Bioinformatics and HIV Latency.

Despite effective treatment, HIV is not completely eliminated from the infected organism because of the existence of viral reservoirs. A major reservoir consists of infected resting CD4+ T cells, mostly of memory type, that persist over time due to the stable proviral insertion and a long cellular lifespan. Resting cells do not produce viral particles and are protected from viral-induced cytotoxicity or immune killing. However, these latently infected cells can be reactivated by stochastic events or by external stimuli. The present review focuses on novel genome-wide technologies applied to the study of integration, transcriptome, and proteome characteristics and their recent contribution to the understanding of HIV latency.

Decoding auditory EEG responses in healthy and clinical populations: A comparative study.

BACKGROUND: Analyses of brain responses to external stimuli are typically based on the means computed across conditions. However in many cognitive and clinical applications, taking into account their variability across trials has turned out to be statistically more sensitive than comparing their means. NEW METHOD: In this study we present a novel implementation of a single-trial topographic analysis (STTA) for discriminating auditory evoked potentials at predefined time-windows. This analysis has been previously introduced for extracting spatio-temporal features at the level of the whole neural response. Adapting the STTA on specific time windows is an essential step for comparing its performance to other time-window based algorithms. RESULTS: We analyzed responses to standard vs. deviant sounds and showed that the new implementation of the STTA gives above-chance decoding results in all subjects (in comparison to 7 out of 11 with the original method). In comatose patients, the improvement of the decoding performance was even more pronounced than in healthy controls and doubled the number of significant results. COMPARISON WITH EXISTING METHOD(S): We compared the results obtained with the new STTA to those based on a logistic regression in healthy controls and patients. We showed that the first of these two comparisons provided a better performance of the logistic regression; however only the new STTA provided significant results in comatose patients at group level. CONCLUSIONS: Our results provide quantitative evidence that a systematic investigation of the accuracy of established methods in normal and clinical population is an essential step for optimizing decoding performance.

Toxicity assessment of refill liquids for electronic cigarettes.

We analyzed 42 models from 14 brands of refill liquids for e-cigarettes for the presence of micro-organisms, diethylene glycol, ethylene glycol, hydrocarbons, ethanol, aldehydes, tobacco-specific nitrosamines, and solvents. All the liquids under scrutiny complied with norms for the absence of yeast, mold, aerobic microbes, Staphylococcus aureus, and Pseudomonas aeruginosa. Diethylene glycol, ethylene glycol and ethanol were detected, but remained within limits authorized for food and pharmaceutical products. Terpenic compounds and aldehydes were found in the products, in particular formaldehyde and acrolein. No sample contained nitrosamines at levels above the limit of detection (1 μg/g). Residual solvents such as 1,3-butadiene, cyclohexane and acetone, to name a few, were found in some products. None of the products under scrutiny were totally exempt of potentially toxic compounds. However, for products other than nicotine, the oral acute toxicity of the e-liquids tested seems to be of minor concern. However, a minority of liquids, especially those with flavorings, showed particularly high ranges of chemicals, causing concerns about their potential toxicity in case of chronic oral exposure.

Effect of prestorage curing on storage life, internal and external qualities of sweet orange (Citrus sinensis)

Orange fruits from two seasons, in April and August 2006 representing late 2005 and early 2006 harvests respectively were cured in hot air at 36-37(0)C to 1%, 3%, 5% and 7% weight loss before storage at 28(0)C and 86% relative humidity (RH). The fruits were observed for incidence of decay, further weight loss, juice content, firmness or softening of the peel, total soluble solids (TSS), pH, titratable acidity, and colour during storage. Curing reduced the incidence of decay. All control fruits were rotten by day 21 in August harvest while 22.5% of the control was rotten by day 56 in the April harvest. Storage life was extended beyond 56 days in fruits cured with 1, 3, 5 and 7% in April harvest as there was no decay throughout, while decay incidence in August harvest was 88.9, 61.1, 22.2 and 31.3% in 1, 3, 5 and 7% respectively. Penicillium digitatum, Phytophthora sp., Alternaria citri and Collectotrichum gloeosporioides were among decay causing moulds detected. Control fruits lost more weight during storage than cured fruits did. Fruit rind hardening was more noticed in the control and those cured to 1% weight loss, especially from the April harvest. It was insignificant in other treatments in both trials. Titratable acidity, pH, juice content and TSS were not affected by the treatment. Colour change to yellow was however retarded by curing. Curing to 5% weight loss was best for decay control and quality retention.

