GenHPF: General Healthcare Predictive Framework with Multi-task Multi-source Learning

Despite the remarkable progress in the development of predictive models for healthcare, applying these algorithms on a large scale has been challenging. Algorithms trained on a particular task, based on specific data formats available in a set of medical records, tend to not generalize well to other tasks or databases in which the data fields may differ. To address this challenge, we propose General Healthcare Predictive Framework (GenHPF), which is applicable to any EHR with minimal preprocessing for multiple prediction tasks. GenHPF resolves heterogeneity in medical codes and schemas by converting EHRs into a hierarchical textual representation while incorporating as many features as possible. To evaluate the efficacy of GenHPF, we conduct multi-task learning experiments with single-source and multi-source settings, on three publicly available EHR datasets with different schemas for 12 clinically meaningful prediction tasks. Our framework significantly outperforms baseline models that utilize domain knowledge in multi-source learning, improving average AUROC by 1.2%P in pooled learning and 2.6%P in transfer learning while also showing comparable results when trained on a single EHR dataset. Furthermore, we demonstrate that self-supervised pretraining using multi-source datasets is effective when combined with GenHPF, resulting in a 0.6%P AUROC improvement compared to models without pretraining. By eliminating the need for preprocessing and feature engineering, we believe that this work offers a solid framework for multi-task and multi-source learning that can be leveraged to speed up the scaling and usage of predictive algorithms in healthcare.Comment: Accepted by IEEE Journal of Biomedical and Health Informatic

Homogeneous bilayer graphene film based flexible transparent conductor

Graphene is considered a promising candidate to replace conventional transparent conductors due to its low opacity, high carrier mobility and flexible structure. Multi-layer graphene or stacked single layer graphenes have been investigated in the past but both have their drawbacks. The uniformity of multi-layer graphene is still questionable, and single layer graphene stacks require many transfer processes to achieve sufficiently low sheet resistance. In this work, bilayer graphene film grown with low pressure chemical vapor deposition was used as a transparent conductor for the first time. The technique was demonstrated to be highly efficient in fabricating a conductive and uniform transparent conductor compared to multi-layer or single layer graphene. Four transfers of bilayer graphene yielded a transparent conducting film with a sheet resistance of 180 {\Omega}_{\square} at a transmittance of 83%. In addition, bilayer graphene films transferred onto plastic substrate showed remarkable robustness against bending, with sheet resistance change less than 15% at 2.14% strain, a 20-fold improvement over commercial indium oxide films.Comment: Published in Nanoscale, Nov. 2011 : http://www.rsc.org/nanoscal

A semi-analytic method with an effect of memory for solving fractional differential equations

In this paper, we propose a new modification of the multistage generalized differential transform method (MsGDTM) for solving fractional differential equations. In MsGDTM, it is the key how to impose an initial condition in each sub-domain to obtain an accurate approximate solution. In several literature works (Odibat et al. in Comput. Math. Appl. 59:1462-1472, 2010; Alomari in Comput. Math. Appl. 61:2528-2534, 2011; Gokdoğan et al. in Math. Comput. Model. 54:2132-2138, 2011), authors have updated an initial condition in each sub-domain by using the approximate solution in the previous sub-domain. However, we point out that this approach is hard to apply an effect of memory which is the basic property of fractional differential equations. Here we provide a new algorithm to impose the initial conditions by using the integral operator that enhances accuracy. Several illustrative examples are demonstrated, and it is shown that the proposed technique is robust and accurate for solving fractional differential equations.close0

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Transmembrane Transport in Biomimetic Assemblies of One-Dimensional Nanomaterials

