Uncertainty and Explainable Analysis of Machine Learning Model for Reconstruction of Sonic Slowness Logs

Logs are valuable information for oil and gas fields as they help to determine the lithology of the formations surrounding the borehole and the location and reserves of subsurface oil and gas reservoirs. However, important logs are often missing in horizontal or old wells, which poses a challenge in field applications. In this paper, we utilize data from the 2020 machine learning competition of the SPWLA, which aims to predict the missing compressional wave slowness and shear wave slowness logs using other logs in the same borehole. We employ the NGBoost algorithm to construct an Ensemble Learning model that can predicate the results as well as their uncertainty. Furthermore, we combine the SHAP method to investigate the interpretability of the machine learning model. We compare the performance of the NGBosst model with four other commonly used Ensemble Learning methods, including Random Forest, GBDT, XGBoost, LightGBM. The results show that the NGBoost model performs well in the testing set and can provide a probability distribution for the prediction results. In addition, the variance of the probability distribution of the predicted log can be used to justify the quality of the constructed log. Using the SHAP explainable machine learning model, we calculate the importance of each input log to the predicted results as well as the coupling relationship among input logs. Our findings reveal that the NGBoost model tends to provide greater slowness prediction results when the neutron porosity and gamma ray are large, which is consistent with the cognition of petrophysical models. Furthermore, the machine learning model can capture the influence of the changing borehole caliper on slowness, where the influence of borehole caliper on slowness is complex and not easy to establish a direct relationship. These findings are in line with the physical principle of borehole acoustics

Serum from patients with ankylosing spondylitis can increase PPARD, fra-1, MMP7, OPG and RANKL expression in MG63 cells

OBJECTIVES: To explore the effects of serum from patients with ankylosing spondylitis on the canonical Wnt/β-catenin pathway and to assess whether the serum has an osteogenic effect in MG63 cells. METHODS: MG63 cells were cultured with serum from 45 ankylosing spondylitis patients, 30 healthy controls, or 45 rheumatoid arthritis patients. The relative PPARD, fra-1, MMP7, OPG and RANKL mRNA levels were measured using quantitative real-time polymerase chain reaction. Associations between gene expression and patient demographics and clinical assessments were then analyzed. RESULTS: MG63 cells treated with serum from ankylosing spondylitis patients had higher PPARD, fra-1, MMP7 and OPG gene expression than did cells treated with serum from controls or rheumatoid arthritis patients (all

Exposure to low-level metalaxyl impacts the cardiac development and function of zebrafish embryos.

Metalaxyl is an anilide pesticide that is widely used to control plant diseases caused by Peronosporales species. In order to study the toxic effects, zebrafish embryos were exposed to metalaxyl at nominal concentrations of 5, 50 and 500 ng/L for 72 hr, and the cardiac development and functioning of larvae were observed. The results showed that metalaxyl exposure resulted in increased rates of pericardial edema, heart hemorrhage and cardiac malformation. The distance between the sinus venosus and bulbus arteriosus, stroke volume, cardiac output and heart rate were significantly increased in larvae exposed to 50 and 500 ng/L metalaxyl compared to solvent control larvae. Significant upregulation in the transcription of tbx5, gata4 and myh6 was observed in the 50 and 500 ng/L treatments, and that of nkx2.5 and myl7 was observed in the 5, 50 and 500 ng/L groups. These disturbances may be related to cardiac developmental and functional defects in the larvae. The activity of Na+/K+-ATPase and Ca2+-ATPase was significantly increased in zebrafish embryos exposed to 500 ng/L metalaxyl, and the mRNA levels of genes related to ATPase (atp2a11, atp1b2b, and atp1a3b) (in the 50 and 500 ng/L groups) and calcium channels (cacna1ab) (in the 500 ng/L group) were significantly downregulated; these changes might be associated with heart arrhythmia and functional failure

Comprehensive Evaluation of Tea Cultivars Suitable for Matcha Production Using Multivariate Statistical Analysis

