEV infection can be blocked by the ECL1 peptide, a functional ligand to GLP2R, or GLP2R antibodies. GLP2R-deficient mice were generated to validate the role of GLP2R in TBEV infection and pathogenesis. Wild-type mice succumbed to TBEV infection and developed >107 TCID50 (median tissue culture infectious dose) virus per gram of brain tissue. In contrast, all GLP2R-deficient mice survived TBEV infection without detectable infectious virus in brain. Altogether, our results support GLP2R as a receptor for TBEV to infect nerve cells.
Airway Pseudomonas aeruginosa Density in Mechanically Ventilated Patients: Clinical Impact and Relation to Therapeutic Efficacy of Antibiotics
Authors: Migiyama Yohei , Sakata Shinya , Iyama Shinji , Tokunaga Kentaro , Saruwatari Koichi , Tomita Yusuke , Saeki Sho , Okamoto Shinichiro , Ichiyasu Hidenori , Sakagami Takuro 
Published: February 2021

Abstract
Background: The bacterial density of Pseudomonas aeruginosa is closely related to its pathogenicity. We evaluated the effect of airway P. aeruginosa density on the clinical course of mechanically ventilated patients and the therapeutic efficacy of antibiotics.Methods: We retrospectively analyzed data of mechanically ventilated ICU patients with P. aeruginosa isolated from endotracheal aspirates. Patients were divided into three groups according to the peak P. aeruginosa density during ICU stay: low (≤104 cfu/mL), moderate (105‒106 cfu/mL), and high (≥107 cfu/mL) peak density groups. The relationship between peak P. aeruginosa density and weaning from mechanical ventilation, risk factors for isolation of high peak density of P. aeruginosa, and antibiotic efficacy were investigated using multivariate and propensity score-matched analyses.Results: Four-hundred-and-sixty-one patients were enrolled. Patients with high peak density of P. aeruginosa had higher inflammation and developed more severe respiratory infections. High peak density of P. aeruginosa was independently associated with few ventilator-free days on day 28 (P < 0.01) and increased ICU mortality (P = 0.047). Risk factors for high peak density of P. aeruginosa were prolonged mechanical ventilation (odd ratio [OR] 3.07 95% confidence interval [CI] 1.35‒6.97), non-antipseudomonal cephalosporins (OR 2.17, 95% CI 1.35‒3.49), hyperglycemia (OR 2.01, 95% CI 1.26‒3.22) during ICU stay, and respiratory diseases (OR 1.9, 95% CI 1.12‒3.23). Isolation of commensal colonizer was associated with lower risks of high peak density of P. aeruginosa (OR 0.43, 95% CI 0.26‒0.73). Propensity score-matched analysis revealed that antibiotic therapy for patients with ventilator-associated tracheobronchitis improved weaning from mechanical ventilation only in the high peak P. aeruginosa group.Conclusions: Patients with high peak density of P. aeruginosa had worse ventilator outcome and ICU mortality. In patients with ventilator-associated tracheobronchitis, antibiotic therapy was associated with favorable ventilator weaning only in the high peak P. aeruginosa density group, and bacterial density could be a good therapeutic indicator for ventilator-associated tracheobronchitis due to P. aeruginosa.
Impact of seasonality and malaria control interventions on Anopheles density and species composition from three areas of Uganda with differing malaria endemicity.
Authors: Mawejje Henry , Kilama Maxwell , Kigozi Simon P. , Musiime Alex K. , Kamya Moses , Lines Jo , Lindsay Steven W. , Smith David , Dorsey Grant , Donnelly Martin J. , Staedke Sarah G. 
Published: February 2021

