bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust Method for Reservoir Simulation History Matching Using Bayesian Inversion and Long-Short-Term Memory Network-Based Proxy
Authors: Zhang Zhen , He Xupeng , AlSinan Marwah , Kwak Hyung , Hoteit Hussein 
Published: November 2022

Summary
History matching is a critical process used for calibrating simulation models and assessing subsurface uncertainties. This common technique aims to align the reservoir models with the observed data. However, achieving this goal is often challenging due to the nonuniqueness of the solution, underlying subsurface uncertainties, and usually the high computational cost of simulations. The traditional approach is often based on trial and error, which is exhaustive and labor-intensive. Some analytical and numerical proxies combined with Monte Carlo simulations are used to reduce the computational time. However, these approaches suffer from low accuracy and may not fully capture subsurface uncertainties. This study proposes a new robust method using Bayesian Markov chain Monte Carlo (MCMC) to perform assisted history matching under uncertainties. We propose a novel three-step workflow that includes (1) multiresolution low-fidelity models to guarantee high-quality matching; (2) long-short-term memory (LSTM) network as a low-fidelity model to reproduce continuous time response based on the simulation model, combined with Bayesian optimization to obtain the optimum low-fidelity model; and (3) Bayesian MCMC runs to obtain the Bayesian inversion of the uncertainty parameters. We perform sensitivity analysis on the LSTM’s architecture, hyperparameters, training set, number of chains, and chain length to obtain the optimum setup for Bayesian-LSTM history matching. We also compare the performance of predicting the recovery factor (RF) using different surrogate methods, including polynomial chaos expansions (PCE), kriging, and support vector machines for regression (SVR). We demonstrate the proposed method using a water flooding problem for the upper Tarbert formation of the 10th SPE comparative model. This study case represents a highly heterogeneous nearshore environment. Results showed that the Bayesian-optimized LSTM has successfully captured the physics in the high-fidelity model. The Bayesian-LSTM MCMC produces an accurate prediction with narrow ranges of uncertainties. The posterior prediction through the high-fidelity model ensures the robustness and accuracy of the workflow. This approach provides an efficient and practical history-matching method for reservoir simulation and subsurface flow modeling with significant uncertainties.
Late-stage Peptide Modification and Cyclization via Maleimidation of C(7)-H Tryptophan
Authors: Wang Peng , Liu Jiang , Yan Zhengqing , Yan Jiahui , Jiang Jitong , Fu Manlin , Kenry Kenry , Zhu Qing 
Published: November 2022

Abstract
Cyclic peptides have attracted tremendous attention in the pharmaceutical industry owing to their excellent cell penetrability, stability, thermostability, and drug-like properties. However, the currently available facile methodologies for creating such peptides are rather limited. Herein, we reported an efficient and direct peptide cyclization via rhodium(III)-catalyzed C(7)-H maleimidation. Notably, this catalytical system has excellent regioselectivity and high tolerance of functional groups which enable late-stage cyclization of peptides. This new architecture of cyclic peptides exhibits higher bioactivity than its parent linear peptides. Moreover, the Trp-substituted maleimide displays excellent reactivity towards Michael addition, indicating its potential as new click functional group for applications in chemical biology and medicinal chemistry.
Identification of key immune-related genes in dilated cardiomyopathy using bioinformatics analysis
Authors: Li Feng , Du Tong-Yue , Wu Li-Da , Zhang Lei , Liu Huan-Huan , Zhang Zhen-Ye , Zhang Jie , Zhang Zhi-Yuan , Qian Ling-Ling , Hao Jian-Feng , Wang Ru-Xing 
Published: November 2022

Abstract
Background:
Dilated cardiomyopathy (DCM) is characterized by the left ventricular dilatation and impaired myocardial systolic dysfunction with high mortality and morbidity. However, the underlying mechanisms remain elusive.
Methods:
Differentially expressed genes (DEGs) analysis was performed using two expression profiles from GSE3585 and GSE84796. Enrichment analysis to explore the potential mechanisms underlying DCM was conducted. A total of four algorithms, including key module of MCODE, degree, maximum neighborhood component (MNC), and maximal clique centrality (MCC), were used within Cytoscape to identify the hub genes. Correlation analysis between hub genes and infiltrated immune cells to identify potential immune-related genes. The expression analysis and diagnosis value analysis of potential immune-related genes were performed. Finally, the expression analysis with GSE57338 and relationship analysis with the comparative toxicogenomics database (CTD) were performed for identification of the key immune-related genes in DCM.
Results:
A total of 80 DEGs were screened for DCM. Enrichment analysisrevealed that DEGs were involved in immune-related pathological process. Immune infiltration analysis indicated a potential immune response abnormal in DCM. Four up-regulated genes, including COL1A2, COL3A1, CD53, and POSTN, were identified as potential immune-related genes. Finally, three genes (COL1A2, COL3A1, and POSTN) were determined as the key immune-related genes in DCM via expression analysis with a validation set (GSE57338) and relationship analysis with CTD.
Conclusions:
Our study suggested that the upregulated COL1A2, COL3A1, and POSTN might be the key immune-related genes for DCM. Further studies are needed to validate the underlying mechanisms.
Characterizing Modifications to a Comparative Effectiveness Research Study – the OPTIMIZE Trial - Using the framework for reporting adaptations and modifications to evidence-based interventions (FRAME)
Authors: Greene Tom , Fritz Julie M , Brennan Gerard P. , Minick Kate , Lane Elizabeth , Wegener Stephen T. , Skolasky Richard L. 
Published: November 2022

