200 research outputs found
Optimization, random resampling, and modeling in bioinformatics
Get PDFQuantitative phenotypes regulated by multiple genes are prevalent in nature and many diseases falls into this category. High-throughput sequencing and high-performance computing provides a basis to understand quantitative phenotypes. However, finding a statistical approach correctly model the phenotypes remain a challenging problem. In this work, I present a resampling-based approach to obtain biological functional categories from gene set and apply the approach to analyze lithium-sensitivity of neurological diseases and cancer. Then, the non-parametrical permutation-based approach is applied to evaluate the performance of a GWAS modeling procedure. While the procedure performs well in statistics, search space reduction is required to address the computation challenge.Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2020-08-01The student, Weihao Ge, accepted the attached license on 2018-07-11 at 15:01.The student, Weihao Ge, submitted this Dissertation for approval on 2018-07-11 at 15:20.This Dissertation was approved for publication on 2018-07-12 at 14:53.DSpace SAF Submission Ingestion Package generated from Vireo submission #12830 on 2018-09-27 at 11:19:09Made available in DSpace on 2018-09-27T16:34:18Z (GMT). No. of bitstreams: 7
GE-DISSERTATION-2018.pdf: 2587074 bytes, checksum: af7295222757484aaacb101c2a1eec14 (MD5)
AllGOTermsInTree_Final.xlsx: 114511 bytes, checksum: aefaec95ed1104987bc7fe79bc1e5b16 (MD5)
Chapter5SupplementaryFigures.docx: 2392428 bytes, checksum: 1bba9d546f1b67c74ecd744b4bee8731 (MD5)
pipeline.gz: 527759 bytes, checksum: f83373d18bb2831dec768ff46cfd16c2 (MD5)
pipelinemanual.docx: 863317 bytes, checksum: f813672fc091f22c7f131d1f4268279d (MD5)
ThesisWeihaoGe.docx: 18721490 bytes, checksum: 3ca2ada1d09dccca4daf4c49bdbb5408 (MD5)
LICENSE.txt: 4206 bytes, checksum: 57d6e5e606dca5f9a8e9e23563f2b5c2 (MD5)
Previous issue date: 2018-07-12Embargo set by: Seth Robbins for item 107807
Lift date: 2020-09-27T16:34:29Z
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemU of I Only Restriction Lifted for Item 107807 on 2020-09-28T09:15:16Z
Moral judgment and cheating: Evidence of a knowledge-behavior link in early childhood
No full textThe data for "Moral Judgment and Cheating:
Evidence of A Knowledge-Behavior Link in Early Childhood" by Li Zhao, Weihao Yan, Junjie Peng, and Paul L. Harri
On power monoids and their automorphisms
Get PDFEndowed with the binary operation of set addition, the family of all finite subsets of containing forms a monoid, with the singleton as its neutral element.
