ADSNARK: Nearly practical and privacy-preserving proofs on authenticated data

We study the problem of privacy-preserving proofs on authenticated data, where a party receives data from a trusted source and is requested to prove computations over the data to third parties in a correct and private way, i.e., the third party learns no information on the data but is still assured that the claimed proof is valid. Our work particularly focuses on the challenging requirement that the third party should be able to verify the validity with respect to the specific data authenticated by the source — even without having access to that source. This problem is motivated by various scenarios emerging from several application areas such as wearable computing, smart metering, or general business-to-business interactions. Furthermore, these applications also demand any meaningful solution to satisfy additional properties related to usability and scalability. In this paper, we formalize the above three-party model, discuss concrete application scenarios, and then we design, build, and evaluate ADSNARK, a nearly practical system for proving arbitrary computations over authenticated data in a privacy-preserving manner. ADSNARK improves significantly over state-of-the-art solutions for this model. For instance, compared to corresponding solutions based on Pinocchio (Oakland’13), ADSNARK achieves up to 25× improvement in proof-computation time and a 20× reduction in prover storage space.

PDMS encasing system for integrated lab-on-chip Ag/AgCl reference electrodes

Poly(dimethylsiloxane) (PDMS) is an organosilicon polymer widely used in the fabrication of microfluidic systems to integrate biochips. In this study, we propose the use of an adapted PDMS mould for the creation of a miniaturized, reusable, reference electrode for in-chip electrochemical measurements. Through its integrated microfluidic system it is possible to replenish internal buffer solutions, unclog critical junctions and treat the electrode’s surface, assuring a long term reuse of the same device. Planar Ag/AgCl reference electrodes were microfabricated over a passivated p-type Silicon Wafer. The PDMS mould, containing an integrated microfluidic system, was fabricated based on patterned SU-8 mould, which includes a lateral horizontal inlet access point. Surface oxidation was used for irreversible permanent bondage between flat surfaces. The final result was planar Ag/AgCl reference electrode with integrated microfluidic that allows for electrochemical analysis in biochips

Risco de suicídio e comorbidades psiquiátricas no transtorno de ansiedade generalizada

RESUMO Objetivo Investigar o risco de suicídio nos pacientes com transtorno de ansiedade generalizada (TAG). Métodos Estudo transversal com 253 pacientes dos ambulatórios de Psiquiatria, Nefrologia e Cardiologia do Hospital Universitário da Universidade Federal de Alagoas. O instrumento utilizado foi o MINI 5.0.0 (Mini-International Neuropsychiatric Interview). Resultados Os indivíduos com TAG corresponderam a 16,6% da amostra, sendo 30,8% nos pacientes entrevistados no ambulatório de psiquiatria e 11,3% nos pacientes entrevistados nos demais ambulatórios. A maioria é do sexo feminino (83,3%), casada (53,8%), sendo a média de idade de 44 (±12,2) anos. Houve comorbidade psiquiátrica em 88,1% dos entrevistados; 54,8% possuíam duas ou mais e 33,3% tinham apenas uma. A mais prevalente foi depressão maior (53,7%), seguida de distimia (21,4%) e depressão recorrente (14,6%). O risco de suicídio foi observado em 54,8% dos indivíduos com TAG. Conclusão A prevalência de TAG foi significativamente maior que na população geral, principalmente no ambulatório de psiquiatria. A maioria dos pacientes apresentou comorbidade psiquiátrica, especialmente transtornos de humor, além de risco de suicídio. O TAG mostrou elevada correlação com transtornos de humor e significativa associação com o risco de suicídio.

Prevalência de transtornos ansiosos e algumas comorbidades em idosos: um estudo de base populacional

RESUMO Objetivo Avaliar a prevalência de transtornos ansiosos e fatores associados em uma amostra populacional de idosos do Sul de Santa Catarina. Métodos Estudo transversal com base em dados populacionais, que avaliou 1.021 indivíduos idosos entre 60 e 79 anos. Foram realizadas entrevistas domiciliares para aferição de variáveis sobre transtornos ansiosos, por meio do questionário MINI, dados sociodemográficos, hipertensão arterial sistêmica (HAS), infarto agudo do miocárdio (IAM) e dosagem de colesterol. Resultados As prevalências entre os transtornos ansiosos foram de 22,0% para o transtorno de ansiedade generalizada (TAG); 14,8% para fobia social (FS); 10,5% para transtorno do pânico (TP); e 8,5% para o transtorno obsessivo-compulsivo (TOC). Além disso, 40,5% dos indivíduos apresentaram pelo menos um transtorno de ansiedade. A distribuição dos transtornos foi semelhante nos dois gêneros; TAG foi mais prevalente nos indivíduos de menor escolaridade; TOC foi mais presente em indivíduos casados ou em união estável. Em relação às variáveis clínicas, HAS foi associada à presença de TOC; FS foi associada com IAM; TOC e FS foram associados com HDL > 40 mg/dL. Conclusão Os dados demonstram que os quadros de ansiedade são muito frequentes em idosos da comunidade, se sobrepõem de forma significativa e estão associados a algumas variáveis clínicas cardiovasculares.

