No description available.

No description available.

No description available.

No description available.

No description available.

<p>Can a critical industrial system, such as a nuclear reactor, be made self-aware and cognizant of its operational history? Can it alert authorities covertly to malicious intrusion without exposing its  defense  mechanisms?  What  if  the  intruders  are  highly  knowledgeable  adversaries,  or  even  insiders that may have designed the system? This thesis addresses these research questions through a novel physical process defense called Covert Cognizance (C2). </p> <p>C2  serves  as  a  last  line  of  defense  to  industrial  systems  when  existing  information  and  operational technology defenses have been breached by advanced persistent threat (APT) actors or insiders. It is an active form of defense that may be embedded in an existing system to induce intelligence,  i.e.,  self-awareness,  and  make  various subsystems  aware  of  each  other.  It  interacts with the system at the process level and provides an additional layer of security to the process data therein without the need of a human in the loop. </p> <p>The C2 paradigm is  founded on two core requirements – zero-impact and zero-observability. Departing from contemporary active defenses, zero-impact requires a successful implementationto leave no footprint on the system ensuring identical operation while zero-observability requires that the embedding is immune to pattern-discovery algorithms.  In other words, a third-party such as  a  malicious  intruder  must  be  unable  to  detect  the  presence  of  the  C2  defense  based  on  observation of the process data, even when augmented by machine learning tools that are adept at pattern discovery. </p> <p>In the present work, nuclear reactor simulations are embedded with the C2 defense to induce awareness across subsystems and defend them against highly knowledgeable adversaries that have bypassed existing safeguards such as model-based defenses.  Specifically, the subsystems are made aware  of  each  other  by  embedding  critical information from  the  process  variables  of  one sub-module  along  the  noise of  the  process  variables  of  another,  thus  rendering  the  implementation  covert and  immune  to  pattern  discovery.   The  implementation  is  validated  using  generative adversarial  nets,  representing  a  state-of-the-art  machine  learning  tool,  and  statistical  analysis  of  the  reactor  states,  control  inputs,  outputs  etc. The  work  is  also  extended  to  data  masking  applications  via  the  deceptive  infusion  of  data  (DIOD)  paradigm.  Future  work  focuses  on  the  development of automated C2 modules for “plug ‘n’ play” deployment onto critical infrastructure and/or their digital twins.</p>

<p>Mass spectrometry (MS) can provide rapid, sensitive, and specific analysis, making it a valuable tool to characterize biomolecules, especially their dynamic changes when involved in significant processes.  Compared to other analytical techniques, which mostly focus on solution-phase or solid-phase characterization, MS enjoys a more general and efficient detection of gas-phase analytes since it ultimately measures abundances of bare ions in vacuum. This unique detection capability of MS has been demonstrated, in this dissertation, by characterizing the neutral serine octamer, a gas-phase amino acid cluster that has been detected by MS only so far. Besides its existence, the progress of chiral enrichment has also been monitored and quantified by MS during octamer formation. The acquired MS data is crucial to interpreting the mechanism of chiral enrichment achieved by serine octamer and might suggest its involvement in the prebiotic world to eventually achieve biohomochirality. The work also showcases the capability of detecting neutral compounds by MS, which breaks the stereotype that MS is exclusively an ion-based technique. </p> <p><br></p> <p>Besides process monitoring in the open air, MS also monitors the highly complicated metabolism processes inside biosamples, primarily benefiting from its excellent sensitivity, specificity, and throughput of ion detection. Since altered cellular metabolism is being recognized as a hallmark of cancer, MS is suitable for cancer diagnostics, whose performance of diagnosing glioma, a common brain cancer, has been tested.  Desorption electrospray ionization(DESI) has been used as it avoids sample preparation and allows direct characterization of raw tissue, therefore well suited for on-site analysis such as in the operating room. In short, we have applied intraoperative DESI-MS analysis on raw brain biopsies to provide glioma diagnostics within 5 min. Specifically, the molecular features revealed by MS are translated into pathological information of analyzed tissue, like genetic mutations and tumor concentrations, which is highly desired during surgeries to guide tumor resection and improve patient management. </p> <p><br></p> <p>Knowledge of diagnostic biomarkers is essential to the translation from MS data to pathology, which can be obtained by metabolic profiling using MS. Despite the tradeoff between comprehensive characterization and analysis time, we have extensively explored endogenous metabolites by using tandem MS and expedited analysis by avoiding the use of chromatography. After fast profiling, statistical analysis of all MS features has been applied to discover diagnostic markers to distinguish healthy brain tissue from cancerous tissue. DESI-MS methods have been developed to facilitate a simple and rapid characterization of these biomarkers in tissue for a smooth clinical transition. </p> <p><br></p> <p>However, the complete characterization of endogenous metabolites in a complicated biomixture, like tissue, is challenging, especially without the orthogonal separation provided by chromatography. This unmet demand calls for the development of novel MS scans to improve the metabolite coverage. For lipidomics by direct infusion MS, the MS scans used for lipid profiling have not been greatly expanded since its introduction. These conventionalMS scans only target one structural moiety of lipids and leave the rest unresolved, which limits the structure elucidation and biological interpretation of diagnostic lipids. We have introduced additional lipid scans that target both the lipid headgroup and one fatty acyl chain, leaving the other fatty acyl chain flexible. These scans with higher specificity can further alleviate the matrix effect by uncovering fewer ions in each scan and provide more structural information to support lipid identification. As a proof-of-concept, we have used them to profile both common phospholipids and the rarer ether lipids that display significant variations between healthy mice tissue and those with metabolic syndrome. The additional structural information provided by these scans ensures a clear message expressed by the disease metabolism and potentially indicates invention points and therapeutic candidates.</p>

