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Calibration after bootstrap for accurate uncertainty quantification in regression models

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npj Computational Materials 2022年第1期8卷 1092-1100页

作者： Glenn Palmer Siqi Du Alexander Politowicz Joshua Paul Emory Xiyu Yang Anupraas Gautam Grishma Gupta Zhelong Li Ryan Jacobs Dane Morgan Department of Computer Sciences University of Wisconsin-MadisonMadisonWIUSA Department of Materials Science and Engineering University of Wisconsin-MadisonMadisonWIUSA

Obtaining accurate estimates of machine learning model uncertainties on newly predicted data is essential for understanding the accuracy of the model and whether its predictions can be trusted.A common approach to such uncertainty quantification is to estimate the variance from an ensemble of models,which are often generated by the generally applicable bootstrap *** this work,we demonstrate that the direct bootstrap ensemble standard deviation is not an accurate estimate of uncertainty but that it can be simply calibrated to dramatically improve its *** demonstrate the effectiveness of this calibration method for both synthetic data and numerous physical datasets from the field of Materials Science and *** approach is motivated by applications in physical and biological science but is quite general and should be applicable for uncertainty quantification in a wide range of machine learning regression models.

关键词： ensemble applicable uncertainty

Long-term outcomes of endoscopic submucosal dissection for undifferentiated type early gastric cancer over 2 cm with R0 resection

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World Journal of Gastrointestinal Endoscopy 2024年第6期16卷 326-334页

作者： Jun Yong Bae Chang Beom Ryu Moon Sung Lee Kulwinder S Dua Internal Medicine and Digestive Disease Center Seoul Medical CenterSeoul 02053South Korea Internal Medicine and Digestive Disease Center and Research Institute Soon Chun Hyang University of School of MedicineBucheon 14584South Korea Department of Medicine Medical College of WisconsinMilwaukeeWI 53226United States

BACKGROUND Endoscopic submucosal dissection(ESD)for over 2 cm in size undifferentiated type(UD type)early gastric cancer(EGC)confined to the mucosa is not only challenging,but also long-term outcomes are not well *** To evaluate the long-term outcomes of ESD done for UD type EGCs confined to the mucosa over 2 cm in size and compare the results with those where the lesions were less than 2 *** 143 patients with UD type EGC confirmed on histology after ESD at a tertiary hospital were *** with synchronous and metachronous lesions and a case with emergency surgery after ESD were excluded.A total of 137 cases were enrolled.79 cases who underwent R0 resection were divided into 2 cm or less(group A)and over 2 cm(group B)in *** Among 79 patients who underwent R0 resection,the number in group A and B were 51 and 28,*** mean follow-up period(SD)was 79.71±45.42 *** was a local recurrence in group A(1/51,2%)and group B(1/28,3.6%)*** patient in group A underwent surgery while the patient in group B underwent repeated ESD with no further recurrences in both *** was no regional lymph node metastasis,distant metastasis,and deaths in both *** R0 resection strategy for ESD on lesions over 2 cm,20.4%(28/137)of patients were able to avoid surgery compared with expanded *** If R0 resection is achieved by ESD,UD type EGCs over 2 cm also showed good and similar clinical outcomes as compared to lesions less than 2 cm when followed for over 5 *** R0 resection strategy,several patients can avoid surgery.

关键词： Undifferentiated type early gastric cancer Endoscopic submucosal dissection Long term outcomes Over 2 cm Early gastric cancer

Micromolded honeycomb scaffold design to support the generation of a bilayered RPE and photoreceptor cell construct

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Bioactive Materials 2023年第12期30卷 142-153页

作者： In-Kyu Lee Ruosen Xie Agustin Luz-Madrigal Seunghwan Min Jingcheng Zhu Jiahe Jin Kimberly L.Edwards M.Joseph Phillips Allison L.Ludwig David M.Gamm Shaoqin Gong Zhenqiang Ma Department of Electrical and Computer Engineering University of Wisconsin-MadisonMadisonWI53706USA wisconsin Institute for Discovery University of Wisconsin-MadisonMadisonWI53715USA Department of Ophthalmology and Visual Sciences University of Wisconsin-MadisonMadisonWI53705USA Department of Biomedical Engineering University of Wisconsin-MadisonMadisonWI53706USA McPherson Eye Research Institute University of Wisconsin-MadisonMadisonWI53705USA Waisman Center University of Wisconsin-MadisonMadisonWI53705USA Department of Comparative Biomedical Sciences University of Wisconsin–MadisonMadisonWI53706USA Department of Materials Science and Engineering University of Wisconsin-MadisonMadisonWI53706USA Department of Engineering Physics University of Wisconsin-MadisonMadisonWI53706USA Grainger Institute for Engineering University of Wisconsin-MadisonMadisonWI53706USA

