Identification of cancer/testis-antigen genes by massively parallel signature sequencing.

Massively parallel signature sequencing (MPSS) generates millions of short sequence tags corresponding to transcripts from a single RNA preparation. Most MPSS tags can be unambiguously assigned to genes, thereby generating a comprehensive expression profile of the tissue of origin. From the comparison of MPSS data from 32 normal human tissues, we identified 1,056 genes that are predominantly expressed in the testis. Further evaluation by using MPSS tags from cancer cell lines and EST data from a wide variety of tumors identified 202 of these genes as candidates for encoding cancer/testis (CT) antigens. Of these genes, the expression in normal tissues was assessed by RT-PCR in a subset of 166 intron-containing genes, and those with confirmed testis-predominant expression were further evaluated for their expression in 21 cancer cell lines. Thus, 20 CT or CT-like genes were identified, with several exhibiting expression in five or more of the cancer cell lines examined. One of these genes is a member of a CT gene family that we designated as CT45. The CT45 family comprises six highly similar (>98% cDNA identity) genes that are clustered in tandem within a 125-kb region on Xq26.3. CT45 was found to be frequently expressed in both cancer cell lines and lung cancer specimens. Thus, MPSS analysis has resulted in a significant extension of our knowledge of CT antigens, leading to the discovery of a distinctive X-linked CT-antigen gene family.

Successful migration of three tracers without identification of sentinel nodes during intraoperative lymphatic mapping for non-small cell lung cancer.

Prospective comparative evaluation of patent V blue, fluorescein and (99m)TC-nanocolloids for intraoperative sentinel lymph node (SLN) mapping during surgery for non-small cell lung cancer (NSCLC). Ten patients with peripherally localised clinical stage I NSCLC underwent thoracotomy and peritumoral subpleural injection of 2 ml of patent V blue dye, 1 ml of 10% fluorescein and 1ml of (99m)Tc-nanocolloids (0.4 mCi). The migration and spatial distribution pattern of the tracers was assessed by direct visualisation (patent V blue), visualisation of fluorescence signalling by a lamp of Wood (fluorescein) and radioactivity counting with a hand held gamma-probe ((99m)Tc-nanocolloids). Lymph nodes at interlobar (ATS 11), hilar (ATS 10) and mediastinal (right ATS 2,4,7; left ATS 5,6,7) levels were systematically assessed every 10 min up to 60 min after injection, followed by lobectomy and formal lymph node dissection. Successful migration from the peritumoral area to the mediastinum was observed for all three tracers up to 60 min after injection. The interlobar lympho-fatty tissue (station ATS 11) revealed an early and preferential accumulation of all three tracers for all tumours assessed and irrespective of the tumour localisation. However, no preferential accumulation in one or two distinct lymph nodes was observed up to 60 min after injection for all three tracers assessed. Intraoperative SLN mapping revealed successful migration of the tracers from the site of peritumoral injection to the mediastinum, but in a diffuse pattern without preferential accumulation in sentinel lymph nodes.

Wireless capsule pH monitoring: does it fulfil all expectations?

pH monitoring has been used as a diagnostic tool in gastro-oesophageal reflux disease (GERD) for many years. Recent studies have shown that wireless capsule pH monitoring is better tolerated and interferes less with daily activities as compared to traditional catheter-based pH monitoring. Moreover, prolonged recording time (48 h instead of 24 h) is possible with wireless pH monitoring. The main secondary effect of wireless capsule pH monitoring is induction of thoracic discomfort in 10-65% of the patients, which can vary from mild foreign body sensation to severe chest pain. Sensitivity and specificity of wireless capsule monitoring is comparable to that of traditional pH monitoring. It has not been proven yet that better tolerability and a longer recording time increases the diagnostic yield of wireless capsule monitoring in GERD.

Identification of Research Portfolio for the Development of Filtration Equipment

This piece of work which is Identification of Research Portfolio for Development of Filtration Equipment aims at presenting a novel approach to identify promising research topics in the field of design and development of filtration equipment and processes. The projected approach consists of identifying technological problems often encountered in filtration processes. The sources of information for the problem retrieval were patent documents and scientific papers that discussed filtration equipments and processes. The problem identification method adopted in this work focussed on the semantic nature of a sentence in order to generate series of subject-action-object structures. This was achieved with software called Knowledgist. List of problems often encountered in filtration processes that have been mentioned in patent documents and scientific papers were generated. These problems were carefully studied and categorized. Suggestions were made on the various classes of these problems that need further investigation in order to propose a research portfolio. The uses and importance of other methods of information retrieval were also highlighted in this work.