<p>  </p> <p>Nuclear reactors operate under extreme environmental conditions, such as neutron bombardment, elevated temperatures, and high pressures. Over time, the harsh environmental conditions affect the material properties of structural materials and fuels. Studying the mechanical properties of structural materials and advanced fuels is common practice that is required to validate the material performance for deployment within the next-generation reactors. Next-generation reactors, such as Generation-IV reactors, will operate in more extreme environments than the current fleet of power reactors, with temperatures reaching potentially over 1,000℃ and the use of corrosive coolants, such as lead, lead-bismuth, and liquid sodium. Studying <em>in-situ</em> mechanical properties, such as irradiation creep, is challenging, particularly in next-generation reactor conditions. The instruments used to measure <em>in-situ</em> irradiation creep must collect data in real-time while experiencing harsh in-reactor conditions. Many historical <em>in-situ</em> creep capsules have implemented a variety of designs to measure irradiation creep. The current study designed, developed, and tested a novel, modular <em>in-situ</em> creep capsule to address the challenges of testing candidate materials for next-generation reactors. The <em>in-situ</em> creep capsule utilizes modern manufacturing methods, instrumentation, and alloying to address extreme environmental temperatures. Implementing modern technology has positioned the critical components of an <em>in-situ</em> creep capsule near the specimen, improving the accuracy of measuring irradiation creep in real-time. The modular design of the <em>in-situ</em> creep capsule allows the testing of various specimen geometries, thus making it a first-of-a-kind.</p>

