bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using Synthetic Production Data from an Open Source Carbonate Reservoir Model to Improve our Understanding of Flow Behaviour
Authors: Costa Gomes Jorge , Geiger Sebastian , Arnold Daniel 
Published: June 2020

Abstract
This work presents a new open access carbonate reservoir case study that uniquely considers the major uncertainties inherent to carbonate reservoirs using one of the most prolific aggradational parasequence carbonate formation sets in the U.A.E., the Upper Kharaib Member (Early Cretaceous), as an analogue. The ensemble considers a range of interpretational scenarios and geomodelling techniques to capture the main components of its reservoir architecture, stratal geometries, facies, pore systems, diagenetic overprints and wettability variations across its shelf-to-basin profile.
Fully anonymized data from 43 wells across 22 fields in the Bab Basin in the U.A.E from different geo-depositional settings and height above the free water level (FWL) was used. The data comprises of a full suite of open-hole logs and core data which has been anonymized, rescaled, repositioned and structurally deformed; FWLs were normalized and the entire model was placed in a unique coordinate system. The resultant static and dynamic models(s) capture the geological setting and reservoir heterogeneities of selected fields but now at a manageable scale. Synthetic production data has been generated by adding wells to an undisclosed ‘truth case’ model to obtain field-wide and well-by-well production data (oil, gas, and water rates, bottom-hole pressures etc.) from simulation runs.
The original oil in place (OOIP) and reserves that have been computed from these models are synthetic and unique. Here we present an initial field development plan and corresponding reservoir simulations that showcase the heterogeneity inherent to the model and demonstrate the variability of the flow and storage capacity of the different reservoir architectures found in and around the Bab Basin. This is an example application of how we can use synthetic production data to improve our understanding of flow behaviours in carbonates.
The novelty of our work is the provision of a unique open access dataset which enables reproducible science in the field of reservoir characterisation and simulation, and helps training new generations of geoscientists and reservoir engineers in the art of characterising, simulating and predicting the reservoir performance of carbonate reservoirs under different recovery processes.
Efficiency and Accuracy Boosts in Exploration and Production from Natural Language Processing Software
Authors: Walker Alec Kennedy 
Published: June 2020

Abstract
In order to fully inform their technical decisions, teams in upstream review reports, journals, and other textual files as references. Facing increasing challenges in the extraction of data and knowledge from a growing body of digital unstructured textual files, exploration geologists are beginning to consider virtual advisors employing natural language processing to expedite this research. This paper explores a use case in which an operator utilized a third-party natural language processing platform to enhance the performance of one of their teams. The paper details how the operator identified the opportunity for improvement using a natural language processing platform, how the project was scoped internally, how the decision was made to seek an external service provider, how the service provider was vetted, how the service provider performed throughout implementation, and what value the resulting tool has delivered to the operator following implementation. The tool was able to take as input a question asked in natural language and return relevant answers from across the unstructured files as well as to take as input a database with missing data and fill it with values from across the unstructured files. Using the tool, the operator has been able to cut out entirely a significant part of the workflow when evaluating geographical areas for prospective development. Before the tool was implemented, this process had become entirely unmanageable. Due to the proliferation of unstructured data, operator personnel were spending rapidly increasing portions of their time accomplishing diminishing portions of the necessary research to inform their decisions. Following deployment of the tool, the operator personnel no longer need to spend time finding the relevant knowledge and data within the unstructured documents, as the virtual advisor takes care of this step for them. This paper aims to inspire operators to consider natural language processing solutions to unstructured file research challenges. More significantly, it highlights in detail a precedent that can serve to inform others in the industry as to an appropriate scope, process, and scale for deployment of such a solution generally.
Salmonella enterica serovar Typhimurium sseK3 induces apoptosis and enhances glycolysis in macrophages
Authors: Yu Chuan , Du Fuyu , Zhang Chunjie , Li Yinju , Liao Chengshui , He Lei , Cheng Xiangchao , Zhang Xiaojie 
Published: June 2020

