Relative to traditional methods, air-liquid interface (ALI) exposures constitute a superior in vitro model for assessing the toxicological activity of complex aerosols. By removing the medium barrier, aerosols can be delivered to the cells at their apical surface. This project investigated the utility of the commercially available VITROCELL® exposure system for comparative toxicological assessment of complex aerosols (freshly-generated diluted diesel exhaust and simulated urban smog). The system setup was modified to improve control of aerosol properties (temperature and humidity) and cellular responses (dynamic range). Following optimization, cytotoxicity (WST-1 and LDH assays) and expression of selected genes involved in proinflammatory signalling and oxidative stress responses (via quantitative RT-PCR) were quantified following 1 hour aerosol exposures. The results showed only limited, variable responses following exposures to high concentrations of diesel exhaust. Lack of consistent and robust responses are likely due to poor deposition of particulate matter from the test aerosols.

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2017-08-01T13:42:24Z No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) JDiogo_Tese Final_Quimica.pdf: 8861608 bytes, checksum: b9ce8a33624820a531c0a5c298600d94 (MD5) / Made available in DSpace on 2017-08-01T13:42:24Z (GMT). No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) JDiogo_Tese Final_Quimica.pdf: 8861608 bytes, checksum: b9ce8a33624820a531c0a5c298600d94 (MD5) Previous issue date: 2017-01-26 / CNPQ / Metodologias te´oricas s˜ao ´uteis para complementar investigac¸˜oes experimentais e guiar novos experimentos envolvendo compostos luminescentes de lantan´ıdeos. A ausˆencia de uma ferramenta computacional contendo tais m´etodos motivou o desenvolvimento do LUMPAC. Se por um lado o LUMPAC difundiu o uso dessas metodologias, por outro as suas limitac¸˜oes tamb´em foram evidenciadas. Nesse sentido, pˆode-se conhecer melhor quais m´etodos merecem uma atenc¸˜ao especial, a saber: c´alculo dos parˆametros de intensidade (Ωλ), c´alculo da energia dos estados excitados dos ligantes e c´alculo da taxa de emiss˜ao n˜ao-radiativa (Anrad). O objetivo geral do presente trabalho de doutoramento consiste em corrigir algumas dessas limitac¸˜oes. Quantoaoc´alculodosΩλ,conseguimosatenuaroproblemacomumanovaformadeajustedos fatores de carga e das polarizabilidades atrav´es de um procedimento que foi denominado de Modelo da UnicidadeQDC, o qual faz uso de um conjunto bastante reduzido de parˆametros (Q,D eC). A importˆancia do ajusteQDC ´e que todas as quantidades derivadas se tornam tamb´em ´unicas para uma dada geometria do complexo, incluindo um esquema proposto de partic¸˜ao qu´ımico da taxa de emiss˜ao radiativa (Arad) em termos dos efeitos dos ligantes. Para demonstrar uma das poss´ıveis aplicac¸˜oes dessa partic¸˜ao, foi considerado o caso de complexos tern´arios de Eu3+ de ligantes n˜ao-iˆonicos repetidos e com os ligantes betadicetonatos DBM, TTA e BTFA. A partic¸˜ao ordenou perfeitamente a combinac¸˜ao n˜ao ´obvia de pares de ligantes n˜ao-iˆonicos que levam aos compostos misturados com os maiores valores deAexp rad. Quanto ao c´alculo dos estados excitados dos ligantes, ´e proposta uma parametrizac¸˜ao do m´etodo CIS baseadonaaproximac¸˜aoNDDO,exclusivamenteparasistemaslantan´ıdicos. Al´emdisso,realizamosumestudoavaliativodemetodologiasTDDFTaplicadasaoc´alculodeestadosexcitados de ligantes em complexos de lantan´ıdeos. Dentre os funcionais e func¸˜oes de base avaliados, a combinac¸˜ao LC-ωPBE/6-31G(d) foi aquela que forneceu as energias tripleto mais concordantes com os dados obtidos na literatura, sendo o erro m´edio absoluto correspondente em torno de 1600 cm−1. Atrav´es da parametrizac¸˜ao do modelo NDDO-CIS implementado no programa ORCA foi poss´ıvel obter um modelo semiemp´ırico para o c´alculo da energia tripleto de complexosdelantan´ıdeocom qualidade bem superiora da melhormetodologiaTDDFT avaliada. / Theoretical methodologies are useful to complement experimental investigations, and to guide new experiments involving luminescent lanthanide compounds. The lack of a software containing these methods motivated us to the development of the user friendly software package LUMPAC. And indeed, LUMPAC is slowly popularising the use of these theoretical methodologies - methodologies that are being put to more frequent tests, and are, consequently, slowly revealing their limitations. In this sense, we identified which aspects of the methods would deserve a more special attention, namely: intensity parameters calculations (Ωλ), calculation of the excited state energies of the ligands, and the calculation of the non-radiative decay rate (Anrad). The overall objective of this doctoral work is to correct some of these limitations as wellastoadvancenewdevelopments. RegardingtheΩλ calculation,wemitigatedthisproblem with a new way to adjust the charge factors and polarizabilities through a procedure we called theQDC Uniqueness Model, which makes use of a fairly small set of adjustaeble parameters (Q,D, andC). The importance of theQDC adjustment is that all derived quantities become also unique for a given complex geometry, including the chemical partition of the radiative emission rate (Arad) in terms of the effects of the ligands, which is being advanced here. To demonstrate one of the possible applications of this chemical partition, we address the case of repeating non-ionic ligand ternary complexes of europium(III) with DBM, TTA, and BTFA. The chemical partition perfectly ordered the non-obvious combination of pairs of non-ionic