Real-time monitoring of protein conformational changes using a nano-mechanical sensor.

Proteins can switch between different conformations in response to stimuli, such as pH or temperature variations, or to the binding of ligands. Such plasticity and its kinetics can have a crucial functional role, and their characterization has taken center stage in protein research. As an example, Topoisomerases are particularly interesting enzymes capable of managing tangled and supercoiled double-stranded DNA, thus facilitating many physiological processes. In this work, we describe the use of a cantilever-based nanomotion sensor to characterize the dynamics of human topoisomerase II (Topo II) enzymes and their response to different kinds of ligands, such as ATP, which enhance the conformational dynamics. The sensitivity and time resolution of this sensor allow determining quantitatively the correlation between the ATP concentration and the rate of Topo II conformational changes. Furthermore, we show how to rationalize the experimental results in a comprehensive model that takes into account both the physics of the cantilever and the dynamics of the ATPase cycle of the enzyme, shedding light on the kinetics of the process. Finally, we study the effect of aclarubicin, an anticancer drug, demonstrating that it affects directly the Topo II molecule inhibiting its conformational changes. These results pave the way to a new way of studying the intrinsic dynamics of proteins and of protein complexes allowing new applications ranging from fundamental proteomics to drug discovery and development and possibly to clinical practice.

Real-time tree-foliage surface estimation using a ground laser scanner

The optimization of most pesticide and fertilizer applications is based on overall grove conditions. In this work we measurements. Recently, Wei [9, 10] used a terrestrial propose a measurement system based on a ground laser scanner to LIDAR to measure tree height, width and volume developing estimate the volume of the trees and then extrapolate their foliage a set of experiments to evaluate the repeatability and surface in real-time. Tests with pear trees demonstrated that the accuracy of the measurements, obtaining a coefficient of relation between the volume and the foliage can be interpreted as variation of 5.4% and a relative error of 4.4% in the linear with a coefficient of correlation (R) of 0.81 and the foliar estimation of the volume but without real-time capabilities. surface can be estimated with an average error less than 5 %.

An embedded real-time red peach detection system based on an OV7670 camera, ARM Cortex-M4 processor and 3D Look-Up Tables

This work proposes the development of an embedded real-time fruit detection system for future automatic fruit harvesting. The proposed embedded system is based on an ARM Cortex-M4 (STM32F407VGT6) processor and an Omnivision OV7670 color camera. The future goal of this embedded vision system will be to control a robotized arm to automatically select and pick some fruit directly from the tree. The complete embedded system has been designed to be placed directly in the gripper tool of the future robotized harvesting arm. The embedded system will be able to perform real-time fruit detection and tracking by using a three-dimensional look-up-table (LUT) defined in the RGB color space and optimized for fruit picking. Additionally, two different methodologies for creating optimized 3D LUTs based on existing linear color models and fruit histograms were implemented in this work and compared for the case of red peaches. The resulting system is able to acquire general and zoomed orchard images and to update the relative tracking information of a red peach in the tree ten times per second.

Real-time Quality of Service Controller for Differentiated Services

IP-verkkojen hyvin tunnettu haitta on, että nämä eivät pysty takaamaan tiettyä palvelunlaatua (Quality of Service) lähetetyille paketeille. Seuraavat kaksi tekniikkaa pidetään lupaavimpina palvelunlaadun tarjoamiselle: Differentiated Services (DiffServ) ja palvelunlaatureititys (QoS Routing). DiffServ on varsin uusi IETF:n määrittelemä Internetille tarkoitettu palvelunlaatumekanismi. DiffServ tarjoaa skaalattavaa palvelujen erilaistamista ilman viestintää joka hypyssä ja per-flow –tilan ohjausta. DiffServ on hyvä esimerkki hajautetusta verkkosuunnittelusta. Tämän palvelutasomekanismin tavoite on viestintäjärjestelmien suunnittelun yksinkertaistaminen. Verkkosolmu voidaan rakentaa pienestä hyvin määritellystä rakennuspalikoiden joukosta. Palvelunlaatureititys on reititysmekanismi, jolla liikennereittejä määritellään verkon käytettävissä olevien resurssien pohjalta. Tässä työssä selvitetään uusi palvelunlaatureititystapa, jota kutsutaan yksinkertaiseksi monitiereititykseksi (Simple Multipath Routing). Tämän työn tarkoitus on suunnitella palvelunlaatuohjain DiffServille. Tässä työssä ehdotettu palvelunlaatuohjain on pyrkimys yhdistää DiffServ ja palvelunlaatureititysmekanismeja. Työn kokeellinen osuus keskittyy erityisesti palvelunlaatureititysalgoritmeihin.

