bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying the Hot Spot Residues of the SARS-CoV-2 Main Protease Using MM-PBSA and Multiple Force Fields
Authors: Byun Jinyoung , Lee Juyong 
Published: June 2021

Abstract
In this study, we investigated the binding affinities between the main protease of SARS-CoV-2 virus and its various ligand to identify the hot spot residues of the protease. To investigate the effect of various force fields, we performed MD simulations with three different force fields: GROMOS54a7, Amber99-SB, and CHARMM36. The total amount of MD simulation time was 1.1 µs. To investigate how known ligands interact with Mpro of SARS-CoV-2, the binding affinities were calculated by using the MMPBSA approach. It is identified that no single force field succeeded in predicting the relative rankings of experimental binding affinities. When compared between different force fields, Amber99-SB and GROMOS54a7 results are fairly correlated while CHARMM36 results show weak or almost no correlations with the others. Additionally, we identified specific residues of Mpro, which contribute more importantly to the binding energies with ligands. It is identified that the residues of the S4 subsite of the binding site, N142, M165, and R188, contribute strongly to ligand binding. In addition, the terminal residues, D295, R298, and Q299 are identified to have attractive interactions with ligands via electrostatic and solvation energy. We believe that our findings will help facilitate develop novel inhibitors of SARS-CoV-2.
Analysis of the Sagittal Balance in Patients with Adult Spinal Deformity: Modified Sagittal Vertical Axis
Authors: Yu Yang , Wu Bing , Wang Zhaohan , Cheng Junyao , Li Bo , Liu Jinjin , Song Kai , Wang Zheng 
Published: June 2021

Abstract
Objective: The overall sagittal balance of patient with adult spinal deformity (ASD) is crucial for satisfactory postoperative outcome. SVA is the parameter often used to assess the sagittal balance. However, pelvis often rotates backward to compensate for sagittal imbalance in patients with ASD. In the case, SVA cannot reflect the real sagittal balance. Modified sagittal vertical axis (MSVA) is the parameter we found to better assess the real sagittal balance in patients with ASD. And we want to explore the relationship between MSVA and the quality of life. Methods: We used sample of 60 patients with ASD who underwent long-segment orthopedic surgery (≥4 vertebrae) between the period of 2015 and 2018. The paired-sample t test and Pearson correlation analysis were used for statistical analysis. P value <0.05 was considered significant. Results: SVA, TK, TLK, LL, SS, PT, PI-LL and MSVA were significantly changed in 60 patients preoperatively and postoperatively (p<0.05). The ODI, SRS22, VAS scores were significantly improved postoperatively (p<0.05). Pearson correlation analysis was used to conclude that postoperative SVA, postoperative MSVA and postoperative quality of life score were related. Postoperative MSVA has the strongest correlation with the quality-of-life score. Conclusions: Through spinal orthopedic surgery, the postoperative spinal parameters and quality of life of patients with ASD were significantly improved. MSVA is of great significance for evaluating postoperative sagittal balance and quality of life of patients with ASD.
Drought Analysis for the Seyhan Basin with NDVI and VCI Vegetation Indices
Authors: Aksel Murat , Dikici Mehmet 
Published: June 2021

Abstract
Various drought indices have been developed to monitor the drought, which is one of the results of climate change and mitigates its adverse effects on water resources, especially agriculture. Vegetation indices determined by remote sensing have been the subject of many studies in recent years and shed light on drought risk management. This study is examined in the Seyhan River Basin, a basin with Turkey’s considerable population density counts and is situated south of the country. Normalized Difference Vegetation Index (NDVI) and Vegetation Condition Index (VCI) are the most widely used vegetation indices and are very useful because they give results only based on satellite images. This study examined the Seyhan Basin by using satellite data in which the vegetation transformation occurring due to the decline of agricultural and forest areas was also seen. An increase in drought frequency was detected in the Seyhan Basin using NDVI and VCI indices. It was determined that climate change and drought increased with a linear uptrend. It is recommended that decision-makers should take the necessary measures by considering the drought risk maps and that long-term drought management plans should be made and implemented.
The Toxicity of Cooking Oil Fumes on Human Bronchial Epithelial Cells Through ROS-Mediated MAPK, NF-κB Signaling Pathways and NLRP3 Inflammasome
Authors: Cao Xiangyu , Fu Mingyang , Miao Jingyi , Sun Yueling , Zhu Rugang , Liu Chengying , Bi Ruochen , Wang Shuai , Liu Jianli 
Published: June 2021