ligands that led to the mixed ligand compounds with the highest values ofAexp rad . Regarding the calculation of the excited states of the ligands, a new parametrization of the CIS method based on the NDDO approximation is being proposed, exclusively for lanthanide complexes. In addition, we carried out a study to evaluate some TDDFT methodologies for the calculation of excited states of ligands in lanthanide complexes. Among the functionals and basis sets evaluated, the combination LC-ωPBE/6-31G(d) was the one that led to the lowest UME (unsigned mean error), of around 1600 cm−1, for the triplet energies in comparison with data from the literature. The parametrization of the NDDO-CIS model implemented into ORCA provided a semiempirical method for the triplet energy calculation of lanthanide complexes with better predictionpower thanthebestassessed TDDFT method.

<p>For many years, researchers have developed ways to diagnose degenerative disease in the retina by utilizing multiple gene analysis techniques. Retinitis pigmentosa (RP) disease can cause either partially or totally blindness in adults. For that reason, it is crucial to find a way to pinpoint the causes in order to develop a proper medication or treatment. One of the common methods is genome-wide analysis (GWA). However, it cannot fully identify the genes that are indirectly related to the changes in eye size. In this research, RNA sequencing (RNA-seq) analysis is used to link the phenotype to genotype, creating a pool of candidate genes that might associate with the RP. This will support future research in finding a therapy or treatment to cure such disease in human adults.</p> <p><br></p> <p>Using the Drosophila Genetic Reference Panel (DGRP) – a gene reference panel of fruit fly – two types of datasets are involved in this analysis: eye-size data and gene expression data with two replicates for each strain. This allows us to create a phenotype-genotype map. In other words, we are trying to trace the genes (genotype) that exhibit the RP disease guided by comparing their eye size (phenotype). The basic idea of the algorithm is to discover the best replicate combination that maximizes the correlation between gene expression and eye-size. Since there are 2N possible replicate combinations, where N is the number of selected strains, the original implementation of sequential algorithm was computationally intensive.</p> <p><br></p> <p>The original idea of finding the best replicate combination was proposed by Nguyen et al. (2022). In this research, however, we restructured the algorithms to distribute the tasks of finding the best replicate combination and run them in parallel. The implementation was done using the R programming language, utilizing doParallel and foreach packages, and able to execute on a multicore machine. The program was tested on both a laptop and a server, and the experimental results showed an outstanding improvement in terms of the execution time. For instance, while using 32 processes, the results reported up to 95% reduction in execution time when compared with the sequential version of the code. Furthermore, with the increment of computational capabilities, we were able to explore and analyze more extreme eye-size lines using three eye-size datasets representing different phenotype models. This further improved the accuracy of the results where the top candidate genes from all cases showed connection to RP.</p>

<p>Ancestry is a complex and layered concept, but it must be operationalized for its objective use in genetic studies. Critical decisions in research analyses, clinical practice, and forensic investigations are based on genetic ancestry inference. For example, in genetic association studies for clinical and applied research, investigators may need to isolate one population of interest from a worldwide dataset to avoid false positive results, or in human identification, ancestry inferences can help reveal the identity of unknown DNA evidence by narrowing down a suspect list. Many studies seek to improve ancestry inference for these reasons. The research presented here offers valuable resources for exploring and improving genetic ancestry inference and intelligence toward identity. </p> <p>First, analyses with ‘big data’ in genomics is a resource-intensive task that requires optimization. Therefore, this research introduces a suite of automated Snakemake workflows, <em>Iliad</em>, that was developed to give the research community an easy-to-learn, hands-off computational tool for genomic data processing of multiple data formats. <em>Iliad</em> can be installed and run on a Google Cloud Platform remote server instance in less than 20 minutes when using the provided installation code in the ReadTheDocs documentation. The workflows support raw data processing from various genetic data types including microarray, sequence, and compressed alignment data, as well as performing micro-workflows on variant call format (VCF) files to merge data or lift over variant positions. When compared to a similar workflow, <em>Iliad </em>completed processing one sample’s raw paired-end sequence reads to a human-legible VCF file in 7.6 hours which was three-times faster than the other workflow. This suite of workflows is paramount towards building reference population panels from human whole-genome sequence (WGS) data which is useful in many research studies including imputation, ancestry estimation, and ancestry informative marker (AIM) discovery.