sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes

Background:Bacterial non-coding small RNAs (sRNAs) have attracted considerable attention due to their ubiquitous nature and contribution to numerous cellular processes including survival, adaptation and pathogenesis. Existing computational approaches for identifying bacterial sRNAs demonstrate varying levels of success and there remains considerable room for improvement. Methodology/Principal Findings: Here we have proposed a transcriptional signal-based computational method to identify intergenic sRNA transcriptional units (TUs) in completely sequenced bacterial genomes. Our sRNAscanner tool uses position weight matrices derived from experimentally defined E. coli K-12 MG1655 sRNA promoter and rho-independent terminator signals to identify intergenic sRNA TUs through sliding window based genome scans. Analysis of genomes representative of twelve species suggested that sRNAscanner demonstrated equivalent sensitivity to sRNAPredict2, the best performing bioinformatics tool available presently. However, each algorithm yielded substantial numbers of known and uncharacterized hits that were unique to one or the other tool only. sRNAscanner identified 118 novel putative intergenic sRNA genes in Salmonella enterica Typhimurium LT2, none of which were flagged by sRNAPredict2. Candidate sRNA locations were compared with available deep sequencing libraries derived from Hfq-co-immunoprecipitated RNA purified from a second Typhimurium strain (Sittka et al. (2008) PLoS Genetics 4: e1000163). Sixteen potential novel sRNAs computationally predicted and detected in deep sequencing libraries were selected for experimental validation by Northern analysis using total RNA isolated from bacteria grown under eleven different growth conditions. RNA bands of expected sizes were detected in Northern blots for six of the examined candidates. Furthermore, the 5'-ends of these six Northern-supported sRNA candidates were successfully mapped using 5'-RACE analysis. Conclusions/Significance: We have developed, computationally examined and experimentally validated the sRNAscanner algorithm. Data derived from this study has successfully identified six novel S. Typhimurium sRNA genes. In addition, the computational specificity analysis we have undertaken suggests that similar to 40% of sRNAscanner hits with high cumulative sum of scores represent genuine, undiscovered sRNA genes. Collectively, these data strongly support the utility of sRNAscanner and offer a glimpse of its potential to reveal large numbers of sRNA genes that have to date defied identification. sRNAscanner is available from: http://bicmku.in:8081/sRNAscanner or http://cluster.physics.iisc.ernet.in/sRNAscanner/.

Effect of Li substitution on dielectric and ferroelectric properties of ZnO thin films grown by pulsed-laser ablation

Li-doped ZnO thin films (Zn1-xLixO, x=0.05-0.15) were grown by pulsed-laser ablation technique. Highly c-axis-oriented films were obtained at a growth temperature of 500 degrees C. Ferroelectricity in Zn1-xLixO was found from the temperature-dependent dielectric constant and from the polarization hysteresis loop. The transition temperature (T-c) varied from 290 to 330 K as the Li concentration increased from 0.05 to 0.15. It was found that the maximum value of the dielectric constant at T-c is a function of Li concentration. A symmetric increase in memory window with the applied gate voltage is observed for the ferroelectric thin films on a p-type Si substrate. A ferroelectric P-E hysteresis loop was observed for all the compositions. The spontaneous polarization (P-s) and coercive field (E-c) of 0.6 mu C/cm(2) and 45 kV/cm were obtained for Zn0.85Li0.15O thin films. These observations reveal that partial replacement of host Zn by Li ions induces a ferroelectric phase in the wurtzite-ZnO semiconductor. The dc transport studies revealed an Ohmic behavior in the lower-voltage region and space-charge-limited conduction prevailed at higher voltages. The optical constants were evaluated from the transmission spectrum and it was found that Li substitution in ZnO enhances the dielectric constant.

An SIMD machine for low-level vision

This paper presents an SIMD machine which has been tuned to execute low-level vision algorithms employing the relaxation labeling paradigm. Novel features of the design include: 1. (1) a communication scheme capable of window accessing under a single instruction. 2. (2) flexible I/O instructions to load overlapped data segments; and 3. (3) data-conditional instructions which can be nested to an arbitrary degree. A time analysis of the stereo correspondence problem, as implemented on a simulated version of the machine using the probabilistic relaxation technique, shows a speed up of almost N2 for an N × N array of PEs.