Matcha was prepared from 36 tea cultivars grown in the same tea garden according to the shading requirements for fresh leaves to be used for the production of matcha and its 11 quality indexes such as sensory quality, major physicochemical properties and chroma values were analyzed. In order to select tea cultivars suitable for the manufacturing of matcha, a comprehensive evaluation model of matcha quality was established by cluster analysis (CA), principal component analysis (PCA) and multiple linear regression analysis. The CA results showed that the 36 cultivars could be divided into three groups. Matcha from group I had the best quality with green color, fresh and mellow taste, and low phenol/ammonia ratio. Matcha from group II had high phenol/ammonia ratio and strong astringent taste. Matcha from Group III, consisting of etiolated and albino cultivars, had poor color and aroma quality. The PCA results showed that the cumulative contribution rate of the first five principal components was 88.152%. Comprehensive evaluation of matcha using the evaluation function constructed based on the first five principal components showed that the top 10 cultivars were Zhongcha 102, Taicha 12, Zhongcha 108, Fuding Dahao, Meizhan, Fuding Dabai, Fuyun 6, Zi Mudan, Maolv and Yingshuang. The model describing the relationship between sensory quality and physicochemical properties established by multiple linear regression analysis was as follows: y = 3.167|a*| + 46.850 (R2 = 0.710, P < 0.001). The scores of matcha cultivars evaluated by this model were highly consistent with the comprehensive evaluation results based on principal components, indicating that the a* value of dried tea could be used as a representative index to evaluate the quality of matcha. The results of this study can provide a reference for evaluating the suitability of tea cultivars for matcha manufacturing

Attitudes of Chinese maternal and child health professionals toward termination of pregnancy for fetal anomaly: a cross-sectional survey

ObjectivesThis study explores the attitudes of Chinese maternal and child health professionals toward the termination of pregnancy for fetal anomaly (TOPFA) based on four case scenarios and further identifies the factors that influence their attitudes.MethodsThis cross-sectional study, conducted from February 14–21, 2022, aimed to explore the attitudes of maternal and child health professionals toward TOPFA in Hunan Province. We targeted health service institutions across 14 prefecture-level cities and the autonomous prefecture. A questionnaire was made available online and shared via the instant communication platform, WeChat. Participants were recruited through the same platform and completed the survey online. Descriptive statistics were used to analyze the data, and binary logistic regression was performed to determine factors affecting the health professionals’ attitudes toward TOPFA, expressed as the odds ratio (OR) and 95% confidence intervals (CI).ResultsThe study found that 63.5% of health professionals approved of the birth of a fetus with cleft lip and palate, while 36.5% opposed it. Similarly, 39.7% approved of the birth of a fetus with phenylketonuria, while 60.3% opposed it. The percentages of those in favor of and against the birth of a fetus with precocious heart disease were 45.5 and 54.5%, respectively, and those for and against the birth of a fetus with missing fingers were 50.8 and 49.2%, respectively. The top three factors considered by health professionals when agreeing on TOPFA were “the impact of fetal disease on fetal function and growth,” “the severity of fetal disease,” and “the assessment of indications for fetal disease by professionals and related professional advice.” The majority of health professionals (75–78%) preferred joint decision-making by parents regarding the right to decide TOPFA.ConclusionOur study indicates that the attitudes of health professionals toward TOPFA can differ significantly depending on the specific birth defect under consideration. Notably, the majority of health professionals prioritized “the impact of fetal abnormalities on fetal function and development” when deciding their support for TOPFA, advocating for the decision to be a joint one between the parents. Additionally, factors such as religious beliefs, professional training, age, and job title appeared to influence these attitudes toward TOPFA. Our findings could serve as a reference point in the development of guidelines for the prevention and management of birth defects

Quantum chemical calculation study on the thermal decomposition of electrolyte during lithium-ion battery thermal runaway

Understanding the behavior of lithium-ion battery electrolytes during thermal runaway is essential for designing safer batteries. However, current reports on electrolyte decomposition behaviors often focus on reactions with electrode materials. Herein we use quantum chemical calculations to develop a model for the thermal decomposition mechanism of electrolytes under both electrolyte and ambient atmosphere conditions. The thermal stability is found to be associated with the dielectric constants of electrolyte constituents. Within the electrolyte, the solvation effects between molecules increase electrolyte stability, making thermal decomposition a more difficult process. Furthermore, Li+ is observed to facilitate electrolyte thermal decomposition, as the energy required for the thermal decomposition reactions of molecules decreases when they are bonded with Li+. It is hoped that this study will offer a theoretical basis for understanding the complex reactions occurring during thermal runaway events

Near-atomic cryo-electron microscopy structures of varicella-zoster virus capsids

