Ulva and Enteromorpha (Ulvaceae, Chlorophyta) from two sides of the Yellow Sea: analysis of nuclear rDNA ITS and plastid rbcL sequence data

Ulvacean green seaweeds are common worldwide; they formed massive green tides in the Yellow Sea in recent years, which caused marine ecological problems as well as a social issue. We investigated two major genera of the Ulvaceae, Ulva and Enteromorpha, and collected the plastid rbcL and nuclear ITS sequences of specimens of the genera in two sides of the Yellow Sea and analyzed them. Phylogenetic trees of rbcL data show the occurrence of five species of Enteromorpha (E. compressa, E. flexuosa, E. intestinalis, E. linza and E. prolifera) and three species of Ulva (U. pertusa, U. rigida and U. ohnoi). However, we found U. ohnoi, which is known as a subtropical to tropical species, at two sites on Jeju Island, Korea. Four ribotypes in partial sequences of 5.8S rDNA and ITS2 from E. compressa were also found. Ribotype network analysis revealed that the common ribotype, occurring in China, Korea and Europe, is connected with ribotypes from Europe and China/Japan. Although samples of the same species were collected from both sides of the Yellow Sea, intraspecific genetic polymorphism of each species was low among samples collected worldwide.

Homology Induction: the use of machine learning to improve sequence similarity searches

Karwath, A. King, R. Homology induction: the use of machine learning to improve sequence similarity searches. BMC Bioinformatics. 23rd April 2002. 3:11 Additional File Describes the title organims species declaration in one string [http://www.biomedcentral.com/content/supplementary/1471- 2105-3-11-S1.doc] Sponsorship: Andreas Karwath and Ross D. King were supported by the EPSRC grant GR/L62849.

Learning styles and performance in the introductory programming sequence

Thomas, L., Ratcliffe, M., Woodbury, J., and Jarman, E. 2002. Learning styles and performance in the introductory programming sequence. SIGCSE Bull. 34, 1 (Mar. 2002), 33-37.

Correction for Eddy Current-Induced Echo-Shifting Effect in Partial-Fourier Diffusion Tensor Imaging.

In most diffusion tensor imaging (DTI) studies, images are acquired with either a partial-Fourier or a parallel partial-Fourier echo-planar imaging (EPI) sequence, in order to shorten the echo time and increase the signal-to-noise ratio (SNR). However, eddy currents induced by the diffusion-sensitizing gradients can often lead to a shift of the echo in k-space, resulting in three distinct types of artifacts in partial-Fourier DTI. Here, we present an improved DTI acquisition and reconstruction scheme, capable of generating high-quality and high-SNR DTI data without eddy current-induced artifacts. This new scheme consists of three components, respectively, addressing the three distinct types of artifacts. First, a k-space energy-anchored DTI sequence is designed to recover eddy current-induced signal loss (i.e., Type 1 artifact). Second, a multischeme partial-Fourier reconstruction is used to eliminate artificial signal elevation (i.e., Type 2 artifact) associated with the conventional partial-Fourier reconstruction. Third, a signal intensity correction is applied to remove artificial signal modulations due to eddy current-induced erroneous T2(∗) -weighting (i.e., Type 3 artifact). These systematic improvements will greatly increase the consistency and accuracy of DTI measurements, expanding the utility of DTI in translational applications where quantitative robustness is much needed.

A non-LTE analysis of the spectra of two narrow lined main sequence stars in the SMC

An analysis of high-resolution VLT/UVES spectra of two B-type main sequence stars, NGC 346-11 and AV 304, in the Small Magellanic Cloud (SMC), has been undertaken, using the non-LTE tlusty model atmospheres to derive the stellar parameters and chemical compositions of each star. The chemical compositions of the two stars are in reasonable agreement. Moreover, our stellar analysis agrees well with earlier analyses of H II regions. The results derived here should be representative of the current base-line chemical composition of the SMC interstellar medium as derived from B-type stars.