Prospective motion correction of 3D echo-planar imaging data for functional MRI using optical tracking.

We evaluated the performance of an optical camera based prospective motion correction (PMC) system in improving the quality of 3D echo-planar imaging functional MRI data. An optical camera and external marker were used to dynamically track the head movement of subjects during fMRI scanning. PMC was performed by using the motion information to dynamically update the sequence's RF excitation and gradient waveforms such that the field-of-view was realigned to match the subject's head movement. Task-free fMRI experiments on five healthy volunteers followed a 2×2×3 factorial design with the following factors: PMC on or off; 3.0mm or 1.5mm isotropic resolution; and no, slow, or fast head movements. Visual and motor fMRI experiments were additionally performed on one of the volunteers at 1.5mm resolution comparing PMC on vs PMC off for no and slow head movements. Metrics were developed to quantify the amount of motion as it occurred relative to k-space data acquisition. The motion quantification metric collapsed the very rich camera tracking data into one scalar value for each image volume that was strongly predictive of motion-induced artifacts. The PMC system did not introduce extraneous artifacts for the no motion conditions and improved the time series temporal signal-to-noise by 30% to 40% for all combinations of low/high resolution and slow/fast head movement relative to the standard acquisition with no prospective correction. The numbers of activated voxels (p<0.001, uncorrected) in both task-based experiments were comparable for the no motion cases and increased by 78% and 330%, respectively, for PMC on versus PMC off in the slow motion cases. The PMC system is a robust solution to decrease the motion sensitivity of multi-shot 3D EPI sequences and thereby overcome one of the main roadblocks to their widespread use in fMRI studies.

When gas analysis assists with postmortem imaging to diagnose causes of death.

Postmortem imaging consists in the non-invasive examination of bodies using medical imaging techniques. However, gas volume quantification and the interpretation of the gas collection results from cadavers remain difficult. We used whole-body postmortem multi-detector computed tomography (MDCT) followed by a full autopsy or external examination to detect the gaseous volumes in bodies. Gases were sampled from cardiac cavities, and the sample compositions were analyzed by headspace gas chromatography-mass spectrometry/thermal conductivity detection (HS-GC-MS/TCD). Three categories were defined according to the presumed origin of the gas: alteration/putrefaction, high-magnitude vital gas embolism (e.g., from scuba diving accident) and gas embolism of lower magnitude (e.g., following a traumatic injury). Cadaveric alteration gas was diagnosed even if only one gas from among hydrogen, hydrogen sulfide or methane was detected. In alteration cases, the carbon dioxide/nitrogen ratio was often >0.2, except in the case of advanced alteration, when methane presence was the best indicator. In the gas embolism cases (vital or not), hydrogen, hydrogen sulfide and methane were absent. Moreover, with high-magnitude vital gas embolisms, carbon dioxide content was >20%, and the carbon dioxide/nitrogen ratio was >0.2. With gas embolisms of lower magnitude (gas presence consecutive to a traumatic injury), carbon dioxide content was <20% and the carbon dioxide/nitrogen ratio was often <0.2. We found that gas analysis provided useful assistance to the postmortem imaging diagnosis of causes of death. Based on the quantifications of gaseous cardiac samples, reliable indicators were determined to document causes of death. MDCT examination of the body must be performed as quickly as possible, as does gas sampling, to avoid generating any artifactual alteration gases. Because of cardiac gas composition analysis, it is possible to distinguish alteration gases and gas embolisms of different magnitudes.

Investigation of defect formation and electronic transport in microcrystalline silicon deposited by hot-wire CVD

We have investigated doped and undoped layers of microcrystalline silicon prepared by hot-wire chemical vapour deposition optically, electrically and by means of transmission electron microscopy. Besides needle-like crystals grown perpendicular to the substrate's surface, all of the layers contained a noncrystalline phase with a volume fraction between 4% and 25%. A high oxygen content of several per cent in the porous phase was detected by electron energy loss spectrometry. Deep-level transient spectroscopy of the crystals suggests that the concentration of electrically active defects is less than 1% of the undoped background concentration of typically 10^17 cm -3. Frequency-dependent measurements of the conductance and capacitance perpendicular to the substrate surface showed that a hopping process takes place within the noncrystalline phase parallel to the conduction in the crystals. The parasitic contribution to the electrical circuit arising from the porous phase is believed to be an important loss mechanism in the output of a pin-structured photovoltaic solar cell deposited by hot-wire CVD.