Abstract
Background The OPTIMIZE trial is a multi-site, comparative effectiveness research (CER) study that uses a sequential multiple assessment randomized trial (SMART) designed to examine the effectiveness of complex health interventions (cognitive behavioral therapy, physical therapy and mindfulness) for adults with chronic low back pain. Modifications are anticipated when implementing complex interventions in CER. Disruptions due to COVID have created unanticipated challenges also requiring modifications. Recent methodologic standards for CER studies emphasize that fully characterizing modifications made is necessary to interpret and implement trial results. The purpose of this paper is to outline the modifications made to the OPTIMIZE trial using the framework for reporting adaptations and modifications to evidence-based interventions (FRAME) to characterize modifications to the OPTIMIZE trial in response to the COVID pandemic and other challenges encountered.
Methods The FRAME outlines a strategy to identify and report modifications to evidence-based interventions or implementation strategies, whether planned or unplanned. We use the FRAME to characterize the process used to modify aspects of the OPTIMIZE trial. Modifications were made to improve lower than anticipated rates of treatment initiation and COVID-related restrictions. Contextual modifications were made to permit telehealth delivery of treatments originally designed for in-person delivery. Training modifications were made with study personnel to provide more detailed information to potential participants, use motivational interviewing communication techniques to clarify potential participants motivation and possible barriers to initiating treatment, and to provide greater assistance with scheduling of assigned treatments.
Results Modifications were developed with input from the trial’s patient and stakeholder advisory panels. Goals of the modifications were to improve trial feasibility without compromising interventions’ core functions. Modifications were approved by the study funder and the trial steering committee.
Conclusions Full and transparent reporting of modifications to clinical trials, whether planned or unplanned, is critical for interpreting the trial’s eventual results and considering future implementation efforts.
Trial Registration: Clinicaltrials.gov NCT03859713, registered March 1, 2019
Uncertain Logistic population model with Allee effect
Authors: Gao Caiwen , Zhang Zhiqiang , Liu Baoliang 
Published: November 2022

Abstract
Any organism in nature will inevitably be affected by uncertain factors. The deterministic model and stochastic model are no longer suitable for population dynamics analysis under uncertain noise environment. In order to simulate these problems more reasonably, we propose an uncertain logistic population model with Allee effect, which describes the population dynamic behavior through uncertain differential equation. In this paper, the solution and Alpha-path of the uncertain Logistic population model with Allee effect are given, and the behavior analysis of the solution is also discussed. Besides, some numerical examples are put forward to illustrate the conclusions obtained in the paper.
Identification of a novel intronic variant of ATP6V0A2 in a Han-Chinese family with Cutis Laxa
Authors: Shu Jianbo , Zhang Ying , Zhao Yiran , Zhang Fang , Liu Yang , Cai Chunquan 
Published: November 2022

Abstract
Background: Cutis laxa is a connective tissue disease caused by abnormal synthesis or secretion of skin elastic fibers, leading to skin flabby and sagging in various body parts. It can be divided into congenital cutis laxa and acquired cutis laxa, and inherited cutis laxa syndromes is more common in clinic.
Methods: In this study, we reported a case of a Han-Chinese male newborn with ATP6V0A2 gene variant leading to cutis laxa. The proband was identified by whole-exome sequencing to determine the novel variant, and their parents were verified by sanger sequencing. Bioinformatics analysis and minigene assay were used to verify the effect of this variant on splicing function.
Results: The main manifestations of the proband are skin laxity, abnormal facial features, and enlargement of the anterior fontanelle. Whole-exome sequencing showed that the newborn carried a non-canonical splicing-site variant c.117+5G>T，p. (?) in ATP6V0A2 gene. Sanger sequencing showed that both parents of the proband carried the heterozygous variant. The results of bioinformatics analysis and minigene assay displayed that the variant site affected the splicing function of pre-mRNA of ATP6V0A2 gene.
Conclusions: In this study, it was identified that ATP6V0A2 gene c. 117+5G>T may be the cause of the disease. Few non-canonical splicing variants of ATP6V0A2 gene were reported in the past, and this variant expands the variants spectrum of the gene. The functional study of minigene assay plays a certain role in improving the evidence level of splicing variants, which lays a foundation for prenatal counseling and follow-up gene therapy.
Precise targeting for 3D cryo-correlative light and electron microscopy volume imaging of tissues using a FinderTOP
Authors: Sommerdijk Nico , de Beer Marit , Daviran Deniz , Roverts Rona , Rutten Luco , Sanchez Elena Macias , Metz Jurriaan , Akiva Anat 
Published: November 2022