AbstractBackground: Salmonella enterica serovar Typhimurium ( S. Typhimurium) is an important infectious disease pathogen that can survive and replicate in macrophages. Glycolysis is essential for immune responses against S. Typhimurium infection in macrophages, and is also associated with apoptosis. S. Typhimurium secreted effector K3 (SseK3) was recently identified as a novel translated and secreted protein. However, there is no study about the role of sseK3 in the relationship between apoptosis and glycolysis in cells infected with S. Typhimurium. It is unclear whether this protein exerts a significant role in the progress of apoptosis and glycolysis in S. Typhimurium-infected macrophages. Results: Macrophages were infected with S. Typhimurium SL1344 wild-type (WT), Δ sseK3 mutant or sseK3 -complemented strain, and the effects of sseK3 on apoptosis and glycolysis were determined. The adherence and invasion in the Δ sseK3 mutant group were similar to that in the WT and sseK3 -complemented groups, indicating that SseK3 was not essential for the adherence and invasion of S. Typhimurium in macrophages. However, the percentage of apoptosis in the Δ sseK3 mutant group was much lower than that in the WT and sseK3 -complemented groups. Caspase-3, caspase-8, and caspase-9 enzyme activity in the Δ sseK3 mutant group were significantly lower than in the WT group and sseK3 -complemented groups, indicating that sseK3 could improve the caspase-3, caspase-8, and caspase-9 enzyme activity. We also found that there were no significant differences in pyruvic acid levels between the three groups, but the lactic acid level in the Δ sseK3 mutant group was much lower than that in the WT and sseK3 -complemented groups. The ATP levels in the Δ sseK3 mutant group were remarkably higher than those in the WT and sseK3 -complemented groups. These indicated that the sseK3 enhanced the level of glycolysis in macrophages infected by S. Typhimurium. Conclusions: S. Typhimurium sseK3 is likely involved in promoting macrophage apoptosis and modulating glycolysis in macrophages. Our results could improve our understanding of the relationship between apoptosis and glycolysis in macrophages induced by S. Typhimurium sseK3 .
Cholecystectomy outcomes after endoscopic sphincterotomy in patients with choledocholithiasis: A meta-analysis
Authors: Xu Jie , Yang Chuang 
Published: June 2020

Abstract
Background Endoscopic sphincterotomy is the standard treatment for common bile duct stones.There is different evidence considering complications specifically biliary pancreatitis and cholangitis with the use of cholecystectomy after endoscopic sphincterotomy.The purpose of this article is to compare the positive cholecystectomy after endoscopic treatment of common bile duct stones, whether the incidence of recurrent pancreatitis cholangitis is reduced, especially in high-risk patients. Methods We searched Pubmed(1990-2019)、Embase(1990-2019)和 Cochrane(1990-2019)database for trials comparing the 2 strategies for gallstones after ES.A related article on the removal of gallbladder after endoscopic sphincterotomy was collected,followed by analysis of each group using RevMan. Results We have adopted a total of 8 studies, including 7 randomized controlled trials and 1 retrospective study. A total of 12718 patients were included in the study, 4922 in the early cholecystectomy group, and 7795 in the gallbladder in situ group.During the follow-up period, 41 patients had pancreatitis after endoscopic sphincterotomy in the cholecystectomy group, and 177 patients in the wait-and-see group. The incidence of pancreatitis in the gallbladder in situ group was significantly reduced(RR 0.38, 95%CI 0.27 to 0.53, P < 0.00001,I 2 =0%).The incidence of cholangitis and jaundice in the removal of the gallbladder group was also less than that in the preserved gallbladder group(RR 0.31, 95%CI 0.26 to 0.38, P < 0.00001,I 2 =0%).There was no significant difference in mortality between the two groups(RR 0.73, 95%CI 0.52 to 1.02, P =0.07,I 2 =14%).There is a significant difference in cholecystitis or biliary colic(RR 0.25, 95% CI 0.21 to 0.29, P < 0.00001,I 2 =28%). Conclusions Early endoscopic cholecystectomy after removal of common bile duct stones can effectively reduce biliary complications such as recurrent pancreatitis, cholangitis and cholecystitis. This is still true for high-risk patients, and has no significant effect on the mortality of patients. After ES,laparoscopic cholecystectomy should be recommended.
The impact of parents' health behaviours on their preferences regarding vaccinations in Bialystok, Poland
Authors: Kraśnicka Jolanta , Krajewska-Kułak Elżbieta , Klimaszewska Krystyna , Cybulski Mateusz , Guzowski Andrzej , Lewko Jolanta , Łukaszuk Cecylia , Kowalczuk Krystyna , Doroszkiewicz Halina , Baranowska Anna , Krajewska-Ferishah Katarzyna , Rolka Hanna , Kulak Wojciech 
Published: June 2020