Användandet av deponier är en av de vanligaste metoderna för avfallshantering globalt. Trots insatser som gjordes för att förbjuda hushållsavfall i deponier under millennieskiftet, deponier skapade innan restriktionerna är fortfarande en risk för miljön. Under 2014 öppnade SÖRAB en kontinuerlig biologisk reningsanläggning (KBR-anläggning) på Löt Avfallsanläggning för att hantera lakvatten från en gammal deponi som under en tid fylldes med hushållsavfall. Sedan dess har SÖRAB arbetat med att förbättra KBR-anläggningen. Målet med denna studie är att utforma en driftstrategi för KBR-anläggningen för att förbättra kvävereningen vid låga temperaturer. Ett antal laborativa försök genomfördes, såsom den mikrobiella konsortiets livsduglighet i lakvattnet och tillväxten i både rumstemperatur och vid 4°C, bioaugmentation genom att berika den mikrobiella cellkulturen som redan finns i lakvattnet och hur detta förbättrar kvävereningen i jämförelse med tillsatser av den kommersiella bakterieblandningen ClearBlu Environmental och andra externa kolkällor. Resultaten från dessa laborativa försök påvisade komplett nitrifikation i både rumstemperatur och 4°C i berikat lakvatten från KBR-anläggningens L2A bassäng efter fem dagar. Försöket visade även på syresatt denitrifikation. Dessutom påvisades komplett denitrifikation inom fem dagar, vid rumstemperatur i lakvatten från anläggningens L2B bassäng. Under efterföljande pilotförsök påvisades möjligheten till upplivandet av den biologiska kvävereningen genom berikningen av den mikrobiella cellkulturen i lakvattnet. I ett pilotförsök då lakvatten från L2B bassängen berikades, komplett denitrifikation skedde under en anaerob fas på 16 dagar samt nitrifikation och aerob denitrifikation under ett påföljande 17 dagar lång aerob fas. Ett annat pilotförsök då lakvatten från L2A bassängen berikades påvisade både aerob och anaerob nitrifikation, då ammoniumrening skedde i både den syresatta och syrefria fasen. Tillsatsen av nutrient broth (näringsbuljong) kan påverka KBR-anläggningen, vilket kväver vidare studier. Resultatet från detta projekt tydligt påvisar att kvävereningen i KBR-anläggningen kan förbättras genom att berika den redan närvarande mikrobiella kulturen. / Landfilling has been one of the most popular methods of handling waste globally. Despite the efforts made to stop the disposal of household waste during the turn of the millennia, the landfills formed before these restrictions are still at risk for causing harm to the environment. In 2014, SÖRAB opened a continuous-flow biological treatment (KBR) facility in Löt to treat the leachate produced in one of their older landfills, once filled with household waste. Since then, SÖRAB has been working on improving the treatment facility. The aim of this the study is to find a suitable process to enhance the nitrogen removal at low temperature. Several laboratory scale experiments were performed, such as viability of microbial consortia in the leachate and growth at room temperature and at 4°C, testing bioaugmentation by enriching the microbial cell culture in the leachate and their efficiency in removing nitrogen, compared to the commercial cell culture ClearBlu Environmental and carbon source addition. The results displayed complete nitrification at both room temperature and 4°C in bioaugmented, enriched leachate originating from the L2A basin of the KBR facility, after five days. These trials also suggested the occurrence of aerated denitrification. Complete denitrification within five days was seen at room temperature in bioaugmented, enriched leachate from the L2B basin of the same facility. The ensuing pilot scale trials proved the possibility to revive the biological nitrogen removal by microbial cell culture enrichment. In one pilot in which leachate from the L2B basin was enriched, complete denitrification in the anaerobic phase consisting of 16 days occurred, along with some nitrification and aerated denitrification in the 17 day long aerated phase that followed. Another pilot scale trail in which leachate from the L2A basin was enriched, both aerobic and anaerobic nitrification occurred, as ammonium removal occurred in both the aerated and unaerated phases. The addition of nutrient broth might influence the KBR system which needs further study. The results from this project clearly demonstrate that nitrogen removal in the KBR facility could be enhanced using a culture naturally present in the facility.

