Dissertations / Theses on the topic 'Large-Scale Screening'

The present project discusses the application of screening techniques in large-scale simulation models with the purpose of determining whether this kind of procedures could be a substitute for or a complement to simulation-based optimization for bottleneck identification and improvement. Based on sensitivity analysis, the screening techniques consist in finding the most important factors in simulation models where there are many factors, in which presumably only a few or some of these factors are important. The screening technique selected to be studied in this project is Sequential Bifurcation. This method consists in grouping the potentially important factors, dividing the groups continuously depending on the response generated from the model of the system under study. The results confirm that the application of the Sequential Bifurcation method can considerably reduce the simulation time because of the number of simulations needed, which decreased compared with the optimization study. Furthermore, by introducing two-factor interactions in the metamodel, the results are more accurate and may even be as accurate as the results from optimization. On the other hand, it has been found that the application of Sequential Bifurcation could become a problem in terms of accuracy when there are many storage buffers in the decision variables list. Due to all of these reasons, the screening techniques cannot be a complete alternative to simulation-based optimization. However, as shown in some initial results, the combination of these two methods could yield a promising roadmap for future research, which is highly recommended by the authors of this project.

An immediate reduction in global CO2 emissions could be accomplished by replacing coal- or oil-based energy sources with purified natural gas. The most important process involved in natural gas purification is the separation of CO2 from CH4, where Pressure Swing Adsorption (PSA) technology on porous materials has emerged as a less energy demanding technology. Among porous materials which are used or could potentially be used in PSA, Metal Organic Frameworks (MOFs) have attracted particular interest owing to their record-breaking surface areas, high-porosity, and high tunability. However, the discovery of optimal MOFs for use in adsorption-based CO2 separation processes is remarkably challenging, as millions of MOFs can potentially be constructed from virtually limitless combinations of inorganic and organic secondary building units. To overcome this combinatorial problem, this thesis aims to (1) identify important design features of MOFs for CO2/CH4 separation through the investigation of currently existing MOFs as well as the high throughput computational screening of a large database of MOFs, and to (2) develop efficient computational tools for aiding the discovery of new MOF materials. To validate the computational methods and models used in this thesis, the first work of this thesis presents the computational modeling of CO2 adsorption on an experimental CuBDPMe MOF using grand canonical Monte Carlo simulations and density functional theory. The simulated CO2 adsorption isotherms are in good agreement with experiment, which confirms the accuracy of the models used in our simulations throughout this thesis. The second work of this thesis investigates the performance of an experimental MIL-47 MOF and its seven functionalized derivatives in the context of natural gas purification, and compares their performance with that of other well-known MOFs and commercially used adsorbents. The computational results show that introducing polar non-bulky functional groups on MIL-47 leads to an enhancement in its performance, and the comparison suggests that MIL-47-NO2 could be a possible candidate as a solid sorbent for natural gas purification. This study is followed by the compactional study of water effects on natural gas purification using MOFs, as traces of water is present in natural gas under pipeline specifications. From the study, it is found that water has a marginal effect on natural gas purification in hydrophobic MOFs under pipeline specifications. Following the aforementioned studies, a database of 324,500 hypothetical MOFs is screened for their performance in natural gas purification using the general protocol defined in this thesis. From the study, we identify 'hit' materials for targeted synthesis, and investigate the structure-property relationships with the intent of finding important MOF design features relevant to natural gas purification. We show that layered sheets consisting of poly-aromatic molecules separated by a perpendicular distance of roughly 7 Å are an important structural-chemical feature that leads to strong adsorption of CO2. Following the screening study, we develop efficient computational tools for the recognition of high-preforming MOFs for methane purification using Machine Learning techniques. A training set of 32,500 MOF structures was used to calibrate support vector machines (SVMs) classifiers that incorporate simple geometrical features including pore size, void fraction and surface area. The SVM machine learning classifiers can be used as a filtering tool when screening large databases. The SVM classifiers were tested on ~290,000 MOFs that were not part of the training set and could correctly identify up to 70% of high-performing MOFs while only flagging a fraction of the MOFs for more rigorous screening. As a complement to this study, we present ML classifier models for CO2/CH4 separation parameters that incorporate separately the Voronoi hologram and AP-RDF descriptors, and we compare their performance with the classifiers composed of simple geometrical descriptors. From the comparison, it is found that including AP-RDF and Voronoi hologram descriptors into the classifiers improves the performance of classifiers by 20% in capturing high-performing MOFs. Finally, from the screening data, we develop a novel chemiformatics tool, MOFFinder, for aiding in the discovery of new MOFs for CO2 scrubbing from natural gas. It has a user-friendly graphical interface to promote easy exploration of over 300,000 hypothetical MOFs. It enables synthetic chemists to find MOFs of interest by searching the database for Secondary Building Units (SBUs), geometric features, functional groups and adsorption properties. MOFFinder provides, for the first time the substructure/similarity query of porous materials for users and is publicly available on titan.chem.uottawa.ca/moffinger.