Abstract
Background. Currently, as the number of vaccinated children in Poland and throughout Europe is decreasing. Many factors impact on the rate vaccination and parents’ health behaviours may affect the frequency of vaccinations. The aim of the study was to assess the association of parents’ health behaviors with children’s vaccinations.Methods. A cross-sectional survey was conducted from July 2015 to June 2016 to assess to assess the association of parents’ health behaviors with children’s vaccinations in Białystok city, Poland. We used the the Inventory of Health Behaviours and an original questionnaire including demographic data and questions about vaccination. Three hundred parents were recruited from the Pro Medica Family Medica Center in Bialystok, Poland.Results: Only 3.7% of respondents did not vaccinate their children. The level of health behaviours was average in 42.3% of the respondents, low in 33%, and high in 24.7%. Significant differences in health behaviours, mainly the level of normal eating habits (p = 0.038) and positive mental attitude (p=0.022), were found in relation to views on the toxicity of vaccines. Participants who reported that vaccines can cause autism engaged in a higher level of prophylactic behaviours. Respondents who vaccinated their children with combined vaccines had a significantly higher level of health practices. Conclusions: Parents preferred health behaviours did not effect on children vaccination. Parents who believed in the toxicity of vaccines were more concerned about proper nutrition, had a positive mental attitude, and engaged in a higher level of preventive behaviours and health practices. Parents who did not vaccinate their children had lower levels of normal eating habits. Parents who vaccinated their children with combined vaccines had a higher level of health behaviours, especially in terms of health practices.
Vitamin D receptor gene polymorphisms and the risk of the Type 1 diabetes: A meta-regression and updated meta-analysis
Authors: Zhai Na , Bidares Ramtin , Makoui Masoud Hassanzadeh , Aslani Saeed , Mohammadi Payam , Razi Bahman , Imani Danyal , Yazdchi Mohammad , Mikaeili Haleh 
Published: June 2020

Abstract
Background: The association between the polymorphisms in the vitamin D receptor (VDR) gene and the risk of type 1 diabetes mellitus (T1DM) has been evaluated in several studies. However, the findings were inconclusive. Thus, we conducted a meta-analysis to comprehensively evaluate the effect of VDR gene polymorphisms on the risk of T1DM.Methods: All relevant studies reporting the association between VDR gene polymorphisms and susceptibility to T1DM published up to May 2020 were identified by comprehensive systematic database search in ISI Web of Science, Scopus, and PubMed/MEDLINE. Strength of association were assessed by calculating of pooled odds ratios (ORs) and 95% confidence intervals (CIs). The methodological quality of each study was assessed according to the Newcastle–Ottawa Scale. To find the potential sources of heterogeneity, meta-regression and subgroup analysis were also performed. Results: A total of 40 case–control studies were included in this meta-analysis. The results of overall population rejected any significant association between VDR gene polymorphisms and T1DM risk. However, the pooled results of subgroup analysis revealed significant negative and positive associations between FokI and BsmI polymorphisms and T1DM in Africans and Americans, respectively. Conclusions: This meta-analysis suggested a significant association between VDR gene polymorphism and T1DM susceptibility in ethnic-specific analysis.
Structure guided protein engineering increases enzymatic activities of the SGNH family esterases
Authors: Li Zhengyang , Li Long , Huo Yingyi , Chen Zijun , Zhao Yu , Huang Jing , Jian Shuling , Rong Zhen , Wu Di , Gan Jianhua , Hu Xiaojian , Li Jixi , Xu Xue-Wei 
Published: June 2020