Tesis por compendio / [ES] La medicina actual se dirige hacia un enfoque más personalizado basándose en el diagnóstico molecular del paciente a través del estudio de biomarcadores específicos. Aplicando este principio molecular, el diagnóstico, pronóstico y selección de la terapia se apoyan en la identificación de variaciones específicas del genoma humano, como variaciones de un único nucleótido (SNV). Para detectar estos biomarcadores se dispone de una amplia oferta de tecnologías. Sin embargo, muchos de los métodos en uso presentan limitaciones como un elevado coste, complejidad, tiempos de análisis largos o requieren de personal y equipamiento especializado, lo que imposibilita su incorporación masiva en la mayoría de los sistemas sanitarios. Por tanto, existe la necesidad de investigar y desarrollar soluciones analíticas que aporten información sobre las variantes genéticas y que se puedan implementar en diferentes escenarios del ámbito de la salud con prestaciones competitivas y económicamente viables. El objetivo principal de esta tesis ha sido desarrollar estrategias innovadoras para resolver el reto de la detección múltiple de variantes genéticas que se encuentran en forma minoritaria en muestras biológicas de pacientes, cubriendo las demandas asociadas al entorno clínico. Las tareas de investigación se centraron en la combinación de reacciones de discriminación alélica con amplificación selectiva de DNA y el desarrollo de sistemas ópticos de detección versátiles. Con el fin de atender el amplio abanico de necesidades, en el primer capítulo, se presentan resultados que mejoran las prestaciones analíticas de la reacción en cadena de la polimerasa (PCR) mediante la incorporación de una etapa al termociclado y de un agente bloqueante amplificando selectivamente las variantes minoritarias que fueron monitorizadas mediante fluorescencia a tiempo real. En el segundo capítulo, se logró la discriminación alélica combinando la ligación de oligonucleótidos con la amplificación de la recombinasa polimerasa (RPA), que al operar a temperatura constante permitió una detección tipo point-of-care (POC). La identificación de SNV se llevó a cabo mediante hibridación en formato micromatriz, utilizando la tecnología Blu-Ray como plataforma de ensayo y detección. En el tercer capítulo, se integró la RPA con la reacción de hibridación alelo especifica en cadena (AS-HCR), en formato array para genotipar SNV a partir de DNA genómico en un chip. La lectura de los resultados se realizó mediante un smartphone. En el último capítulo, se presenta la síntesis de un nuevo reactivo bioluminiscente que se aplicó a la monitorización de biomarcadores de DNA a tiempo real y final de la RPA basada en la transferencia de energía de resonancia de bioluminiscencia (BRET), eliminando la necesidad de una fuente de excitación. Todas las estrategias permitieron un reconocimiento especifico de la variante de interés, incluso en muestras que contenían tan solo 20 copias de DNA genómico diana. Se consiguieron resultados sensibles (límite de detección 0.5% variante/total), reproducibles (desviación estándar relativa < 19%), de manera sencilla (3 etapas o menos), rápida (tiempos cortos de 30-200 min) y permitiendo el análisis simultaneo de varios genes. Como prueba de concepto, estas estrategias se aplicaron a la detección e identificación en muestras clínicas de biomarcadores asociados a cáncer colorrectal y enfermedades cardiológicas. Los resultados se validaron por comparación con los métodos de referencia NGS y PCR, comprobándose que se mejoraban los requerimientos técnicos y la relación coste-eficacia. En conclusión, las investigaciones llevadas a cabo posibilitaron desarrollar herramientas de genotipado con propiedades analíticas competitivas y versátiles, aplicables a diferentes escenarios sanitarios, desde hospitales a entornos con pocos recursos. Estos resultados son prometedores al dar respuesta a la demanda de tecnologías alternativas para el diagnóstico molecular personalizado. / [CA] La medicina actual es dirigeix cap a un enfocament més personalitzat basant-se en el diagnòstic molecular del pacient a través de l'estudi de biomarcadors específics. Aplicant aquest principi molecular, el diagnòstic, pronòstic i selecció de la teràpia es recolzen en la identificació de variacions específiques del genoma humà, com variacions d'un únic nucleòtid (SNV). Per a detectar aquests biomarcadors, es disposa d'una àmplia oferta de tecnologies. No obstant això, molts dels mètodes en ús presenten limitacions com un elevat cost, complexitat, temps d'anàlisis llargues o requereixen de personal i equipament especialitzat, la qual cosa impossibilita la seua incorporació massiva en la majoria dels sistemes sanitaris. Per tant, existeix la necessitat d'investigar i desenvolupar solucions analítiques que aporten informació sobre les variants genètiques i que es puguen implementar en diferents escenaris de l'àmbit de la salut amb prestacions competitives i econòmicament viables. L'objectiu principal d'aquesta tesi ha sigut desenvolupar estratègies innovadores per a resoldre el repte de la detecció múltiple de variants genètiques que es troben en forma minoritària en mostres biològiques de pacients, cobrint les demandes associades a l'entorn clínic. Les tasques d'investigació es van centrar en la combinació de reaccions de discriminació al·lèlica amb amplificació selectiva de DNA i al desenvolupament de sistemes òptics de detecció versàtils. Amb la finalitat d'atendre l'ampli ventall de necessitats, en el primer capítol, es presenten resultats que milloren les prestacions analítiques de la reacció en cadena de la polimerasa (PCR) mitjançant la incorporació d'una etapa al termociclat i d'un agent bloquejant amplificant selectivament les variants minoritàries que van ser monitoritzades mitjançant fluorescència a temps real. En el segon capítol, es va aconseguir la discriminació al·lèlica combinant el lligament d'oligonucleòtids