La robotique et l’automatisation des microscopes ont ouvert la voie aux cribles cellulaires à haut contenu : des marqueurs fluorescents ciblant l’ADN ou d’autres composants sont utilisés pour imager des centaines de milliers de cellules dans différentes conditions. Il a été montré que les cribles cellulaires sont efficaces pour découvrir des médicaments de nouvelles classes thérapeutiques, cad ceux qui agissent sur une nouvelle cible. Les cribles permettent d’identifier des composés prometteurs et de les caractériser en leur associant des annotations fonctionnelles, comme leur cible moléculaire ou leur mécanisme d’action (MOA).J’ai étudié l'hétérogénéité des réponses cellulaires à différents niveaux et comment cette hétérogénéité phénotypique peut être exploitée pour mieux caractériser les composés. Au premier niveau, j’ai étudié l'hétérogénéité entre patients. Nous avons montré qu’utiliser différentes lignées cellulaires dérivées de patients augmente la probabilité de prédire la cible moléculaire du composé testé. Le second niveau correspond à la diversité des réponses cellulaires de la même lignée cellulaire soumise au même traitement. Des méthodes de clustering appropriées peuvent être utilisées pour clarifier cette complexité et pour grouper les cellules en sous-populations. Les proportions de chaque sous-population par traitement permettent de prédire le bon MOA. Le troisième niveau regarde comment les sous-populations cellulaires sont organisées spatialement. J’ai trouvé que les cellules voisines s’influencent les unes les autres et affichent un phénotype similaire plus fréquemment qu’attendu par chance. Ces résultats obtenus sur une centaine de traitements montrent que des cellules génétiquement identiques ne sont pas identiques et indépendantes mais sont à l’origine d’une hétérogénéité spatiale par le lignage cellulaire et les interactions. En utilisant l’information spatiale ainsi que l'hétérogénéité phénotypique, les méthodes à noyaux de graphes améliorent la classification en MOA sous certaines conditions. Parallèlement, comme l’analyse spatiale peut s’appliquer à n’importe quelle image de microscopie, j’ai développé une librairie d’analyse Python, PySpacell, pour étudier l’aléatoire spatial de marqueurs quantitatifs et qualitatifs
Robotics and automated fluorescence microscopes have promoted high-content cell-based screenings: fluorescent probes targeting DNA or other major components are used to image hundreds of thousands of cells under many different conditions. Cell-based assays have proven to be efficient at discovering first-in-class therapeutic drugs, i.e. drugs acting on a new target. They allow to detect promising molecules and to profile them, by associating functional annotations to them, like their molecular target or mechanism of action (MOA). I studied heterogeneity of cell responses at different levels and how this phenotypic heterogeneity can be leveraged to better profile drugs. The first level is about studying heterogeneity between patients. We showed that using different patient-derived cell lines increases the chance of predicting the correct molecular target of the tested drug. The second level corresponds to the diversity of cell responses within the same cell line under the same treatment. Appropriate clustering approaches can be used to unravel this complexity and group cells into subpopulations. The proportions of each subpopulation per treatment allow to predict the correct MOA. The third level looks at how the cell subpopulations are spatially organized. I found that neighboring cells influence each others, and display a similar phenotype more frequently than expected at random. These results assessed across a hundred of treatments, show that even genetically identical cells are not all alike and independent, but create spatial heterogeneity via cell lineage and interaction. Using spatial information as well as phenotypic heterogeneity with graph kernel methods improves the MOA classification under some conditions. Alongside, as spatial analysis could be applied on any cell microscopy image, I developed a Python analysis package, pySpacell, to study spatial randomness from quantitative and qualitative cell markers