Idealised operation of zero-voltage-switching series-L/parallel-tuned Class-E power amplifier

An analysis of a modified series-L/parallel-tuned Class-E power amplifier is presented, which includes the effects that a shunt capacitance placed across the switching device will have on Class-E behaviour. In the original series L/parallel-tuned topology in which the output transistor capacitance is not inherently included in the circuit, zero-current switching (ZCS) and zero-current derivative switching (ZCDS) conditions should be applied to obtain optimum Class-E operation. On the other hand, when the output transistor capacitance is incorporated in the circuit, i.e. in the modified series-L/parallel-tuned topology, the ZCS and ZCDS would not give optimum operation and therefore zero-voltage-switching (ZVS) and zero-voltage-derivative switching (ZVDS) conditions should be applied instead. In the modified series-L/parallel-tuned Class-E configuration, the output-device inductance and the output-device output capacitance, both of which can significantly affect the amplifier's performance at microwave frequencies, furnish part, if not all, of the series inductance L and the shunt capacitance COUT, respectively. Further, when compared with the classic shunt-C/series-tuned topology, the proposed Class-E configuration offers some advantages in terms of 44% higher maximum operating frequency (fMAX) and 4% higher power-output capability (PMAX). As in the classic topology, the fMAX of the proposed amplifier circuit is reached when the output-device output capacitance furnishes all of the capacitance COUT, for a given combination of frequency, output power and DC supply voltage. It is also shown that numerical simulations agree well with theoretical predictions.

Ca2+-activated Cl- current in retinal arteriolar smooth muscle.

PURPOSE: To characterize the biophysical, pharmacologic, and functional properties of the Ca(2+)-activated Cl(-) current in retinal arteriolar myocytes. METHODS: Whole-cell perforated patch-clamp recordings were made from myocytes within intact isolated arteriolar segments. Arteriolar tone was assessed using pressure myography. RESULTS: Depolarizing of voltage steps to -40 mV and greater activated an L-type Ca(2+) current (I(Ca(L))) that was followed by a sustained current. Large tail currents (I(tail)) were observed on stepping back to -80 mV. The sustained current and I(tail) reversed close to 0 mV in symmetrical Cl(-) concentrations. The ion selectivity sequence for I(tail) was I(-)> Cl(-)> glucuronate. Outward I(tail) was sensitive to the Cl(-) channel blockers 9-anthracene-carboxylic acid (9-AC; 1 mM), 4-acetamido-4'-isothiocyanatostilbene-2,2'-disulfonic acid (SITS; 1 mM), and disodium 4,4'-diisothiocyanatostilbene-2,2'-disulfonate (DIDS; 1 mM), but only DIDS produced a substantial (78%) block of inward tail currents at -100 mV. I(tail) was decreased in magnitude when the normal bathing medium was substituted with Ca(2+)-free solution or if I(Ca(L)) was inhibited by 1 microM nimodipine. Caffeine (10 mM) produced large transient currents that reversed close to the Cl(-) equilibrium potential and were blocked by 1 mM DIDS or 100 microM tetracaine. DIDS had no effect on basal vascular tone in pressurized arterioles but dramatically reduced the level of vasoconstriction observed in the presence of 10 nM endothelin-1. CONCLUSIONS: Retinal arteriolar myocytes have I(Cl(Ca)), which may be activated by Ca(2+) entry through L-type Ca(2+) channels or Ca(2+) release from intracellular stores. This current appears to contribute to agonist-induced retinal vasoconstriction.

A Novel Multilocus Sequence Typing Scheme for the Opportunistic Pathogen Propionibacterium acnes and Characterisation of Type I Cell Surface-Associated Antigens.