Análisis y optimización del radio enlace en un sistema RFID

El proyecto tiene como principal objetivo lograr mejorar el enlace entre el tag y el Reader, en un sistema RFID (Radio Frecuency IDentification). El mismo será abordado desde dos ópticas de trabajo; La primera, es lograr el mismo alcance de los sistemas actuales, reduciendo la potencia aportada por el Reader. En esta situación su principal aplicación será en los implantes en seres vivos, disminuyendo la radiación electromagnética en los mismos. La segunda, es lograr aumentar la distancia del alcance del enlace, sin aumentar la potencia del Reader.

Perfil glicometabólico inicial em pacientes com síndrome coronariana aguda e síndrome metabólica

FUNDAMENTO: Pacientes com síndrome metabólica (SM) têm alto risco coronariano e a disfunção da célula beta ou resistência à insulina pode prever um risco adicional de eventos cardiovasculares precoces. OBJETIVO: Avaliar as alterações glicometabólicas precoces em pacientes com SM, mas sem diagnóstico de diabete tipo 2, após síndrome coronariana aguda. MÉTODOS: Um total de 114 pacientes foi submetido ao teste oral de tolerância à glicose (TOTG), 1-3 dias da alta hospitalar, após infarto agudo do miocárdio ou angina instável. Baseado no TOTG, definimos três grupos de pacientes: tolerância normal à glicose (TNG; n=26), tolerância alterada à glicose (TAG; n=39) ou diabetes mellitus (DM; n=49). O Modelo de Avaliação da Homeostase (HOMA-IR) foi usado para estimar a resistência à insulina; a responsividade da célula beta foi avaliada através do índice insulinogênico de 30 minutos (ΔI30/ΔG30). RESULTADOS: Baseado no HOMA-IR, os pacientes com DM eram mais insulino-resistentes do que aqueles com TNG ou TAG (p<0,001). De acordo com o índice insulinogênico, a responsividade da célula beta também estava alterada em indivíduos com DM (p<0,001 vs TNG ou TAG). CONCLUSÃO: Altas taxas de alterações glicometabólicas foram encontradas após síndrome coronariana aguda em pacientes com SM. Como essas anormalidades acentuadamente aumentam o risco de desfechos adversos, o TOTG precoce pode ser utilizado em pacientes com SM para identificar aqueles que apresentam maior risco coronariano.

Funktionelle Charakterisierung von mtch2 im Zebrafischmodell

Die steigende Zahl von Erkrankungen in Folge von Adipositas ist ein weltweites Gesundheitsproblem unserer Zeit. Genomweite Assoziationsstudien konnten single-nucleotide polymorphisms identifizieren, die in Zusammenhang mit Adipositas stehen könnten, darunter auch MTCH2. Weiterführende Untersuchungen konnten zeigen, dass MTCH2 eine regulatorische Rolle bei der Adipogenese einnimmt. Da mtch2 auch im Zebrafisch in verschiedenen Geweben und Organen wie Leber, Darm und Fettgewebe exprimiert wird, liegt die Vermutung nahe, dass es in diesen Organen und Geweben eine Funktion aufweist. Diese Funktion sollte über einen Morpholino-induzierten Knockdown des Gens und die Analyse des Phänotyps der Morpholino-injizierten Fische näher analysiert werden. Der Knockdown von mtch2 im Zebrafisch wurde mit Hilfe zweier Splice-Morpholinos induziert und über quantitative Real Time PCR identifiziert. Die Auswirkungen des Knockdowns auf die Entwicklung von Leber und Darm der Fische wurde über spezifische Marker mit der Methode der In situ Hybridisierung untersucht. Die Adipozytenbildung wurde durch Nilrotfärbung analysiert und über die Fütterung der Fische mit fluoreszierenden Beads mit dem Essverhalten in Zusammenhang gebracht. Bei beiden Morpholinos führte der Knockdown von mtch2 an Tag 4 der Entwicklung der Morpholino-injizierten Zebrafische zu Auffälligkeiten in der Ausbildung von Leber und Darm der Fische, die aber nicht mit einer generellen Störung der Entwicklung der Tiere einherging. An Tag 8 der Entwicklung der Zebrafische zeigte sich hingegen, dass die Tiere im Gegensatz zu den Kontroll-injizierten Fischen insgesamt kleiner beziehungsweise unterentwickelt waren, wobei dieser Umstand nicht mit ihrem Essverhalten in Zusammenhang gebracht werden konnte. Zudem konnte eine reduzierte Adipozytenbildung in den Morpholino-injizierten Zebrafischen festgestellt werden. (...)