Abstract Requirements engineering (RE) is an important process in systems development. This research was carried out in the context of Very Large-Scale Requirements Engineering (VLSRE) within the scope of a requirement screening (RS) process. The RS process is defined as a front-end process for screening incoming requests, which are received in a constant flow. The goal of the RS process is to efficiently identify the most promising requests for further analysis, development and implementation while filtering out non-valuable ones as early as possible. The objective of this study was to understand the challenges related to the RS process and develop solutions to address those challenges. A qualitative research approach was utilised to achieve the research goals. The overall research process follows an action research method, in which each action research cycle includes at least one individually defined and executed case study. Action research and case studies are research methods that are well suited to studying real-life phenomena in their natural settings. This research was carried out in two case companies in the information and communication technology domain. Data from 45 interviews were analysed for preparing publications I–V, which are included in this thesis. In addition, during the longitudinal action research study described in this thesis, data from 26 interviews and 132 workshops were utilised to develop solutions for the RS process, which is an industrial implementation of the VLSRE process. The conducted action research contributes to the field of software engineering, in which such research efforts are currently lacking. This research has identified a number of significant challenges that different stakeholders face related to requirements processing and decision making in the VLSRE context. Examples of these challenges are the great number of incoming requirements, the lack of information for decision making and the feasibility of utilised tools. To address the identified challenges, a requirements architecting method was developed. The method includes a dynamic requirement template, which gathers structured information content for eliciting requests, documenting and communicating requirements and forming features while considering the needs of different stakeholders. The method was piloted, validated and deployed in industry
Tiivistelmä Tutkimus toteutettiin laajamittaisen vaatimusmäärittelyprosessin kontekstissa keskittyen vaatimusten seulontaprosessiin. Vaatimusten seulontaprosessi määritellään tuotekehityksen alkuvaiheen prosessiksi, jossa käsitellään jatkuvana vuona tulevia kehityspyyntöjä. Vaatimusten seulontaprosessissa pyritään tunnistamaan tehokkaasti lupaavimmat pyynnöt jatkoanalyysiä, tuotekehitystä ja toteutusta ajatellen sekä suodattamaan pois niin aikaisessa vaiheessa, kun mahdollista ne pyynnöt, joilla ei ole arvontuotto-odotuksia. Tutkimuksen tavoite oli ymmärtää haasteita, jotka liittyvät vaatimusten seulontaprosessiin sekä kehittää ratkaisuja näihin haasteisiin. Tutkimuksessa käytettiin laadullisen tutkimuksen menetelmiä. Kokonaisuutena tutkimusprosessi noudattaa toimintatutkimuksen periaatteita siten, että jokainen sykli tai sen vaihe sisältää yhden tai useamman itsenäisesti määritellyn tapaustutkimuksen suunnittelun ja läpiviennin. Valitut tutkimusmenetelmät soveltuvat hyvin tilanteisiin, joissa tutkimuskohteina ovat reaalimaailman ilmiöt niiden luonnollisissa ympäristöissä havainnoituina. Tutkimusaineisto kerättiin kahdesta informaatio- ja kommunikaatioteknologia-alan kohdeorganisaatiosta. Väitöskirjaan sisällytettyihin julkaisuihin I-V on analysoitu 45 haastattelun aineisto. Näiden lisäksi väitöskirjassa kuvatun pitkäkestoisen toimintatutkimuksen aikana hyödynnettiin 26 haastattelun ja 132 työpajan aineistoa kehitettäessä ratkaisuja vaatimusten seulontaprosessin haasteisiin. Vaatimusten seulontaprosessi on laajamittaisen vaatimusmäärittelyprosessin teollinen toteutus. Tutkimuksessa tunnistettiin useita merkittäviä haasteta, joita eri sidosryhmillä on liittyen vaatimusten seulontaprosessiin ja päätöksentekoon laajamittaisessa vaatimusmäärittelyprosessissa. Vaatimusten suuri määrä, päätöksentekoon tarvittavan tiedon puute ja käytössä olevien työkalujen soveltumattomuus ovat esimerkkejä tunnistetuista haasteista. Ratkaisuna haasteisiin kehitettiin vaatimusten seulonta- ja analyysimenetelmä. Kehitetty menetelmä sisältää dynaamisen vaatimusdokumentin, jonka avulla voidaan kerätä kehityspyyntöjen tietosisältö jäsennellysti, dokumentoida ja kommunikoida vaatimukset sekä muodostaa niistä tuotteisiin toteutettavia ominaisuuksia ottaen huomioon eri sidosryhmien tarpeet. Kehitetty menetelmä on koestettu, validoitu ja soveltuvin osin otettu käyttöön teollisuudessa

