Automated segmentation of multiple red blood cells with digital holographic microscopy.

We present a method to automatically segment red blood cells (RBCs) visualized by digital holographic microscopy (DHM), which is based on the marker-controlled watershed algorithm. Quantitative phase images of RBCs can be obtained by using off-axis DHM along to provide some important information about each RBC, including size, shape, volume, hemoglobin content, etc. The most important process of segmentation based on marker-controlled watershed is to perform an accurate localization of internal and external markers. Here, we first obtain the binary image via Otsu algorithm. Then, we apply morphological operations to the binary image to get the internal markers. We then apply the distance transform algorithm combined with the watershed algorithm to generate external markers based on internal markers. Finally, combining the internal and external markers, we modify the original gradient image and apply the watershed algorithm. By appropriately identifying the internal and external markers, the problems of oversegmentation and undersegmentation are avoided. Furthermore, the internal and external parts of the RBCs phase image can also be segmented by using the marker-controlled watershed combined with our method, which can identify the internal and external markers appropriately. Our experimental results show that the proposed method achieves good performance in terms of segmenting RBCs and could thus be helpful when combined with an automated classification of RBCs.

Measurement with an automated oscillometric wrist device with position sensor leads to lower values than measurements obtained with an automated oscillometric arm device from the same manufacturer in elderly persons.

OBJECTIVE: Home blood pressure (BP) monitoring is recommended by several clinical guidelines and has been shown to be feasible in elderly persons. Wrist manometers have recently been proposed for such home BP measurement, but their accuracy has not been previously assessed in elderly patients. METHODS: Forty-eight participants (33 women and 15 men, mean age 81.3±8.0 years) had their BP measured with a wrist device with position sensor and an arm device in random order in a sitting position. RESULTS: Average BP measurements were consistently lower with the wrist than arm device for systolic BP (120.1±2.2 vs. 130.5±2.2 mmHg, P<0.001, means±SD) and diastolic BP (66.0±1.3 vs. 69.7±1.3 mmHg, P<0.001). Moreover, a 10 mmHg or greater difference between the arm and wrist device was observed in 54.2 and 18.8% of systolic and diastolic measures, respectively. CONCLUSION: Compared with the arm device, the wrist device with position sensor systematically underestimated systolic as well as diastolic BP. The magnitude of the difference is clinically significant and questions the use of the wrist device to monitor BP in elderly persons. This study points to the need to validate BP measuring devices in all age groups, including in elderly persons.

Automated User Interface testing in Symbian Operating System

Tässä diplomityössä tutkitaan automatisoitua testausta ja käyttöliittymätestauksen tekemistä helpommaksi Symbian-käyttöjärjestelmässä. Työssä esitellään Symbian ja Symbian-sovelluskehityksessä kohdattavia haasteita. Lisäksi kerrotaan testausstrategioista ja -tavoista sekä automatisoidusta testaamisesta. Lopuksi esitetään työkalu, jolla testitapausten luominen toiminnalisuus- ja järjestelmätestaukseen tehdään helpommaksi. Graafiset käyttöliittymättuovat ainutlaatuisia haasteita ohjelmiston testaamiseen. Ne tehdään usein monimutkaisista komponenteista ja niitä suunnitellaan jatkuvasti uusiksi ohjelmistokehityksen aikana. Graafisten käyttöliittymien testaukseen käytetään usein kaappaus- ja toistotyökaluja. Käyttöliittymätestauksen testitapausten suunnittelu ja toteutus vaatii paljon panostusta. Koska graafiset käyttöliittymät muodostavat suuren osan koodista, voitaisiin säästää paljon resursseja tekemällä testitapausten luomisesta helpompaa. Käytännön osuudessa toteutettu projekti pyrkii tähän tekemällä testiskriptien luomisesta visuaalista. Näin ollen itse testien skriptikieltä ei tarvitse ymmärtää ja testien hahmottaminen on myös helpompaa.

