Post-transcriptional regulation in the nucleus and cytoplasm: study of mean time to threshold (MTT) and narrow escape problem

Messenger RNAs (mRNAs) can be repressed and degraded by small non-coding RNA molecules. In this paper, we formulate a coarsegrained Markov-chain description of the post-transcriptional regulation of mRNAs by either small interfering RNAs (siRNAs) or microRNAs (miRNAs). We calculate the probability of an mRNA escaping from its domain before it is repressed by siRNAs/miRNAs via cal- culation of the mean time to threshold: when the number of bound siRNAs/miRNAs exceeds a certain threshold value, the mRNA is irreversibly repressed. In some cases,the analysis can be reduced to counting certain paths in a reduced Markov model. We obtain explicit expressions when the small RNA bind irreversibly to the mRNA and we also discuss the reversible binding case. We apply our models to the study of RNA interference in the nucleus, examining the probability of mRNAs escaping via small nuclear pores before being degraded by siRNAs. Using the same modelling framework, we further investigate the effect of small, decoy RNAs (decoys) on the process of post-transcriptional regulation, by studying regulation of the tumor suppressor gene, PTEN : decoys are able to block binding sites on PTEN mRNAs, thereby educing the number of sites available to siRNAs/miRNAs and helping to protect it from repression. We calculate the probability of a cytoplasmic PTEN mRNA translocating to the endoplasmic reticulum before being repressed by miRNAs. We support our results with stochastic simulations

Quantum first-passage problem

Formulation of quantum first passage problem is attempted in terms of a restricted Feynman path integral that simulates an absorbing barrier as in the corresponding classical case. The positivity of the resulting probability density, however, remains to be demonstrated.

First real-time experimental demonstrations of 11.25Gb/s optical OFDMA PONs with adaptive dynamic bandwidth allocation.

End-to-end real-time experimental demonstrations are reported, for the first time, of aggregated 11.25Gb/s over 26.4km standard SMF, optical orthogonal frequency division multiple access (OOFDMA) PONs with adaptive dynamic bandwidth allocation (DBA). The demonstrated intensity-modulation and direct-detection (IMDD) OOFDMA PON system consists of two optical network units (ONUs), each of which employs a DFB-based directly modulated laser (DML) or a VCSEL-based DML for modulating upstream signals. Extensive experimental explorations of dynamic OOFDMA PON system properties are undertaken utilizing identified optimum DML operating conditions. It is shown that, for simultaneously achieving acceptable BERs for all upstream signals, the OOFDMA PON system has a >3dB dynamic ONU launch power variation range, and the BER performance of the system is insusceptible to any upstream symbol offsets slightly smaller than the adopted cyclic prefix. In addition, experimental results also indicate that, in addition to maximizing the aggregated system transmission capacity, adaptive DBA can also effectively reduce imperfections in transmission channel properties without affecting signal bit rates offered to individual ONUs.

FIRST PASSAGE APPROXIMATION FOR NORMAL STATIONARY RANDOM PROCESSES.

A new approximate solution for the first passage probability of a stationary Gaussian random process is presented which is based on the estimation of the mean clump size. A simple expression for the mean clump size is derived in terms of the cumulative normal distribution function, which avoids the lengthy numerical integrations which are required by similar existing techniques. The method is applied to a linear oscillator and an ideal bandpass process and good agreement with published results is obtained. By making a slight modification to an existing analysis it is shown that a widely used empirical result for the asymptotic form of the first passage probability can be deduced theoretically.

The first real-time worldwide ionospheric predictions network: an advance in support of spaceborne experimentation, on-line model validation, and space weather

We report on the first realtime ionospheric predictions network and its capabilities to ingest a global database and forecast F-layer characteristics and "in situ" electron densities along the track of an orbiting spacecraft. A global network of ionosonde stations reported around-the-clock observations of F-region heights and densities, and an on-line library of models provided forecasting capabilities. Each model was tested against the incoming data; relative accuracies were intercompared to determine the best overall fit to the prevailing conditions; and the best-fit model was used to predict ionospheric conditions on an orbit-to-orbit basis for the 12-hour period following a twice-daily model test and validation procedure. It was found that the best-fit model often provided averaged (i.e., climatologically-based) accuracies better than 5% in predicting the heights and critical frequencies of the F-region peaks in the latitudinal domain of the TSS-1R flight path. There was a sharp contrast however, in model-measurement comparisons involving predictions of actual, unaveraged, along-track densities at the 295 km orbital altitude of TSS-1R In this case, extrema in the first-principle models varied by as much as an order of magnitude in density predictions, and the best-fit models were found to disagree with the "in situ" observations of Ne by as much as 140%. The discrepancies are interpreted as a manifestation of difficulties in accurately and self-consistently modeling the external controls of solar and magnetospheric inputs and the spatial and temporal variabilities in electric fields, thermospheric winds, plasmaspheric fluxes, and chemistry.