Abstract
Cryo-correlative light and electron microscopy (cryoCLEM) is a powerful strategy to high resolution imaging in the unperturbed hydrated state, in particular for in combination with cryo-electron tomography (cryoET). In this approach fluorescence microscopy aids localizing the area of interest, and cryogenic focused ion beam/scanning electron microscopy (cryoFIB/SEM) allows preparation of thin cryo-lamellae for cryoET. However, the current method cannot be accurately applied on bulky (3D) samples such as tissues and organoids.
3D cryo-correlative imaging of large volumes is needed to close the resolution gap between cryo-light microscopy and cryoET, placing sub-nanometer observations in a larger biological context. Currently technological hurdles render 3D cryoCLEM an unexplored approach.
Here we demonstrate a cryoCLEM workflow for tissues, correlating 3D cryo-Airyscan confocal microscopy with 3D cryoFIB/SEM volume imaging. Accurate correlation is achieved by imprinting a FinderTOP pattern in the sample surface during high pressure freezing, and allows precise targeting for cryoFIB/SEM volume imaging and cryo-lift out for cryoTEM.
Institutional Integrity and Carbon Emissions
Authors: Khurana Ritika , Elbakidze Levan , Etienne Xiaoli 
Published: November 2022

Abstract
Institutions affect environmental quality by enabling economic growth, supporting environmental protection policies, and regulating industries. In this paper, we empirically examine the impact of institutions on carbon emissions. Using the Generalized Methods of Moments and an unbalanced panel of 120 countries from 1984 to 2016, we examine the impact of institutional integrity on per capita carbon emissions and carbon intensity of energy use. We also explore the heterogeneous effect of institutions on carbon emissions across income groups and regions. Lastly, we examine the impact of disaggregated institutional quality factors on carbon emissions. Our results confirm the presence of the Environmental Kuznets Curve in the models with and without institutions. However, the marginal effect of GDP per capita on carbon emissions is lower in the models that account for institutional integrity than the models that do not. Therefore, carbon policies should account for economic growth as well as institutional contexts. The results also show that although the combined institutional integrity is an important determinant of carbon emissions, individual institutional factors in isolation have minor effects.
Multiplicity of Zn coordination sites at cubic spinel ferrites: magnetism and influence of the Zn d band.
Authors: Tejera-Centeno Cesar , Rico Rubén , Gallego Silvia 
Published: November 2022

Abstract
Zinc substituted nickel ferrite (ZnxNi1 − xFe2O4) is investigated under density functional theory (DFT) within the DFT + U approximation for x ≤ 0.50, with particular interest in understanding the effect of Zn on the net magnetization. Using as a reference ZnFe2O4, the localization of the Zn d band is proved to have a large impact on the preference for Zn to occupy either tetrahedral (ZnA) or octahedral (ZnB) coordination sites, which in ZnFe2O4 is equivalent to the relative stability of the direct and inverse spinel forms. This affects the lattice volume and has important consequences on the magnetism of the system, as ZnA and ZnB alter the balance of interactions between magnetic sublattices in a different way. Our simulations support the presence of a significant ratio of Zn atoms at octahedral positions at ZnxNi1 − xFe2O4, mainly as the Zn concentration increases, putting limits to the ability to increase the magnetization of NiFe2O4 by Zn substitution.
Application of Moringa leaves as soil amendment to Tiger-nut suppressed weeds in the Nigerian Guinea Savanna
Authors: Fadeyi Olasupo James , Fabunmi Thomas Oladeji , Soretire Adeniyi Adebowale , Olowe Victor Idowu Olugbenga , Adeyemi Olusegun Raphael 
Published: November 2022