</p> <p>Second, there are persistent challenges in ancestry inference for individuals of the Middle East, especially with the use of AIMs. This research demonstrates a population genomics study pertaining to the Middle East, novel population data from Lebanon (n=190), and an unsupervised genetic clustering approach with WGS data from the 1000 Genomes Project and Human Genome Diversity Project. These efforts for AIM discovery identified two single nucleotide polymorphisms (SNPs) based on their high allelic frequency differences between the Middle East and populations in Eurasia, namely Europe and South/Central Asia. These candidate AIMs were evaluated with the most current and comprehensive AIM panel to date, the VISAGE Enhanced Tool (ET), using an external validation set of Middle Eastern WGS data (n=137). Instead of relying on pre-defined biogeographic ancestry labels to confirm the accuracy of validation sample ancestry inference, this research produced a deep, unsupervised ADMIXTURE analysis on 3,469 worldwide WGS samples with nearly 2 million independent SNPs (r2 < 0.1) which provided a genetic “ground truth”. This resulted in 136/137 validation samples as Middle East and provided valuable insights toward reference samples with varying co-ancestries that ultimately affects the classification of admixed individuals. Novel deep learning methods, specifically variational autoencoders, were introduced for visualizing one hundred percent of the genetic variance found using these AIMS in an alternative method to PCA and presents distinct population clusters in a robust ancestry space that remains static for the projection of unknown samples to aid in ancestry inference and human identification. </p> <p>Third, this research delves into a craniofacial study that makes improvements toward key intelligence information about physical identity by exploring the relationship between dentition and facial morphology with an advanced phenotyping approach paired with robust dental parameters used in clinical practice. Cone-beam computed tomography (CBCT) imagery was used to analyze the hard and soft tissue of the face at the same time. Low-to-moderate partial correlations were observed in several comparisons of dentition and soft tissue segments. These results included partial correlations of: i) inter-molar width and soft tissue segments nearest the nasal aperture, the lower maxillary sinuses, and a portion of the upper cheek, and ii) of lower incisor inclination and soft tissue segments overlapping the mentolabial fold. These results indicate that helpful intelligence information, potentially leading towards identity in forensic investigations, may be present where hard tissue structures are manifested in an observable way as a soft tissue phenotype. This research was a valuable preliminary study that paves the way towards the addition of facial hard tissue structures in combination with external soft tissue phenotypes to advance fundamental facial genetic research. Thus, CBCT scans greatly add to the current facial imagery landscape available for craniofacial research and provide hard and soft tissue data, each with measurable morphological variation among individuals. When paired with genetic association studies and functional biological experiments, this will ultimately lead to a greater understanding of the intricate coordination that takes place in facial morphogenesis, and in turn, guide clinical orthodontists to better treatment modalities with an emphasis on personalized medicine. Lastly, it aids intelligence methodologies when applied within the field of forensic anthropology.</p>

Genomic DNA is the template of life - the entity which is characterized by a self-sustaining anatomical development, regulated signaling processes, the ability to reproduce and to respond to stimuli. Through what is classically known as the central dogma, the genome is transcribed into mRNA, which in turn is translated into proteins. The proteins take part in most, if not all, cellular processes, and it is by unraveling these processes that we can begin to understand life and disease-causing mechanisms. In vitro and in vivo assays are two levels at which protein communication may be studied, and which permit manipulation and control over the proteins under investigation. But in order to retrieve a representation of the processes as close to reality as possible, in situ analysis may instead be applied as a complement to the other two levels of study. In situ PLA offers the ability to survey protein activity in tissue samples and primary cell lines, at a single cell level, detecting single targets in their natural unperturbed environment.   In this thesis new developments of the in situ PLA are described, along with a new technique offering in situ enzyme-free detection of proximity between biomolecules. The dynamic range of in situ PLA has now been increased by several orders of magnitude to cover analogous ranges of protein expression; the output signals have been modified to offer a greater signal-to-noise ratio and to limit false-positive-rates while also extending the dynamic range further; simultaneous detection of multiple protein complexes is now possible; proximity-HCR is presented as a robust and inexpensive enzyme-free assay for protein complex detection. The thesis also covers descriptions on how the techniques may be simultaneously applied, also together with other techniques, for the multiple data-point acquisition required by the emerging realm of systems biology. A future perspective is presented for how much more information may be simultaneously acquired from tissue samples to describe biomolecular interactions in a new manner. This will allow new types of biomarkers and drugs to be discovered, and a new holistic understanding of life.

