Efficient targeted transcript discovery via array-based normalization of RACE libraries.

Rapid amplification of cDNA ends (RACE) is a widely used approach for transcript identification. Random clone selection from the RACE mixture, however, is an ineffective sampling strategy if the dynamic range of transcript abundances is large. To improve sampling efficiency of human transcripts, we hybridized the products of the RACE reaction onto tiling arrays and used the detected exons to delineate a series of reverse-transcriptase (RT)-PCRs, through which the original RACE transcript population was segregated into simpler transcript populations. We independently cloned the products and sequenced randomly selected clones. This approach, RACEarray, is superior to direct cloning and sequencing of RACE products because it specifically targets new transcripts and often results in overall normalization of transcript abundance. We show theoretically and experimentally that this strategy leads indeed to efficient sampling of new transcripts, and we investigated multiplexing the strategy by pooling RACE reactions from multiple interrogated loci before hybridization.

Subtelomeric 6p deletion: clinical and array-CGH characterization in two patients

We report on two patients with de novo subtelomeric terminal deletion of chromosome 6p. Patient 1 is an 8-month-old female born with normal growth parameters, typical facial features of 6pter deletion, bilateral corectopia, and protruding tongue. She has severe developmental delay, profound bilateral neurosensory deafness, poor visual contact, and hypsarrhythmia since the age of 6 months. Patient 2 is a 5-year-old male born with normal growth parameters and unilateral hip dysplasia; he has a characteristic facial phenotype, bilateral embryotoxon, and moderate mental retardation. Further characterization of the deletion, using high-resolution array comparative genomic hybridization (array-CGH; Agilent Human Genome kit 244 K), revealed that Patient 1 has a 8.1 Mb 6pter-6p24.3 deletion associated with a contiguous 5.8 Mb 6p24.3-6p24.1 duplication and Patient 2 a 5.7 Mb 6pter-6p25.1 deletion partially overlapping with that of Patient 1. Complementary FISH and array analysis showed that the inv del dup(6) in Patient 1 originated de novo. Our results demonstrate that simple rearrangements are often more complex than defined by standard techniques. We also discuss genotype-phenotype correlations including previously reported cases of deletion 6p.

Real-time full field laser Doppler imaging.

We present a full field laser Doppler imaging instrument, which enables real-time in vivo assessment of blood flow in dermal tissue and skin. This instrument monitors the blood perfusion in an area of about 50 cm(2) with 480 × 480 pixels per frame at a rate of 12-14 frames per second. Smaller frames can be monitored at much higher frame rates. We recorded the microcirculation in healthy skin before, during and after arterial occlusion. In initial clinical case studies, we imaged the microcirculation in burned skin and monitored the recovery of blood flow in a skin flap during reconstructive surgery indicating the high potential of LDI for clinical applications. Small animal imaging in mouse ears clearly revealed the network of blood vessels and the corresponding blood perfusion.

Comparative study of upper lip frenectomy with the CO2 laser versus the Er, Cr: YSGG laser

Objectives: To compare upper lip frenulum reinsertion, bleeding, surgical time and surgical wound healing in frenectomies performed with the CO2 laser versus the Er, Cr:YSGG laser. Study design: A prospective study was carried out on 50 randomized pediatric patients who underwent rhomboidal resection of the upper lip frenulum with either the CO2 laser or the Er,Cr:YSGG laser. Twenty-five patients were assigned to each laser system. All patients were examined at 7, 14, 21 days and 4 months after the operation in order to assess the surgical wound healing. Results: Insertion of the frenulum, which was preoperatively located between the upper central incisors, migrated to the mucogingival junction as a result of using both laser systems in all patients. Only two patients required a single dose of 650 mg of paracetamol, one of either study group. CO2 laser registered improved intraoperative bleeding control results and shorter surgical times. On the other hand, the Er,Cr:YSGG laser achieved faster healing. Conclusions: Upper lip laser frenectomy is a simple technique that results in minimum or no postoperative swelling or pain, and which involves upper lip frenulum reinsertion at the mucogingival junction. The CO2 laser offers a bloodless field and shorter surgical times compared with the Er,Cr:YSGG laser. On the other hand, the Er,Cr:YSGG laser achieved faster wound healing.