Untersuchungen zum Einfluss von OLED Licht auf in vitro Zellkulturen

In der vorliegenden Arbeit werden Untersuchungen zum Einfluss von Licht auf humane in vitro-Zellkulturen beschrieben. Zunächst wird das Licht technisch erläutert und das Farbspektrum des Lichts betrachtet. Das natürliche Farbspektrum der Sonne ändert sich über den Tag, des Weiteren werden die Farben des Lichts in der Wissenschaft in verschiedenen Bereichen verwendet. Der Mensch hat einen geregelten Tagesablauf, der mit dem Tagesverlauf der Sonne parallel abläuft. Durch verschiedene Einflüsse kann diese Parallelität gestört werden. Für die Untersuchungen zum Einfluss des Lichts werden in vitro Modellsysteme verwendet, insbesondere Keratinozyten, die genauer beschrieben werden. Außerdem werden für die Untersuchungen organische Leuchtdioden (kurz: OLED) verwendet. Es wird eine Auswahl an Versuchs-OLEDs getroffen, welche für erste Versuche verwendet werden. In dieser Arbeit sollen erste Erkenntnisse über die Auswirkungen von Licht auf humane Zellen ermittelt werden, um aus der großen Auswahl von OLEDs Farbspektren zur genaueren Betrachtung herauszuziehen und später eine Anwendung in der Medizin zu ermöglichen. Hierzu werden das Wachstum und der Stoffwechselumsatz der Zellen betrachtet. Die Zellen werden mit Hilfe eines Versuchsaufbaus aus einer vorangegangenen Praktikumsarbeit beleuchtet. Als Lichtspektrum wurden 5 Farben ausgewählt: blau, grün, orange, warmweiß und kaltweiß. Als weitere Parameter werden eine feste Beleuchtungszeit, sowie eine identische Leuchtdichte bei allen Farben festgelegt. Aus den Versuchen können erste Erkenntnisse gezogen werden, jedoch müssen diese durch weitere Versuche bestätigt bzw. genauer betrachtet werden.

A novel gene expression signature in peripheral blood mononuclear cells for early detection of colorectal cancer.

BACKGROUND: Early detection and treatment of colorectal adenomatous polyps (AP) and colorectal cancer (CRC) is associated with decreased mortality for CRC. However, accurate, non-invasive and compliant tests to screen for AP and early stages of CRC are not yet available. A blood-based screening test is highly attractive due to limited invasiveness and high acceptance rate among patients. AIM: To demonstrate whether gene expression signatures in the peripheral blood mononuclear cells (PBMC) were able to detect the presence of AP and early stages CRC. METHODS: A total of 85 PBMC samples derived from colonoscopy-verified subjects without lesion (controls) (n = 41), with AP (n = 21) or with CRC (n = 23) were used as training sets. A 42-gene panel for CRC and AP discrimination, including genes identified by Digital Gene Expression-tag profiling of PBMC, and genes previously characterised and reported in the literature, was validated on the training set by qPCR. Logistic regression analysis followed by bootstrap validation determined CRC- and AP-specific classifiers, which discriminate patients with CRC and AP from controls. RESULTS: The CRC and AP classifiers were able to detect CRC with a sensitivity of 78% and AP with a sensitivity of 46% respectively. Both classifiers had a specificity of 92% with very low false-positive detection when applied on subjects with inflammatory bowel disease (n = 23) or tumours other than CRC (n = 14). CONCLUSION: This pilot study demonstrates the potential of developing a minimally invasive, accurate test to screen patients at average risk for colorectal cancer, based on gene expression analysis of peripheral blood mononuclear cells obtained from a simple blood sample.

Expression of Staphylococcus aureus clumping factor A in Lactococcus lactis subsp. cremoris using a new shuttle vector.