Impact of the introduction of real-time therapeutic drug monitoring on empirical doses of carbapenems in critically ill burn patients.

PURPOSE: Adequate empirical antibiotic dose selection for critically ill burn patients is difficult due to extreme variability in drug pharmacokinetics. Therapeutic drug monitoring (TDM) may aid antibiotic prescription and implementation of initial empirical antimicrobial dosage recommendations. This study evaluated how gradual TDM introduction altered empirical dosages of meropenem and imipenem/cilastatin in our burn ICU. METHODS: Imipenem/cilastatin and meropenem use and daily empirical dosage at a five-bed burn ICU were analyzed retrospectively. Data for all burn admissions between 2001 and 2011 were extracted from the hospital's computerized information system. For each patient receiving a carbapenem, episodes of infection were reviewed and scored according to predefined criteria. Carbapenem trough serum levels were characterized. Prior to May 2007, TDM was available only by special request. Real-time carbapenem TDM was introduced in June 2007; it was initially available weekly and has been available 4 days a week since 2010. RESULTS: Of 365 patients, 229 (63%) received antibiotics (109 received carbapenems). Of 23 TDM determinations for imipenem/cilastatin, none exceeded the predefined upper limit and 11 (47.8%) were insufficient; the number of TDM requests was correlated with daily dose (r=0.7). Similar numbers of inappropriate meropenem trough levels (30.4%) were below and above the upper limit. Real-time TDM introduction increased the empirical dose of imipenem/cilastatin, but not meropenem. CONCLUSIONS: Real-time carbapenem TDM availability significantly altered the empirical daily dosage of imipenem/cilastatin at our burn ICU. Further studies are needed to evaluate the individual impact of TDM-based antibiotic adjustment on infection outcomes in these patients.

Methods of Design and Testing of Real Time Systems

Teollusuussovelluksissa vaaditaan nykyisin yhä useammin reaaliaikaista tiedon käsittelyä. Luotettavuus on yksi tärkeimmistä reaaliaikaiseen tiedonkäsittelyyn kykenevän järjestelmän ominaisuuksista. Sen saavuttamiseksi on sekä laitteisto, että ohjelmisto testattava. Tämän työn päätavoitteena on laitteiston testaaminen ja laitteiston testattavuus, koska luotettava laitteistoalusta on perusta tulevaisuuden reaaliaikajärjestelmille. Diplomityössä esitetään digitaaliseen signaalinkäsittelyyn soveltuvan prosessorikortin suunnittelu. Prosessorikortti on tarkoitettu sähkökoneiden ennakoivaa kunnonvalvontaa varten. Uusimmat DFT (Desing for Testability) menetelmät esitellään ja niitä sovelletaan prosessorikortin sunnittelussa yhdessä vanhempien menetelmien kanssa. Kokemukset ja huomiot menetelmien soveltuvuudesta raportoidaan työn lopussa. Työn tavoitteena on kehittää osakomponentti web -pohjaiseen valvontajärjestelmään, jota on kehitetty Sähkötekniikan osastolla Lappeenrannan teknillisellä korkeakoululla.

Beaming into the rat world: enabling real-time intereaction between rat and human each at their own scale

Immersive virtual reality (IVR) typically generates the illusion in participants that they are in the displayed virtual scene where they can experience and interact in events as if they were really happening. Teleoperator (TO) systems place people at a remote physical destination embodied as a robotic device, and where typically participants have the sensation of being at the destination, with the ability to interact with entities there. In this paper, we show how to combine IVR and TO to allow a new class of application. The participant in the IVR is represented in the destination by a physical robot (TO) and simultaneously the remote place and entities within it are represented to the participant in the IVR. Hence, the IVR participant has a normal virtual reality experience, but where his or her actions and behaviour control the remote robot and can therefore have physical consequences. Here, we show how such a system can be deployed to allow a human and a rat to operate together, but the human interacting with the rat on a human scale, and the rat interacting with the human on the rat scale. The human is represented in a rat arena by a small robot that is slaved to the human"s movements, whereas the tracked rat is represented to the human in the virtual reality by a humanoid avatar. We describe the system and also a study that was designed to test whether humans can successfully play a game with the rat. The results show that the system functioned well and that the humans were able to interact with the rat to fulfil the tasks of the game. This system opens up the possibility of new applications in the life sciences involving participant observation of and interaction with animals but at human scale.