Comparison of Fundus Autofluorescence Between Fundus Camera (Topcon) and Confocal Scanning Laser Ophthalmoscope (HRA) in Various Pathologies

Purpose: To investigate the differences between the Fundus Camera (Topcon TRC-50X) and Confocal Scanning Laser Ophthalmoscope (Heidelberg retina angiogram (HRA)) on the fundus autofluorescence (FAF) imaging (resolution and FAF characteristics). Methods: Eighty nine eyes of 46 patients with various retinal diseases underwent FAF imaging with HRA (488nm exciter / 500nm barrier filter) before fluorescein angiography (FFA) and Topcon Fundus Camera (580nm exciter / 695nm barrier filter) before and after FFA. The quality of the FAF images was estimated, compared for their resolution and analysed for the influence of fixation stability and cataracts. Hypo- and hyper-FAF behaviour was analysed for the healthy disc, healthy fovea, and a variety of pathological features. Results: HRA images were found to be of superior quality in 18 eyes, while Topcon images were estimated superior in 21 eyes. No difference was found in 50 eyes. Both poor fixation (p=0.009) and more advanced cataract (p=0.013) were found to strongly increase the likelihood of better image quality by Topcon. Images acquired by Topcon before and after FFA were identical (100%). The healthy disc was usually dark on HRA (71%), but showed mild autofluorescence on Topcon (88%). The healthy fovea showed in 100% Hypo-FAF on HRA, while Topcon showed in 52% Iso-FAF, in 43% mild Hypo-FAF, and in 5% Hypo-FAF as on HRA. No difference of FAF was found for geographic atrophy, pigment changes, and drusen, although Topcon images were often more detailed. Hyper-FAF due to exudation showed better on HRA. Pigment epithelium detachment showed identical FAF behaviour on the border, but reduced FAF with Topcon in the center. Cystic edema was visible only on HRA in a petaloid pattern. Hard exsudates caused Hypo-FAF only on HRA, hardly visible on Topcon. Blocage phenomenon by blood however was identical. Conclusions: The filter set of Topcon and the single image acquisition appear to be an advantage for patients with cataract or poor fixation. Preceding FFA does not alter the Topcon FAF image. Regarding the FAF behaviour, there are differences between the two systems which need to be taken into account when interpreting the images.

Rockfall monitoring by Terrestrial Laser Scanning ¿ case study of the basaltic rock face at Castellfollit de la Roca (Catalonia, Spain)

This case study deals with a rock face monitoring in urban areas using a Terrestrial Laser Scanner. The pilot study area is an almost vertical, fifty meter high cliff, on top of which the village of Castellfollit de la Roca is located. Rockfall activity is currently causing a retreat of the rock face, which may endanger the houses located at its edge. TLS datasets consist of high density 3-D point clouds acquired from five stations, nine times in a time span of 22 months (from March 2006 to January 2008). The change detection, i.e. rockfalls, was performed through a sequential comparison of datasets. Two types of mass movement were detected in the monitoring period: (a) detachment of single basaltic columns, with magnitudes below 1.5 m3 and (b) detachment of groups of columns, with magnitudes of 1.5 to 150 m3. Furthermore, the historical record revealed (c) the occurrence of slab failures with magnitudes higher than 150 m3. Displacements of a likely slab failure were measured, suggesting an apparent stationary stage. Even failures are clearly episodic, our results, together with the study of the historical record, enabled us to estimate a mean detachment of material from 46 to 91.5 m3 year¿1. The application of TLS considerably improved our understanding of rockfall phenomena in the study area.

Résultats à deux ans de la trabéculoplastie sélective au laser dans le glaucome à angle ouvert et l'hypertonie oculaire