Abstract
The allelopathic effect of Moringa (Moringa oleifera Lam.) leaves applied as organic manure in tiger nut (Cyperus esculentus L.) production on associated weeds was investigated in the guinea savanna of South West Nigeria, during the 2014 (September - November) and 2015 (June - August) wet seasons. Five Moringa leaves rates (0, 2.5, 5.0, 7.5 and 10 t/ha) and three tuber sizes (0.28 g, 0.49 g and 0.88 g dry weight) were laid out in the main plot and sub-plot, respectively in a split-plot arrangement fitted into randomized complete block design and replicated three times. Parameters measured, weed cover score (WCS), weed density (WD) and weed dry matter production (WDMP) were significantly (p<0.05) influenced in both years by Moringa leaf. In 2015, WCS, WD and WDMP significantly (p<0.05) reduced by 25-73%, 35-78% and 26-70% on Moringa leaves-treated plots respectively. There were significant (p<0.05) interactions between quantity of Moringa leaves incorporated and tuber size. The bigger the tuber and the higher the quantity of Moringa leaves incorporated the lower the WCS, WD and WDMP. Consequently, application of 10 t.ha-1 Moringa leaves and planting of large or medium-sized tubers are recommended for optimum weed suppression in tiger nut production in South West Nigeria.
Is it a better option for young patients with femoral neck fracture to be placed with four cannulated screws during reduction and internal fixation
Authors: Sun Weijun 
Published: November 2022

Abstract
Aim: To compare the efficacy of three cannulated screws and four cannulated screws in the treatment of femoral neck fracture.
Methods: This is a retrospective study.A total of 215 patients were enrolled for the study. Patients who received four cannulated screws were included in the observation group, while patients who received three cannulated screws were included in the control group. Both groups were followed up for at least 1 year. The general data and surgical conditions of the two groups were compared.
Results: A total of 213 patients were included in the study. Among them, 97 patients received four cannulated screws and were included in the observation group. The remaining patients were included in the control group. There was no significant difference in the basic data of these patients. The patients in the observation group had longer actual operation and more intraoperative bleeding, and the difference was statistically significant.At the same time, the patients in the observation group also need to receive more intraoperative X-ray fluoroscopy times, and the difference is statistically significant.Compared with the patients in the control group, the patients in the observation group had better Harris score and hip joint activity, whether 6 months or 1 year after operation, and the difference was statistically significant.At the same time, the number of patients with delayed fracture healing or nonunion in the observation group was also relatively low, and the difference was also statistically significant.There were fewer cases of femoral head necrosis or unequal length of lower limbs in the observation group than in the control group, but the difference was not statistically significant.
Conclusion:Four cannulated screws should be considered for fracture fixation in young patients with femoral neck fractures. This fixation method has the advantage of fast healing time, and the range of motion and functional score of patients' hip joint will also have more advantages.
Acalculous cholecystitis is a common extrahepatic manifestation of hepatitis E and suggests a more serious condition
Authors: Cao Xuemei , Jiang Wei , Shi Lingfeng , Wang Yanping , Chen Jie , Huang Wenxiang , Zhang Shujun 
Published: November 2022

Abstract
Background The purpose of this study was to understand the incidence and clinical significance of acalculous cholecystitis in acute hepatitis E.
Patients and methods A single center enrolled 114 patients with acute hepatitis E. All these patients had imaging of the gallbladder, and patients with gallstones and cholecystectomy were excluded.
Results Acalculous cholecystitis was found in 66 patients (57.89%) with acute hepatitis E. The incidence of males was 63.95%, which was significantly higher than that of females (39.29%) (P=0.022). The mean hospital stays and the incidence of spontaneous peritonitis in patients with cholecystitis were significantly higher than those in patients without cholecystitis 20.12 ± 9.43 days and 9.09%, respectively, and significantly higher than those in patients without cholecystitis 12.98 ± 7.26 days and 0% (P<0.001 and P=0.032, respectively). ALB, TB, DB, CHE and PTA in patients with cholecystitis were significantly inferior to those without cholecystitis (P<0.001, P<0.001, P<0.001, P<0.001 and P= 0.003, respectively).
Conclusion Acalculous cholecystitis is very common in patients with acute hepatitis E, and it may serve as a predictor of increased peritonitis, synthetic decompensation, and longer hospital stay with hepatitis E.
Radio Map Construction based on BERT for Fingerprint-based Indoor Positioning System
Authors: Wang Zhuang , Kong Qun , Wei Bingcai , Zhang Liye , Tian Aikui 
Published: November 2022

Abstract
Due to the heavy workload of RSS collection, the instability of WLAN signal strength and the disappearance of signals caused by complex indoor environments, the construction of Radio Map for Wireless local area network (WLAN) fingerprint-based indoor positioning system is time-consuming and laborious. In order to rapidly deploy indoor WLAN positioning system, the Bidirectional Encoder Representation from Transformers (BERT) model is used to fill the missing signal in Radio Map and quickly build Radio Map. The Radio Map is imported into the BERT model in the form of natural language text, the missing signal is filled by the BERT model. Since the number of input data in BERT model cannot exceed 512 words, the structure of BERT model is not suitable for WLAN signals with large data volume. Therefore, we redefine the model structure based on the original BERT model and fill in the missing signals in the radio map in parallel. In addition, the loss function is redefined. Except that each segment has a loss function, the weighted average value of all segment loss functions is defined as the total loss function. The experimental results show that using the improved BERT model to fill the missing signal in Radio Map is much more accurate and time-saving.