System identification using a linear combination of cumulant slices

In this paper we develop a new linear approach to identify the parameters of a moving average (MA) model from the statistics of the output. First, we show that, under some constraints, the impulse response of the system can be expressed as a linear combination of cumulant slices. Then, thisresult is used to obtain a new well-conditioned linear methodto estimate the MA parameters of a non-Gaussian process. Theproposed method presents several important differences withexisting linear approaches. The linear combination of slices usedto compute the MA parameters can be constructed from dif-ferent sets of cumulants of different orders, providing a generalframework where all the statistics can be combined. Further-more, it is not necessary to use second-order statistics (the autocorrelation slice), and therefore the proposed algorithm stillprovides consistent estimates in the presence of colored Gaussian noise. Another advantage of the method is that while mostlinear methods developed so far give totally erroneous estimates if the order is overestimated, the proposed approach doesnot require a previous estimation of the filter order. The simulation results confirm the good numerical conditioning of thealgorithm and the improvement in performance with respect to existing methods.

RFID-tekniikan käyttö betonielementtien tunnistamiseen

RFID on 2000-luvulla yleisesti saatavilla tullut tekniikka erilaisten kohteiden tunnistamiseen. RFID-tekniikassa tunnistamiseen käytetään pienikokoisia tunnisteita, joiden tietosisältö pystytään lukemaan langattomasti ilman näköyhteyttä tarkoitukseen soveltuvalla lukulaitteella. Tunnisteet ovat halpoja ja yksinkertaisia. Yleensä ne eivät sisällä omaa virtalähdettä, vaan ne toimivat ainoastaan lukulaitteen luoman kentän voimalla. Tässä työssä tutkitaan RFID-tekniikan soveltuvuutta betonista valmistettujen rakennuselementtien tunnistamiseen. Ympäristön vaikutukset tekniikan käyttöön tutkitaan ja selvitetään, mitkä ovat parhaat toimintatavat elementtien tunnistamiseen nämä vaikutukset huomioon ottaen. Työssä esitellään ensin RFID-tekniikan toimintaperiaatteet sekä tunnisteiden ja lukulaitteiden rakenne. Tunnisteiden jaottelu erilaisten ominasisuuksien perusteella käydään läpi ja sovellusalan kannalta tärkeimmät standardit esitellään. Käytännön osuudessa esitellään RFID-tekniikan soveltamista betonista valmistettujen rakennuselementtien tunnistamiseen. Työssä esitellään saavutetut mittaustulokset sekä betonielementtien tunnistamiseen ja tietojen hallintaan toteutetun järjestelmän rakenne.

Identification of Multiple Mechanisms of Resistance to Vemurafenib in a Patient with BRAFV600E-Mutated Cutaneous Melanoma Successfully Rechallenged after Progression.

PURPOSE: To investigate the mechanism(s) of resistance to the RAF-inhibitor vemurafenib, we conducted a comprehensive analysis of the genetic alterations occurring in metastatic lesions from a patient with a BRAF(V600E)-mutant cutaneous melanoma who, after a first response, underwent subsequent rechallenge with this drug. EXPERIMENTAL DESIGN: We obtained blood and tissue samples from a patient diagnosed with a BRAF(V600E)-mutant cutaneous melanoma that was treated with vemurafenib and achieved a near-complete response. At progression, he received additional lines of chemo/immunotherapy and was successfully rechallenged with vemurafenib. Exome and RNA sequencing were conducted on a pretreatment tumor and two subcutaneous resistant metastases, one that was present at baseline and previously responded to vemurafenib (PV1) and one that occurred de novo after reintroduction of the drug (PV2). A culture established from PV1 was also analyzed. RESULTS: We identified two NRAS-activating somatic mutations, Q61R and Q61K, affecting two main subpopulations in the metastasis PV1 and a BRAF alternative splicing, involving exons 4-10, in the metastasis PV2. These alterations, known to confer resistance to RAF inhibitors, were tumor-specific, mutually exclusive, and were not detected in pretreatment tumor samples. In addition, the oncogenic PIK3CA(H1047R) mutation was detected in a subpopulation of PV1, but this mutation did not seem to play a major role in vemurafenib resistance in this metastasis. CONCLUSIONS: This work describes the coexistence within the same patient of different molecular mechanisms of resistance to vemurafenib affecting different metastatic sites. These findings have direct implications for the clinical management of BRAF-mutant melanoma. Clin Cancer Res; 19(20); 5749-57. ©2013 AACR.