Abstract
Cooking oil fumes (COFs) are main pollutants in kitchen and indoor air, which threaten human health. Exposure to COFs can cause respiratory diseases and impair pulmonary function. To investigate the toxicity of COFs on human bronchial epithelial cells (Beas-2B) and explore the underlying mechanisms, MTT assay was conducted to detect the viability of Beas-2B. Intracellular reactive oxygen species (ROS) levels and nitric oxide (NO) levels were determined with DCFH-DA assay and DAF-FM assay. The expression of genes involved in inflammation were measured with quantitative real-time PCR (qRT-PCR). The phosphorylation and the expression of proteins related to Mitogen-activated protein kinase (MAPK), NF-κB signaling pathways were measured with western blot. Our results revealed that COFs decreased Beas-2B cells viability, increased the ROS levels and NO levels in cells and induced apoptosis in Beas-2B cells. The results of qRT-PCR and western blot showed that the expression of NLRP3, p65, iNOS, IL-1β, and the factors related to oxidative stress and inflammation increased, NF-κB signaling pathway and MAPK signaling pathway were activated. This study provided some useful information to alleviate the toxicity of COFs and revealed the possible mechanism for the damage on respiratory system induced by COFs.
A Multi-Objective Cloud Workflow Scheduling Optimization Based on Evolutionary Multi-objective Algorithm with Decomposition
Authors: Yao XueLi 
Published: June 2021

Abstract
In the cloud computing environment, cost-effective workflow task scheduling is the key problem that cloud computing service providers need to solve. However, previous scheduling methods only consider one-sided demands, such as minimizing running time or running cost. In this paper, the cloud workflow scheduling model including two minimizing time and execution cost are established, and then the MOEA/D algorithm based on weight vector adjustment and local search is proposed, and the algorithm is applied in the model solving process. Firstly, the weight vector adjustment method is employed to obtain more evenly distributed solutions; and in order to obtain more evenly distributed solutions and hope to speed up the convergence speed of the solution process, this paper adds local search operators into the solution process of evolutionary algorithm, and proposes MOEA/D algorithm based on local search and weight vector adjustment as an improved multi-objective optimization algorithm to solve the cloud workflow scheduling model based on time and execution cost, it can be turned out that MOEA/D algorithm based on local search and weight vector adjustment can obtain more evenly distributed solutions than MOEA/D algorithm and NSGA-II algorithm on the basis of faster convergence speed, which provides decision support for cloud workflow scheduling decision-makers.
A Family of Quaternion-valued Pipelined Second-order Volterra Adaptive Filters for Nonlinear System Identification
Authors: Liu Qianqian , He Yigang 
Published: June 2021

Abstract
This paper primarily proposes a family of quaternion Volterra filters based on the feedforward pipelined structure (QPSOVAFs) for nonlinear quaternion system identification to reduce the computational complexity. Then, the strictly nonlinear QPSOVAF (SNL-QPSOVAF), semi-widely nonlinear QPSOVAF(SWNL-QPSOVAF), and widely nonlinear QPSOVAF (WNL-QPSOVAF), are proposed. This architecture consists of several quaternion-valued second-order Volterra (SOV) modules. The structure's nonlinear subsection executes a nonlinear mapping from the input space to an intermediate space using the feedforward SOV; the linear combiner subsection performs a linear mapping from the intermediate space to the output space. Moreover, the theoretical analysis expresses the effectiveness of the proposed QPSOVAFs in a specific condition. Finally, simulation results further prove that the proposed QPSOVAFs have good performance in identifying the quaternion-valued nonlinear system.
Global fishing and seafood trade burdens places with ineffective fisheries management
Authors: Klein Carissa , Kuempel Caitlin , Watson Reg , Coll Marta , Teneva Lida , Mora Camilo 
Published: June 2021