Monitoring System Resources During Automated Testing in Symbian Operating System

Tässä diplomityössä esitellään ohjelmistotestauksen ja verifioinnin yleisiä periaatteita sekä käsitellään tarkemmin älypuhelinohjelmistojen verifiointia. Työssä esitellään myös älypuhelimissa käytettävä Symbian-käyttöjärjestelmä. Työn käytännön osuudessa suunniteltiin ja toteutettiin Symbian-käyttöjärjestelmässä toimiva palvelin, joka tarkkailee ja tallentaa järjestelmäresurssien käyttöä. Verifiointi on tärkeä ja kuluja aiheuttava tehtävä älypuhelinohjelmistojen kehityssyklissä. Kuluja voidaan vähentää automatisoimalla osa verifiointiprosessista. Toteutettu palvelin automatisoijärjestelmäresurssien tarkkailun tallentamalla tietoja niistä tiedostoon testien ajon aikana. Kun testit ajetaan uudestaan, uusia tuloksia vertaillaan lähdetallenteeseen. Jos tulokset eivät ole käyttäjän asettamien virherajojen sisällä, siitä ilmoitetaan käyttäjälle. Virherajojen ja lähdetallenteen määrittäminen saattaa osoittautua vaikeaksi. Kuitenkin, jos ne määritetään sopivasti, palvelin tuottaa hyödyllistä tietoa poikkeamista järjestelmäresurssien kulutuksessa testaajille.

Automated detection of patient-ventilator asynchrony: new tool or new toy?

Although severe patient-ventilator asynchrony is frequent during invasive and non-invasive mechanical ventilation, diagnosing such asynchronies usually requires the presence at the bedside of an experienced clinician to assess the tracings displayed on the ventilator screen, thus explaining why evaluating patient-ventilator interaction remains a challenge in daily clinical practice. In the previous issue of Critical Care, Sinderby and colleagues present a new automated method to detect, quantify, and display patient-ventilator interaction. In this validation study, the automatic method is as efficient as experts in mechanical ventilation. This promising system could help clinicians extend their knowledge about patient-ventilator interaction and further improve assisted mechanical ventilation.

Blind docking of 260 protein-ligand complexes with EADock 2.0.

Molecular docking softwares are one of the important tools of modern drug development pipelines. The promising achievements of the last 10 years emphasize the need for further improvement, as reflected by several recent publications (Leach et al., J Med Chem 2006, 49, 5851; Warren et al., J Med Chem 2006, 49, 5912). Our initial approach, EADock, showed a good performance in reproducing the experimental binding modes for a set of 37 different ligand-protein complexes (Grosdidier et al., Proteins 2007, 67, 1010). This article presents recent improvements regarding the scoring and sampling aspects over the initial implementation, as well as a new seeding procedure based on the detection of cavities, opening the door to blind docking with EADock. These enhancements were validated on 260 complexes taken from the high quality Ligand Protein Database [LPDB, (Roche et al., J Med Chem 2001, 44, 3592)]. Two issues were identified: first, the quality of the initial structures cannot be assumed and a manual inspection and/or a search in the literature are likely to be required to achieve the best performance. Second the description of interactions involving metal ions still has to be improved. Nonetheless, a remarkable success rate of 65% was achieved for a large scale blind docking assay, when considering only the top ranked binding mode and a success threshold of 2 A RMSD to the crystal structure. When looking at the five-top ranked binding modes, the success rate increases up to 76%. In a standard local docking assay, success rates of 75 and 83% were obtained, considering only the top ranked binding mode, or the five top binding modes, respectively.

Automated formulation of optimisation models for steel beam structures

Over 70% of the total costs of an end product are consequences of decisions that are made during the design process. A search for optimal cross-sections will often have only a marginal effect on the amount of material used if the geometry of a structure is fixed and if the cross-sectional characteristics of its elements are property designed by conventional methods. In recent years, optimalgeometry has become a central area of research in the automated design of structures. It is generally accepted that no single optimisation algorithm is suitable for all engineering design problems. An appropriate algorithm, therefore, mustbe selected individually for each optimisation situation. Modelling is the mosttime consuming phase in the optimisation of steel and metal structures. In thisresearch, the goal was to develop a method and computer program, which reduces the modelling and optimisation time for structural design. The program needed anoptimisation algorithm that is suitable for various engineering design problems. Because Finite Element modelling is commonly used in the design of steel and metal structures, the interaction between a finite element tool and optimisation tool needed a practical solution. The developed method and computer programs were tested with standard optimisation tests and practical design optimisation cases. Three generations of computer programs are developed. The programs combine anoptimisation problem modelling tool and FE-modelling program using three alternate methdos. The modelling and optimisation was demonstrated in the design of a new boom construction and steel structures of flat and ridge roofs. This thesis demonstrates that the most time consuming modelling time is significantly reduced. Modelling errors are reduced and the results are more reliable. A new selection rule for the evolution algorithm, which eliminates the need for constraint weight factors is tested with optimisation cases of the steel structures that include hundreds of constraints. It is seen that the tested algorithm can be used nearly as a black box without parameter settings and penalty factors of the constraints.