Beaming into the rat world: enabling real-time intereaction between rat and human each at their own scale

Immersive virtual reality (IVR) typically generates the illusion in participants that they are in the displayed virtual scene where they can experience and interact in events as if they were really happening. Teleoperator (TO) systems place people at a remote physical destination embodied as a robotic device, and where typically participants have the sensation of being at the destination, with the ability to interact with entities there. In this paper, we show how to combine IVR and TO to allow a new class of application. The participant in the IVR is represented in the destination by a physical robot (TO) and simultaneously the remote place and entities within it are represented to the participant in the IVR. Hence, the IVR participant has a normal virtual reality experience, but where his or her actions and behaviour control the remote robot and can therefore have physical consequences. Here, we show how such a system can be deployed to allow a human and a rat to operate together, but the human interacting with the rat on a human scale, and the rat interacting with the human on the rat scale. The human is represented in a rat arena by a small robot that is slaved to the human"s movements, whereas the tracked rat is represented to the human in the virtual reality by a humanoid avatar. We describe the system and also a study that was designed to test whether humans can successfully play a game with the rat. The results show that the system functioned well and that the humans were able to interact with the rat to fulfil the tasks of the game. This system opens up the possibility of new applications in the life sciences involving participant observation of and interaction with animals but at human scale.

The contribution of real-time mirror reflections of motor actions on virtual body ownership in an immersive virtual environment

This paper reports an experiment that investigated people"s body ownership of an avatar that was observed in a virtual mirror. Twenty subjects were recruited in a within-groups study where 10 first experienced a virtual character that synchronously reflected their upper-body movements as seen in a virtual mirror, and then an asynchronous condition where the mirror avatar displayed prerecorded actions, unrelated to those of the participant. The other 10 subjects experienced the conditions in the opposite order. In both conditions the participant could carry out actions that led to elevation above ground level, as seen from their first person perspective and correspondingly in the mirror. A rotating virtual fan eventually descended to 2m above the ground. The hypothesis was that synchronous mirror reflection would result in higher subjective sense of ownership. A questionnaire analysis showed that the body ownership illusion was significantly greater for thesynchronous than asynchronous condition. Additionally participants in the synchronous condition avoided collision with the descending fan significantly more often than those in the asynchronous condition. The results of this experiment are put into context within similar experiments on multisensory correlation and body ownership within cognitive neuroscience.

Real-time Linux in electric drive systems

Reaaliaikaisten käyttöjärjestelmien käyttö sulautetuissa järjestelmissä on kasvamassa koko ajan. Sulautettuja tietokoneita käytetään yhä useammassa kohteessa kuten sähkökäyttöjen ohjauksessa. Sähkökäyttöjen ohjaus hoidetaan nykyisin yleensä nopealla digitaalisella signaaliprosessorilla (DSP), jolloin ohjelmointi ja päivittäminen on hidasta ja vaikeaa johtuen käytettävästä matalan tason Assembler-kielestä. Ratkaisuna yleiskäyttöisten prosessorien ja reaaliaikakäyttöjärjestelmien käyttö. Kaupalliset reaaliaikakäyttöjärjestelmät ovat kalliita ja lähdekoodin saaminen omaan käyttöön jopa mahdotonta. Linux on ei-kaupallinen avoimen lähdekoodin käyttöjärjestelmä, joten sen käyttö on ilmaista ja sitä voi muokata vapaasti. Linux:iin on saatavana useita laajennuksia, jotka tekevät siitä reaaliaikaisen käyttöjärjestelmän. Vaihtoehtoina joko kova (hard) tai pehmeä (soft) reaaliaikaisuus. Linux:iin on olemassa valmiita kehitysympäristöjä mutta ne kaipaavat parannusta ennen kuin niitä voidaan käyttää suuressa mittakaavassa teollisuudessa. Reaaliaika Linux ei sovellus nopeisiin ohjauslooppeihin (<100 ms) koska nopeus ei riitä vielä mutta nopeus kasvaa samalla kun prosessorit kehittyvät. Linux soveltuu hyvin rajapinnaksi nopean ohjauksen ja käyttäjän välille ja hitaampaan ohjaukseen.