Cellulosic biomass is the major organic matter produced in the biosphere. The biodegradation of this cellulosic material is achieved by enzymatic activities of the cellulose degrading microorganisms. These organisms usually express a complex extracellular or a membrane bound cellulolytic system comprising combination of several cellulase enzymes. Cellulases are the group of hydrolytic enzymes capable of hydrolysing insoluble cellulose to glucose. Phlebia gigantea is an aggressive white rot basidiomycete with ability to tolerate resinous extracts on freshly cut wood and higher growth rate. This helps the fungus to colonise the sapwood preventing other fungi from becoming established. Early research on the cellulase system of this organism reported the presence of a cellulase system composed of P-glucosidase, endoglucanase and a cellobiohydrolase. Based on these unpublished studies, our aim was to obtain a complete sequence of putative cellobiohydrolase I (CbhI) from this organism. Attempts to identify and isolate the cellulase gene resulted in an incomplete cDNA sequence of I 154 bp. To understand the cellulase system, expression and regulation of the cellulase enzymatic activity was examined for incubation of P. gigantea on substrates glucose, xylose, Avicel, carboxymethyl cellulose and cellobiose. The pH, total protein and biomass production results indicated that the capacity of P. gigantea to degrade cellulose is dependent upon the nature of the carbon source and the regulation of the cellulase synthesis is repressed in the presence of simple sugars like glucose and xylose. The study employed the highly effective method of purification by affinity adsorption and purified cellulase complex in large quantity. Characterisation of the kinetic properties of this cellulase complex revealed that the rate of cellulase catalysis were optimum at pH 5.0 and temperature 50GC. The purified complex was comprised of multiple proteins and demonstrated significant CMCase and CBHase activity on zymogram analysis. The purified cellulase complex was characterised by 2D gel electrophoresis and by peptide mass finger printing using MALDI-TOF massspectrometry analysis. The 2D gel analysis of the purified cellulase complex showed 15 spots within the range of pI 3.5 to pI 7 and the molecular weight between 20KDa to 100KDa. Three protein spots were selected based on the IEF and SDS zymogram and identified using MALDI-TOF MS analysis. These proteins were identified based on the peptide mass data belonging to the 6-phospho-a-glucosidase, p-glucosidase and glycosyl hydrolase family 13 a-amylase or pullulanases, suggesting the divergent evolution of specific cellulase proteins. This study showed P. gigantea as a potential cellulase source and the cellulase complex secreted by the induction of substrate, comprises a variety of enzymes related to hydrolysis of cellulose biomass. It is evident from this and previous studies that P. gigantea cellulase complex comprises of a specific set of enzymes that possess the ability to degrade crystalline cellulose and is one of the first organisms to colonise freshly cut wood. Further studies on the cellulase system of this primary colonist may open up the prospects to utilise this organism as the potential onsite bioreactor agent, pre-treating the biomass and increasing the economic feasibility of the industrial bioenergy processes.

Metastasis is one of the critical hallmarks of malignancy tumor and the principal cause of death in patients with cancer. Cell migration is the basic and essential step in cancer metastasis process. To systematically investigate functional genes regulating cell migration and cancer metastasis on large scale, we developed a novel on-chip method, SAMcell (self-assembled cell microarray). This method was demonstrated to be particularly suitable for loss-of-function high-throughput screening because of its unique advantages. The first application of SAMcell was to screen human genome miRNAs, considering that more and more miRNAs had been proved to govern cancer metastasis. We found that over 20 % of miRNAs have migratory regulation activity in diverse cell types, indicating a general involvement of miRNAs in migratory regulation. Through triple-round screenings, we discovered miR-23b, which is down-regulated in human colon cancer samples, potently mediates the multiple steps of metastasis, including cell motility, cell growth and cell survival. In parallel, the second application of SAMcell was to screen human genome kinase genes, considering that more and more kinase genes had become successful diagnostic marker or drug targets. We found over 11% migratory kinase genes, suggesting the important role of kinase group in metastasis regulation. Through both functional screening and bioinformatics analysis, we discovered and validated 6 prospective metastasis-related kinase genes, which can be new potential targets in cancer therapy. These findings allow the understanding of regulation mechanism in human cancer progression, especially metastasis and provide the new insight into the biological and therapeutical importance of miRNAs or kinases in cancer.