BACKGROUND: Selective laser trabeculoplasty (SLT) is a relatively new treatment strategy for the treatment of glaucoma. Its principle is similar to that of argon laser trabeculoplasty (ALT), but may lead to less damage to the trabecular meshwork. METHODS: We assessed the 2-year efficacy of SLT in a noncomparative consecutive case series. Any adult patient either suspected of having glaucoma or with open-angle glaucoma, whose treatment was judged insufficient to reach target intraocular pressure (IOP), could be recruited. IOP and number of glaucoma treatments were recorded over 2 years after the procedure. RESULTS: Our sample consisted of 44 consecutive eyes of 26 patients, aged 69+/-8 years. Eyes were treated initially on the lower 180 degrees . Three of them were retreated after 15 days on the upper 180. Fourteen eyes had ocular hypertension, 17 primary open-angle/normal-tension glaucoma, 11 pseudoexfoliation (PEX) glaucoma, and two pigmentary glaucoma. Thirty-six eyes had previously been treated and continued to be treated with topical anti-glaucoma medication, ten had had prior ALT, nine iridotomy, and 12 filtering surgery. The 2-year-follow up could not be completed for eight eyes because they needed filtering surgery. In the remaining 36 eyes, IOP decreased by a mean of 17.2%, 3.3 mmHg, (19.2+/-4.7 to 15+/-3.6 mmHg) after 2 years (p<0.001). As a secondary outcome, the number of glaucoma treatments decreased from 1.44 to 1.36 drops/patient. Other results according to subgroups of patients are analyzed: the greatest IOP decrease occurred in eyes that had never been treated with anti-glaucoma medication or with PEX glaucoma. SLT was probably valuable in a few eyes after filtering surgery; however, the statistical power of the study was not strong enough to draw a firm conclusion. When expressed in survival curves after 2 years, however, only 48% and 41% of eyes experienced a decrease of more than 3 mmHg or more than 20% of preoperative intraocular pressure, respectively. CONCLUSION: SLT decreases IOP somewhat for at least 2 years without an increase in topical glaucoma treatment. However, it cannot totally replace topical glaucoma treatment. In the future, patient selection should be improved to decrease the cost/effectiveness ratio.

Fetoscopic laser therapy for twin-twin transfusion syndrome: beyond current gestational age limits.

Both "early" (< 16 weeks' gestation) and "late" (> 26 weeks' gestation) presentations of twin-twin transfusion syndrome (TTTS) are rare and challenging complications of monochorionic/diamniotic twin pregnancies. Growing evidence suggests that fetoscopic laser therapy for both "early" and "late" TTTS is feasible, safe, and yields similar outcomes to cases treated between 16 and 26 weeks' gestation. We suggest reevaluation of conventional gestational age guidelines for laser therapy for TTTS.

Evaluation of spatial distribution of flatfish by laser scannig

Peer reviewed

Via-configurable transistor array: a regular design technique to improve ICs yield

Process variations are a major bottleneck for digital CMOS integrated circuits manufacturability and yield. That iswhy regular techniques with different degrees of regularity are emerging as possible solutions. Our proposal is a new regular layout design technique called Via-Configurable Transistors Array (VCTA) that pushes to the limit circuit layout regularity for devices and interconnects in order to maximize regularity benefits. VCTA is predicted to perform worse than the Standard Cell approach designs for a certain technology node but it will allow the use of a future technology on an earlier time. Ourobjective is to optimize VCTA for it to be comparable to the Standard Cell design in an older technology. Simulations for the first unoptimized version of our VCTA of delay and energy consumption for a Full Adder circuit in the 90 nm technology node are presented and also the extrapolation for Carry-RippleAdders from 4 bits to 64 bits.

Joint array combining and MLSE for single-user receivers in multipath Gaussian multiuser channels

The well-known structure of an array combiner along with a maximum likelihood sequence estimator (MLSE) receiveris the basis for the derivation of a space-time processor presentinggood properties in terms of co-channel and intersymbol interferencerejection. The use of spatial diversity at the receiver front-endtogether with a scalar MLSE implies a joint design of the spatialcombiner and the impulse response for the sequence detector. Thisis faced using the MMSE criterion under the constraint that thedesired user signal power is not cancelled, yielding an impulse responsefor the sequence detector that is matched to the channel andcombiner response. The procedure maximizes the signal-to-noiseratio at the input of the detector and exhibits excellent performancein realistic multipath channels.

Pintaemittoivan VCSEL-diodin käyttö aallonpituusmodulaatiospektroskopiaan perustuvissa hapen konsentraation mittauksissa

Teollisuuden sovelluksissa kaasun mittauslaitteilta vaaditaan suurta luotettavuutta sekä niiden huollontarve tulee olla minimaalista. Jatkuva-aikaisissa mittauksissa nämä vaatimuksetlunastaa viritettävän diodilaser-spektroskopian käyttö. Pienen kokonsa, vähäisten tehohäviöiden ja hyvien säätömahdollisuuksien ansiosta, VCSEL:t (vertical cavity surface emitting laser) ovat sopivia vaihtoehtoja valonlähteeksi mitattaessapäästökaasuja, tässä tapauksessa happea. Työssä rakennettiin mittauslaitteisto, jota käytettiin hapen konsentraation määrittämiseen. Mittauslaitteistolla suoritettiin hapen pitoisuusmittauksia ja saatuja tuloksia verrattiin teoreettisen mallin antamien tulosten kesken. Mittaukset perustuvat toisen harmonisen signaalin havainnointiin. Lisäksi tarkasteltiin paineen ja lämpötilanvaikutusta mittaustuloksiin.