Wavelets in real-time paper web analysis

Online paper web analysis relies on traversing scanners that criss-cross on top of a rapidly moving paper web. The sensors embedded in the scanners measure many important quality variables of paper, such as basis weight, caliper and porosity. Most of these quantities are varying a lot and the measurements are noisy at many different scales. The zigzagging nature of scanning makes it difficult to separate machine direction (MD) and cross direction (CD) variability from one another. For improving the 2D resolution of the quality variables above, the paper quality control team at the Department of Mathematics and Physics at LUT has implemented efficient Kalman filtering based methods that currently use 2D Fourier series. Fourier series are global and therefore resolve local spatial detail on the paper web rather poorly. The target of the current thesis is to study alternative wavelet based representations as candidates to replace the Fourier basis for a higher resolution spatial reconstruction of these quality variables. The accuracy of wavelet compressed 2D web fields will be compared with corresponding truncated Fourier series based fields.

Analysis of TRIP expression in different types of skin tumor

TRAF-interacting protein (TRIP) is a ubiquitously expressed nucleolar E3 ubiquitin ligase. Ubiquitination of proteins is a post-translational modification, which decides on the cellular fate of the protein. TRIP in vivo substrate has not been yet identified. However, TRIP has been shown to play an important role in cellular proliferation, especially in keratinocytes. TRIP was found to be up-regulated in basal cell carcinoma (BCC) at the mRNA level. This prompted us to elucidate its role in skin proliferative diseases such as cancer by analyzing its expression in BCCs at protein level and in squamous cell carcinoma (SCC) at mRNA and protein level. To that purpose, we performed a real-time PCR (qPCR) analysis followed by an immunohistochemistry (IHC) on formalin-fixed, paraffin-embedded (FFPE) biopsies. The real-time PCR was performed on 12 RNA samples of which 6 were extracted from SCC biopsies and 6 from normal human skin. The results were statistically insignificant. Further analyses are needed on new RNA samples. The IHC assay was performed on 20 biopsies from BCCs, 21 biopsies from SCCs and on 5 tissues from normal human skin. The results obtained showed an extensive expression of TRIP in keratinocytes nuclei. Due to various limitations related to the technique and to doubts about preservation of the antigens in the tissues from normal human skin, we could not highlight a clear difference in TRIP expression between the different tissues. In conclusion, further analyses are needed on new RNA samples (qPCR) and on better preserved FFPE tissues from normal skin (IHC) to assess TRIP relative expression in BCCs and SCCs versus normal human skin.

Capillary thermal desorption unit for near real-time analysis of VOCs at sub-trace levels. Application to the analysis of environmental air contamination and breath samples

A capillary microtrap thermal desorption module is developed for near real-time analysis of volatile organic compounds (VOCs) at sub-ppbv levels in air samples. The device allows the direct injection of the thermally desorbed VOCs into a chromatographic column. It does not use a second cryotrap to focalize the adsorbed compounds before entering the separation column so reducing the formation of artifacts. The connection of the microtrap to a GC–MS allows the quantitative determination of VOCs in less than 40 min with detection limits of between 5 and 10 pptv (25 °C and 760 mmHg), which correspond to 19–43 ng m−3, using sampling volumes of 775 cm3. The microtrap is applied to the analysis of environmental air contamination in different laboratories of our faculty. The results obtained indicate that most volatile compounds are easily diffused through the air and that they also may contaminate the surrounding areas when the habitual safety precautions (e.g., working under fume hoods) are used during the manipulation of solvents. The application of the microtrap to the analysis of VOCs in breath samples suggest that 2,5-dimethylfuran may be a strong indicator of a person's smoking status