Abstract
Background Long lasting insecticidal nets (LLINs) and indoor residual spraying (IRS) are malaria control interventions primarily responsible for reductions in transmission intensity across sub-Saharan Africa. These interventions, however, may have differential impact on Anopheles species composition and density. Here, we studied the changing pattern of Anopheles species in three areas of Uganda with markedly different transmission intensities and different levels of vector control. Methods From October 2011 to June 2016 mosquitoes were collected monthly using CDC light traps from 100 randomly selected households in three areas: Walukuba (low transmission), Kihihi (moderate transmission) and Nagongera (high transmission). LLINs were distributed in November 2013 in Walukuba and Nagongera and in June 2014 in Kihihi. IRS was implemented only in Nagongera, with three rounds of bendiocarb delivered between December 2014 and June 2015. Mosquito species were identified morphologically and by PCR (Polymerase Chain Reaction). Results In Walukuba, LLIN distribution was associated with a decline in Anopheles funestus vector density (0.07 vs 0.02 mosquitoes per house per night, density ratio [DR] 0.34, 95% CI: 0.18-0.65, p=0.001), but not An. gambiae s.s. nor An. arabiensis. In Kihihi, over 98% of mosquitoes were An. gambiae s.s. and LLIN distribution was associated with a decline in An. gambiae s.s. vector density (4.00 vs 2.46, DR 0.68, 95% CI: 0.49-0.94, p=0.02). In Nagongera, the combination of LLINs and multiple rounds of IRS was associated with almost complete elimination of An. gambiae s.s. (28.0 vs 0.17, DR 0.004, 95% CI: 0.002-0.009, p<0.001), and An. funestus s.l. (3.90 vs 0.006, DR 0.001, 95% CI: 0.0005-0.004, p<0.001), with a less pronounced decline in An. arabiensis (9.18 vs 2.00, DR 0.15 95% CI: 0.07-0.33, p<0.001). Conclusions LLIN distribution was associated with reductions in An. funestus s.l. in the lowest transmission site and An. gambiae s.s. in the moderate transmission site. In the highest transmission site, a combination of LLINs and multiple rounds of IRS was associated with the near collapse of An. gambiae s.s. and An. funestus s.l. Following IRS, An. arabiensis, a behaviorally resilient vector, became the predominant species, which may have implications for malaria vector control activities. Development of interventions targeted at outdoor biting remains a priority.
Performance of liver stiffness measurements obtained with FibroScan is affected by glucose metabolism in patients with nonalcoholic fatty liver disease
Authors: Yang Xinyu , Chang Xinxia , Wu Shengdi , Sun Xiaoyang , Zhu Xiaopeng , Wang Liu , Xu Yushan , Yao Xiuzhong , Rao Shengxiang , Hu Xiqi , Xia Mingfeng , Bian Hua , Yan Hong-Mei , Gao Xin 
Published: February 2021

Abstract
Background: The performance of liver stiffness measurements (LSMs) obtained using FibroScan can be affected by several factors, and cut-off values are different for fibrosis caused by various aetiologies. The study aims to evaluate the diagnostic accuracy of LSM in nonalcoholic fatty liver disease (NAFLD) patients with abnormal glucose metabolism and investigate whether the LSM value would be affected by metabolic indicators.Methods: The study involved 91 NAFLD patients with abnormal glucose metabolism who underwent liver biopsy. The diagnostic accuracy of LSM value was evaluated by the receiver operator characteristic (ROC) curves, with the biopsy results taken as the gold standard. Multivariate linear regression and subgroup analysis were performed to determine the correlated indicators.Results: The areas under the ROC curves (AUROCs) of LSM values for detecting fibrosis stage ≥1, 2, 3 and 4 were 0.793 (95% confidence interval [CI]: 0.695-0.871), 0.764 (95% CI: 0.663-0.846), 0.837 (95% CI: 0.744-0.906) and 0.902 (95% CI: 0.822-0.955), with cut-off values of 6.3, 7.6, 8.3 and 13.8 kPa, respectively. Multivariate linear regression demonstrated that haemoglobin A1c (HbA1c, β = 0.200, P = 0.038) and aspartate aminotransferase (AST, β = 0.200, P = 0.044) were independently associated with the LSM value after adjustment for fibrosis stage, ballooning and inflammation grade from liver biopsy. Subgroup analysis demonstrated that LSM values were slightly higher in patients with HbA1c ≥7% than in those with HbA1c <7% and in patients with body mass index (BMI) ≥30 kg/m2 than in those with BMI <30 kg/m2.Conclusions: FibroScan was valuable for the evaluation of liver fibrosis in NAFLD patients with abnormal glucose metabolism. FibroScan is recommended to evaluate severe fibrosis, especially to exclude advanced fibrosis. Glucose metabolism state may affect LSM values.
High expression of CDCA7 predicts poor prognosis for clear cell renal cell carcinoma and explores its associations with immunity
Authors: Liu Shouyong , Wang Yi , Miao Chenkui , Xing Qianwei , Wang Zengjun 
Published: February 2021