We have developed a novel Multilocus Sequence Typing Scheme (MLST) and database (http://pubmlst.org/pacnes/) for Propionibacterium acnes based on the analysis of seven core housekeeping genes. The scheme, which was validated against previously described antibody, single locus and Random Amplification of Polymorphic DNA (RAPD) typing methods, displayed excellent resolution and differentiated 123 isolates into 37 sequence types (ST). An overall clonal population structure was detected with six eBURST groups representing the major clades I, II and III, along with two singletons. Two highly successful and global clonal lineages, ST6 (type IA) and ST10 (type IB1), representing 65% of this current MLST isolate collection were identified. The ST6 clone and closely related single locus variants (SLV), which comprise a large clonal complex CC6, dominated isolates from patients with acne, and were also significantly associated with ophthalmic infections. Our data therefore supports an association between acne and P. acnes strains from the type IA cluster and highlights the role of a widely disseminated clonal genotype in this condition. Characterisation of type I cell surface-associated antigens that are not detected in ST10 or strains of type II and III identified two dermatan-sulphate-binding proteins with putative phase/antigenic variation signatures. We propose that the expression of these proteins by type IA organisms contributes to their role in the pathophysiology of acne and helps explain the recurrent nature of the disease. The MLST scheme and database described in this study should provide a valuable platform for future epidemiological and evolutionary studies of P. acnes.

Validation of Next Generation Sequencing Technologies in Comparison to Current Diagnostic Gold Standards for BRAF, EGFR and KRAS Mutational Analysis

Next Generation Sequencing (NGS) has the potential of becoming an important tool in clinical diagnosis and therapeutic decision-making in oncology owing to its enhanced sensitivity in DNA mutation detection, fast-turnaround of samples in comparison to current gold standard methods and the potential to sequence a large number of cancer-driving genes at the one time. We aim to test the diagnostic accuracy of current NGS technology in the analysis of mutations that represent current standard-of-care, and its reliability to generate concomitant information on other key genes in human oncogenesis. Thirteen clinical samples (8 lung adenocarcinomas, 3 colon carcinomas and 2 malignant melanomas) already genotyped for EGFR, KRAS and BRAF mutations by current standard-of-care methods (Sanger Sequencing and q-PCR), were analysed for detection of mutations in the same three genes using two NGS platforms and an additional 43 genes with one of these platforms. The results were analysed using closed platform-specific proprietary bioinformatics software as well as open third party applications. Our results indicate that the existing format of the NGS technology performed well in detecting the clinically relevant mutations stated above but may not be reliable for a broader unsupervised analysis of the wider genome in its current design. Our study represents a diagnostically lead validation of the major strengths and weaknesses of this technology before consideration for diagnostic use.

5.9-keV Mn K-shell X-ray luminosity from the decay of 55Fe in Type Ia supernova models

We show that the X-ray line flux of the Mn Kα line at 5.9 keV from the decay of 55Fe is a promising diagnostic to distinguish between Type Ia supernova (SN Ia) explosion models. Using radiation transport calculations, we compute the line flux for two three-dimensional explosion models: a near-Chandrasekhar mass delayed detonation and a violent merger of two (1.1 and 0.9 M⊙) white dwarfs. Both models are based on solar metallicity zero-age main-sequence progenitors. Due to explosive nuclear burning at higher density, the delayed-detonation model synthesizes ˜3.5 times more radioactive 55Fe than the merger model. As a result, we find that the peak Mn Kα line flux of the delayed-detonation model exceeds that of the merger model by a factor of ˜4.5. Since in both models the 5.9-keV X-ray flux peaks five to six years after the explosion, a single measurement of the X-ray line emission at this time can place a constraint on the explosion physics that is complementary to those derived from earlier phase optical spectra or light curves. We perform detector simulations of current and future X-ray telescopes to investigate the possibilities of detecting the X-ray line at 5.9 keV. Of the currently existing telescopes, XMM-Newton/pn is the best instrument for close (≲1-2 Mpc), non-background limited SNe Ia because of its large effective area. Due to its low instrumental background, Chandra/ACIS is currently the best choice for SNe Ia at distances above ˜2 Mpc. For the delayed-detonation scenario, a line detection is feasible with Chandra up to ˜3 Mpc for an exposure time of 106 s. We find that it should be possible with currently existing X-ray instruments (with exposure times ≲5 × 105 s) to detect both of our models at sufficiently high S/N to distinguish between them for hypothetical events within the Local Group. The prospects for detection will be better with future missions. For example, the proposed Athena/X-IFU instrument could detect our delayed-detonation model out to a distance of ˜5 Mpc. This would make it possible to study future events occurring during its operational life at distances comparable to those of the recent supernovae SN 2011fe (˜6.4 Mpc) and SN 2014J (˜3.5 Mpc).