Automated monitoring of medical protocols: a secure and distributed architecture

The control of the right application of medical protocols is a key issue in hospital environments. For the automated monitoring of medical protocols, we need a domain-independent language for their representation and a fully, or semi, autonomous system that understands the protocols and supervises their application. In this paper we describe a specification language and a multi-agent system architecture for monitoring medical protocols. We model medical services in hospital environments as specialized domain agents and interpret a medical protocol as a negotiation process between agents. A medical service can be involved in multiple medical protocols, and so specialized domain agents are independent of negotiation processes and autonomous system agents perform monitoring tasks. We present the detailed architecture of the system agents and of an important domain agent, the database broker agent, that is responsible of obtaining relevant information about the clinical history of patients. We also describe how we tackle the problems of privacy, integrity and authentication during the process of exchanging information between agents.

Comparison of Inoculation with the InoqulA and WASP Automated Systems with Manual Inoculation.

The quality of sample inoculation is critical for achieving an optimal yield of discrete colonies in both monomicrobial and polymicrobial samples to perform identification and antibiotic susceptibility testing. Consequently, we compared the performance between the InoqulA (BD Kiestra), the WASP (Copan), and manual inoculation methods. Defined mono- and polymicrobial samples of 4 bacterial species and cloudy urine specimens were inoculated on chromogenic agar by the InoqulA, the WASP, and manual methods. Images taken with ImagA (BD Kiestra) were analyzed with the VisionLab version 3.43 image analysis software to assess the quality of growth and to prevent subjective interpretation of the data. A 3- to 10-fold higher yield of discrete colonies was observed following automated inoculation with both the InoqulA and WASP systems than that with manual inoculation. The difference in performance between automated and manual inoculation was mainly observed at concentrations of >10(6) bacteria/ml. Inoculation with the InoqulA system allowed us to obtain significantly more discrete colonies than the WASP system at concentrations of >10(7) bacteria/ml. However, the level of difference observed was bacterial species dependent. Discrete colonies of bacteria present in 100- to 1,000-fold lower concentrations than the most concentrated populations in defined polymicrobial samples were not reproducibly recovered, even with the automated systems. The analysis of cloudy urine specimens showed that InoqulA inoculation provided a statistically significantly higher number of discrete colonies than that with WASP and manual inoculation. Consequently, the automated InoqulA inoculation greatly decreased the requirement for bacterial subculture and thus resulted in a significant reduction in the time to results, laboratory workload, and laboratory costs.

Social sensing for psychology: Automated interpersonal behavior assessment

In this article, we show how the use of state-of-the-art methods in computer science based on machine perception and learning allows the unobtrusive capture and automated analysis of interpersonal behavior in real time (social sensing). Given the high ecological validity of the behavioral sensing, the ease of behavioral-cue extraction for large groups over long observation periods in the field, the possibility of investigating completely new research questions, and the ability to provide people with immediate feedback on behavior, social sensing will fundamentally impact psychology.

Toward on-the-fly quantum mechanical/molecular mechanical (QM/MM) docking: development and benchmark of a scoring function.

We address the challenges of treating polarization and covalent interactions in docking by developing a hybrid quantum mechanical/molecular mechanical (QM/MM) scoring function based on the semiempirical self-consistent charge density functional tight-binding (SCC-DFTB) method and the CHARMM force field. To benchmark this scoring function within the EADock DSS docking algorithm, we created a publicly available dataset of high-quality X-ray structures of zinc metalloproteins ( http://www.molecular-modelling.ch/resources.php ). For zinc-bound ligands (226 complexes), the QM/MM scoring yielded a substantially improved success rate compared to the classical scoring function (77.0% vs 61.5%), while, for allosteric ligands (55 complexes), the success rate remained constant (49.1%). The QM/MM scoring significantly improved the detection of correct zinc-binding geometries and improved the docking success rate by more than 20% for several important drug targets. The performance of both the classical and the QM/MM scoring functions compare favorably to the performance of AutoDock4, AutoDock4Zn, and AutoDock Vina.

Structure of a-Si:H/a-Si1-xCx:H multilayers deposited in a reactor with automated substrate holder

This paper deals with the structural properties of a-Si:H/a-Si1-xCx: H multilayers deposited by glow-discharge decomposition of SiH4 and SiH4 and CH4 mixtures. The main feature of the rf plasma reactor is an automated substrate holder. The plasma stabilization time and its influence on the multilayer obtained is discussed. A series of a-Si:H/a-Si1-xCx: H multilayers has been deposited and characterized by secondary ion mass spectrometry (SIMS), X-ray diffraction (XRD) and transmission electron microscopy (TEM). No asymmetry between the two types of interface has been observed. The results show that the multilayers present a very good periodicity and low roughness. The difficulty of determining the abruptness of the multilayer at the nanometer scale is discussed.