This thesis describes the on-road analysis of criteria air pollutants (CAPs) and volatile organic compounds (VOCs) from a moving vehicle. CAPs and VOCs have numerous direct and indirect effects on the environment and public health and are generated from a variety of point and diffuse sources. The concentration of these pollutants can vary on the scale of metres and seconds due to variable emission rates of sources, meteorology, and the topography of an area. CAPs are conventionally measured on a spatial scale of tens of kilometres and one hour or longer time resolution, which limits the understanding of their impact and leaving many communities lacking information regarding their air quality. VOCs are not measured as frequently as CAPs, owing to the difficulty, challenges, and cost associated with sampling. The Mobile Mass Spectrometry Lab (MMSL) was developed to collect high geospatial (15 – 1,500 m) and temporal (1 – 10 s) resolution measurements of CAPs (O3, NOx, PM2.5), CO2, CH4, and VOCs. CAPs and greenhouse gases were monitored using standard analyzers, while VOCs were measured using a proton-transfer reaction time-of-flight mass spectrometer (PTR-MS). PTR-MS is a real-time, direct, in situ technique that can monitor VOCs in the ambient atmosphere without sample collection. The PTR-MS monitored up to mass-to-charge 330 with a sample integration time of 1 or 10 seconds and had detection limits into the low- to mid-ppt. PTR-MS is a soft ionization technique that is selective to all compounds with a proton affinity less than water, which excludes the atmospheric matrix and includes most VOCs. The measurements provided by the PTR-MS provided a rich dataset for which to develop workflow and processing methods alongside sampling strategies for the collection of high geospatial and temporal VOC data. The first on-road deployment of the MMSL was performed across the Regional District of Nanaimo and the Alberni-Clayoquot Regional District in British Columbia, Canada, from July iv 2018 – April 2019 to monitor the geospatial and temporal variation in the concentration of CAPs and VOCs. VOCs detected in the areas include hydrocarbons like toluene, C2-benzenes, and terpenes, organic acids like acetic acid, oxygenated compounds like acetone and acetaldehyde, and reduced sulfur compounds like methanethiol and dimethyl sulfide. While observed concentrations of VOCs were mostly below detection limits, concentration excursions upwards of 2,200 ppb for C2-benzenes (reported as ethylbenzene) for instance, were observed across the various communities and industries that comprise central Vancouver Island. VOCs like monoterpenes, were observed near the wood industries up to 229 ppb. Combustion related VOCs, like toluene and C2-benzenes, were often observed on major transportation corridors and was found to vary significantly between seasons, with winter measurements often exceeding those made in the summer. Reduced sulfur compounds, common components of nuisance odours, were measured around a few industries like waste management and wood industries. The second on-road deployment of the MMSL focused on the analysis of VOCs in the community around a wastewater treatment plant (WWTP) to identify the source of odours in the area. VOCs were also monitored in the odour control process of the WWTP to identify the VOCs being emitted, how much were emitted, and where potential deficiencies were in the process in a unique study. Median emission rates at the facility for methanethiol, dimethyl sulfide, and dimethyl disulfide were determined to be 100, 19, and 21 kg yr-1, respectively. VOC monitoring in the community encompassed the WWTP and the other major industries in the area, including agricultural land, a composting facility, and a marina. The highest measurements of odorous reduced sulfur compounds were observed around the WWTP, upwards of 36 ppb for methanethiol. Unsupervised multivariate analysis was performed to identify groups of VOCs present and their potential sources. Three groups were identified, one of which was related to reduced sulfur compounds. This group was observed around the WWTP, indicating that the WWTP was the likely source of malodours in the community. / Graduate