碩士
國立中山大學
化學系研究所
103
Ambient mass spectrometry （AMS） is known for its unique feature to perform analysis without sample pretreatment, and has been used for direct, rapid, and real-time detection of chemical compounds. Techniques such as DESI, DART, and ELDI have been demonstrated to be useful for rapidly characterizing chemical and biological compounds. In this study, we have developed an ambient mass spectrometric technique known as thermal desorption electrospray ionization mass spectrometry （TD-ESI/MS）. A direct metallic sampling probe was used to collect analytes from sample surfaces regardless of sample size or shape. Analytes were thermally desorbed, post-ionized by reacting with charged solvent species in an electrospray plume, and the ions were subsequently detected by the mass analyzer attached to the ion source. .The residual sample on the metallic probe is rapidly removed by burning the probe with a flame from a torch. The time required to complete an analysis was less than 15 seconds. In the first study, TD-ESI/MS was used to screen phthalates [ Dibutyl Phthalate （DBP）, Dimethyl Phthalate （DMP）, Di-octyl Phthalate （DOP）, Di（2-ethylhexyl）Phthalate （DEHP）, Di-iso-nonyl Phthalate （DINP）, Benzyl Butyl Phthalate （BBP）, Di-isodecyl Phthalate （DIDP）and Diethyl Phthalate （DEP） ] on the objects in two kindergartens. Approximately one thousand samples were collected, analyzed and the results were reported within two days. Sample collection was completed in approximately 3hrs, TD-ESI/MS analysis was completed in 10 hrs, and data organization and report writing took another 5 hrs. The results indicate that approximately 30% and 20% of the objects in the two kindergartens contain higher level of phthalates. The success in screening phthalates in all the objects found in the two kindergartens suggests that performing large scale screening of phthalates in the living environment is possible. In the second study, liquid-phase microextraction （LPME） was coupled with an ambient ionization technique, known as thermal desorption electrospray ionization （TD-ESI） for rapid screening of veterinary drug residues in foods. The ambient TD-ESI ion source consisted of （1）a metal loop suspending 5 μL of organic solvent was used for analyte extraction in liquids, （2）after equilibrium among analytes, sample solution, and extraction solvent was reached, a heating oven for desorbing analytes on the LPME probe.Preliminary results of LPME/TD-ESI/MS/ showed that reproducibility tests （n=5） for 10 µg/mL of sulfonamides（sulfamethazine, sulfamethoxazole） and β-agonists （clenbuterol, salbutamol, terbutaline） were less than 7.6 % and 10.2 %, respectively. The sensitivities of sulfamethazine（m/z 279） and clenbuterol（m/z 277）improved,; where detection limits could be decreased as low as 1.0 µg/mL, and 0.1 µg/mL while using the LPME fiber as a sampling probe. Furthermore, the capacity of LPME/TD-ESI/MS for quantitative analysis was evaluated using milk, honey and pork blood spiked with spiked veterinary drugs. Excellent correlations of determination were achieved for analytes with R2values greater than 0.997、0.998 and 0.972, respectively.

碩士
國立暨南國際大學
應用化學系
104
Micro-RNAs (miRNAs) are small non-coding RNAthat only need to pair partially to the target mRNA in order to elicit translational repression.Previously, our lab used behavioral screening to define 11 distinct dm-miRNAs from the collection of 160 UAS-miRNA lines that drove expression in elav-expressing (pan-neuronal) cells of adult Drosophila males, which can prompt inter-male courtship behavior.In my study, the underling same experimental approachto find outthe role of the individual miRNA involves the male or female fly heterosexualcourtship activity. Our result showed that 15 miRNAs affected male courtship responses and 36 miRNAs affected female courtship responses.We highlight the importance of these miRNAs in neuronal system, and expect to identify the miRNAs targets and gain molecular insights in the mechanisms of fly courtship activity.Our long-term goal is todissect sex processes at biochemical, genetic, anatomical, and behavioral levels. Such “translational” studies of the flysystems neuroscience generate clinically relevant insight into human brain function and ultimately may lead to important advances in the understanding in vertebrate.