We show that the only non-trivial automorphism of is the involution . The proof leverages ideas from additive number theory and proceeds through an unconventional induction on what we call the boxing dimension of a finite set of integers, that is, the smallest number of (discrete) intervals whose union is the set itself.11 pages, no figures. Fixed many typos and a couple of mistakes from the previous version. To appear in J Combinatorial Theory Ser
Friluftslif : Mobility for Free Air Living
No full textUME Friluftsliv is a mobility solution focusingon Rural coliving communities. The author hasexperienced the huge transition of urbaniza-tion. After more than 15 years of urban life,the author occasionally missed the old daysand questioned if there was any other choice.During the study in Sweden, the author learnedthe Scandinavian concept “Friluftsliv” whichtranslates literally as free air living. It is a lifestyleattaching much importance to connecting withnature and spending time outdoors. The authorhad practiced along the journey and benefitedfrom it a lot. Hence, Friluftsliv was chosen as theproject theme to promote such a lifestyle and toevoke the audience to join.During the research, it was found that with amore flexible working pattern, coliving becameincreasingly popular and promising. And thecommunity spirit is the core. Among diversecoliving spaces, coliving in rural regions offerscommunities and more outdoor explorationopportunities, while the locations are likely onthe radar. For better understanding, the authorconducted a case study on the Arctic Cowork-ing Lodge, which is located in Lofoten Islands,Norway.The creative process is based on the case studyresults of Arctic Coworking Lodge, enhancingthe rural coliving experience for everyone wasthe priority. Collaborating with colleagues, thepackage was defined by mock-up in the stu-dio as a space configuration of concentrate,exchange and relax. Hand sketching was usedprimarily for initial exploration, and then build-ing up 3D drafts helped to coordinate variouscomponents into the package. The design focusof this project is the community spirit. Modulardesign was applied to make the vehicle versatilefor the different persona in different scenarios.The concept is the modular interior componentscan be detached and shared out to supportoutdoor activities
PDE-Constrained Machine Learning with Gaussian Processes towards Digital Twins
No full textThe development of trustworthy digital twins for complex physical systems, often governed by high-dimensional partial differential equations (PDEs), demands predictive models that are both highly accurate and provide reliable uncertainty quantification (UQ). This thesis addresses the complementary weaknesses of two leading machine learning paradigms: the powerful expressiveness of deep neural networks (NNs), which often lack robust UQ, and the principled probabilistic nature of Gaussian processes (GPs), which struggle with the curse of dimensionality.This work presents a unified framework that synergizes these approaches through physics-constrained deep kernel learning (DKL). In this hybrid architecture, an NN learns a low-dimensional, feature representation, which in turn defines the kernel of a GP. This design leverages the representation learning power of NNs to make GP inference tractable and effective in high-dimensional settings.The core contributions are twofold. For forward problems, we introduce a PDE-constrained DKL model that effectively mitigates the curse of dimensionality. By embedding physical laws into deep kernel, the framework learns physically consistent solutions and provides reliable uncertainty estimates even from sparse data. For inverse problems, such as estimating unknown PDE parameters, we propose a novel two-stage Bayesian inference strategy to overcome computational intractability. An initial physics-informed pretraining stage optimizes the high-dimensional NN weights and provides robust point estimates. In the second stage, these weights are fixed, enabling efficient Hamiltonian Monte Carlo (HMC) sampling of the posterior distribution for only the low-dimensional PDE parameters and kernel hyperparameters.Collectively, this dissertation delivers a cohesive and robust framework for scientific machine learning. By systematically addressing architectural foundations, forward modeling in high dimensions, and tractable Bayesian inference for inverse problems, this work provides a significant step towards building trustworthy, uncertainty-aware digital twins for complex systems in science and engineering