<p dir="ltr">Open-access bioinformatics data enables accessible public health research for a variety of stakeholders, including teachers and low-resourced researchers. This project outlines two case studies utilizing open-access bioinformatics data sets and analysis software as proofs of concept for the types of research projects that can be adapted for workforce development purposes. The first case study is a spatial temporal analysis of Lyme disease rates in the United States from 2008 to 2020 using freely available data from the United States Department of Agriculture and Centers for Disease Control and Prevention to determine how urbanization and other changes in land use have impacted Lyme disease rates over time. The second case study conducts a pangenome analysis using bacteriophage data from the Actinobacteriophage Database to determine conserved gene regions related to host specificity.</p>

In der vorliegenden Arbeit wird eine Methodik zur Entwicklung mechanischer Simulationen der Interaktion Sportler-Sportgerät-Umwelt zur Untersuchung der Funktionalität von Sportgeräten konzipiert und vorgestellt. Die mechanische Simulation ist die gegenständliche Nachbildung spezieller Teilaspekte des Sportlers, z.B. der Körperform, der Trägheitseigenschaften, der Masse, der Interaktionskräfte zur Umwelt oder charakteristischer Bewegungsabläufe zum Zweck der Durchführung gezielter Experimente zur Untersuchung des dynamischen Systemverhaltens Sportler-Sportgerät-Umwelt. Dazu werden drei Fallbeispiele aus der Forschungstätigkeit der Arbeitsgruppe HLST an der Technischen Universität Chemnitz mit Methoden zur Verifikation von Simulationsmodellen – dem strukturierten Durchgehen, der Validierung im Dialog und dem Schreibtischtest – analysiert. Die Analyseergebnisse werden in eine Grobstruktur eingebettet, die aus relevanten Vorarbeiten zur Anwendung der Allgemeinen Modelltheorie abgeleitet ist. Die in den jeweiligen Fallbeispielen verwendeten Prozessschritte, Methoden und Werkzeuge werden dargestellt und die Entwicklungsergebnisse erörtert. Im Abschluss jedes Fallbeispiels wird der Entwicklungsprozess anhand von einheitlichen Kriterien bewertet. In einem abschließenden Schritt erfolgt die Zusammenführung der im Stand der Technik dargelegten Grundlagen und der in den drei Fallbeispielen gewonnenen Informationen zu einer strukturieren und kommentierten Methodik.:1 Einleitung 8 1.1 Definitionen 8 1.2 Einsatzgebiete der mechanischen Simulation 11 1.2.1 Überblick 11 1.2.2 Sicherheit gegen Versagen 12 1.2.3 Konformität 14 1.2.4 Funktionalität 15 1.3 Motivation und Zielsetzung 16 1.4 Aufbau der Arbeit 16 2 Theoretische Grundlagen 18 2.1 Experimentelle Methoden der Sportgeräteentwicklung 18 2.1.1 Einordnung nach Odenwald (2006) 18 2.1.2 Einordnung nach Witte (2013) 19 2.1.3 Einordnung nach Senner (2001) 20 2.1.4 Eigene Systematisierung 23 2.2 Allgemeine Modelltheorie 26 2.3 Existierende Ansätze für die Applikation der Allgemeinen Modelltheorie 29 2.3.1 Anwendung der AMT in der Chemie 29 2.3.2 Anwendung der AMT in der Biomechanik 30 2.3.3 Anwendung der AMT in Logistik und Produktion 32 2.3.4 Fazit 37 3 Präzisierung der Problemstellung 38 4 Methodik 39 5 Fallbeispiel Schwimmanzug – Strömungswiderstand 41 5.1 Vorbemerkungen 41 5.2 Aufgabenanalyse 42 5.2.1 Definition der zu untersuchenden Funktionalität des Sportgeräts 42 5.2.2 Analyse der zugrundeliegenden technischen Funktion des Sportgeräts 42 5.2.3 Analyse der Simulationswürdigkeit 43 5.2.4 Identifikation des Originals 47 5.3 Modellformulierung 48 5.3.1 Modellansatz 48 5.3.2 Modellsynthese 50 5.4 Modellimplementierung 53 5.4.1 Herstellung des Strömungskörpers 53 5.4.2 Simulation der Fortbewegung im Wasser 