Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay

The transcriptome in a cell is finely regulated by a large number of molecular mechanisms able to control the balance between mRNA production and degradation. Recent experimental findings have evidenced that fine and specific regulation of degradation is needed for proper orchestration of a global cell response to environmental conditions. We developed a computational technique based on stochastic modeling, to infer condition-specific individual mRNA half-lives directly from gene expression time-courses. Predictions from our method were validated by experimentally measured mRNA decay rates during the intraerythrocytic developmental cycle of Plasmodium falciparum. We then applied our methodology to publicly available data on the reproductive and metabolic cycle of budding yeast. Strikingly, our analysis revealed, in all cases, the presence of periodic changes in decay rates of sequentially induced genes and co-ordination strategies between transcription and degradation, thus suggesting a general principle for the proper coordination of transcription and degradation machinery in response to internal and/or external stimuli. Citation: Cacace F, Paci P, Cusimano V, Germani A, Farina L (2012) Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay. PLoS Comput Biol 8(11): e1002772. doi:10.1371/journal.pcbi.100277

Distributed infinite-horizon optimal control of continuous-time linear systems over network

This article deals with the distributed infinite-horizon linear-quadratic-Gaussian optimal control problem for continuous-time systems over networks. In particular, the feedback controller is composed of local control stations, which receive some measurement data from the plant process and regulates a portion of the input signal. We provide a solution when the nodes have information on the structural data of the whole network but takes local actions, and also when only local information on the network are available to the nodes. The proposed solution is arbitrarily close to the optimal centralized one (in terms of cost index) when a design parameter is set sufficiently large. Numerical simulation validate the theoretical results

Stochastic Leader-Following for Heterogeneous Linear Agents with Communication Delays

We study the leader-following problem for linear stochastic multi-agent systems with uniform and constant communication delays on directed or undirected graphs. We consider both the state feedback and output feedback solutions. In the latter case, the agents can be a set of heterogeneous linear systems. By resorting to a new approach based on the scalar Lambert equation we obtain a constructive design with less conservative closed-form delay bounds. In particular, it is possible to compensate arbitrarily large delays if the agents are not unstable

Distributed kalman filtering over sensor networks with unknown random link failures

In this letter we consider the distributed consensus-based filtering problem for linear time-invariant systems over sensor networks subject to random link failures when the failure sequence is not known at the receiving side. We assume that the information exchanged, traveling along the channel, is corrupted by a noise and hence, it is no more possible to discriminate with certainty if a link failure has occurred. Therefore, in order to process the only significant information, we endow each sensor with detectors which decide on the presence of link failures. At each sensor the proposed approach consists of three steps: 1) failure detection; 2) local data aggregation; and 3) Kalman consensus filtering. Numerical examples show the effectiveness of this method

Fault Control on a Thermal Anomaly: Conceptual and Numerical Modeling of a Low\u2010Temperature Geothermal System in the Southern Alps Foreland Basin (NE Italy)

The interest on low\u2010temperature geothermal resources is progressively increasing since their renewability and widespread availability. Despite their frequency, these resources and their development have been only partially investigated. This paper unravels the major physical processes driving a low\u2010temperature geothermal resource in NE Italy (Euganean Geothermal System) through conceptual and numerical modeling. Dense fracturing associated to regional fault zones and a relay ramp enhances regional to local flow of thermal waters. Their rapid upwelling in the Euganean Geothermal Field is favored by open extensional fractures deforming the relay ramp. The water (65\u201386 \ub0C) is intensively exploited for balneotherapy, rendering it a profitable resource. Three\u2010dimensional coupled flow and heat transport numerical simulations based on this conceptual model are performed. Despite the presence of a uniform basal heat flow, a thermal anomaly corresponding to field observations develops in the modeling domain reproducing the relay ramp. Intensive fracturing extending across a wide area and a slightly anomalous heat flow favors a local increase in convection that drives the upwelling of deep\u2010seated hot waters. The simulations corroborate and refine the conceptual model, revealing that water of up to 115 \ub0C is likely to be found in the unexplored part of the thermal field. This study furthers knowledge on fault\u2010controlled low\u2010temperature geothermal resources where the geological setting could enhance local convection without anomalous heat flows, creating temperatures favorable for energy production. Conceptual and numerical modeling based on solid geological and hydrogeological reconstructions can offer a support tool for further detailed explorations of these prominent resources

Adaptive Streaming On Heterogeneous Networks”,

ABSTRACT Specific network protocols, like MobileIP, offer seamless connectivity to mobile systems. However, the QoS requirements of streaming applications and video conferencing systems require an approach that spans across different layers of the network stack. In this paper we study how to integrate an efficient method for vertical handoff and adaptation support for multimedia streaming through heterogeneous networks. We also present experimental results obtained with our prototype on IEEE 802.11 and UMTS networks

Tumor induced osteomalacia: a systematic review and individual patient's data analysis

Context: Tumor induced osteomalacia (TIO) is a rare paraneoplastic syndrome, usually caused by small, benign and slow-growing phosphaturic mesenchymal tumors. Clinically, TIO is characterized by renal phosphate leak, causing hypophosphatemia and osteomalacia. This review was performed to assess the clinical characteristics of TIO patients described worldwide so far. Evidence acquisition: On 06/26/2021, a systematic search was performed in Medline, Google Scholar, Google book, and Cochrane Library using the terms: "tumor induced osteomalacia", "oncogenic osteomalacia", "hypophosphatemia". There were no language restrictions. This review was performed according to PRISMA criteria. Evidence results: Overall, 1725 TIO cases were collected. TIO was more frequent in adult men, who showed a higher incidence of fractures compared to TIO women. The TIO causing neoplasms were identified in 1493 patients. The somatostatin receptor-based imaging modalities have the highest sensitivity for the identification of TIO-causing neoplasms. TIO causing neoplasms were equally located in bone and soft tissues; these latter showed a higher prevalence of fractures and deformities. The surgery is the preferred TIO definitive treatment (successful in >90% of patients). Promising non-surgical therapies are treatments with burosumab in TIO patients with elevated Fibroblast Growth Factor-23 levels, and with radiolabeled somatostatin analogs in patients with TIO-causing neoplasm identified by somatostatin receptor-based imaging techniques. Conclusion: TIO occurs preferentially in adult men. The TIO clinical expressiveness is more severe in men as well as in patients with TIO-causing neoplasms located to soft tissues. Treatments with burosumab and with radiolabeled somatostatin analogs are the most promising non-surgical therapies

Filtering Continuous-Time Linear Systems with Time-Varying Measurement Delay

We consider the filtering problem of LTI continuous-time systems with known and bounded measurement delays. The aim of the technical note is the design of a finite-dimensional sub-optimal filter whose performance in terms of the estimation error is comparable to optimal infinite-dimensional approaches. We show that the proposed approach allows for a precise characterization of the relationship between measurement delay and the covariance of the estimation error. In the time-varying case no restrictive hypotheses on the delay function are needed. The proposed filter can therefore be applied to delay functions for which traditional infinite-dimensional approaches cannot be straightforwardly applied