Spontaneous Emergence of Chirality in the Limited Enantioselectivity Model: Autocatalytic Cycle Driven by an External Reagent

The emergence of chirality in enantioselective autocatalysis for compounds unable to transform according to the Frank-like reaction network is discussed with respect to the controversial limited enantioselectivity (LES) model composed of coupled enantioselective and non-enantioselective autocatalyses. The LES model cannot lead to spontaneous mirror symmetry breaking (SMSB) either in closed systems with a homogeneous temperature distribution or in closed systems with a stationary non-uniform temperature distribution. However, simulations of chemical kinetics in a two-compartment model demonstrate that SMSB may occur if both autocatalytic reactions are spatially separated at different temperatures in different compartments but coupled under the action of a continuous internal flow. In such conditions, the system can evolve, for certain reaction and system parameters, toward a chiral stationary state; that is, the system is able to reach a bifurcation point leading to SMSB. Numerical simulations in which reasonable chemical parameters have been used suggest that an adequate scenario for such a SMSB would be that of abyssal hydrothermal vents, by virtue of the typical temperature gradients found there and the role of inorganic solids mediating chemical reactions in an enzyme-like role.

Disc Filter External Models in an Integrated Simulation Environment

Työssä tutkittiin kiekkosuodattimeen liittyviä ulkoisia simulointimalleja integroidussa simulointiympäristössä. Työn tarkoituksena oli parantaa olemassa olevaa mekanistista kiekkosuodatinmallia. Malli laadittiin dynaamiseen paperiteollisuuden tarpeisiin tehtyyn simulaattoriin (APMS), jossa olevaan alkuperäiseen mekanistiseen malliin tehtiin ulkoinen lisämalli, joka käyttää hyväkseen kiekkosuodatinvalmistajan mittaustuloksia. Laitetiedon saatavuutta suodattimien käyttäjille parannettiin luomalla Internetissä sijaitsevalle palvelimelle kiekkosuodattimen laitetietomäärittelyt. Suodatinvalmistaja voi palvella asiakkaitaan viemällä laitetiedot palvelimelle ja yhdistämällä laitetiedon simulointimalliin. Tämä on mahdollista Internetin ylitse käytettävän integroidun simulointiympäristön avulla, jonka on tarkoitus kokonaisvaltaisesti yhdistää simulointi ja prosessisuunnittelu. Suunnittelijalle tarjotaan työkalut, joilla dynaaminen simulointi, tasesimulointi ja kaavioiden piirtäminen onnistuu prosessilaitetiedon ollessa saatavilla. Nämä työkalut on tarkoitus toteuttaa projektissa nimeltä Galleria, jossa luodaan prosessimalli- ja laitetietopalvelin Internetiin. Gallerian käyttöliittymän avulla prosessisuunnittelija voi käyttää erilaisia simulointiohjelmistoja ja niihin luotuja valmiita malleja, sekä saada käsiinsä ajan tasalla olevaa laitetietoa. Ulkoinen kiekkosuodatinmalli laskee suodosvirtaamat ja suodosten pitoisuudet likaiselle, kirkkaalle ja superkirkkaalle suodokselle. Mallin syöttöparametrit ovat kiekkojen pyörimisnopeus, sisään tulevan syötön pitoisuus, suotautuvuus (freeness) ja säätöparametri, jolla säädetään likaisen ja kirkkaan suodoksen keskinäinen suhde. Suotautuvuus kertoo mistä massasta on kyse. Mitä suurempi suotautuvuus on, sitä paremmin massa suodattuu ja sitä puhtaampia suodokset yleensä ovat. Mallin parametrit viritettiin regressioanalyysillä ja valmistajan palautetta apuna käyttäen. Käyttäjä voi valita haluaako hän käyttää ulkoista vai alkuperäistä mallia. Alkuperäinen malli täytyy ensin alustaa antamalla sille nominaaliset toimintapisteet virtaamille ja pitoisuuksille tietyllä pyörimisnopeudella. Ulkoisen mallin yhtälöitä voi käyttää alkuperäisen mallin alustamiseen, jos alkuperäinen malli toimii ulkoista paremmin. Ulkoista mallia voi käyttää myös ilman simulointiohjelmaa Galleria-palvelimelta käsin. Käyttäjälle avautuu näin mahdollisuus tarkastella kiekkosuodattimien parametreja ja nähdä suotautumistulokset oman työasemansa ääreltä mistä tahansa, kunhan Internetyhteys on olemassa. Työn tuloksena kiekkosuodattimien laitetiedon saatavuus käyttäjille parani ja alkuperäisen simulointimallin rajoituksia ja puutteita vähennettiin.