Abstract
Background: Cell division cycle-associated 7 (CDCA7), as a member of the cell division cycle associated family, was reported to be aberrantly expressed in both solid tumors and hematological tumors, suggesting its essential role in promoting tumorigenesis. Hence, we aimed to explore its comprehensive roles of overall survival (OS) in clear cell renal cell carcinoma (ccRCC) and emphasize its associations with immunity.Methods: The RNA sequencing data and corresponding clinical information were downloaded from The Cancer Genome Atlas (TCGA) database. Gene set enrichment analysis (GSEA) was adopted to explore CDCA7 associated signaling pathways. Univariate and multivariate Cox regression analyses were carried out to assess independent prognostic factors. Furthermore, roles of CDCA7 in human immunity were also investigated.Results: Our results suggested that CDCA7 was overexpressed in ccRCC and its elevated expression was related to shorter OS (P<0.01). Univariate and multivariate Cox regression analyses identified CDCA7 as an independent prognostic factor (both P<0.05). The prognostic nomogram integrating CDCA7 expression level and clinicopathologic variables was constructed to predict 1-, 3- and 5-year OS. GSEA indicated that high CDCA7 expression was related to the apoptosis pathway, cell cycle pathway, JAK-STAT pathway, NOD like receptor pathway, P53 pathway, T cell receptor pathway and toll like receptor pathway, etc. Moreover, CDCA7 was significantly related to microsatellite instability (MSI, P<0.001) and tumor mutational burden (TMB, P<0.001). As for immunity, CDCA7 was remarkably associated with immune infiltration, tumor microenvironment, immune checkpoint molecules and immune pathways.Conclusions: CDCA7 could serve as an independent prognostic factor for ccRCC and it was closely related to MSI, TMB, and immunity.
Extra Large Sequence Transformer Model for Chinese Word Segment
Authors: Shen Dezhou 
Published: February 2021

Abstract
Chinese word segment is widely studied in document analysis.
The accuracy of the current popular word segment model, LSTM+CRF, is still not satisfactory.
Models trained by the popular dataset often fails in the out-domain situation.
In this paper, combining the Transformer-XL layer, the Fully-Connect layer, and the Conditional Random Field layer, the proposed model improved 3.23% in the macro-F1 score, comparing to the BERT+CRF model, on the MSR2005 Chinese word segment test dataset.
Effect of adding hydrochlorothiazide to usual treatment of patients with acute decompensated heart failure: a randomized clinical trial
Authors: Piardi Diogo , Butzke Mauricio , Mazzuca Ana Carolina , Gomes Bruna , Alves Sofia , Kotzian Bruno , Ghisleni Eduarda , Giaretta Vanessa , Bellaver Priscila , Varaschin Gabrielle , Garbin Arthur , Beck-da-Silva Luís 
Published: February 2021

Abstract
Introduction:
Acute decompensated heart failure (ADHF) is the leading cause of hospitalization in patients aged 65 years or older, and most of them present with congestion. The use of hydrochlorothiazide (HCTZ) may increase the response to loop diuretics.
Objective
To evaluate the effect of adding HCTZ to furosemide on congestion and symptoms in patients with ADHF.
Methods
This randomized clinical trial compared HCTZ 50 mg versus placebo for 3 days in patients with ADHF and signs of congestion. The primary outcome of the study was daily weight reduction. Secondary outcomes were change in creatinine, need for vasoactive drugs, change in natriuretic peptides, congestion score, dyspnea, thirst, and length of stay.
Results
Fifty-one patients were randomized — 26 to the HCTZ group and 25 to the placebo group. There was a trend towards additional weight reduction in the HCTZ group (HCTZ: -1.78 ± 1.08 kg/day vs placebo: -1.05 ± 1.51 kg/day; p = 0.062). In post hoc analysis, the HCTZ group demonstrated significant weight reduction for every 40 mg of intravenous furosemide (HCTZ: -0.74 ± 0.47 kg/40 mg vs placebo: -0.33 ± 0.80 kg/40 mg; p = 0.032). There was a trend to increase in creatinine in the HCTZ group (HCTZ: 0.50 ± 0.37 vs placebo: 0.27 ± 0.40; p = 0.05) but no significant difference in onset of acute renal failure (HCTZ: 58% vs placebo: 41%; p = 0.38). No differences were found in the remaining outcomes.
Conclusion
There was a trend towards greater daily weight reduction in the HCTZ group. In analysis adjusted to the dose of intravenous furosemide, adding HCTZ 50 mg to furosemide resulted in a significant synergistic effect on weight loss.