VZV是一种广泛存在并且具有高度传染性的人类α-疱疹病毒。初次感染VZV可导致水痘，人群普遍易感（感染率约为61%～100%）。该病毒可在背根神经节潜伏感染，持续终生。夏宁邵教授团队长期开展VZV相关基础与新型疫苗研究，通过系统和精细探索建立了高效的VZV规模化培养和病毒颗粒纯化技术体系，成功获得高质量的VZV颗粒样品。首次揭示了疱疹病毒α家族的水痘-带状疱疹病毒（VZV）不同类型核衣壳的近原子分辨率结构，阐明了VZV核衣壳不同组成蛋白的相互作用网络与衣壳装配机制，可为进一步开展新型载体疫苗设计及抗病毒药物等研究提供重要支持。 我校博士后王玮、高级工程师郑清炳、博士生潘德全和俞海副教授为该论文共同第一作者，我校夏宁邵教授、程通副教授、李少伟教授以及美国罗格斯大学朱桦（Hua Zhu）教授、加利福尼亚大学洛杉矶分校周正洪（Z. Hong Zhou）教授为该论文的共同通讯作者。【Abstract】Varicella-zoster virus (VZV) is a medically important human herpesvirus that causes chickenpox and shingles, but its cell-associated nature has hindered structure studies. Here we report the cryo-electron microscopy structures of purified VZV A-capsid and C-capsid, as well as of the DNA-containing capsid inside the virion. Atomic models derived from these structures show that, despite enclosing a genome that is substantially smaller than those of other human herpesviruses, VZV has a similarly sized capsid, consisting of 955 major capsid protein (MCP), 900 small capsid protein (SCP), 640 triplex dimer (Tri2) and 320 triplex monomer (Tri1) subunits. The VZV capsid has high thermal stability, although with relatively fewer intra- and inter-capsid protein interactions and less stably associated tegument proteins compared with other human herpesviruses. Analysis with antibodies targeting the N and C termini of the VZV SCP indicates that the hexon-capping SCP—the largest among human herpesviruses—uses its N-terminal half to bridge hexon MCP subunits and possesses a C-terminal flexible half emanating from the inner rim of the upper hexon channel into the tegument layer. Correlation of these structural features and functional observations provide insights into VZV assembly and pathogenesis and should help efforts to engineer gene delivery and anticancer vectors based on the currently available VZV vaccine.This research was supported by grants from the National Science and Technology Major Projects for Major New Drugs Innovation and Development (no. 2018ZX09711003-005-003), the National Science and Technology Major Project of Infectious Diseases (no. 2017ZX10304402), the National Natural Science Foundation of China (no. 81871648, 81601762), the Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences (no. 2019RU022) and the US National Institutes of Health (DE025567/028583). 该研究获得了国家自然科学基金、新药创制国家科技重大专项和传染病防治国家科技重大专项等资助

Safety, tolerability, pharmacokinetics, and pharmacodynamics of single and multiple doses of aficamten in healthy Chinese participants: a randomized, double-blind, placebo-controlled, phase 1 study

Objectives: Aficamten is a selective, small-molecule allosteric inhibitor of cardiac sarcomere being developed as a chronic oral treatment for patients with symptomatic obstructive hypertrophic cardiomyopathy. This was the first-in-Chinese study aiming to investigate the safety, tolerability, pharmacokinetics, and pharmacodynamics of aficamten in healthy adults.Methods: This double-blind, randomized, placebo-controlled, phase 1 study was conducted in 28 healthy male and female Chinese participants after single ascending dose (SAD) and multi-dose (MD) administrations of aficamten. In the SAD cohort, 16 participants were randomized to receive a single oral dose of aficamten: 10 mg, 20 mg, or placebo. In the MD cohort, 12 participants were randomized to receive multiple doses of aficamten: 5 mg or placebo once daily for 14 days. Safety was monitored throughout the study with electrocardiograms, echocardiograms, clinical laboratory tests, and reporting of adverse events (AEs). Pharmacokinetic profiles of aficamten and metabolites, as well as CYP2D6 genetic impact, were evaluated.Results: A total of 35 treatment-emergent AEs were reported by 14 (50%) participants with mild severity. There were no serious AEs or adverse decreases in left ventricular ejection fraction below 50% during the study. Aficamten was dose-proportional over the dose range of 5–20 mg and accumulated in the MD cohort.Conclusion: Aficamten was safe and well-tolerated in the healthy Chinese adult participants. The pharmacokinetics of aficamten in the Chinese population was comparable to those previously found in Western participants. These phase 1 data support the progression of aficamten into future clinical studies in Chinese patients.Clinical Trial registration:https://clinicaltrials.gov, identifier: NCT04783766