Interplay between multiple length and time scales in complex chemical systems

Processes in complex chemical systems, such as macromolecules, electrolytes, interfaces, micelles and enzymes, can span several orders of magnitude in length and time scales. The length and time scales of processes occurring over this broad time and space window are frequently coupled to give rise to the control necessary to ensure specificity and the uniqueness of the chemical phenomena. A combination of experimental, theoretical and computational techniques that can address a multiplicity of length and time scales is required in order to understand and predict structure and dynamics in such complex systems. This review highlights recent experimental developments that allow one to probe structure and dynamics at increasingly smaller length and time scales. The key theoretical approaches and computational strategies for integrating information across time-scales are discussed. The application of these ideas to understand phenomena in various areas, ranging from materials science to biology, is illustrated in the context of current developments in the areas of liquids and solvation, protein folding and aggregation and phase transitions, nucleation and self-assembly.

Pietismin kuva - ikkuna yksityiseen hengellisyyteen : Johann Arndtin opetukset pietistisen embleemin perustana

The image of Pietism a window to personal spirituality. The teachings of Johann Arndt as the basis of Pietist emblems The Pietist effect on spiritual images has to be scrutinised as a continuum initiating from the teachings of Johann Arndt who created a protestant iconography that defended the status of pictures and images as the foundation of divine revelation. Pietist artworks reveal Arndtian part of secret, eternal world, and God. Even though modern scholars do not regarded him as a founding father of Pietism anymore, his works have been essential for the development of iconography, and the themes of the Pietist images are linked with his works. For Arndt, the starting point is in the affecting love for Christ who suffered for the humankind. The reading experience is personal and the words point directly at the reader and thus appear as evidence of the guilt of the reader as well as of the love of God. Arndt uses bounteous and descriptive language which has partially affected promoting and picturing of many themes. Like Arndt, Philipp Jakob Spener also emphasised the heart that believes. The Pietist movement was born to oppose detached faith and the lack of the Holy Ghost. Christians touched by the teachings of Arndt and Spener began to create images out of metaphors presented by Arndt. As those people were part of the intelligentsia, it was natural that the fashionable emblematics of the 17th century was moulded for the personal needs. For Arndt, the human heart is manifested as a symbol of soul, personal faith or unbelief as well as an allegory of the burning love for Jesus. Due to this fact, heart emblems were gradually widely used and linked with the love of Christ. In the Nordic countries, the introduction of emblems emanated from the gentry s connections to the Central Europe where emblems were exploited in order to decorate books, artefacts, interiors, and buildings as well as visual/literal trademarks of the intelligentsia. Emblematic paintings in the churches of the castles of Venngarn (1665) and Läckö (1668), owned by Magnus Gabriel De la Gardie, are one of the most central interior paintings preserved in the Nordic countries, and they emphasise personal righteous life. Nonetheless, it was the books by Arndt and the Poet s Society in Nurnberg that bound the Swedish gentry and the scholars of the Pietist movement together. The Finnish gentry had no castles or castle churches so they supported county churches, both in building and in maintenance. As the churches were not private, their iconography could not be private either. Instead, people used Pietist symbols such as Agnus Dei, Cor ardens, an open book, beams, king David, frankincense, wood themes and Virtues. In the Pietist images made for public spaces, the attention is focused on pedagogical, metaphorical, and meaningful presentation as well as concealed statements.

High-temperature dielectric response in pulsed laser deposited Bi1.5Zn1.0Nb1.5O7 thin films

Cubic pyrochlore Bi1.5Zn1.0Nb1.5O7 thin films were deposited by pulsed laser ablation on Pt(200)/SiO2/Si at 500, 550, 600, and 650 degrees C. The thin films with (222) preferred orientation were found to grow at 650 degrees C with better crystallinity which was established by the lowest full-width half maxima of similar to 0.38. The dielectric response of the thin films grown at 650 degrees C have been characterized within a temperature range of 270-650 K and a frequency window of 0.1-100 kHz. The dielectric dispersion in the thin films shows a Maxwell-Wagner type relaxation with two different kinds of response confirmed by temperature dependent Nyquist plots. The ac conduction of the films showed a varied behavior in two different frequency regions. The power law exponent values of more than 1 at high frequency are explained by a jump-relaxation-model. The possibility of grain boundary related large polaronic hopping, due to two different power law exponents and transformation of double to single response in Nyquist plots at high temperature, has been excluded. The ``attempt jump frequency'' obtained from temperature dependent tangent loss and real part of dielectric constants, has been found to lie in the range of their lattice vibronic frequencies (10(12)-10(13) Hz). The activation energy arising from a large polaronic hopping due to trapped charge at low frequency region has been calculated from the ac conduction behavior. The range of activation energies (0.26-0.59. eV) suggests that the polaronic hopping at low frequency is mostly due to oxygen vacancies. (C) 2010 American Institute of Physics. doi:10.106311.3457335]