Age-related macular degeneration(AMD)causes blindness due to loss of retinal pigment epithelium(RPE)and photoreceptors(PRs),which comprise the two outermost layers of the *** the small size of the macula and the importance of direct contact between RPE and PRs,the use of scaffolds for targeted reconstruction of the outer retina in later stage AMD and other macular dystrophies is particularly *** developed microfabricated,honeycomb-patterned,biodegradable poly(glycerol sebacate)(PGS)scaffolds to deliver organized,adjacent layers of RPE and PRs to the subretinal ***,an optimized process was developed to photocure PGS,shortening scaffold production time from days to *** resulting scaffolds robustly supported the seeding of human pluripotent stem cell-derived RPE and PRs,either separately or as a dual celllayered *** advanced,economical,and versatile scaffolds can accelerate retinal cell transplantation efforts and benefit patients with AMD and other retinal degenerative diseases.

关键词： Microfabrication Retina Scaffolds Stem cells Tissue engineering

Delivery Outcomes in Non-Tertiary Referral Centers for Women with Congenital Heart Disease

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Congenital Heart Disease 2023年第3期18卷 315-323页

作者： Daniel Sweeney Scott Cohen Salil Ginde Jennifer Gerardin Peter Bartz Matthew Buelow Medical College of wisconsin MilwaukeeWIUSA Department of Pediatrics Medical College of WisconsinMilwaukeeWIUSA Department of Internal Medicine Medical College of WisconsinMilwaukeeWIUSA

Background:Women with congenital heart disease(CHD)have increased risk for adverse events during pregnancy and *** studies have assessed pregnancy and delivery outcomes at tertiary referral centers(TRC).The aim of our study was to assess pregnancy outcomes in women with CHD who deliver in a non-tertiary referral center(non-TRC).Methods:Clinical demographics were collected,including anatomic complexity,physiologic state and pre-pregnancy risk *** were stratified by delivery location,either TRC or *** and neonatal complications of pregnancy were ***:Women with CHD who delivered in a TRC had a higher pre-pregnancy risk when assessed by the Zahar and CARPREG-II scores,and had more patients fall into a higher WHO *** was no difference in rates of maternal cardiac complications between delivery locations(11%)and neonatal complications(20%)between deliveries at TRC and ***:There were not increased maternal cardiac or neonatal complications when delivery occurred at a *** complications remained high regardless of delivery *** study suggests that proper risk assessment may help identify women who are candidates for safe delivery at non-TRC in women with CHD,and that neonatal resources should be considered when planning delivery location.

关键词： Congenital heart disease pregnancy delivery outcome

Consistency of Tropospheric Water Vapor between Reanalyses and Himawari-8/AHI Measurements over East Asia

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Advances in Atmospheric Sciences 2024年第1期41卷 19-38页

作者： Di DI Jun LI Yunheng XUE Min MIN Bo LI Zhenglong LI Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters Nanjing University of Information Science and TechnologyNanjing 210044China Key Laboratory for Aerosol-Cloud-Precipitation China Meteorological AdministrationSchool of Atmospheric PhysicsNanjing University of Information Science and TechnologyNanjing 210044China FYSIC National Satellite Meteorological CenterChina Meteorological AdministrationBeijing 100081China Chengdu University of Information Science and Technology Chengdu 610225China School of Atmospheric Sciences and Guangdong Province Key laboratory for Climate Change and Natural Disaster Studies Sun Yat-sen University and Southern Laboratory of Ocean Science and EngineeringZhuhai 519082China Cooperative Institute for Meteorological Satellite Studies University of Wisconsin–MadisonMadison WI 53706WisconsinUSA Wuxi University Wuxi 214105China