Identification and characterization of pathogenic Pestalotiopsis species to pecan tree in Brazil

The objective of this work was to characterize and cluster isolates of Pestalotiopsis species and to identify those that are pathogenic to pecan, based on morphological and molecular characters. Pestalotiopsis spp. isolates were identified by sequencing the internal transcribed spacer (ITS) and β?tubulin regions. Identification methods were compared to indicate the key morphological characters for species characterization. Thirteen isolates were used for the pathogenicity tests. Morphological characterization was performed using the following variables: mycelial growth rate, sporulation, colony pigmentation, and conidial length and width. Ten pathogenic isolates were identified, three as -tubulin regions. Identification methods were compared to indicate the key morphological characters for species characterization. Thirteen isolates were used for the pathogenicity tests. Morphological characterization was performed using the following variables: mycelial growth rate, sporulation, colony pigmentation, and conidial length and width. Ten pathogenic isolates were identified, three as Pestalotiopsis clavispora and three as P. cocculi. The other isolates remained as an undefined species. The morphological characters were efficient for an initial separation of the isolates, which were grouped according to differences at species level, mainly colony diameter, which was identified as an important morphological describer. Beta-tubulin gene sequencing was less informative than the ITS region sequencing for species identification.

Syndrome de vasoconstriction cérébrale réversible : identifications de facteurs pronostiques = [Reversible cerebral vasoconstriction syndrome identification of pronostic factors]

Objectif : Le syndrome de vasoconstriction cérébrale réversible (SVCR) est une entité clinico-radiologique associant des céphalées paroxystiques à un vasospasme uni- ou multifocal réversible des artères cérébrales avec ou sans déficit neurologique transitoire ou crise comitiale. Le but de notre étude est de rechercher les facteurs de mauvais pronostic des patients présentant un SVCR. Méthode : Nous avons réalisé une étude rétrospective des imageries vasculaires cérébrales invasives et non invasives entre janvier 2006 et 2011 et avons retenu 10 patients présentant les critères du RCVS. Les données démographiques, facteurs de risque vasculaires ainsi que l'évolution de chaque patient ont été noté. Résultats : Sept des 10 patients sont des femmes, avec un âge médian de 46 ans. Quatre patients ne présentaient pas de facteur étiologique, deux femmes se trouvaient en période post-partum (entre la première et la troisième semaine) et les trois autres cas sont induits par des drogues vaso-actives (cannabis pour 2 cas dont un associé à la cyclosporine, sumatriptan pour un cas). La durée moyenne du suivi est de 10,2 mois (0¬28 mois). Deux patients ont présentés une séquelle neurologique : un a gardé des troubles phasiques et l'autre une hémianopsie latérale homonyme. Deux autres patients sont décédés dans les suites, ce qui est inhabituel. Nous n'avons pas trouvé de corrélation d'évolution différente entre les cas de SVCR primaire ou secondaire. Les seules facteurs corrélaient à l'évolution clinique sont le status neurologique à l'admission et la présence de lésion parenchymateuse (ischémie ou hématome) à l'imagerie. Conclusion : La vasoconstriction cérébrale réversible impliquant des déficits neurologiques ou la mort a été, rarement, rapportée. Nous devons garder à l'esprit qu'une telle évolution peut survenir notamment pour les cas présentant un état neurologique dégradé à l'admission ou présentant des lésions parenchymateuses à l'imagerie.

Intrinsic subspace convergence in TDD MIMO communication

In numerical linear algebra, students encounter earlythe iterative power method, which finds eigenvectors of a matrixfrom an arbitrary starting point through repeated normalizationand multiplications by the matrix itself. In practice, more sophisticatedmethods are used nowadays, threatening to make the powermethod a historical and pedagogic footnote. However, in the contextof communication over a time-division duplex (TDD) multipleinputmultiple-output (MIMO) channel, the power method takes aspecial position. It can be viewed as an intrinsic part of the uplinkand downlink communication switching, enabling estimationof the eigenmodes of the channel without extra overhead. Generalizingthe method to vector subspaces, communication in thesubspaces with the best receive and transmit signal-to-noise ratio(SNR) is made possible. In exploring this intrinsic subspace convergence(ISC), we show that several published and new schemes canbe cast into a common framework where all members benefit fromthe ISC.