Coordinate and time-dependent diffusion dynamics in protein folding

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Treatment of developmental defect of upper lip with carbon dioxide laser radiation (CO2): First surgical time

With the exception of the cleft lip, developmental defects (DD) of the lip are rare. The upper lip originates from the ectomesenchyme and is formed by the merging of the nasal medial and lateral processes with the maxillary process. Disturbances during this formation period can cause DD with functional and/or esthetic repercussions. We present a case of DD of the upper lip in a patient with a history of progressive growth of the left lateral portion of the upper lip that occurred from the time of birth until the age of 22 years. Clinical examination revealed hypertrophy of the area from the left philtral columns to the left commissure of the lip, extending the portion of the surface mucosa creating a flaccid and asymptomatic tissue mass. All other buccal structures appeared to be within normal limits and without any evidence of defects or deformities. In the surgical planning we decided to carry out corrective surgery in two phases. The first phase accomplished a conservative excision of the total abnormal labial tissue mass with a CO2 laser radiation (5 W in continuous mode, bunch diameter φ = 0.6 mm with a power density of 768 W/cm2 and fluency of 0.231 J/cm2) being careful to preserve the vermilion portion of the lip. Postsurgical clinical evaluations were done every three days until the skin sutures were removed and then every seven days until two months post surgery. While the entire mass of excessive tissue could not be completely removed, the removal of the excessive mucosal tissue produced a very good outcome relative to lip function, with a good esthetic result without scarring, and good tissue mobility. The results showed that the CO2 laser is an extremely useful instrument that can provide excellent control of the surgical field and allow for healing that produces excellent functional and esthetic results. © 2005 Taylor & Francis.

The von Mises-Fisher distribution of the first exit point from the hypersphere of the drifted Brownian motion and the density of the first exit time

A characterization is provided for the von Mises–Fisher random variable, in terms of first exit point from the unit hypersphere of the drifted Wiener process. Laplace transform formulae for the first exit time from the unit hypersphere of the drifted Wiener process are provided. Post representations in terms of Bell polynomials are provided for the densities of the first exit times from the circle and from the sphere.

The Mice at play in the CALIFA survey. A case study of a gas-rich major merger between first passage and coalescence

We present optical integral field spectroscopy (IFS) observations of the Mice, a major merger between two massive (≳10^11 M_⊙) gas-rich spirals NGC 4676A and B, observed between first passage and final coalescence. The spectra provide stellar and gas kinematics, ionised gas properties, and stellar population diagnostics, over the full optical extent of both galaxies with ~1.6 kpc spatial resolution. The Mice galaxies provide a perfect case study that highlights the importance of IFS data for improving our understanding of local galaxies. The impact of first passage on the kinematics of the stars and gas has been significant, with strong bars most likely induced in both galaxies. The barred spiral NGC 4676B exhibits a strong twist in both its stellar and ionised gas disk. The edge-on disk galaxy NGC 4676A appears to be bulge free, with a strong bar causing its “boxy” light profile. On the other hand, the impact of the merger on the stellar populations has been minimal thus far. By combining the IFS data with archival multiwavelength observations we show that star formation induced by the recent close passage has not contributed significantly to the total star formation rate or stellar mass of the galaxies. Both galaxies show bicones of high ionisation gas extending along their minor axes. In NGC 4676A the high gas velocity dispersion and Seyfert-like line ratios at large scaleheight indicate a powerful outflow. Fast shocks (vs ~ 350 km s^-1) extend to ~6.6 kpc above the disk plane. The measured ram pressure (P/k = 4.8 × 10^6 K cm^-3) and mass outflow rate (~8−20 M_⊙ yr^-1) are similar to superwinds from local ultra-luminous infrared galaxies, although NGC 4676A only has a moderate infrared luminosity of 3 × 10^10 L_⊙. Energy beyond what is provided by the mechanical energy of the starburst appears to be required to drive the outflow. Finally, we compare the observations to mock kinematic and stellar population maps extracted from a hydrodynamical merger simulation. The models show little enhancement in star formation during and following first passage, in agreement with the observations. We highlight areas where IFS data could help further constrain the models.

Laminar-turbulent transition in Raman fiber lasers:a first passage statistics based analysis

Loss of coherence with increasing excitation amplitudes and spatial size modulation is a fundamental problem in designing Raman fiber lasers. While it is known that ramping up laser pump power increases the amplitude of stochastic excitations, such higher energy inputs can also lead to a transition from a linearly stable coherent laminar regime to a non-desirable disordered turbulent state. This report presents a new statistical methodology, based on first passage statistics, that classifies lasing regimes in Raman fiber lasers, thereby leading to a fast and highly accurate identification of a strong instability leading to a laminar-turbulent phase transition through a self-consistently defined order parameter. The results have been consistent across a wide range of pump power values, heralding a breakthrough in the non-invasive analysis of fiber laser dynamics.

Probabilistic approach of water residence time and connectivity using Markov Chains with application to tidal embayments

Markov Chain analysis was recently proposed to assess the time scales and preferential pathways into biological or physical networks by computing residence time, first passage time, rates of transfer between nodes and number of passages in a node. We propose to adapt an algorithm already published for simple systems to physical systems described with a high resolution hydrodynamic model. The method is applied to bays and estuaries on the Eastern Coast of Canada for their interest in shellfish aquaculture. Current velocities have been computed by using a 2 dimensional grid of elements and circulation patterns were summarized by averaging Eulerian flows between adjacent elements. Flows and volumes allow computing probabilities of transition between elements and to assess the average time needed by virtual particles to move from one element to another, the rate of transfer between two elements, and the average residence time of each system. We also combined transfer rates and times to assess the main pathways of virtual particles released in farmed areas and the potential influence of farmed areas on other areas. We suggest that Markov chain is complementary to other sets of ecological indicators proposed to analyse the interactions between farmed areas - e.g. depletion index, carrying capacity assessment. Markov Chain has several advantages with respect to the estimation of connectivity between pair of sites. It makes possible to estimate transfer rates and times at once in a very quick and efficient way, without the need to perform long term simulations of particle or tracer concentration.