A stacked Late Quaternary fluvio-periglacial sequence from the Axe valley, southern England with implications for landscape evolution and Palaeolithic archaeology

The current model of mid-latitude late Quaternary terrace sequences, is that they are uplift-driven but climatically controlled terrace staircases, relating to both regional-scale crustal and tectonic factors, and palaeohydrological variations forced by quasi-cyclic climatic conditions in the 100 K world (post Mid Pleistocene Transition). This model appears to hold for the majority of the river valleys draining into the English Channel which exhibit 8–15 terrace levels over approximately 60–100 m of altitudinal elevation. However, one valley, the Axe, has only one major morphological terrace and has long-been regarded as anomalous. This paper uses both conventional and novel stratigraphical methods (digital granulometry and terrestrial laser scanning) to show that this terrace is a stacked sedimentary sequence of 20–30 m thickness with a quasi-continuous (i.e. with hiatuses) pulsed, record of fluvial and periglacial sedimentation over at least the last 300–400 K yrs as determined principally by OSL dating of the upper two thirds of the sequence. Since uplift has been regional, there is no evidence of anomalous neotectonics, and climatic history must be comparable to the adjacent catchments (both of which have staircase sequences) a catchment-specific mechanism is required. The Axe is the only valley in North West Europe incised entirely into the near-horizontally bedded chert (crypto-crystalline quartz) and sand-rich Lower Cretaceous rocks creating a buried valley. Mapping of the valley slopes has identified many large landslide scars associated with past and present springs. It is proposed that these are thaw-slump scars and represent large hill-slope failures caused by Vauclausian water pressures and hydraulic fracturing of the chert during rapid permafrost melting. A simple 1D model of this thermokarstic process is used to explore this mechanism, and it is proposed that the resultant anomalously high input of chert and sand into the valley during terminations caused pulsed aggradation until the last termination. It is also proposed that interglacial and interstadial incision may have been prevented by the over-sized and interlocking nature of the sub-angular chert clasts until the Lateglacial when confinement of the river overcame this immobility threshold. One result of this hydrogeologically mediated valley evolution was to provide a sequence of proximal Palaeolithic archaeology over two MIS cycles. This study demonstrates that uplift tectonics and climate alone do not fully determine Quaternary valley evolution and that lithological and hydrogeological conditions are a fundamental cause of variation in terrestrial Quaternary records and landform evolution.

Electron-impact ionization and recombination of M -shell atomic ions in the argon isonuclear sequence

Electron-impact ionization and recombination cross sections and rate coefficients are calculated for M-shell Ar atomic ions using a configuration-average distorted-wave method. The electron-impact ionization calcula- tions are for all atomic ions in the Ar isonuclear sequence. Ionization contributions include both direct ioniza- tion and excitation-autoionization processes. Good agreement is found between theory and experimental crossed-beam measurements for moderately charged ion stages. Comparisons are made with previous theoret- ical calculations where possible.We also generate rate coefficients for neutral argon ionization, based on recent R-matrix with pseudostates calculations. Electron-impact dielectronic recombination is calculated for all M-shell ions of argon. For Ar6+ and Ar7+ the current theoretical results agree well with previous level-resolved distorted-wave calculations. In order to compare with published ionization balance results our dielectronic recombination data are combined with literature values for the higher ion stages and with recent radiative recombination data for all the ion stages. We find significant differences in our equilibrium fractional abun- dances for the M-shell ions, compared with literature values. We relate these differences to the underlying atomic data.