Experts' consensus on use of electronic cigarettes: a Delphi survey from Switzerland.

OBJECTIVES: In some countries, nicotine-containing electronic cigarettes (e-cigarettes) are considered a consumer product without specific regulations. In others (eg, Switzerland), the sale of e-cigarettes containing nicotine is forbidden, despite the eagerness of many smokers to obtain them. As scientific data about efficacy and long-term safety of these products are scarce, tobacco control experts are divided on how to regulate them. In order to gain consensus among experts to provide recommendations to health authorities, we performed a national consensus study. SETTING: We used a Delphi method with electronic questionnaires to bring together the opinion of Swiss experts on e-cigarettes. PARTICIPANTS: 40 Swiss experts from across the country. OUTCOME MEASURES: We measured the degree of consensus between experts on recommendations regarding regulation, sale, use of and general opinion about e-cigarettes containing nicotine. New recommendations and statements were added following the experts' answers and comments. RESULTS: There was consensus that e-cigarettes containing nicotine should be made available, but only under specific conditions. Sale should be restricted to adults, using quality standards, a maximum level of nicotine and with an accompanying list of authorised ingredients. Advertisement should be restricted and use in public places should be forbidden. CONCLUSIONS: These recommendations encompass three principles: (1) the reality principle, as the product is already on the market; (2) the prevention principle, as e-cigarettes provide an alternative to tobacco for actual smokers, and (3) the precautionary principle, to protect minors and non-smokers, since long-term effects are not yet known. Swiss authorities should design specific regulations to sell nicotine-containing e-cigarettes.

Supplier Evaluation on the Standard Material and Component Markets in the Electronic Manufacturing Equipment Industry

Työn tavoitteena oli arvioida ja selvittää toimittajasuhteeseen vaikuttavia tekijöitä JOT Automation Group Oyj.n ja sen alihankkijoiden välisessä yhteistyössä ja muodostaa yrityksen kilpailukykyä parantava toimittaja-arviointiprosessi. Työssä keskityttiin tarkastelemaan yleisillä materiaali- ja komponenttimarkkinoilla toimivia toimittajia elektroniikkateollisuuden tuotantojärjestelmien valmistuksessa. Ensin tutustuttiin toimittajasuhdetta ja sen arviointia käsitelleeseen kirjallisuuteen. Teorian tueksi tehtiin haastatteluja ja kartoitettiin ensisijaisia tarpeita ja tavoitteita arviointiprosessille. Valmis prosessi testattiin käytännössä kahden eri case-esimerkin avulla. Prosessista muodostui kahteen eri työkaluun jakautunut kokonaisuus, joista auditointi arvioi toimittajan kyvykkyyttä vastatta sille asetettuihin vaatimuksiin. Toimittajan suorituskyvyn mittaaminen puolestaan testaa ja vertaa jatkuvasti toiminnan todellista tasoa auditoinnissa saatuihin tuloksiin. Työ sisältää selvityksen ja ohjeistuksen toimittaja-arviointiprosessin käytöstä. Prosessin käyttö alentaa toimittajaan kohdistuvaa materiaalien saatavuuteen ja hankintaan liittyviä riskejä. Esimerkeistä saadut kokemukset osoittivat, että prosessin avulla päästään pureutumaan tärkeisiin ydinalueisiin ja kehittämään niitä sekä toimittajalle, että ostajayritykselle edullisella tavalla. Toimittaja-arviointiprosessista kehittyy toimintatapa yrityksen ja sen toimittajan välisen suhteen ylläpitämiseksi.

Lymphoepithelial carcinoma in the maxillary sinus: a case report.