Staphylococcus aureus harbors redundant adhesins mediating tissue colonization and infection. To evaluate their intrinsic role outside of the staphylococcal background, a system was designed to express them in Lactococcus lactis subsp. cremoris 1363. This bacterium is devoid of virulence factors and has a known genetic background. A new Escherichia coli-L. lactis shuttle and expression vector was constructed for this purpose. First, the high-copy-number lactococcal plasmid pIL253 was equipped with the oriColE1 origin, generating pOri253 that could replicate in E. coli. Second, the lactococcal promoters P23 or P59 were inserted at one end of the pOri253 multicloning site. Gene expression was assessed by a luciferase reporter system. The plasmid carrying P23 (named pOri23) expressed luciferase constitutively at a level 10,000 times greater than did the P59-containing plasmid. Transcription was absent in E. coli. The staphylococcal clumping factor A (clfA) gene was cloned into pOri23 and used as a model system. Lactococci carrying pOri23-clfA produced an unaltered and functional 130-kDa ClfA protein attached to their cell walls. This was indicated both by the presence of the protein in Western blots of solubilized cell walls and by the ability of ClfA-positive lactococci to clump in the presence of plasma. ClfA-positive lactococci had clumping titers (titer of 4,112) similar to those of S. aureus Newman in soluble fibrinogen and bound equally well to solid-phase fibrinogen. These experiments provide a new way to study individual staphylococcal pathogenic factors and might complement both classical knockout mutagenesis and modern in vivo expression technology and signature tag mutagenesis.

Dispositius handheld per a aplicacions mèdiques: disseny i implementació d'interfícies del protocol Start

Els sistemes dʼatenció mèdica en situacions de pèrdues humanes massives necessiten classificar un número molt elevat de víctimes en un temps limitat i amb pocs recursos disponibles. Els mètodes clàssics es basen en una etiqueta de triatge de paper on el personal dʼemergències anota lʼestat del pacient juntament amb una quantitat reduïda dʼinformació. En aquest projecte descrivim lʼanàlisi, disseny i implementació dʼinterfícies gràfiques per dispositius mòbils pel protocol de triatge START, per ser utilitzades pels equips dʼemergència. Els components del projecte inclouen un dispositiu portàtil Nokia N810 amb connexió GPS, i IDBlue, un lector dʼetiquetes RFID per Bluetooth.

Radio frequency identification (RFID) of dentures in long-term care facilities.

STATEMENT OF PROBLEM: The difficulty of identifying the ownership of lost dentures when found is a common and expensive problem in long term care facilities (LTCFs) and hospitals. PURPOSE: The purpose of this study was to evaluate the reliability of using radiofrequency identification (RFID) in the identification of dentures for LTCF residents after 3 and 6 months. MATERIAL AND METHODS: Thirty-eight residents of 2 LTCFs in Switzerland agreed to participate after providing informed consent. The tag was programmed with the family and first names of the participants and then inserted in the dentures. After placement of the tag, the information was read. A second and third assessment to review the functioning of the tag occurred at 3 and 6 months, and defective tags (if present) were reported and replaced. The data were analyzed with descriptive statistics. RESULTS: At the 3-month assessment of 34 residents (63 tags) 1 tag was unreadable and 62 tags (98.2%) were operational. At 6 months, the tags of 27 of the enrolled residents (50 tags) were available for review. No examined tag was defective at this time period. CONCLUSIONS: Within the limits of this study (number of patients, 6-month time span) RFID appears to be a reliable method of tracking and identifying dentures, with only 1 of 65 devices being unreadable at 3 months and 100% of 50 initially placed tags being readable at the end of the trial.

Design and analysis of ChIP-Seq experiments for nuclear factor I DNA-binding proteins