High spatiotemporal resolution radiances from the advanced imagers onboard the new generation of geostationary weather satellites provide a unique opportunity to evaluate the abilities of various reanalysis datasets to depict multilayer tropospheric water vapor(WV),thereby enhancing our understanding of the deficiencies of WV in reanalysis *** on daily measurements from the Advanced Himawari Imager(AHI)onboard the Himawari-8 satellite in 2016,the bias features of multilayer WV from six reanalysis datasets over East Asia are thoroughly *** assessments show that wet biases exist in the upper troposphere in all six reanalysis datasets;in particular,these biases are much larger in ***,we find better depictions of WV in the middle troposphere than in the upper *** accuracy of WV in the ERA5 dataset is the highest,in terms of the bias magnitude,dispersion,and pattern *** characteristics of the WV bias over the Tibetan Plateau are significantly different from those over other parts of East *** addition,the reanalysis datasets all capture the shift of the subtropical high very well,with ERA5 performing better overall.

关键词： AHI reanalysis dataset multilayer water vapor assessment radiative transfer model

Surface-enhanced Raman spectroscopy for emerging contaminant analysis in drinking water

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Frontiers of Environmental Science & Engineering 2023年第5期17卷 51-65页

作者： Seo Won Cho Haoran Wei Environmental Chemistry and Technology Program University of Wisconsin–MadisonMadisonWI 53706USA Department of Civil and Environmental Engineering University of Wisconsin–MadisonMadisonWI 53706USA

Emerging contaminants(ECs)in drinking water pose threats to public health due to their environmental prevalence and potential *** occurrence of ECs in our drinking water supplies depends on their physicochemical properties,discharging rate,and susceptibility to removal by water treatment *** health effects of long-term exposure to ECs justify their regular monitoring in drinking water *** this review article,we will summarize the current status and future opportunities of surface-enhanced Raman spectroscopy(SERS)for EC analysis in drinking *** principles of SERS are first introduced and a comparison of SERS and liquid chromatography-tandem mass spectrometry in terms of cost,time,sensitivity,and availability is ***,we discuss the strategies for designing effective SERS sensors for EC analysis based on five categories—per-and polyfluoroalkyl substances,novel pesticides,pharmaceuticals,endocrine-disrupting chemicals,and *** addition to maximizing the intrinsic enhancement factors of SERS substrates,strategies to improve hot spot accessibilities to the targeting ECs are equally *** is a review article focusing on SERS analysis of ECs in drinking *** discussions are not only guided by numerous endeavors to advance SERS technology but also by the drinking water regulatory policy.

关键词： Emerging contaminant Surface-enhanced Raman spectroscopy Drinking water monitoring Sensor Regulatory policy

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不可忽略的无响应缺失下的协变量选择

应用概率统计 2024年第2期40卷 287-297页

作者：邵军王磊华东师范大学统计学院上海200062 美国威斯康星大学麦迪逊分校统计系麦迪逊WI53706 南开大学统计与数据科学学院天津300071

本文旨在建立一个存在不可忽略的无响应缺失时高维协变量向量的协变量选择方法.由于有不可忽略的缺失响应数据,必须建立一种新的协变量选择方法来删除既与响应变量也与缺失机制无关的协变量.一旦冗余协变量被删除,现有的缺失机制估计和... 详细信息

本文旨在建立一个存在不可忽略的无响应缺失时高维协变量向量的协变量选择方法.由于有不可忽略的缺失响应数据,必须建立一种新的协变量选择方法来删除既与响应变量也与缺失机制无关的协变量.一旦冗余协变量被删除,现有的缺失机制估计和其他基于逆缺失机制加权的分析方法可以被应用.我们提供了一些模拟结果来展示我们方法的有效性.

关键词：构造的响应变量高维非随机丢失缺失机制半参数方法

Nano-STING agonist-decorated microrobots boost innate and adaptive anti-tumor immunity

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Nano Research 2023年第7期16卷 9848-9858页

作者： Yixin Wang Zhaoting Li Yu Chen Allie Barrett Fanyi Mo Quanyin Hu Pharmaceutical Sciences Division School of PharmacyUniversity of Wisconsin-MadisonMadisonWI 53705USA Carbone Cancer Center School of Medicine and Public HealthUniversity of Wisconsin-MadisonMadisonWI 53705USA wisconsin Center for NanoBioSystems School of PharmacyUniversity of Wisconsin-MadisonMadisonWI 53705USA