A molecular dynamics study of cage-to-cage migration in sodium Y zeolite: role of surface-mediated diffusion

The details of cage-to-cage migration have been obtained from an analysis of the molecular dynamics trajectory of a probe adsorbate. It is observed that particles utilize the region within a radius of 2 angstrom from the window center but with diffusion taking place predominantly at 1.6 angstrom from the window center and a potential energy of nearly -12 kJ/mol. A barrier of about 0.5 kJ/mol is observed for surface-mediated diffusion. Surprisingly, for diffusion without surface mediation for a particle going from one cage center to another, there is an attractive well near the window instead of a barrier. At low adsorbate concentrations and room temperature, the predominant mode for cage-to-cage migration is surface-mediated diffusion. The analysis suggests that particles slide along the surface of the inner walls of the alpha-cages during migration from one cage to another.

CowLog

We have developed CowLog, which is open-source software for recording behaviors from digital video and is easy to use and modify. CowLog tracks the time code from digital video files. The program is suitable for coding any digital video, but the authors have used it in animal research. The program has two main windows: a coding window, which is a graphical user interface used for choosing video files and defining output files that also has buttons for scoring behaviors, and a video window, which displays the video used for coding. The windows can be used in separate displays. The user types the key codes for the predefined behavioral categories, and CowLog transcribes their timing from the video time code to a data file. CowLog comes with an additional feature, an R package called Animal, for elementary analyses of the data files. With the analysis package, the user can calculate the frequencies, bout durations, and total durations of the coded behaviors and produce summary plots from the data.

CowLog

We have developed CowLog, which is open-source software for recording behaviors from digital video and is easy to use and modify. CowLog tracks the time code from digital video files. The program is suitable for coding any digital video, but the authors have used it in animal research. The program has two main windows: a coding window, which is a graphical user interface used for choosing video files and defining output files that also has buttons for scoring behaviors, and a video window, which displays the video used for coding. The windows can be used in separate displays. The user types the key codes for the predefined behavioral categories, and CowLog transcribes their timing from the video time code to a data file. CowLog comes with an additional feature, an R package called Animal, for elementary analyses of the data files. With the analysis package, the user can calculate the frequencies, bout durations, and total durations of the coded behaviors and produce summary plots from the data.

Enhanced photodynamic effect of cobalt(III) dipyridophenazine complex on thyrotropin receptor expressing HEK293 cells

Ternary cobalt(III) complexes CoL(B)] (1-3) of a trianionic tetradentate phenolate-based ligand (L) and phenanthroline bases (B), viz. 1,10-phenanthroline (phen in 1), dipyridoquinoxaline (dpq in 2) and dipyridophenazine (dppz in 3) are synthesized, characterized from X-ray crystallographic, analytical and spectral techniques, and their utility in photodynamic therapy (PDT) of thyroid diseases caused by TSH receptor dysfunction is probed. The complexes display a visible spectral band within the PDT spectral window at similar to 690 nm. Photodynamic potential was estimated through DNA cleavage activity of the dpq and dppz complexes in UV-A light of 365 nm and red light of 676 nm. The reactions proceed via the hydroxyl radical pathway. The complexes retain their DNA photocleavage activity in red light under anaerobic conditions, a situation normally prevails in hypoxic tumor core. Investigation into the photocytotoxic potential of these complexes showed that the dppz complex 3 is approximately 4-fold more active in the HEK293 cells expressing human thyrotropin receptor (HEK293-hTSHR) than in the parental cell line and has an insignificant effect on an unrelated human cervical carcinoma cell line (HeLa). Photoexcitation of complex 3 in HEK293-hTSHR cells leads to damage hTSHR as evidenced from the decrease in cAMP formation both in absence and presence of hTSH and decrease in the TSHR immunofluorescence with a concomitant cytoplasmic translocation of the membrane protein, cadherin. The involvement of hTSHR is evidenced from the ability of complex 3 to bind to the extracellular domain of hTSHR (hTSHR-ECD) with a K-d value of 81 nM and from the photocleavage of hTSHR-ECD.