Wireless Application Test Bed and Simulations for Broadband Mobile Communications Systems

Langattoman laajakaistaisen tietoliikennetekniikan kehittyminen on herättänyt kiinnostuksen sen ammattimaiseen hyödyntämiseen yleisen turvallisuuden ja kriisinhallinnan tarpeisiin. Hätätilanteissa usein olemassa olevat kiinteät tietoliikennejärjestelmät eivät ole ollenkaan käytettävissä tai niiden tarjoama kapasiteetti ei ole riittävä. Tästä syystä on noussut esiin tarve nopeasti toimintakuntoon saatettaville ja itsenäisille langattomille laajakaistaisille järjestelmille. Tässä diplomityössä on tarkoitus tutkia langattomia ad hoc monihyppy -verkkoja yleisen turvallisuuden tarpeiden pohjalta ja toteuttaa testialusta, jolla voidaan demonstroida sekä tutkia tällaisen järjestelmän toimintaa käytännössä. Työssä tutkitaan pisteestä pisteeseen sekä erityisesti pisteestä moneen pisteeseen suoritettavaa tietoliikennettä. Mittausten kohteena on testialustan tiedonsiirtonopeus, lähetysteho ja vastaanottimen herkkyys. Näitä tuloksia käytetään simulaattorin parametreina, jotta simulaattorin tulokset olisivat mahdollisimman aidot ja yhdenmukaiset testialustan kanssa. Sen jälkeen valitaan valikoima yleisen turvallisuuden vaatimusten mukaisia ohjelmia ja sovellusmalleja, joiden suorituskyky mitataan erilaisten reititysmenetelmien alaisena sekä testialustalla että simulaattorilla. Tuloksia arvioidaan ja vertaillaan. Multicast monihyppy -video päätettiin sovelluksista valita tutkimusten pääkohteeksi ja sitä sekä sen ominaisuuksia on tarkoitus myös oikeissa kenttäkokeissa.

Identification of parasitoid species using PCR amplification and restriction enzyme digestion

Spodoptera frugiperda is a pest of great economic importance in the Americas. It is attacked by several species of parasitoids, which act as biological control agents. Parasitoids are morphologically identifiable as adults, but not as larvae. Laboratory rearing conditions are not always optimal to rear out parasitic wasps from S. frugiperda larvae collected from wild populations, and it frequently happens that parasitoids do not complete their life cycle and stop developing at the larval stage. Therefore, we explored ways to identify parasitoid larvae using molecular techniques. Sequencing is one possible technique, yet it is expensive. Here we present an alternate, cheaper way of identifying seven species of parasitoids (Cotesia marginiventris, Campoletis sonorensis, Pristomerus spinator, Chelonus insularis, Chelonus cautus, Eiphosoma vitticolle and Meteorus laphygmae) using PCR amplification of COI gene followed by a digestion with a combination of four restriction endonucleases. Each species was found to exhibit a specific pattern when the amplification product was run on an agarose gel. Identifying larvae revealed that conclusions on species composition of a population of parasitic wasps can be biased if only the emerging adults are taken into account.

Optimal use of SSR markers for varietal identification of upland cotton

Abstract: The objective of this work was to identify polymorphic simple sequence repeat (SSR) markers for varietal identification of cotton and evaluation of the genetic distance among the varieties. Initially, 92 SSR markers were genotyped in 20 Brazilian cotton cultivars. Of this total, 38 loci were polymorphic, two of which were amplified by one primer pair; the mean number of alleles per locus was 2.2. The values of polymorphic information content (PIC) and discrimination power (DP) were, on average, 0.374 and 0.433, respectively. The mean genetic distance was 0.397 (minimum of 0.092 and maximum of 0.641). A panel of 96 varieties originating from different regions of the world was assessed by 21 polymorphic loci derived from 17 selected primer pairs. Among these varieties, the mean genetic distance was 0.387 (minimum of 0 and maximum of 0.786). The dendrograms generated by the unweighted pair group method with arithmetic average (UPGMA) did not reflect the regions of Brazil (20 genotypes) or around the world (96 genotypes), where the varieties or lines were selected. Bootstrap resampling shows that genotype identification is viable with 19 loci. The polymorphic markers evaluated are useful to perform varietal identification in a large panel of cotton varieties and may be applied in studies of the species diversity.