54 5.5 Modellanwendung 57 5.6 Modellüberprüfung 60 5.6.1 Abgleich zwischen den experimentellen Ergebnissen und dem theoretischen Modell 60 5.6.2 Vergleich mit dem Original 62 5.7 Fazit 67 6 Fallbeispiel Laufschuh – Stoßabsorption 69 6.1 Vorbemerkungen 69 6.2 Aufgabenanalyse 69 6.2.1 Definition der zu untersuchenden Funktionalität 69 6.2.2 Analyse der zugrundeliegenden technischen Funktion des Sportgeräts 71 6.2.3 Analyse der Simulationswürdigkeit 71 6.2.4 Definition des Originals 72 6.3 Modellformulierung 72 6.3.1 Modellansatz 72 6.3.2 Systemanalyse 72 6.3.3 Modellsynthese 77 6.4 Modellimplementierung 78 6.4.1 Krafterzeugung 78 6.4.2 Kraftübertragung 79 6.5 Modellanwendung 81 6.6 Modellüberprüfung 82 6.6.1 Soll-Istwert-Vergleich 82 6.6.2 Reliabilität 83 6.6.3 Korrelation zu Stoßbelastungsvariablen 85 6.6.4 Ereignisvaliditätstest: Sohlentemperatur 86 6.6.5 Ereignisvaliditätstest: Sohlendeformation 88 6.7 Fazit 91 7 Fallbeispiel Fußballschuh – Traktionseigenschaften 94 7.1 Vorbemerkungen 94 7.2 Aufgabenanalyse 94 7.2.1 Definition der zu untersuchenden Funktionalität 94 7.2.2 Analyse der zugrundeliegenden technischen Funktion des Sportgeräts 95 7.2.3 Analyse der Simulationswürdigkeit 96 7.2.4 Definition des Originals 97 7.3 Modellformulierung 98 7.3.1 Modellansatz 98 7.3.2 Systemanalyse 98 7.3.3 Modellsynthese 106 7.4 Modellimplementierung 107 7.5 Modellanwendung 110 7.6 Modellüberprüfung 114 7.6.1 Reliabilität 114 7.6.2 Sensitivitätsanalyse: Normalkraft 114 7.6.3 Sensitivitätsanalyse: Kraftanstieg horizontal 116 7.6.4 Vergleich mit der Realität 116 7.7 Fazit 117 8 Methodik zur Entwicklung mechanischer Simulationen der Interaktion Sportler-Sportgerät-Umwelt 119 8.1 Schematische Darstellung 119 8.2 Erläuterung der Vorgehensempfehlung 120 8.2.1 Klärung der Problemstellung 120 8.2.2 Modellbildung 122 8.2.3 Modellanwendung 124 9 Schlussbetrachtung 126 Literaturverzeichnis 128 Tabellenverzeichnis 133 Abbildungsverzeichnis 135 Danksagung 138 Selbstständigkeitserklärung 139 Lebenslauf 140 / In this dissertation a methodology is conceived that aims to structure the development process of test arrangements that mechanically simulate the interaction of athlete, sports equipment and environment. Mechanical simulation in this context is defined as the physical replication of specific properties of the athlete (e.g. the shape of the human body, body weight, joint kinematics, inertia, external forces in specific movements) in order to conduct experiments to investigate the dynamic behavior of the system athlete-equipment-environment. Therefore, three case studies of mechanical simulation models that have been developed at Technische Universität Chemnitz are analyzed by applying the validation and verification methods “structured walkthrough”, “face validity” and “desk checking”. The results of that analysis are embedded into a framework that is derived by literature review on applied model theory. For each of the three development processes the procedure model is identified and main tools and methods are discussed. Every case study is finally assessed by using standardized evaluation criterions. Finally, the main findings of the analysis of the case studies as well as knowledge obtained by reviewing the state of the art in model theory and simulation methods are used to build up a structured and commentated guideline.:1 Einleitung 8 1.1 Definitionen 8 1.2 Einsatzgebiete der mechanischen Simulation 11 1.2.1 Überblick 11 1.2.2 Sicherheit gegen Versagen 12 1.2.3 Konformität 14 1.2.4 Funktionalität 15 1.3 Motivation und Zielsetzung 16 1.4 Aufbau der Arbeit 16 2 Theoretische Grundlagen 18 2.1 Experimentelle Methoden der Sportgeräteentwicklung 18 2.1.1 Einordnung nach Odenwald (2006) 18 2.1.2 Einordnung nach Witte (2013) 19 2.1.3 Einordnung nach Senner (2001) 20 2.1.4 Eigene Systematisierung 23 2.2 Allgemeine Modelltheorie 26 2.3 Existierende Ansätze für die Applikation der Allgemeinen Modelltheorie 29 2.3.1 Anwendung der AMT