High-throughput transcriptomic profiling has become a ubiquitous tool to assay an organism transcriptome and to characterize gene expression patterns in different cellular states or disease conditions, as well as in response to molecular and pharmacologic perturbations. Refinements to data preparation techniques have enabled integration of transcriptomic profiling into large-scale biomedical studies, generally devised to elucidate phenotypic factors contributing to transcriptional differences across a cohort of interest. Understanding these factors and the mechanisms through which they contribute to disease is a principal objective of numerous projects, such as The Cancer Genome Atlas and the Cancer Cell Line Encyclopedia. Additionally, transcriptomic profiling has been applied in toxicogenomic screening studies, which profile molecular responses of chemical perturbations in order to identify environmental toxicants and characterize their mechanisms-of-action. Further adoption of high-throughput transcriptomic profiling requires continued effort to improve and lower the costs of implementation. Accordingly, my dissertation work encompasses both the development and assessment of cost-effective RNA sequencing platforms, and of novel machine learning techniques applicable to the analyses of large-scale transcriptomic data sets. The utility of these techniques is evaluated through their application to a toxicogenomic screen in which our lab profiled exposures of adipocytes to metabolic disrupting chemicals. Such exposures have been implicated in metabolic dyshomeostasis, the predominant cause of obesity pathogenesis. Considering that an estimated 10% of the global population is obese, understanding the role these exposures play in disrupting metabolic balance has the potential to help combating this pervasive health threat. This dissertation consists of three sections. In the first section, I assess data generated by a highly-multiplexed RNA sequencing platform developed by our section, and report on its significantly better quality relative to similar platforms, and on its comparable quality to more expensive platforms. Next, I present the analysis of a toxicogenomic screen of metabolic disrupting compounds. This analysis crucially relied on novel supervised and unsupervised machine learning techniques which I specifically developed to take advantage of the experimental design we adopted for data generation. Lastly, I describe the further development, evaluation, and optimization of one of these methods, K2Taxonomer, into a computational tool for unsupervised molecular subgrouping of bulk and single-cell gene expression data, and for the comprehensive in-silico annotation of the discovered subgroups.

碩士
國立臺灣大學
生物科技研究所
105
Type VI secretion system (T6SS) is molecular machine that is widespread among phylum Proteobacteria to mediate interactions with neighboring eukaryotic and prokaryotic cells. The legume symbiont, Azorhizobium caulinodans ORS571 (α-proteobacteria), possess one deduced T6SS cluster harboring impA~impL genes on the genome. However, the T6SS hallmark protein, Hcp (hemolysin-coregulated protein) is not detectable in the extracellular matrix of ORS571 under current culture conditions. To facilitate the study of the role and regulatory pathway of T6SS in ORS571 life cycle, I screened for T6SS-active mutants from a transposon mutant library using colony lift immunoassay. The genome-wide mutant library was constructed by conjugative transfer of mini-Tn5 vector (pFAJ1819) into ORS571 cells followed by irreversible random Tn5 insertions into the genome. Efficiency of the transposon-based mutagenesis was increased 3~20 fold by refrigerating (3~11oC) the post-conjugation suspension for 2 days ~ 4 weeks before spreading on antibiotic selection plates. The improved mutation efficiency enabled colony development at high density, and these mutant colonies were directly transferred onto membrane and incubated overnight for accumulation of secreted Hcp protein. Background noise caused by adherent colonies was effectively reduced by using the dispersing chemical NaIO4 followed by a thorough vortex step. Accordingly, the detection limit was improved down to 6.3 ng Hcp protein. Approximately 68,000 mutants were analyzed, and 4 Hcp-secreting mutants and 1 Hcp-overexpression mutant were identified. Among the 4 Hcp-secreting mutants, strain Tn-A3 displayed decreased viability and imp-independent Hcp release caused by overexpression of phage-related loci (Azc_2137-2139); strain Tn-A2 and Tn-h91 showed compromised vitality and imp-independent Hcp secretion/release caused by C-terminal disruption of alanine racemase (alr, Azc_2065); strain Tn-A4 was disrupted in hypothetical gene Azc_0044, so it was pending further investigation. On the other hand, Hcp-overexpression strain Tn-A1 was unexpectedly identified by its phenotype of hyper-adherence presumably due to phosphate dyshomeostasis (pstS, Azc_4037). Further genetic verifications are required to assert the regulatory role of phosphate homeostasis on T6SS. Overall, the near-saturation screen suggests pathway(s) other than the deduced T6SS (Azc_2586-2605) participating in Hcp secretion/ release in A. caulinodans ORS571, and the mechanism(s) await future elucidation.