The creation of biomimetic structures based on one-dimensional nanomaterials and lipid membranes will provide a unique platform for achieving functionalities of biological machines and mimicking nature at the nanoscale. Silicon nanowires (SiNW) and carbon nanotubes (CNT) are of significant interest due to the novel properties not present in bulk materials as well as characteristic dimensions comparable to the size of biological molecules. My thesis describes the creation of fabricated nanomaterials integrated with biomaterials such lipid membranes and their constitutive proteins to create biomimetic assemblies. In the first part of my dissertation, I report transmembrane carbon nanotube pores as a biological ion channel analogs. Biological ion channels in nature transport ions across cellular membranes showing two functions of gating and ion selectivity. CNT pores give structural and functional mimic of an ion channel, in part because smooth, narrow and hydrophobic inner pores of the CNT are remarkably similar to natural biological pores. First, CNTs served as a materials platform that can replicate the features of biological channels. I successfully created ultrashort CNTs (ca. ~10nm) using lipid-assisted sonication-cutting method. Lipid molecules self-assemble on the long CNTs to form a template for sonication cutting. These short CNT pores with their length comparable to the lipid membrane thickness provide a much closer match to protein-channel dimensions. Short CNT pores were incorporated into lipid vesicles to mimic membrane ion channels and study transport properties through CNT pores. These short CNTs in a lipid membrane can transport water, protons, and small ions and reject large uncharged species. Ion rejection in CNT channels is determined by charge repulsion at the CNT rim. Electrophoretic ion transport measurements for individual CNT pores revealed an ion conductance value of 0.63ns which is comparable to those of biological channels. CNT pores inserted in the membrane exhibited stochastic gating behavior common for biological ion channels. These fluctuations result from a spontaneous reversible ionic penetration-exclusion transition previously reported in nanofluidic transport of sub-2-nm pores. Electrophoretically-driven translocation of individual single-stranded DNA molecules through CNT pores produced well-defined ion current blockades. Overall, short CNT mimics transport properties of a biological protein channel. Since the structure and functionality of short CNT pores self-inserted in a lipid membrane resemble the β-barrel structure of a porin, they are termed as "carbon nanotube porins".In the second part, I describe synthesis of SiNWs grown via vapor-liquid-solid (VLS) mechanism. Silicon nanowires were grown on silicon substrates via chemical vapor deposition (CVD) using silane as a precursor gas and diborane for p-type doing of wires. These nanowires were utilized for a bioelectronics platform for integration of membrane protein functionality based on one-dimensional lipid bilayer. This lipid bilayer provides shielding the nanowires from the solution species and environment for proteins preserving their functionality, integrity, and even vectorality. Here, I report a hybrid lipid bilayer- silicon nanowire bioelectronic device with output controlled via light-induced proton pump protein, bacteriorhodopsin (bR). SiNW field effect transistors (FET) were fabricated via conventional micro/nanofabrication process. bR proteins were incorporated into SiNW transistors covered with a lipid bilayer shell and different ionophore molecules, valinomycin and nigericin were co-assembled to create biologically-tunable bioelectronics devices. In this way, the devices convert photoactivated proton transport by bR protein into an electronic signal. The addition of ionophores tuned the device output by altering membrane ion permeability and the two ionophores were able to modulate different system parameters

Epoxidation of vegetable oils using the heterogeneous catalysis, amorphous Ti-SiO2

Epoxidation of the double bond is an interesting reaction because it opens up a wide variety of reactions that can be carried out under mild conditions. The formed epoxide is an intermediate that can be converted to a variety of products by the addition of nucleophiles to form lubricants because of high reactivity of the oxirane ring and the physical and chemical properties can be changed depending upon the kind of nucleophiles are added. For example, alkoxy alcohol, hydroxy ester, amino alcohol, hydroxynitrile, etc. can be produced by reaction of epoxide with different nucleophile. In industry, the epoxidation of plant oils has been already carried out homogeneously with a percarboxylic acid, such as peracetic acid and performic acid, obtained by oxidation with hydrogen peroxide, using mineral acid, like sulfuric acid, as catalyst. However, there are several drawbacks in the process: (i) high selectivity of epoxidation is not achieved due to acid-catalysed oxirane ring opening reaction; (ii) the separation of acidic by-products is difficult; (iii) the handling of concentrated hydrogen peroxide and strong acids is dangerous and causes corrosion problems and additionally, they are environmentaly harmful. Thus, recently, a lot of interests of academia researchers and chemical companies have been made on the catalytic processes in order to overcome these disadvantages. Even though many investigations in this field have been carried out already, there are still many possibilities in developing higher efficiency and economical benefit and new ways for environmentally friendly reactions. The aim of this thesis is to investigate the heterogeneously catalyzed epoxidation of vegetable oils, like oleic acid methyl ester and oleic acid, in a batch-reactor. The scope of this work includes the preparation and analysis of amorphous Ti-SiO2 catalysts using different silica sources and different methods. Furthermore, scaling-up of the reaction was carried out and the efficiency was compared with that in small scale one. Additionally, the separation of product from the reaction mixture by distillation was briefly tested in order to see the possibility of the re-cycling process