Friluftslif : Mobility for Free Air Living
No full textUME Friluftsliv is a mobility solution focusingon Rural coliving communities. The author hasexperienced the huge transition of urbaniza-tion. After more than 15 years of urban life,the author occasionally missed the old daysand questioned if there was any other choice.During the study in Sweden, the author learnedthe Scandinavian concept “Friluftsliv” whichtranslates literally as free air living. It is a lifestyleattaching much importance to connecting withnature and spending time outdoors. The authorhad practiced along the journey and benefitedfrom it a lot. Hence, Friluftsliv was chosen as theproject theme to promote such a lifestyle and toevoke the audience to join.During the research, it was found that with amore flexible working pattern, coliving becameincreasingly popular and promising. And thecommunity spirit is the core. Among diversecoliving spaces, coliving in rural regions offerscommunities and more outdoor explorationopportunities, while the locations are likely onthe radar. For better understanding, the authorconducted a case study on the Arctic Cowork-ing Lodge, which is located in Lofoten Islands,Norway.The creative process is based on the case studyresults of Arctic Coworking Lodge, enhancingthe rural coliving experience for everyone wasthe priority. Collaborating with colleagues, thepackage was defined by mock-up in the stu-dio as a space configuration of concentrate,exchange and relax. Hand sketching was usedprimarily for initial exploration, and then build-ing up 3D drafts helped to coordinate variouscomponents into the package. The design focusof this project is the community spirit. Modulardesign was applied to make the vehicle versatilefor the different persona in different scenarios.The concept is the modular interior componentscan be detached and shared out to supportoutdoor activities
可調控細胞行為和組織再生的工程化動態生物材料
No full textCells continuously interact with their surrounding microenvironment, and these interactions regulate a series of cellular processes, thereby directing cell behaviors and fate. Engineered biomaterials provide an artificial microenvironment for the seeded or encapsulated cells, where cell–material interaction can be rationally modulated to realize effective cell lineage commitment. Elegant previous studies have achieved significant progress in the biomedical applications of biomimetic materials emulating the biochemical complexity of extracellular matrix (ECM). However, the field of dynamic synthetic biointerfaces, which can be utilized for manipulation of cell–material interaction, is still in its infancy. In this dissertation, we present three different dynamic platforms to emulate the inherent properties of the ECM, manipulate the cell behaviors, and promote the tissue regeneration.Among various biomaterials, hydrogels are the promising candidates for tissue engineering and regenerative medicine. We next moved our focus to dynamic hydrogels based on metal ions and bisphosphonates. Doping of metal ions such as Mg2+, Ca2+ and Fe2+ provides the hydrogels with unique attributes, including bioactivity, conductivity, and tunability. We first developed a versatile and general strategy to fabricate a family of nanocomposite hydrogels based on a wide array of metal ions. We demonstrated that the hydrogels exhibited a wide spectrum of remarkable dynamic properties, such as excellent injectability, rapid stress relaxation, efficient ion diffusion, and triggered disassembly for harvesting encapsulated cells. Moreover, we demonstrated that the nanocomposite hydrogels doped with lanthanide ions exhibited highly tunable fluorescent