Abstract
Seafood is the most traded food commodity globally, but is underpinned by unsustainable fishing practices. When a country obtains seafood from outside its jurisdiction, any negative social and environmental impacts associated with fishing are displaced to the fished location. ‘Unequal displacement’ occurs when seafood is obtained from a place with poorer, less-effective, fisheries management than the country that catches or imports the seafood. We found that up to 22% (19.9 MT) of wild-capture seafood was unequally displaced, much of which is caught in the high seas, Russia, Malaysia, and Angola. Unequal displacement occurs for up to 50% (10.0 MT) of traded seafood. Almost all 172 countires that we assessed unequally displace seafood, but few are responsible for the majority (China, India, Thailand, Russia, South Korea, Spain, Netherlands, UK, USA). Achieving both sustainable food provision and ocean health requires new policies that encourage the reduction of unequal seafood displacement.
Modified Extended Object Tracker for Lidar Data Using Random Matrix Model
Authors: Li Peng , Chen Cheng , You Congzhe , Qiu Junda 
Published: June 2021

Abstract
Random Matrix (RM) model is an effective method for modeling extended objects, and has been widely used in extended object tracking. However, the existing RM based tracking methods usually assume that the measurement models obey Gaussian distribution, which will lead to the decrease of accuracy when applied to Lidar system. This paper proposed a new observation model and used it to modified the RM smoother by considering the characteristics of Lidar data. Simulation results show that the proposed approach achieved better performance compared with the original RM tracker in Lidar system.
Intrauterine Adhesions Combined with Robert's Uterus : A Case Report and Literature Review
Authors: Gao Kexin , Zhang Han , Zhu Jihong , Yu Meiling 
Published: June 2021

Abstract
Background: Robert's uterus, a rare congenital abnormality of Mullerian duct development, has oblique septum and non-communicating asymmetric hemi-cavity. Key clinical characterization of the congenital disorder is presence of hematometra and severe dysmenorrhea, some patients experience acute abdominal pain in association with menstruation. Due to the difficulty of preoperative diagnosis and high rate of misdiagnosis, Preoperative assessment matters the choice of emergency surgery and avoid a second surgery. No systematic literature review in detail has been reported previously.Case presentation: We reported a rare case of Robert’s uterus with severe abdominal pain during menstruation, in which the patient initially underwent emergency laparoscopic right ovarian cystectomy, right salpingectomy, and pelvic adhesiolysis on suspicion of ovarian teratoma torsion. However, dysmenorrhea still existed or even aggravated after the operation, hysteroscopic surgery was performed three month later, which revealed two asymmetric uterine cavities, hematometra was located in the right-side blind cavity, and thus diagnosed as Robert’s uterus and severe uterine adhesion, which, to our knowledge, has not been reported previously. Hysteroscopic incision of the septum and intrauterine adhesion were performed. Subsequently, Two-year follow-up showed no obvious dysmenorrhea recurrence. Conclusion: Robert's uterus is uncommon but can mimic other common and acute abdominal disease. Advance imaging technologies, such as three-dimensional ultrasound and magnetic resonance imaging combined with hysteroscopy and laparoscopy are less invasive for diagnosis and treatment of Robert’s uterus. Septal resection is main surgical procedure, combining laparoscopy and hysteroscopy is conducive and less invasive treatment.
Analgesic Comparison of Perineural With Intravenous Dexamethasone on Interscalene Block for Shoulder Arthroscopy: a Meta-analysis of Randomized Controlled Trials
Authors: Huang Liangku , Li Peng , Zhang Liang , Kang Guangming , Zhou Haizhen , Zhao Zandong 
Published: June 2021