Investigation into the determination of arsenic by direct current plasma atomic emission spectrometer

Improvements have been made on the currently available hydride generator system manufactured by SpectraMetrics Incorporated, because the system was found to be unsatisfactory with respect to the following: 1. the drying agent, anhydrous calcium chloride, 2. the special sample tube, 3. the direction of argon flow through the Buchner funnel when it came to dealing with real sample, that is, with reference only to aqueous extracts of soil samples. Changes that were made on the system included the replacement of anhydrous calcium chloride with anhydrous calcium sulphate and the replacement of the special sample tube with a modified one made from silica. Re-directing the flow of argon through the top of the Buchner funnel appeared to make the system compatible with aqueous extracts of soil samples. The interferences from 1000 ~g/mL of nickel(II) , cobalt(II), iron(III), copper(II) have been eliminated with the aid of 1.4 M hydrochloric acid and 1% (weight/volume) L-cystine. Greater than 90% recovery of 0.3 ~g/mL arsenic signal was achieved in each case. Furthermore, 103% of arsenic signal was accomplished in the presence of 1000 ~g/mL cadmium with 5 M Hel. tVhen each of the interferents was present in solution at 1000 ppm, a recovery of 85% was achieved by using 5 M hydrochloric acid and 3% (weight/volume) L-cystine. Without L-cystine and when 1.4 M hydrochloric acid was used, the recoveries were 0% (Ni), 0% (Co), 88% (Fe), 15% (Cu), 18% (Cd). Similarly, a solution containing 1000 ppm of each interferent gave a zero percent recovery of arsenic. The reduction of trivalent and pentavalent arsenic at a pH less than one has also been investigated and shown to be quantitative if peak areas are measured. The reproducibility determination of a 0.3 Vg/mL standard arsenic solution by hydride generation shows a relative standard deviation of 3.4%. The detection limits with and without Porapak Q have been found to be 0.6 ng/mL and 1.0 ng/mL, respectively.

Postures et mutations du plan-séquence fixe, du cinéma des premiers temps à YouTube

Pour respecter les droits d'auteur, la version électronique de ce mémoire a été dépouillée de ses documents visuels. La version intégrale du mémoire a été déposée au Service de la gestion des documents et des archives de l'Université de Montréal.

An Alternative Approach To Computer System Security Monitoring And Enhancement Through System Call Sequence Analysis

Modern computer systems are plagued with stability and security problems: applications lose data, web servers are hacked, and systems crash under heavy load. Many of these problems or anomalies arise from rare program behavior caused by attacks or errors. A substantial percentage of the web-based attacks are due to buffer overflows. Many methods have been devised to detect and prevent anomalous situations that arise from buffer overflows. The current state-of-art of anomaly detection systems is relatively primitive and mainly depend on static code checking to take care of buffer overflow attacks. For protection, Stack Guards and I-leap Guards are also used in wide varieties.This dissertation proposes an anomaly detection system, based on frequencies of system calls in the system call trace. System call traces represented as frequency sequences are profiled using sequence sets. A sequence set is identified by the starting sequence and frequencies of specific system calls. The deviations of the current input sequence from the corresponding normal profile in the frequency pattern of system calls is computed and expressed as an anomaly score. A simple Bayesian model is used for an accurate detection.Experimental results are reported which show that frequency of system calls represented using sequence sets, captures the normal behavior of programs under normal conditions of usage. This captured behavior allows the system to detect anomalies with a low rate of false positives. Data are presented which show that Bayesian Network on frequency variations responds effectively to induced buffer overflows. It can also help administrators to detect deviations in program flow introduced due to errors.