Determinação do volume de madeira em povoamento de eucalipto por escâner a laser aerotransportado

O objetivo deste trabalho foi avaliar a possibilidade de se estimar o diâmetro à altura do peito (DAP) com os dados de altura e de número de árvores derivados do escâner a laser aerotransportado (LiDAR, "light detection and ranging"), e determinar o volume de madeira de talhão de Eucalyptus sp. a partir dessas variáveis. O número total de árvores detectadas foi obtido com uso da filtragem de máxima local. A altura de plantas estimada pelo LiDAR apresentou tendência não significativa à subestimativa. A estimativa do DAP foi coerente com os valores encontrados no inventário florestal; porém, também mostrou tendência à subestimativa, em razão do comportamento observado quanto à altura. A variável número de fustes apresentou valores próximos aos observados nas parcelas do inventário. O LiDAR subestimou o volume total de madeira do talhão em 11,4%, em comparação ao volume posto na fábrica. A tendência de subestimação da altura das árvores (em média, cerca de 5%) impactou a estimativa do volume individual de árvores e, consequentemente, a do volume do talhão. No entanto, é possível gerar equações de regressão que estimam o DAP com boa precisão, a partir de dados de altura de plantas obtidos pelo LiDAR. O modelo parabólico é o que possibilita as melhores estimativas da produção volumétrica dos talhões de eucalipto.

Laser-MAG-hybridihitsauksen käyttöönotto laivan rungon valmistuksessa

Perinteisten kaarihitsausmenetelmien suhteellisen suuri lämmöntuonti aiheuttaa huomattavia muodonmuutoksia laivan rungon valmistusprosessin alkuvaiheessa. Muodonmuutosten seurauksena rakenteiden mitta- ja muototarkkuus heikkenee, mikä lisää oikaisu- ja sovitustyötä myöhemmissä työvaiheissa. Hitsausmuodonmuutoksia voidaan vähentää siirtymällä käyttämään laser-MAG-hybridihitsausta, jossa lämmöntuonti on merkittävästi pienempi kuin kaarihitsauksessa. Näin kyetään oleellisesti leikkaamaan oikaisu- ja sovitustyöstä syntyviä kustannuksia. Tämän diplomityön tavoitteena oli kehittää tuotantovalmiiksi kuitulaser- ja MAG-hitsauksen yhdistelmäprosessi Aker Yards Oy:n Turun telakalla loppuvuoden 2006 aikana. Hitsauslaitteiston asennus oli valmistunut kesäkuussa 2006, minkä jälkeen aloitettiin luokituslaitoksen hyväksymän koeohjelman hitsaukset. Käyttöönotto suunnitelmaan sisältyvä koehitsausohjelma oli laadittu Det Norske Veritaksen julkaisemaa ohjetta (Guidelines no. 19) mukaillen. Ensimmäiseksi määritettiin hitsauskokeiden avulla prosessille laadun ja tehokkuuden suhteen optimaalinen railogeometria. Seuraavaksi optimoitiin prosessin hitsausparametrit 6 mm:n aineenpaksuudelle hyödyntäen Taguchi-koesuunnittelumenetelmää. Tämän jälkeen optimiparametreilla hitsattiin koekappale väsytyskokeisiin, jotka suoritettiin Teknillisen korkeakoulun laivalaboratoriossa. Väsytyskoetulokset täyttivät luokituslaitoksen vaatimukset. Myös hitsauksen menetelmäkoe suoritettiin hyväksytetysti. Viimeinen koeohjelman mukainen hitsauskoesarja tehtiin prosessiparametrien sallittujen vaihtelurajojen määrittämiseksi. Diplomityön tavoite täyttyi joulukuussa 2006, jolloin 'laivan kansipaneeli hitsattiin ensimmäistä kertaa uudella hitsausprosessilla. Hitsauksen laatu korreloi hyvin menetelmäkokeen tulosten kanssa ¿ hitsit olivat tasalaatuisia ja ne täyttivät B-luokan vaatimukset.