Abstract
Introduction: The analgesic comparison of perineural with intravenous dexamethasone on interscalene block for pain management of shoulder arthroscopy remains controversial. We conduct a systematic review and meta-analysis to explore the influence of perineural with intravenous dexamethasone on interscalene block on the postoperative pain intensity of shoulder arthroscopy.Methods: We have searched PubMed, EMbase, Web of science, EBSCO, and Cochrane library databases through April 2021 for randomized controlled trials (RCTs) assessing the effect of perineural with intravenous dexamethasone on interscalene block for pain control of shoulder arthroscopy. This meta-analysis is performed using the random-effect model.Results: Five RCTs are included in the meta-analysis. Overall, compared with intravenous dexamethasone for shoulder arthroscopy, perineural dexamethasone leads to similar block duration (SMD=0.12; 95% CI=-0.12 to 0.35; P=0.33), pain scores at 12 h (SMD=-0.67; 95% CI=-1.48 to 0.15; P=0.11), pain scores at 24 h (SMD=-0.33; 95% CI=-0.79 to 0.14; P=0.17), opioid consumption (SMD=0.01; 95% CI=-0.18 to 0.19; P=0.95) and nausea/vomiting (OR=0.74; 95% CI=0.38 to 1.44; P=0.38).Conclusions: Perineural and intravenous dexamethasone demonstrated comparable pain control after shoulder arthroscopy when supplemented to interscalene block.
A Pilot Study of Participatory and Rapid Implementation Approaches to Increase Depression Screening in Primary Care
Authors: Last Briana S. , Buttenheim Alison M. , Futterer Anne C. , Livesey Cecilia , Jaeger Jeffrey , Stewart Rebecca E. , Reilly Megan , Press Matthew J. , Peifer Maryanne , Wolk Courtney Benjamin , Beidas Rinad S. 
Published: June 2021

Abstract
Background: Most individuals with depression go unidentified and untreated. In 2016 the US Preventive Services Task Force released guidelines recommending universal screening in primary care to identify patients with depression and to link them to treatment. Feasible, acceptable, and effective strategies to implement these guidelines are needed. Methods: This three-phased study employed rapid participatory methods to design and test strategies to increase depression screening at Penn Medicine, a large health system with 90 primary care practices. First, researchers solicited ideas and barriers from stakeholders to increase screening using an innovation tournament—a crowdsourcing method that invites stakeholders to submit ideas to address a workplace challenge. Second, a panel of stakeholders and scientists deliberated over and ranked the tournament ideas. An instant runoff election was held to select the winning idea. Third, the research team piloted the winning idea in a primary care practice using rapid prototyping, an approach that quickly refines and iterates strategy designs. Results: The innovation tournament yielded 31 ideas and 32 barriers from diverse stakeholders (12 primary care physicians, 10 medical assistants, 4 nurse practitioners, 2 practice managers, and 4 patient support assistants). A panel of 6 stakeholders and scientists deliberated on the ideas and voted for patient self-report (i.e., through tablet computers, text message, or an online patient portal) as the winning idea. The research team rapid prototyped tablets in one primary care practice with one physician over 5 five-hour shifts to examine the feasibility, acceptability, and effectiveness of the strategy. Most patients, the physician, and medical assistants found the tablets acceptable and feasible. However, patient support assistants struggled to incorporate them in their workflow and expressed concerns about scaling up the process. Depression screening rates were higher using tablets compared to usual care; follow-up was comparable between tablets and usual care. Conclusions: Rapid participatory methods engaged and amplified the voices of diverse stakeholders in primary care. These methods helped design an acceptable and feasible implementation strategy that showed promise for increasing depression screening in a primary care setting. The next step is to evaluate the strategy in a randomized controlled trial across primary care practices.
Machine Learning Identifies ICU Outcome Predictors in a Multicenter COVID-19 Cohort.
Authors: Magunia Harry , Lederer Simone , Verbuecheln Raphael , Gilot Bryant Joseph , Koeppen Michael , Haeberle Helene A , Mirakaj Valbona , Hofmann Pascal , Marx Gernot , Bickenbach Johannes , Nohe Boris , Lay Michael , Spies Claudia , Edel Andreas , Schiefenhövel Fridtjof , Rahmel Tim , Putensen Christian , Sellmann Timur , Koch Thea , Brandenburger Timo , Kindgen-Milles Detlef , Brenner Thorsten , Berger Marc , Zacharowski Kai , Adam Elisabeth , Posch Matthias , Moerer Onnen , Scheer Christian S , Sedding Daniel , Weigand Markus A , Fichtner Falk , Nau Carla , Prätsch Florian , Wiesmann Thomas , Koch Christian , Schneider Gerhard , Lahmer Tobias , Straub Andreas , Meiser Andreas , Weiss Manfred , Jungwirth Bettina , Wappler Frank , Meybohm Patrick , Herrmann Johannes , Malek Nisar , Kohlbacher Oliver , Biergans Stephanie , Rosenberger Peter 
Published: June 2021