Rate Control State-of-the-art Survey

The majority of Internet traffic use Transmission Control Protocol (TCP) as the transport level protocol. It provides a reliable ordered byte stream for the applications. However, applications such as live video streaming place an emphasis on timeliness over reliability. Also a smooth sending rate can be desirable over sharp changes in the sending rate. For these applications TCP is not necessarily suitable. Rate control attempts to address the demands of these applications. An important design feature in all rate control mechanisms is TCP friendliness. We should not negatively impact TCP performance since it is still the dominant protocol. Rate Control mechanisms are classified into two different mechanisms: window-based mechanisms and rate-based mechanisms. Window-based mechanisms increase their sending rate after a successful transfer of a window of packets similar to TCP. They typically decrease their sending rate sharply after a packet loss. Rate-based solutions control their sending rate in some other way. A large subset of rate-based solutions are called equation-based solutions. Equation-based solutions have a control equation which provides an allowed sending rate. Typically these rate-based solutions react slower to both packet losses and increases in available bandwidth making their sending rate smoother than that of window-based solutions. This report contains a survey of rate control mechanisms and a discussion of their relative strengths and weaknesses. A section is dedicated to a discussion on the enhancements in wireless environments. Another topic in the report is bandwidth estimation. Bandwidth estimation is divided into capacity estimation and available bandwidth estimation. We describe techniques that enable the calculation of a fair sending rate that can be used to create novel rate control mechanisms.

Dielectric and Impedance Studies on 0.5Li(2)O-0.5K(2)O-2B(2)O(3) Glasses

Transparent glasses in the system 0.5Li(2)O-0.5K(2)O-2B(2)O(3) (LKBO) were fabricated via the conventional melt quenching technique. Amorphous and glassy nature of the samples was confirmed by X-ray diffraction and differential scanning calorimetry (DSC) respectively. Complex dielectric and impedance studies were conducted on the samples at different temperatures in the 100 Hz-10 MHz frequency range. ac conductivity was calculated from the dielectric data and the conductivity relaxation was found to obey the Jonscher's law. The Nyquist's plots (Z `'(omega) vs. Z'(omega)) showed single suppressed semicircles at all the temperatures under study indicating the non ideal Debye type relaxation process to be active. Activation energies for conduction and relaxation process were calculated using the Arrhenius relation. The UV-visible optical transmission spectra was shown a wide transmission window and calculated optical band gap was found to be 5.67 eV.

Ultimate Strength of RC Wall Panels with Openings

Test results of 12 reinforced concrete (RC) wall panels with openings are presented. The panels have been subjected to in-plane vertical loads applied at an eccentricity to represent possible accidental eccentricity that occurs in practice due to constructional imperfections. The 12 specimens consist of two identical groups of six panels each. One group of panels is tested in one-way in-plane action (i.e., supported at top and bottom edges against lateral displacement). The second group of panels is tested in two-way in-plane action (i.e., supported on all the four edges against lateral displacement). Openings in the panels represent typical door and window openings. Cracking loads, ultimate loads, crack patterns, and lateral deflections of the panels are studied. Empirical methods have been developed for the prediction of ultimate load. Also, lateral deflections, cracking loads, and ultimate loads of identical loads tested under one-way and two-way action are compared.