in der Chemie 29 2.3.2 Anwendung der AMT in der Biomechanik 30 2.3.3 Anwendung der AMT in Logistik und Produktion 32 2.3.4 Fazit 37 3 Präzisierung der Problemstellung 38 4 Methodik 39 5 Fallbeispiel Schwimmanzug – Strömungswiderstand 41 5.1 Vorbemerkungen 41 5.2 Aufgabenanalyse 42 5.2.1 Definition der zu untersuchenden Funktionalität des Sportgeräts 42 5.2.2 Analyse der zugrundeliegenden technischen Funktion des Sportgeräts 42 5.2.3 Analyse der Simulationswürdigkeit 43 5.2.4 Identifikation des Originals 47 5.3 Modellformulierung 48 5.3.1 Modellansatz 48 5.3.2 Modellsynthese 50 5.4 Modellimplementierung 53 5.4.1 Herstellung des Strömungskörpers 53 5.4.2 Simulation der Fortbewegung im Wasser 54 5.5 Modellanwendung 57 5.6 Modellüberprüfung 60 5.6.1 Abgleich zwischen den experimentellen Ergebnissen und dem theoretischen Modell 60 5.6.2 Vergleich mit dem Original 62 5.7 Fazit 67 6 Fallbeispiel Laufschuh – Stoßabsorption 69 6.1 Vorbemerkungen 69 6.2 Aufgabenanalyse 69 6.2.1 Definition der zu untersuchenden Funktionalität 69 6.2.2 Analyse der zugrundeliegenden technischen Funktion des Sportgeräts 71 6.2.3 Analyse der Simulationswürdigkeit 71 6.2.4 Definition des Originals 72 6.3 Modellformulierung 72 6.3.1 Modellansatz 72 6.3.2 Systemanalyse 72 6.3.3 Modellsynthese 77 6.4 Modellimplementierung 78 6.4.1 Krafterzeugung 78 6.4.2 Kraftübertragung 79 6.5 Modellanwendung 81 6.6 Modellüberprüfung 82 6.6.1 Soll-Istwert-Vergleich 82 6.6.2 Reliabilität 83 6.6.3 Korrelation zu Stoßbelastungsvariablen 85 6.6.4 Ereignisvaliditätstest: Sohlentemperatur 86 6.6.5 Ereignisvaliditätstest: Sohlendeformation 88 6.7 Fazit 91 7 Fallbeispiel Fußballschuh – Traktionseigenschaften 94 7.1 Vorbemerkungen 94 7.2 Aufgabenanalyse 94 7.2.1 Definition der zu untersuchenden Funktionalität 94 7.2.2 Analyse der zugrundeliegenden technischen Funktion des Sportgeräts 95 7.2.3 Analyse der Simulationswürdigkeit 96 7.2.4 Definition des Originals 97 7.3 Modellformulierung 98 7.3.1 Modellansatz 98 7.3.2 Systemanalyse 98 7.3.3 Modellsynthese 106 7.4 Modellimplementierung 107 7.5 Modellanwendung 110 7.6 Modellüberprüfung 114 7.6.1 Reliabilität 114 7.6.2 Sensitivitätsanalyse: Normalkraft 114 7.6.3 Sensitivitätsanalyse: Kraftanstieg horizontal 116 7.6.4 Vergleich mit der Realität 116 7.7 Fazit 117 8 Methodik zur Entwicklung mechanischer Simulationen der Interaktion Sportler-Sportgerät-Umwelt 119 8.1 Schematische Darstellung 119 8.2 Erläuterung der Vorgehensempfehlung 120 8.2.1 Klärung der Problemstellung 120 8.2.2 Modellbildung 122 8.2.3 Modellanwendung 124 9 Schlussbetrachtung 126 Literaturverzeichnis 128 Tabellenverzeichnis 133 Abbildungsverzeichnis 135 Danksagung 138 Selbstständigkeitserklärung 139 Lebenslauf 140

<p>Neutrophils are the first cells recruited to an immune stimulus stemming from infection or sterile injuries via a mixture of chemoattractant cues. In addition to eliminating pathogens, neutrophils coordinate the overall inflammation by activating and producing inflammatory signals in the tissue while modulating the activation of other immune cells which in some cases leads to adverse tissue damage. Over amplified or chronic neutrophil recruitment directly leads to autoimmune diseases including rheumatic arthritis, diabetes, neurodegenerative diseases, and cancer. Dampening neutrophil recruitment is a strategy to intervene in neutrophil-orchestrated chronic inflammation. Despite intensive research over the past several decades, clinical studies targeting neutrophil migration have been largely unsuccessful, possibly due to the prominent redundancy of adhesion receptors and chemokines. Additional challenges lie in the balance of dampening detrimental inflammation while preserving immunity. Neutrophils are terminally differentiated cells that are hard to study in cell culture. Mouse models are often used to study hematopoiesis, migration, and chemotaxis of neutrophils but is very labor intensive. To discover novel therapeutic targets that modulate neutrophil migration, we performed a neutrophil-specific microRNA (miRNA) overexpression screen in zebrafish and identified eight miRNAs as potent suppressors of neutrophil migration. We have generated transgenic zebrafish lines that overexpresses these candidate miRNAs where we recapitulated the mitigation in neutrophil motility and chemotaxis to tissue injury or infection. Among those we further characterized two miRNAs which have not been reported to regulate neutrophil migration, namely miR-722 and miR-199.