Identification of antibodies with non-overlapping neutralization sites that target coxsackievirus A16

手足口病（Hand, Foot and Mouth Disease，HFMD）是一种由人肠道病毒引起的全球性传染病，主要发生于5岁以下的婴幼儿。2月5日，我校夏宁邵教授团队在《细胞》子刊《细胞•宿主与微生物》（Cell Host & Microbe）上在线发表题为“Identification of antibodies with non-overlapping neutralization sites that target coxsackievirus A16”的研究论文。该研究首次揭示了手足口病主要病原体柯萨奇病毒A组16型（CVA16）三种衣壳颗粒形式与三种不同类型的治疗性中和抗体的全面相互作用细节和非重叠的中和表位结构信息，阐明了CVA16成熟颗粒是疫苗候选主要保护性免疫原的理论基础，建立了可指导疫苗研制的免疫原特异检测方法，为CVA16疫苗及抗病毒药物研究提供关键基础。我校夏宁邵教授、李少伟教授、程通副教授和美国加州大学洛杉矶分校纳米系统研究所Z. Hong Zhou（周正洪）教授为该论文的共同通讯作者。我校博士生何茂洲、徐龙发博士后、郑清炳高级工程师、博士生朱瑞和尹志超为该论文共同第一作者。【Abstract】Hand, foot, and mouth disease is a common childhood illness primarily caused by coxsackievirus A16 (CVA16), for which there are no current vaccines or treatments. We identify three CVA16-specific neutralizing monoclonal antibodies (nAbs) with therapeutic potential: 18A7, 14B10, and NA9D7. We present atomic structures of these nAbs bound to all three viral particle forms—the mature virion, A-particle, and empty particle—and show that each Fab can simultaneously occupy the mature virion. Additionally, 14B10 or NA9D7 provide 100% protection against lethal CVA16 infection in a neonatal mouse model. 18A7 binds to a non-conserved epitope present in all three particles, whereas 14B10 and NA9D7 recognize broad protective epitopes but only bind the mature virion. NA9D7 targets an immunodominant site, which may overlap the receptor-binding site. These findings indicate that CVA16 vaccines should be based on mature virions and that these antibodies could be used to discriminate optimal virion-based immunogens.This work was supported by grants from the Major Program of National Natural Science Foundation of China ( 81991490 ), the National Science and Technology Major Projects for Major New Drugs Innovation and Development ( 2018ZX09711003-005-003 ), the National Science and Technology Major Project of Infectious Diseases ( 2017ZX10304402-002-003 ), the National Natural Science Foundation of China ( 31670933 and 81801646 ), the China Postdoctoral Science Foundation ( 2018M640599 and 2019T120557 ), the Principal Foundation of Xiamen University ( 20720190117 ), and the National Institutes of Health ( R37-GM33050 , GM071940 , DE025567 , and AI094386 ). 该研究获得了国家自然科学基金、新药创制国家科技重大专项、传染病防治国家科技重大专项和美国国立卫生研究院基金的资助

Foxp3+ regulatory T cells maintain the bone marrow microenvironment for B cell lymphopoiesis

Foxp3+ regulatory T cells (Treg cells) modulate the immune system and maintain self-tolerance, but whether they affect haematopoiesis or haematopoietic stem cell (HSC)-mediated reconstitution after transplantation is unclear. Here we show that B-cell lymphopoiesis is impaired in Treg-depleted mice, yet this reduced B-cell lymphopoiesis is rescued by adoptive transfer of affected HSCs or bone marrow cells into Treg-competent recipients. B-cell reconstitution is abrogated in both syngeneic and allogeneic transplantation using Treg-depleted mice as recipients. Treg cells can control physiological IL-7 production that is indispensable for normal B-cell lymphopoiesis and is mainly sustained by a subpopulation of ICAM1+ perivascular stromal cells. Our study demonstrates that Treg cells are important for B-cell differentiation from HSCs by maintaining immunological homoeostasis in the bone marrow microenvironment, both in physiological conditions and after bone marrow transplantation