Activating the cyclic guanosine monophosphate-adenosine monophosphate synthase/stimulator of interferon genes(cGAS/STING)signaling has emerged as a promising anti-tumor strategy due to the important role of the pathway in innate and adaptive immunity,yet the selective delivery of STING agonists to tumors following systemic administration remains ***,we develop a nano-STING agonist-decorated microrobot platform to achieve the enhanced anti-tumor *** ions and the STING agonist 2’3’-cyclic guanosine monophosphate-adenosine monophosphate(cGAMP)are co-encapsulated in the mitochondria-targeting nanoparticles(mTNPs),which can trigger the release of mitochondrial DNA(mtDNA)by Fenton reactioninduced mitochondria oxidative *** exogenous cGAMP and the endogenous mtDNA can work synergistically to induce potent cGAS/STING signaling ***,we decorate mTNPs onto Salmonella typhimurium VNP20009(VNP)bacteria to facilitate tumor accumulation and deep *** demonstrate that the systemic administration of this microrobot activates both innate and adaptive immunity,improving the immunotherapeutic efficacy of the STING agonists.

关键词： drug delivery mitochondrial DNA(mtDNA) Fenton reaction stimulator of interferon genes(STING) tumor immunotherapy bacteria

Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway

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Synthetic and Systems Biotechnology 2022年第2期7卷 738-749页

作者： Francesca V.Gambacorta Ellen R.Wagner Tyler B.Jacobson Mary Tremaine Laura K.Muehlbauer Mick A.McGee Justin J.Baerwald Russell L.Wrobel John F.Wolters Mike Place Joshua J.Dietrich Dan Xie Jose Serate Shabda Gajbhiye Lisa Liu Maikayeng Vang-Smith Joshua J.Coon Yaoping Zhang Audrey P.Gasch Daniel Amador-Noguez Chris Todd Hittinger Trey K.Sato Brian F.Pfleger DOE Great Lakes Bioenergy Research Center University of Wisconsin-MadisonMadisonWIUSA Department of Chemical and Biological Engineering University of Wisconsin-MadisonMadisonWIUSA Laboratory of Genetics Center for Genomic Science InnovationUniversity of Wisconsin-MadisonMadisonWIUSA Department of Bacteriology University of Wisconsin-MadisonMadisonWIUSA Department of Chemistry University of Wisconsin-MadisonMadisonWIUSA wisconsin Energy Institute J.F.Crow Institute for the Study of EvolutionUniversity of Wisconsin-MadisonMadisonWIUSA Department of Biomolecular Chemistry University of Wisconsin-MadisonMadisonWIUSA

Metabolic engineering strategies have been successfully implemented to improve the production of isobutanol,a next-generation biofuel,in Saccharomyces ***,we explore how two of these strategies,pathway re-localization and redox cofactor-balancing,affect the performance and physiology of isobutanol producing *** equipped yeast with isobutanol cassettes which had either a mitochondrial or cytosolic localized isobutanol pathway and used either a redox-imbalanced(NADPH-dependent)or redox-balanced(NADH-dependent)ketol-acid reductoisomerase *** then conducted transcriptomic,proteomic and metabolomic analyses to elucidate molecular differences between the engineered *** localization had a large effect on isobutanol production with the strain expressing the mitochondrial-localized enzymes producing 3.8-fold more isobutanol than strains expressing the cytosolic ***-balancing did not improve isobutanol titers and instead the strain with the redox-imbalanced pathway produced 1.5-fold more isobutanol than the balanced version,albeit at low overall pathway *** genomic analyses suggested that the poor performances of the cytosolic pathway strains were in part due to a shortage in cytosolic Fe-S clusters,which are required cofactors for the dihydroxyacid dehydratase *** then demonstrated that this cofactor limitation may be partially recovered by disrupting iron homeostasis with a fra2 mutation,thereby increasing cellular iron *** resulting isobutanol titer of the fra2 null strain harboring a cytosolic-localized isobutanol pathway outperformed the strain with the mitochondrial-localized pathway by 1.3-fold,demonstrating that both localizations can support flux to isobutanol.

关键词： Saccharomyces cerevisiae Isobutanol Functional genomics analysis Pathway localization Fe incorporation