Onttojen puiden lahopuukovakuoriaiset — kolmen pyydystyypin vertailu

Vanhat ja ontot puut ovat tärkeä elinympäristö monelle lahopuusta riippuvaiselle eliölajille. Onttoihin puihin on erikoistunut suuri määrä myös vaarantuneita ja harvinaisia hyönteislajeja, jotka elävät puun onkalon seinämillä tai onkalon pohjalle kerääntyvässä orgaanisessa aineksessa, ns. mulmissa. Tutkimuksen tavoitteena oli selvittää, mikä kolmesta pyydystyypistä (ikkuna-, vuoka- ja kuoppapyydys) soveltuu parhaiten onttojen puiden lahopuukovakuoriaisten pyyntiin. Lisäksi tavoitteena oli kartoittaa hyönteisnäytteiden ensimmäiseen laboratoriokäsittelyyn vaadittua aikaa. Tutkimuksessa oli mukana vanhoja rungostaan onttoutuneita lehmuksia, tammia ja vaahteroita pääkaupunkiseudun puisto- ja kartanoalueilta. Puiden onkaloiden sisään aseteltiin ikkuna-, vuoka- ja kuoppapyydyksiä, kaksi kutakin tyyppiä ja ne tyhjennettiin kolmen viikon välein touko-heinäkuussa 2006. Pyydyksiä oli siis yhteensä 90 per pyyntijakso. Kun näytteistä eroteltiin halutut hyönteislahkot (mukaanlukien kovakuoriaiset) niiden käsittelyyn käytetty aika kirjattiin ylös. Aineistosta tunnistettiin yhteensä 3825 kovakuoriaisyksilöä ja 212 lajia, joista lahopuusta riippuvaisia oli yhteensä 3398 yksilöä ja 121 lajia. Ikkunapyydyksissä esiintyi yhteensä 1639 yksilöä ja 140 lajia, vuokapyydyksissä 1506 yksilöä ja 134 lajia, kuoppapyydyksissä 680 yksilöä ja 111 lajia. Näytteiden käsittelyaikojen keskiarvot olivat 48,3 minuuttia ikkunapyydykselle, 65,5 minuuttia vuokapyydykselle ja 34,1 kuoppapyydykselle. Lajistokoostumuksen huomioiva ?-diversiteetti erosi huomattavasti pyydysten välillä, se oli 36,5 % ikkuna- ja vuokapyydysten välillä, 13,1 % ikkuna- ja kuoppapyydysten välillä ja 14,2 % vuoka- ja kuoppapyydysten välillä. Ikkuna- ja vuokapyydysten välillä ei havaittu tilastollisesti merkitsevää eroa saproksyylilajien (p<0,05), -yksilöiden (p<0,05) tai käsittelyaikojen (p<0,05) keskiarvoissa. Ikkuna- ja vuokapyydyksillä saatiin keskimäärin selvästi enemmän saproksyylilajeja ja –yksilöitä kuoppapyydykseen verrattuna. Kuoppapyydyksellä saatiin kokonaisyksilömäärään verrattuna suhteellisesti vähemmän saproksyylejä (59 %) kuin ikkuna- (69 %) ja vuokapyydyksillä (71 %). Ikkunapyydykset olivat tehokkain pyydystyyppi vertailtaessa pyydysten keräämää saproksyyliyksilömäärää suhteessa aineiston käsittelyn vaatimaan aikaan. Tehokkuus (yksilöä minuutissa) ikkunapyydykselle oli 0,74, vuokapyydykselle 0,43 ja kuoppapyydykselle 0,21. Ikkunapyydyksiä ei ole aikaisemmin käytetty puun onkalon sisällä hyönteisiä pyydettäessä vaan ne ovat aikaisemmissa tutkimuksissa roikkuneet onkalon ulkopuolella. Ikkunapyydykset kuitenkin toimivat erinomaisesti myös onkaloiden sisällä. Ikkuna- sekä vuokapyydys toimivatkin selkeästi paremmin lahopuukovakuoriaisten pyynnissä verrattuna kuoppapyydykseen, jonka poisjättäminen olisi kuitenkin tuottanut huomattavasti lajiköyhemmän aineiston. Mahdollisimman monimuotoisen onttojen puiden lahopuukovakuoriaislajiston keräämiseksi tulisi käyttää ikkuna- tai vuokapyydyksiä yhdessä kuoppapyydysten kanssa.

Diffusion of sorbates in zeolites Y and A novel dependence on sorbate size and strength of sor ba t e-Zeoli t e interaction

A systematic investigation of monatomic spherical sorbates in the supercages of zeolites Y and A by molecular dynamics technique is presented. Rates of intercage diffusion, rates of cage visits, and the diffusion coefficients have been calculated as a function of the sorbate-zeolite interaction strength. These properties exhibit markedly different dependences on interaction strength for the two zeolites. The observed behavior is shown to be a consequence of the two principal mechanisms of intercage diffusion and the energetic barrier associated with them. The diffusion coefficient and other properties associated with intercage diffusion are found to be directly proportional to the reciprocal of the square of the sorbate diameter when the sorbate diameter is significantly smaller than the window diameter. As the sorbate diameter increases, a peak is observed in all the transport properties investigated including the diffusion coefficient. We call this surprising effect as the ring or levitation effect and it explains several anomalous results reported in the literature and suggests a breakdown of the geometrical criterion for diffusion of sorbates. It shows that under certain conditions nongeometrical factors play a major role and geometrical factors become secondary in the determination of the molecular sieve property. A generalized parameter has been proposed which suggests conditions under which one can expect the ring or levitation effect in any porous medium. Inverse size selectivity becomes operative under these conditions.