碩士
國立暨南國際大學
應用化學系
103
Courtship, an instinct of animals in the nature, normally occurs in between opposite sexes. Nevertheless, a lot of evidences proved that courtship and sexual behaviors existed between the same sexes in many species. It involved cellular or molecular mechanism is poorly understood. Drosophila melanogaster as an idea model provides advanced genetic tools for the neuronal circuit manipulations combined with sophispicated animal behaviors to realize the physiological mechanism underlying the homo-sexual behavior. We used behavioral screening to define 11 distinct dm-miRNAs (mir-10, -11, -34, -124, -252, -276b, -984, -985, -987, -989 and -1012) from the collection of 160 UAS-dme-miRNA lines that drove expression in elav-expressing cells of adult Drosophila males, which can prompt inter-male courtship behavior. Some of miRNA targets were also further predicted using some of miRNA target prediction resources. It should be noted that many common target genes, and some targets associated with same signaling pathway was predicted from 11 miRNAs. Therefore, it is of particular interest to reliably these predict potential miRNA targets which might be involved in this phenomenon. Finally, our data further confirm that 3 miRNAs (miRNA-10, -252 and -987) have a significant impact on the mRNA levels of porcupine (por) and demonstrate that down-regulate por level in adult male fly’ neuronal system can also induce the inter-male courtship behavior. An evolutionary perspective of homo-sexual that incorporates mechanisms related in flies, may lead to important advances in the understanding targeting molecules in human males.

碩士
國立清華大學
工業工程與工程管理學系所
105
Screening experiments are often conducted before optimization in order to reduce computation resources by identifying the important factors of the problem. In the literatures, factor screening and simulation optimization approaches mostly adopted expectation as performance measures. The methodologies that are focused on other alternatives, however, are difficult to develop due to a lack of nice statistical properties as expectation. Quantile is an important alternative to the expectation for spatial data and moreover, it enables risk control. In this study, we propose a novel approach called STRONG-Q that integrates efficient quantile-based factor screening methods into the framework of STRONG, which is a newly-developed Response-Surface-based framework, for large-scale quantile-based simulation optimization problems. The quantile-based factor screening method can effectively control the Type I error and enables the large-scale quantile-based simulation optimization problems to be solved efficiently when it is integrated into STRONG.

碩士
高雄醫學大學
藥學系碩士在職專班
106
Background: Outcomes of Hepatitis B prevention and control in Taiwan is outstanding in the world. Hepatitis B, significant efforts have also been devoted to the prevention and control of Hepatitis C, including reimbursement of oral direct-acting antiviral drugs by the National Health Insurance. DAA can block disease progression for patients with chronic Hepatitis C infection. In Taiwan, screening by liver-related foundations has been widely known under the spread of newspaper media, and also believed by some to be a good screening model. In this study, we re-appraised this screening model from the epidemiological and clinical perspectives. Aims: To retrospectively analyze community-based screening data and discuss the effectiveness and unresolved issues of large-scale community screening from clinical perspectives. Methods: Two non-governmental organizations conducted a two-stage liver cancer screening in Daliao District, Kaohsiung City. The first stage was blood sampling to test HBsAg anti-HCV, AST , ALT and AFP. For those who were positive for HBsAg or anti-HCV, further confirmation were performed on HBV DNA and HCV RNA. The second stage was ultrasonography examination for participants who were positive for any of the above five markers. Results: A total of 1495 subjects participate in this screening. The median coverage rates of 22 villages were 7.93/1000. Overall prevalence of HBsAg and anti-HCV were 11.6% and 3.7%. To identify the candidates of antiviral treatment for chronic Hepatitis B and C virus infection, participants were stratified by viral load and ALT levels. Among the positive subjects, only less than half were positive for HBV DNA (5.3%) or HCV RNA (1.5%). To identify the high risk for HCC by REACH-B risk score, only 16 (9.2%) of HBsAg carrier were with score higher than 10. Five subjects had AFP levels higher than 20 ng/ml. Discussion: In the study area with same prevalence of HBsAg and anti-HCV as the whole of Taiwan, we found that only few candidates for anti-viral treatment or HCC screening can be detected through such a community-based screening. We noted that geographic representation of participants to the whole population was poor. Conclusion: Due to biased geographic sampling and low rate of candidates for intervention, community-based screening should be conducted with well-coverage design in high risk areas.