spectrum. We next applied the developed hydrogels to treat peripheral nerve injuries, which are of great clinical significance. We demonstrated that the nanocomposite hydrogels containing magnesium and bisphosphonates promoted peripheral nerve regeneration and achieved partial functional recovery in s sciatic nerve injury rat model.To further investigate the applications of tissue regeneration assisted by the dynamic hydrogels, we next designed a supramolecular cell-adaptable gelatin host-guest (GHG) hydrogel with various dynamic properties, including injectability, shear-thinning and self-healing. The GHG hydrogel can be loaded with various therapeutic agents for a series of tissue regeneration. We first examined the skin regeneration of the GHG hydrogel-based wound dressing on a full-thickness burn mice model. Prolonged inflammatory response and insufficient vascularization cause delayed and poor wound healing. We demonstrated that the GHG hydrogel loaded with resveratrol and histatin-1 suppressed inflammation and promoted vascularization at skin burn wound sites. We next evaluated the efficacy of dynamic hydrogels to treat a debilitating injury, traumatic spinal cord injury. We demonstrated that the GHG hydrogel loaded with adipose-derived stromal cells promoted spinal cord regeneration via enhanced in-situ neurogenesis and efficient pro-healing immunomodulation. We next studied the efficacy of GHG hydrogels to promote osteochondral regeneration both in small and large animals. We demonstrated that the GHG hydrogel with tunable degradation kinetic supported effective hyaline cartilage repair in cartilage defect model of pig.We then moved to utilize the engineered nanocomposite dynamic hydrogels mimicking the hierarchical biomechanical structures of the natural ECM. We demonstrated that the chemical incorporation of acryloyl nanoparticle-based cross-linkers creates regionally stiff network structures in the dynamic supramolecular hydrogels without compromising the dynamic properties of the cell-adaptable inter-nanoparticle hydrogel network. The obtained dynamic hydrogels with a heterogeneous hydrogel network topology expedite the development of adhesion structures, 3D spreading, and mechanosensing of the encapsulated stem cells, as evidenced by the upregulated expression of key biomarkers such as vinculin, FAK, and YAP. This enhanced spreading and mechanotransduction promote the osteogenic differentiation of the encapsulated stem cells. In contrast, doping with physically entrapped nanoparticles or molecular cross-linkers (PEGDA) cannot locally reinforce the dynamic hydrogel network and therefore fails to facilitate cell mechanosensing or differentiation in the 3D hydrogels. We further show that the dynamic hydrogels with locally stiffened network promote the in-situ regeneration of bone defects in an animal model.在正常組織中，細胞不斷與其周圍的微環境相互作用，並且這些相互作用可以調節一系列細胞過程，從而指導細胞行為和命運。工程化的生物材料為包封的細胞提供了人工微環境，可以合理地調節細胞與材料之間的相互作用，以實現有效的細胞命運調控。先前的研究已經在仿生材料的生物醫學應用中取得了顯著進展，實現了對細胞外基質生化複雜性的有效模擬。然而，可用於調控細胞與材料相互作用的合成動態生物界面領域仍處於起步階段。在本文中，我們提出了三種不同的動態平台來模擬細胞外基質的固有特性，從而調控細胞行為和命運，並促進組織再生。在各種生物材料中，水凝膠是組織工程和再生醫學的有前途的候選者。我們首先將重點放到了基於金屬離子和雙膦酸鹽的動態水凝膠。金屬離子（例如Mg2+，Ca2+和Fe2+）的摻雜為水凝膠提供了獨特的屬性，包括生物活性，導電性和可調性。我們首先開發了一種通用策略來製造一系列基於多種金屬離子的納米複合水凝膠。我們證明了所獲得的水凝膠具有廣譜的顯著動態特性，例如出色的可注射性，快速的應力鬆弛，有效的離子擴散以及可觸發的降解。此外，我們證明摻雜鑭系元素離子的納米複合水凝膠表現出高度可調的熒光光譜。接下來，我們將開發的水凝膠用於治療周圍神經損傷，這具有重要的臨床意義。我們證明了含有鎂和雙膦酸鹽的納米複合水凝膠促進了坐骨神經損傷大鼠模型的周圍神經再生並實現了部分功能恢復。為了進一步研究由動態水凝膠輔助的組織再生的應用，我們接下來設計了一種具有多種動態特性（包括可注射性，剪切變稀和自我修復）的超分子細胞明膠主客體水凝膠。超分子細胞明膠主客體水凝膠可用於負載各種治療劑，並相應地應用到一系列組織再生。我們首先在全厚度燒傷小鼠模型上檢查了基於超分子細胞明膠主客體水凝膠的傷口敷料對於皮膚再生的促進作用。由於炎性反應時間延長和血管生成不足會導致傷口癒合延遲和不良，我們證明了載有白藜蘆醇和組蛋白-1的超分子細胞明膠主客體水凝膠可抑制炎症並促進皮膚燒傷創面的血管形成。接下來，我們評估了動態水凝膠對於脊髓橫斷模型修復的功效。我們證明，載有脂肪來源的基質細胞的超分子細胞明膠主客體水凝膠通過增強的原位神經生成和有效的炎性免疫調節促進了脊髓再生。接下來，我們研究了超分子細胞明膠主客體水凝膠在大小動物中促進骨軟骨再生的功效。我們證明了具有可調節降解動力學的超分子細胞明膠主客體水凝膠在豬軟骨缺損模型中支持有效的透明軟骨修復。接下來，我們使用工程化的納米復合動態水凝膠來模擬天然細胞外基質的分層異質化的力學結構。我們證明了基於丙烯酰基納米粒子的交聯劑的化學摻入在動態超分子水凝膠中創建了區域剛性的網絡結構，而不損害細胞適應性納米粒子間水凝膠網絡的動力學特性。所獲得的具有異質水凝膠網絡拓撲結構的動態水凝膠可加快封裝的干細胞的黏附結構，三維鋪展和機械感測的形成和成熟，這主要是由關鍵生物標誌物的上調表達所證明的。這種增強的擴散和機械轉導促進了包封的干細胞的成骨分化。相比之下，摻雜有物理包裹的納米顆粒或分子交聯劑不能局部增強動態水凝膠網絡，因此無法促進三維水凝膠中的細胞機械感測或分化。我們進一步表明，具有局部強化網絡的動態水凝膠可促進動物模型中骨缺損的原位再生。YUAN, Weihao.Ph.D. Chinese University of Hong Kong 2021.Includes bibliographical references (leaves )Abstracts in English and ChineseTitle from PDF title page (viewed on …