</p> <p> </p> <p>MiR-722 downregulates the transcript level of <i>rac2</i> through binding to the <i>rac2</i> 3'UTR. Furthermore, miR-722-overexpressing larvae display improved outcomes in both sterile and bacterial systemic models, which correlates with a robust upregulation of the anti-inflammatory cytokines in the whole larvae and isolated neutrophils. miR-722 protects zebrafish from lethal lipopolysaccharide challenge. In addition, overexpression of mir-722 reduced chemotaxis of human neutrophil like cells, indicating that miR-722 is a potential agent to reduce inflammation in humans. </p> <p>MiR-199<i>,</i> decreases neutrophil chemotaxis in zebrafish and human neutrophil-like cells. Intriguingly, in terminally differentiated neutrophils, miR-199 alters the cell cycle-related pathways and directly suppresses cyclin-dependent kinase 2 (<i>cdk2</i>), whose known activity is restricted to cell cycle progression and cell differentiation. Inhibiting Cdk2, but not DNA replication, disrupts cell polarity and chemotaxis of zebrafish neutrophils without inducing cell death. Human neutrophil-like cells deficient in CDK2 fail to polarize and display altered signaling downstream of the formyl peptide receptor. Chemotaxis of primary human neutrophils is also reduced upon CDK2 inhibition. Furthermore, miR-199 overexpression or CDK2 inhibition significantly improves the outcome of lethal systemic inflammation challenges in zebrafish. </p> <p> </p> <p>In summary, our results reveal previously unknown functions of these miRNAs, and provide potential avenues to modulate neutrophil migration as well as lead to discoveries of novel factors which can regulate this process. We have also discovered a non-classical role of CDK2 in regulating neutrophil migration which provides directions for alleviating systemic inflammation and a better understanding of neutrophil biology. </p>

<p dir="ltr">The genetic perturbations caused by spaceflight on biological systems tend to have a system-wide effect which is often difficult to deconvolute into individual signals with specific points of origin. Single cell multi-omic data can provide a profile of the perturbational effects but does not necessarily indicate the initial point of interference within a network. The objective of this project is to take advantage of large scale and genome-wide perturbational or Perturb-Seq datasets by using them to pre-train a generalist machine learning model that is capable of predicting the effects of unseen perturbations in new data. Perturb-Seq datasets are large libraries of single cell RNA sequencing data collected from CRISPR knock out screens in cell culture. The advent of generative machine learning algorithms, particularly transformers, make it an ideal time to re-assess large scale data libraries in order to grasp cell and even organism-wide genomic expression motifs. By tailoring an algorithm to learn the downstream effects of the genetic perturbations, we present a pre-trained generalist model capable of predicting the effects of multiple perturbations in combination, locating points of origin for perturbation in new datasets, predicting the effects of known perturbations in new datasets, and annotation of large-scale network motifs. We demonstrate the utility of this model by identifying key perturbational signatures in RNA sequencing data from spaceflown biological samples from the NASA Open Science Data Repository.</p>