SUMMARY : Eukaryotic DNA interacts with the nuclear proteins using non-covalent ionic interactions. Proteins can recognize specific nucleotide sequences based on the sterical interactions with the DNA and these specific protein-DNA interactions are the basis for many nuclear processes, e.g. gene transcription, chromosomal replication, and recombination. New technology termed ChIP-Seq has been recently developed for the analysis of protein-DNA interactions on a whole genome scale and it is based on immunoprecipitation of chromatin and high-throughput DNA sequencing procedure. ChIP-Seq is a novel technique with a great potential to replace older techniques for mapping of protein-DNA interactions. In this thesis, we bring some new insights into the ChIP-Seq data analysis. First, we point out to some common and so far unknown artifacts of the method. Sequence tag distribution in the genome does not follow uniform distribution and we have found extreme hot-spots of tag accumulation over specific loci in the human and mouse genomes. These artifactual sequence tags accumulations will create false peaks in every ChIP-Seq dataset and we propose different filtering methods to reduce the number of false positives. Next, we propose random sampling as a powerful analytical tool in the ChIP-Seq data analysis that could be used to infer biological knowledge from the massive ChIP-Seq datasets. We created unbiased random sampling algorithm and we used this methodology to reveal some of the important biological properties of Nuclear Factor I DNA binding proteins. Finally, by analyzing the ChIP-Seq data in detail, we revealed that Nuclear Factor I transcription factors mainly act as activators of transcription, and that they are associated with specific chromatin modifications that are markers of open chromatin. We speculate that NFI factors only interact with the DNA wrapped around the nucleosome. We also found multiple loci that indicate possible chromatin barrier activity of NFI proteins, which could suggest the use of NFI binding sequences as chromatin insulators in biotechnology applications. RESUME : L'ADN des eucaryotes interagit avec les protéines nucléaires par des interactions noncovalentes ioniques. Les protéines peuvent reconnaître les séquences nucléotidiques spécifiques basées sur l'interaction stérique avec l'ADN, et des interactions spécifiques contrôlent de nombreux processus nucléaire, p.ex. transcription du gène, la réplication chromosomique, et la recombinaison. Une nouvelle technologie appelée ChIP-Seq a été récemment développée pour l'analyse des interactions protéine-ADN à l'échelle du génome entier et cette approche est basée sur l'immuno-précipitation de la chromatine et sur la procédure de séquençage de l'ADN à haut débit. La nouvelle approche ChIP-Seq a donc un fort potentiel pour remplacer les anciennes techniques de cartographie des interactions protéine-ADN. Dans cette thèse, nous apportons de nouvelles perspectives dans l'analyse des données ChIP-Seq. Tout d'abord, nous avons identifié des artefacts très communs associés à cette méthode qui étaient jusqu'à présent insoupçonnés. La distribution des séquences dans le génome ne suit pas une distribution uniforme et nous avons constaté des positions extrêmes d'accumulation de séquence à des régions spécifiques, des génomes humains et de la souris. Ces accumulations des séquences artéfactuelles créera de faux pics dans toutes les données ChIP-Seq, et nous proposons différentes méthodes de filtrage pour réduire le nombre de faux positifs. Ensuite, nous proposons un nouvel échantillonnage aléatoire comme un outil puissant d'analyse des données ChIP-Seq, ce qui pourraient augmenter l'acquisition de connaissances biologiques à partir des données ChIP-Seq. Nous avons créé un algorithme d'échantillonnage aléatoire et nous avons utilisé cette méthode pour révéler certaines des propriétés biologiques importantes de protéines liant à l'ADN nommés Facteur Nucléaire I (NFI). Enfin, en analysant en détail les données de ChIP-Seq pour la famille de facteurs de transcription nommés Facteur Nucléaire I, nous avons révélé que ces protéines agissent principalement comme des activateurs de transcription, et qu'elles sont associées à des modifications de la chromatine spécifiques qui sont des marqueurs de la chromatine ouverte. Nous pensons que lés facteurs NFI interagir uniquement avec l'ADN enroulé autour du nucléosome. Nous avons également constaté plusieurs régions génomiques qui indiquent une éventuelle activité de barrière chromatinienne des protéines NFI, ce qui pourrait suggérer l'utilisation de séquences de liaison NFI comme séquences isolatrices dans des applications de la biotechnologie.

Diseño de antenas UHF para aplicaciones RFID

Aquest projecte es basa en l'estudi, disseny i avaluació d'antenes per a aplicacions RFID a la banda UHF. Les etiquetes RFID estan compostes per un xip i una antena que han de presentar una bona adaptació per a aconseguir màxima transferència de potència. Els dos objectius principals en els diferents fases de disseny de cada antena han estat optimitzar les seves dimensions, i incrementar l'ample de banda.

trEST, trGEN and Hits: access to databases of predicted protein sequences.

High throughput genome (HTG) and expressed sequence tag (EST) sequences are currently the most abundant nucleotide sequence classes in the public database. The large volume, high degree of fragmentation and lack of gene structure annotations prevent efficient and effective searches of HTG and EST data for protein sequence homologies by standard search methods. Here, we briefly describe three newly developed resources that should make discovery of interesting genes in these sequence classes easier in the future, especially to biologists not having access to a powerful local bioinformatics environment. trEST and trGEN are regularly regenerated databases of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Hits is a web-based data retrieval and analysis system providing access to precomputed matches between protein sequences (including sequences from trEST and trGEN) and patterns and profiles from Prosite and Pfam. The three resources can be accessed via the Hits home page (http://hits. isb-sib.ch).