Abstract
Background: Esterases and lipases hydrolyze short-chain esters and long-chain triglycerides, respectively, and therefore play essential roles in the synthesis and decomposition of ester bonds in the pharmaceutical and food industries. Many SGNH family esterases share high similarity in sequences. However, they have distinct enzymatic activities toward the same substrates. Due to a lack of structural information, the detailed catalytic mechanisms of these esterases remain barely investigated. Results: In this study, we identified two SGNH family esterases, CrmE10 and AlinE4, from marine bacteria with significantly different preferences for pH, temperature, metal ion, and organic solvent tolerance despite high sequence similarity. The crystal structures of these two esterases, including wild type and mutants, were determined to high resolutions ranging from 1.18 Å to 2.24 Å. Both CrmE10 and AlinE4 were composed of five β-strands and nine α-helices, which formed one compact N-terminal α/β globular domain and one extended C-terminal domain. The aspartic residues (D178 in CrmE10/ D162 in AlinE4) destabilized the conformations of the catalytic triad (Ser-Asp-His) in both esterases, and the metal ion Cd2+ might reduce enzymatic activity by blocking proton transfer or substrate binding. CrmE10 and AlinE4 showed distinctly different electrostatic surface potentials, despite the similar atomic architectures and a similar swap catalytic mechanism. When five negative charged residues (Asp or Glu) were mutated to residue Lys, CrmE10 obtained elevated alkaline-adaptability and significantly increased the enzymatic activity from 0% to 20% at pH 10.5. Also, CrmE10 mutants exhibited dramatic change for enzymatic properties when compared with the wide-type enzyme. Conclusions: These findings offer a perspective for understanding the catalytic mechanism of different esterases and might facilitate the industrial biocatalytic applications.
Low-arginine and low-protein diets induce hepatic lipid accumulation through different mechanisms in growing rats
Authors: Otani Lila , Nishi Hiroki , Koyama Ayaka , Akasaka Yuta , Taguchi Yusuke , Toyoshima Yuka , Yamanaka Daisuke , Hakuno Fumihiko , Jia Huijuan , Takahashi Shin-Ichiro , Kato Hisanori 
Published: June 2020

Abstract
Background Dietary protein deficiency and amino acid imbalance cause hepatic fat accumulation. We previously demonstrated that only arginine deficiency or total amino acid deficiency in a diet caused significant hepatic triglyceride (TG) accumulation in young Wistar rats. In this study, we explored the mechanisms of fatty liver formation in these models.Dietary protein deficiency and amino acid imbalance cause hepatic fat accumulation. We previously demonstrated that only arginine deficiency or total amino acid deficiency in a diet caused significant hepatic triglyceride (TG) accumulation in young Wistar rats. In this study, we explored the mechanisms of fatty liver formation in these models. Methods We fed 6-week-old male Wistar rats a control diet (containing an amino acid mixture equivalent to 15% protein), a low-total-amino acid diet (equivalent to 5% protein; 5PAA), and a low-arginine diet (only the arginine content is as low as that of the 5PAA diet) for 2 weeks. Results Much greater hepatic TG accumulation was observed in the low-arginine group than in the low-total-amino acid group. The lipid consumption rate and fatty acid uptake in the liver did not significantly differ between the groups. In contrast, the low-total-amino acid diet potentiated insulin sensitivity and related signaling in the liver and enhanced de novo lipogenesis. The low-arginine diet also inhibited hepatic very-low-density lipoprotein secretion without affecting hepatic insulin signaling and lipogenesis. Conclusions : Although the arginine content of the low-arginine diet was as low as that of the low-total-amino acid diet, the two diets caused fatty liver via completely different mechanisms. Enhanced lipogenesis was the primary cause of a low-protein diet-induced fatty liver, whereas lower very-low-density lipoprotein secretion caused low-arginine diet-induced fatty liver.
Prevalence of Crowding, Boarding and Staffing Levels in Swedish Emergency Departments - a National Cross Sectional Study
Authors: Wretborn Jens , Henricson Joakim , Ekelund Ulf , Wilhelms Daniel B 
Published: June 2020