amb l'amplificació de la recombinasa polimerasa (RPA), que en operar a temperatura constant va permetre una detecció tipus point-of-care (POC). La identificació de SNV es va dur a terme mitjançant hibridació en format micromatriu, utilitzant la tecnologia Blu-Ray com a plataforma d'assaig i detecció. En el tercer capítol, es va integrar la RPA amb la reacció d'hibridació al·lel específica en cadena (AS-HCR), en format matriu per a genotipar SNV a partir de DNA genòmic en un xip. La lectura dels resultats es va realitzar mitjançant un telèfon intel·ligent. En l'últim capítol, es presenta la síntesi d'un nou reactiu bioluminescent que es va aplicar al monitoratge de biomarcadors de DNA a temps real i final de la RPA basada en la transferència d'energia de ressonància de bioluminescència (BRET), eliminant la necessitat d'una font d'excitació. Totes les estratègies van permetre un reconeixement específic de la variant d'interès, fins i tot en mostres que només contenien 20 còpies de DNA genòmic diana. Es van aconseguir resultats sensibles (límit de detecció 0.5% variant/total), reproduïbles (desviació estàndard relativa < 19%), de manera senzilla (3 etapes o menys), ràpida (temps curts de 30-200 min) i permetent l'anàlisi simultània de diversos gens. Com a prova de concepte, aquestes estratègies es van aplicar a la detecció i identificació en mostres clíniques de biomarcadors associats a càncer colorectal i a malalties cardiològiques. Els resultats es van validar per comparació amb els mètodes de referència NGS i PCR, comprovant-se que es milloraven els requeriments tècnics i la relació cost-eficàcia. En conclusió, les investigacions dutes a terme van possibilitar desenvolupar eines de genotipat amb propietats analítiques competitives i versàtils, aplicables a diferents escenaris sanitaris, des d'hospitals a entorns amb pocs recursos. Aquests resultats són prometedors en donar resposta a la demanda de tecnologies alternatives per al diagnòstic molecular personalitzat. / [EN] Current medicine is moving towards a more personalized approach based on the patients' molecular diagnosis through the study of specific biomarkers. Diagnosis, prognosis and therapy selection, applying this molecular principle, rely on identifying specific variations in the human genome, such as single nucleotide variations (SNV). A wide range of technologies is available to detect these biomarkers. However, many of the employed methods have limitations such as high cost, complexity, long analysis times, or requiring specialized personnel and equipment, making their massive incorporation in most healthcare systems impossible. Therefore, there is a need to research and develop analytical solutions that provide information on genetic variants that can be implemented in different health scenarios with competitive and economically feasible performances. The main objective of this thesis has been to develop innovative strategies to solve the challenge of multiple detection of genetic variants that are found in a minority amount in patient samples, covering the demands associated with the clinical setting. Research tasks focused on the combination of allelic discrimination reactions with selective DNA amplification and the development of versatile optical detection systems. In order to meet the wide range of needs, in the first chapter, the analytical performances of the polymerase chain reaction (PCR) were improved by incorporating a thermocycling step and a blocking agent to amplify selectively minority variants that were monitored by real-time fluorescence. In the second chapter, allelic discrimination was achieved by combining oligonucleotide ligation with recombinase polymerase amplification (RPA), which operates at a constant temperature, allowing point-of-care (POC) detection. SNV identification was carried out by hybridization in microarray format, using Blu-Ray technology as the assay platform and detector. RPA was integrated with allele-specific hybridization chain reaction (AS-HCR), in an array format to genotype SNV from genomic DNA on a chip in the third chapter. The reading of the results was performed using a smartphone. In the last chapter, a new bioluminescent reagent was synthesized. It was applied to real-time and endpoint DNA biomarker monitoring based on bioluminescence resonance energy transfer (BRET), eliminating the need for an excitation source. All the strategies allowed specific recognition of the target variant, even in samples containing as few as 20 copies of target genomic DNA. Sensitive (limit of detection 0.5% variant/total), reproducible (relative standard deviation < 19%), simple (3 steps or less), fast (short times of 30-200 min) results were achieved, allowing simultaneous analysis of several genes. As proof of concept, these strategies were applied to detect and identify biomarkers associated with colorectal cancer and cardiological diseases in clinical samples. The results were validated by comparison with reference methods such as NGS and PCR, proving that the technical requirements and cost-effectiveness were improved. In conclusion, the developed research made it possible to develop genotyping tools with competitive analytical properties and versatile, applicable to different healthcare scenarios, from hospitals to limited-resource environments. These results are promising since they respond to the demand for alternative technologies for personalized molecular diagnostics. / The authors acknowledge the financial support received from the Generalitat Valenciana PROMETEO/2020/094, GRISOLIA/2014/024 PhD Grant and GVA-FPI-2017 PhD grant, the Spanish Ministry of Economy and Competitiveness MINECO projects CTQ2016-75749-R and PID2019-110713RB-I00 and European Regional Development Fund (ERDF). / Lázaro Zaragozá, A. (2022). Study of Strategies for Genetic Variant Discrimination and Detection by Optosensing [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/185216 / Compendio