INTRODUCTION: Lymphoepithelial carcinoma of the maxillary sinus is a very rare malignancy and it can be difficult to make a pre-operative diagnosis. CASE PRESENTATION: A 72-year-old Caucasian woman presented to our facility with an isolated right-side epistaxis that had been present for three months, with the results of a computed tomography scan showing a soft tissue mass in the right maxillary sinus with an impacted tooth. The results of a transnasal endoscopic biopsy were compatible with a lymphoepithelial carcinoma, following which our patient underwent a radical excision of the mass. The final histology results revealed lymphoepithelial carcinoma of the maxillary sinus with negative assays for Epstein-Barr virus. Our patient was given post-operative external radiotherapy and has remained disease-free at three-year follow-up. CONCLUSIONS: This report details the diagnosis and management of a case of lymphoepithelial carcinoma of the maxillary sinus, which is a very rare malignant tumor with very little mention in the literature. Only a strong suspicion with systematic use of various patho-immunological tests helps to arrive at a definitive diagnosis by excluding other better-known tumors.

Developing customer-based e-solutions

Logistiikkapalveluiden markkinat ovat viime vuosina muuttuneet. Kilpailtu toimiala ja asiakasvaatimusten muuttuminen ovat pakottaneet yritykset pyrkimään entistä tehokkaampaan jakeluketjuun. Työn tarkoituksena oli tutkia sähköisten asiakasliittymien toimivuutta asiakkaan näkökulmasta Euro Express tuotannossa ja prosessissa. Tarkoituksena oli selvittää eri sidosryhmien vaatimukset prosessille huomioiden sähköisen liiketoiminnan tuomat edut ja ominaispiirteet. Tavoitteena oli kuvata olemassa oleva prosessi ja tutkia prosessin rajapinnat –asiakas, tuotanto ja ulkoiset sidosryhmät. Tutkielmassa sähköisten ratkaisujen ominaispiirteet on käyty läpi ja tulevaisuuden kehitysnäkökulmista keskusteltu. Kehittyneiden tietoteknisten ratkaisujen avulla jatkuva prosessien uudistaminen (Business Process Reengineering) on mahdollista. Yleisesti epäolennaisuudet asiakasrajapinnassa, informaation kulussa ja yhteyksissä eri järjestelmien välillä aiheuttavat ongelmia sähköisten ratkaisujen toteuttamisessa. Tulevaisuudessa logistiikka yritykset ottavat entistä enemmän käyttöönsä uudenaikaisia teknologisia ratkaisuja tilaukseen, tuotantoon ja asiakaspalveluun. Näiden uudenlaisten ratkaisujen kehittämisestä on hyötyä sekä käyttäjälle että tarjoajalle, mutta ne ovat myös pakollisia palveluntarjoajalle kehittyäkseen markkinoilla. Tulevaisuudessa kilpailun tiivistyessä ja asiakkaiden vaatimusten kasvaessa on kiinnitettävä entistä suurempaa huomiota koko prosessiketjun toimivuuteen. Uudet teknologiset ratkaisut ja niiden käyttäminen tehokkaasti tuovat yrityksille kilpailuetuja, joita ei muuten olisi saavutettavissa.

Electronic Commerce - Advantages and Requirements through Supply Chain

Työ käsittelee Metso Paper Servicen varaosa- ja kulutusosatuotelinjojen mahdollisuuksia sähköiseen liiketoimintaan ulkoisten asiakkaiden kanssa sekä sähköisten transaktioiden vaikutuksia, etuja ja edellytyksiä. Työssä selvitetään Metson ja sen kymmenen kotimaisen asiakastehtaan myynti- ja ostoprosessin toiminta. Prosessimallin avulla arvioidaan valmiuksia sähköisiin transaktioihin nykyisessä myynti- ja ostotoiminnassa. Tarkastelu painottuu toimintoihin tarjontaketjun eri vaiheissa. Teknisiä näkökohtia käsitellään kokonaiskuvan luomiseksi. Lisäksi työssä arvioidaan muutoksia, joita sähköinen liiketoiminta aiheuttaisi. Haastatteluin tehdyssä tutkimuksessa kartoitetaan näkemyksiä sähköiseen liiketoimintaan erilaisilla organisaation tasoilla. Kokonaisnäkemys syntyy erilaisista näkökulmista sähköiseen kauppaan. Sähköiseen liiketoimintaan suhtaudutaan myönteisesti. Kokemuksia on kuitenkin vielä vähän. Vaikka hankkeita sähköisen liiketoiminnan lisäämiseksi on vireillä, yhtä tärkeää on parantaa valmiuksia tehostamalla paitsi informaatiovirtaa, myös materiaalivirtaa.