Efficacy and Safety of Novel Oral Antivirals in Hospitalized COVID-19 Patients: A Network Meta-Analysis of Randomized Clinical Trials
No full textHaoshuang Liu,1,2 Jingfeng Chen,1,2 Weihao Shao,3 Su Yan,1,2 Suying Ding1,2 1Health Management Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People’s Republic of China; 2College of Public Health, Zhengzhou University, Zhengzhou, 450001, People’s Republic of China; 3School of Population Medicine and Public Health, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, People’s Republic of ChinaCorrespondence: Suying Ding, Department of Health Management Center, the First Affiliated Hospital of Zhengzhou University, Longhu Zhonghuan Road, Jinshui District, Zhengzhou, Henan, 450052, People’s Republic of China, Tel +86 158 3802 3097, Email [email protected]: Numerous pharmacological interventions are now under investigation for the treatment of the 2019 coronavirus pandemic (COVID-19), and the evidence is rapidly evolving. Our aim is to evaluate the comparative efficacy and safety of these drugs.Methods: We searched for randomized clinical trials (RCTs) on the efficacy and safety of novel oral antivirals for the treatment of hospitalized COVID-19 patients until November 30, 2022, including baricitinib, ivermectin (IVM), favipiravir (FVP), chloroquine (CQ), lopinavir and ritonavir (LPV/RTV), hydroxychloroquine (HCQ), and hydroxychloroquine plus azithromycin (HCQ+AZT). The main outcomes of this network meta-analysis (NMA) were in-hospital mortality, adverse event (AE), recovery time, and improvement in peripheral capillary oxygen saturation (SpO2). For dichotomous results, the odds ratio (OR) was used, and the 95% confidence interval (CI) was determined. We also used meta-regression to explore whether different treatments affected efficacy and safety. STATA 15.0 was used to conduct the NMA. The research protocol was registered with PROSPERO (#CRD 42023415743).Results: Thirty-six RCTs, with 33,555 hospitalized COVID-19 patients, were included in this analysis. First, we compared the efficacy of different novel oral antivirals. Baricitinib (OR 0.56, 95% CI: 0.35 to 0.90) showed the highest probability of being the optimal probiotic species in reducing in-hospital mortality and suggested that none of the interventions reduced AE better than placebo. In terms of safety outcomes, IVM ranked first in improving the recovery time of hospitalized COVID-19 patients (mean difference (MD) − 1.36, 95% CI: − 2.32 to − 0.39). In addition, patients were most likely to increase SpO2 (OR 1.77, 95% CI: 0.09 to 3.45). The meta-regression revealed no significant differences between participants using different novel oral antivirals in all outcomes in hospitalized COVID-19 patients.Conclusion: Currently, baricitinib has reduced in-hospital mortality in hospitalized COVID-19 patients, with moderate certainty of evidence. IVM appeared to be a safer option than placebo in improving recovery time, while FVP was associated with increased SpO2 safety outcomes. These preliminary evidence-based observations should guide clinical practice until more data are made public.Keywords: COVID-19, network meta-analysis, pharmacological intervention, efficacy, safet
Protection Testing for Multiterminal High-Voltage dc Grid: Procedures and Assessment
Get PDFeAssessment The application of multiterminal (MT), high-voltage dc (HVdc) (MTdc) grid technology requires test procedures for the operation and implementation of the protection solutions. The test procedures are usually derived from experience and from extensive measurement data, which, at present, are still not widely available. Based on a hardware-inthe- loop (HIL) method, advanced dc protection testing strategies, utilizing existing experience for ac grids and requirements for MTdc grids, may overcome this gap.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Intelligent Electrical Power Grid
- …