Abstract
Background. Intensive Care Resources are heavily utilized during the COVID-19 pandemic. However, risk stratification and prediction of SARS-CoV-2 patient clinical outcomes upon ICU admission remain inadequate. This study aimed to develop a machine learning model, based on retrospective & prospective clinical data, to stratify patient risk and predict ICU survival and outcomes.Methods. A Germany-wide electronic registry was established to pseudonymously collect admission, therapeutic and discharge information of SARS-CoV-2 ICU patients retrospectively and prospectively. Machine learning approaches were evaluated for the accuracy and interpretability of predictions. The Explainable Boosting Machine approach was selected as the most suitable method. Individual, non-linear shape functions for predictive parameters and parameter interactions are reported. Results. 1,039 patients were included in the Explainable Boosting Machine model, 596 patients retrospectively collected, and 443 patients prospectively collected. The model for prediction of general ICU outcome was shown to be more reliable to predict “survival”. Age, inflammatory and thrombotic activity, and severity of ARDS at ICU admission were shown to be predictive of ICU survival. Patients’ age, pulmonary dysfunction and transfer from an external institution were predictors for ECMO therapy. The interaction of patient age with D-dimer levels on admission and creatinine levels with SOFA score without GCS were predictors for renal replacement therapy. Conclusions. Using Explainable Boosting Machine analysis, we confirmed and weighed previously reported and identified novel predictors for outcome in critically ill COVID-19 patients. Using this strategy, predictive modeling of COVID-19 ICU patient outcomes can be performed overcoming the limitations of linear regression models.Trial registration. “ClinicalTrials” (clinicaltrials.gov) under NCT04455451
Isolated Progressive Enlargement of Head Mass as the First Symptom: A Rare Case Report of Cranial Metastasis of Hepatocellular Carcinoma and Literature Review
Authors: Liu Yuan-yuan , Zhou Zhi-hua , Hu Shuai , Su Xin , zhou jinxu 
Published: June 2021

Abstract
Background: This article presents a rare case of skull metastasis of primary hepatocellular carcinoma that manifests the isolated progressive enlargement of the head mass as the first symptom. Case presentation:A 65-year-old female patient presented an isolated painless mass in the head, which grew rapidly over the last month. Head CT revealed a 6.4 cm×5.6cm osteolytic destruction in the right parietal bone. MRI further revealed that the occupation was significantly enhanced in the T1 reinforced phase. The patient underwent total surgical resection. Postoperative pathology confirmed that the head mass was the skull metastasis from hepatocellular carcinoma (HCC). Conclusion: The case of skull metastasis from primary hepatocellular carcinoma is rare, and HCC patient with intracranial metastasis tends to have a rather poor prognosis. Surgical excision of the metastatic mass and radiotherapy can improve the life quality and prolong the survival time of the patient.
Prognostic Impact of Pathological Adverse Features in Surgically Resected Adenocarcinoma of Esophagogastric Junction
Authors: Liao Qianchao , Zheng Jiabin , Xiong Wenjun , Wang Junjiang , Hu Xu , Zheng Chengbin , Feng Huolun , Deng Zhenru , Wang Wei , Li Yong 
Published: June 2021

Abstract
Objective The prognostic value of lymphovascular invasion (LVI), perineural invasion (PNI), and poor differentiation (PD) has been widely studied in different solid tumors. However, it was still controversial in adenocarcinoma of esophagogastric junction (AEG). We investigated the prognostic impact of combining LVI, PNI and PD for predicting the survival in patients with AEG.Methods We retrospectively investigated the data of patients who performed surgical resection of AEG on Guangdong Provincial Hospital and Guangdong Provincial Hospital of Chinese Medicine from Jan. 2004 to Dec. 2018. According to the status of LVI, PNI and differentiation, pathological adverse features were divided into three groups: 0, 1 or 2 and 3 adverse features, their impact on prognosis was evaluated. Results Univariate analysis indicated pT, pN, LVI , PNI , PD and pathological adverse features were risk factors for both overall survival (OS) and disease-specific survival (DSS), and multivariate analysis indicated that pathological adverse feature was independent risk factor for both OS and DSS. In subgroup analyses, adverse features were independent risk factor for DSS of stage II AEG but not for stage I or III.Conclusions The pathological adverse features were independent prognostic factors for AEG patients and they can help for further risk stratification in stage II patients.