Abstract
Background: Emergency Department (ED) crowding occurs when demand for care exceeds the available resources. Crowding has been associated with decreased quality of care and increased mortality, but the prevalence on a national level is unknown in most countries. Method: We performed a national, cross-sectional study on staffing levels, staff workload, occupancy rate and patients waiting for an in-hospital bed (boarding) at five time points during 24 hours in Swedish EDs. Results: Complete data were collected from 37 (51% of all) EDs in Sweden. High occupancy rate indicated crowding at twelve hospitals (37.5 %) at 31 out of 170 (18.2%) time points. Mean workload (measured on a scale from 1, no workload to 6, very high workload) was moderate at 2.65 (±1.25). Boarding was more prevalent in academic EDs than rural EDs (median 3 vs 0). There were an average of 2.6, 4.6 and 3.2 patients per registered nurse, enrolled nurse and physician, respectively. Conclusion: ED crowding based on occupancy rate was prevalent on a national level in Sweden and comparable with international data. Staff workload, boarding and patient to staff ratios were generally lower than previously described.
A long non-coding RNA, HOTAIR, promotes cartilage degradation in osteoarthritis by inhibiting WIF-1 expression and activating Wnt pathway
Authors: Yang Yang , Xing Dan , Wang Yawei , Jia Haobo , Li Bing , Li Jiao Jiao 
Published: June 2020

Abstract
Background: Long noncoding RNAs (lncRNAs) are recently found to be critical regulators of the epigenome. However, our knowledge of their role in osteoarthritis (OA) development is limited. This study investigates the mechanism by which HOTAIR, a key lncRNA with elevated expression in OA, affects OA disease progression. Results: HOTAIR expression was greatly elevated in osteoarthritic compared to normal chondrocytes. Silencing and over-expression of HOTAIR in SW1353 cells respectively reduced and increased the expression of genes associated with cartilage degradation in OA. Investigation of molecular pathways revealed that HOTAIR acted directly on Wnt inhibitory factor 1 (WIF-1) by increasing histone H3K27 trimethylation in the WIF-1 promoter, leading to WIF-1 repression that favours activation of the Wnt/β-catenin pathway. Conclusions: Activation of Wnt/β-catenin signalling by HOTAIR through WIF-1 repression in osteoarthritic chondrocytes increases catabolic gene expression and promotes cartilage degradation. This is the first study to demonstrate a direct link between HOTAIR, WIF-1 and OA progression, which may be useful for future investigations into disease biomarkers or therapeutic targets.
Veno-Arterial Extracorporeal Membrane Oxygenation for Electrical Injury Induced Cardiogenic Shock Support: A Case Report
Authors: Jamal Tamer , Shalabi Amjad , Grosman-Rimon Liza , Ghanim Diab , Amir Offer , Kachel Erez 
Published: June 2020

Abstract
Background High voltage electrical injury (HVEI) of more than 1,000V is a potentially devastating form of a multisystem injury associated with high morbidity and mortality. We present the first case of veno-arterial extracorporeal membrane oxygenation (VA-ECMO) as a life saving device for treating a patient with severe cardiogenic shock after a high voltage electrical injury.Case Presentation A 26-year-old male sustained HVEI while working with a concrete mixer pump that came in contact with a high voltage cable of 10,000 volts. He was immediately disconnected from the mixer pump, underwent cardiopulmonary resuscitation and was transported to the nearest medical centre with severe cardiogenic shock with an ejection fraction (EF) of < 10%. Upon arrival, he was in critical condition, sedated and mechanically ventilated, haemodynamically unstable and supported by intravenous (IV) inotropes after a few events of ventricular fibrillation, with an electrical entry point on the left hand and an exit point located on his right leg. Blood pH was 6.8, PCO2 53 mmHg, PaO2 of 57 mmHg, lactate 8 mmol/L, and Troponin 38000 ng/dl. The EF was 10% with global severe left ventricular dysfunction. During cardiopulmonary resuscitation (CPR), including cardiac massage and few electrical shocks, he was immediately connected to the VA-ECMO via open right femoral approach with distal arterial leg perfusion.He was treated with IV broad spectrum antibiotics, and high volume fluids to prevent rhabdomyolysis-induced acute kidney injury, total parenteral nutrition, topical silver sulfadiazine cream, and Granuflex for severe electrical burns. He was gradually weaned from inotropes over the next 3 days, during which his clinical condition and bloodwork improved tremendously. His EF gradually increased to 50% and he was weaned from the VA-ECMO, and underwent decannulation 86 hours after initialization. He was discharged on day 27 without any sequelae.Conclusion The VA-ECMO treatment can be a lifesaving device for treating severe cardiogenic shock caused by high voltage electrical injury, and should be considered while treating these “high-mortality risk” patients.