Analytical description of finite size effects for RNA secondary structures

The ensemble of RNA secondary structures of uniform sequences is studied analytically. We calculate the partition function for very long sequences and discuss how the cross-over length, beyond which asymptotic scaling laws apply, depends on thermodynamic parameters. For realistic choices of parameters this length can be much longer than natural RNA molecules. This has to be taken into account when applying asymptotic theory to interpret experiments or numerical results.Comment: 10 pages, 13 figures, published in Phys. Rev.

Serologic Evidence of Widespread Everglades Virus Activity in Dogs, Florida

Everglades virus (EVEV), an alphavirus in the Venezuelan equine encephalitis complex, circulates among rodents and vector mosquitoes in Florida and occasionally infects humans. It causes febrile disease, sometimes accompanied by neurologic manifestations. Although previous surveys showed high seroprevalence in humans, EVEV infections may be underdiagnosed because the disease is not severe enough to warrant a clinic visit or the undifferentiated presentations complicate diagnosis. Documented EVEV activity, as recent as 1993, was limited to south Florida. Using dogs as sentinels, a serosurvey was conducted to evaluate whether EVEV circulated recently in Florida and whether EVEV's spatial distribution parallels that of the mosquito vector, Culex cedecei. Four percent of dog sera contained neutralizing EVEV antibodies, and many seropositive animals lived farther north than both recorded EVEV activity and the principal vector. These results indicate that EVEV is widespread in Florida and may be an important, unrecognized cause of human illness

An Assessment of HIV/AIDS Risk in Higher Education Students in Yerevan, Armenia

Armenia\u27s current sociopolitical and economic instability and the alarming HIV incidence rates in neighboring countries amplify its risk for a national epidemic. The goals of this study were to assess HIV/AIDS knowledge and risk behaviors among higher education students in Yerevan. Knowledge of HIV transmission through sexual intercourse was markedly higher than that on intravenous transmission and prevailing myths; however, HIV/AIDS knowledge was not related to risk behaviors. Tobacco and alcohol prevalence was relatively high. Students reported risky sexual behaviors, including inconsistent condom use, casual sex, and multiple partners. In addition to descriptive statistics delineating gender differences across the target behavioral domains, bivariate and multivariate statistical analyses were used to understand factors that contributed to increased risk, including early age of initiation and the relationship between substance use and risky sexual activity. The study results provide much-needed information for the development of school- and community-based AIDS prevention programs in Armenia

Regulation of the ESC transcriptome by nuclear long non-coding RNAs

Long noncoding (lnc)RNAs have recently emerged as key regulators of gene expression. Here, we performed high-depth poly(A)+ RNA sequencing across multiple clonal populations of mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs) to comprehensively identify differentially regulated lncRNAs. We establish a biologically robust profile of lncRNA expression in these two cell types and further confirm that the majority of these lncRNAs are enriched in the nucleus. Applying weighted gene co-expression network analysis, we define a group of lncRNAs that are tightly associated with the pluripotent state of ESCs. Among these, we show that acute depletion of PAT-14 using antisense oligonucleotides impacts the differentiation- and development-associated gene expression program of ESCs. Furthermore, we demonstrate that Firre, a lncRNA highly enriched in the nucleoplasm and previously reported to mediate chromosomal contacts in ESCs, controls a network of genes related to RNA processing. Together, we provide a comprehensive, up-to-date and high resolution compilation of lncRNA expression in ESCs and NPCs and show that nuclear lncRNAs are tightly integrated into the regulation of ESC gene expression

Flexible Session Management in a Distributed Environment

Many secure communication libraries used by distributed systems, such as SSL, TLS, and Kerberos, fail to make a clear distinction between the authentication, session, and communication layers. In this paper we introduce CEDAR, the secure communication library used by the Condor High Throughput Computing software, and present the advantages to a distributed computing system resulting from CEDAR's separation of these layers. Regardless of the authentication method used, CEDAR establishes a secure session key, which has the flexibility to be used for multiple capabilities. We demonstrate how a layered approach to security sessions can avoid round-trips and latency inherent in network authentication. The creation of a distinct session management layer allows for optimizations to improve scalability by way of delegating sessions to other components in the system. This session delegation creates a chain of trust that reduces the overhead of establishing secure connections and enables centralized enforcement of system-wide security policies. Additionally, secure channels based upon UDP datagrams are often overlooked by existing libraries; we show how CEDAR's structure accommodates this as well. As an example of the utility of this work, we show how the use of delegated security sessions and other techniques inherent in CEDAR's architecture enables US CMS to meet their scalability requirements in deploying Condor over large-scale, wide-area grid systems

BIOHYBRID – Biohybrid templates for peripheral nerve regeneration

[Excerpt] Peripheral nerve injuries represent a major cause for morbidity and disability in affected patients and cause substantial costs for society in a global perspective. It has been estimated that peripheral nerve injuries affect 2.8% of trauma patients,many of whom acquire life-long disability (Noble et al., 1998). With respect to an incidence of nerve injuries of 13.9/100,000 inhabitants per year (Asplund et al., 2009) and the number of inhabitants in the EU (495,000,000 inhabitants in 2007), the number of peripheral nerve injuries requiring repair and reconstruction, excluding nerve injuries by amputations, may be 70,000 annually only in EU countries. Related to peripheral nerve injuries, the costs for society are substantial and consist of direct (costs for surgery, outpatient visits and rehabilitation) and indirect (lost production) costs. Individual median and ulnar nerve injuries in the forearm have total costs of EUR 51,000 and 31,000, respectively, where around 85% of the costs consist of loss of production (Rosberg et al., 2005), still excluding costs for adjusted quality of life ( Eriksson et al., 2011) . Thus, one may estimate that the annual costs only in the EU may be as high as EUR 2.2 billion, indicating that improved treatment strategies for peripheral nerve injuries may not only improve the situation for patients, but may also significantly reduce costs for society. [...](undefined

Egulating gene expression through RNA nuclear retention

Multiple mechanisms have evolved to regulate the eukaryotic genome. We have identified CTN-RNA, a mouse tissue-specific w8 kb nuclear-retained poly(A) + RNA that regulates the level of its protein-coding partner. CTN-RNA is transcribed from the protein-coding mouse cationic amino acid transporter 2 (mCAT2) gene through alternative promoter and poly(A) site usage. CTN-RNA is diffusely distributed in nuclei and is also localized to paraspeckles. The 3�UTR of CTN-RNA contains elements for adenosine-to-inosine editing, involved in its nuclear retention. Interestingly, knockdown of CTN-RNA also downregulates mCAT2 mRNA. Under stress, CTN-RNA is posttranscriptionally cleaved to produce protein-coding mCAT2 mRNA. Our findings reveal a role of the cell nucleus in harboring RNA molecules that are not immediately needed to produce proteins but whose cytoplasmic presence is rapidly required upon physiologic stress. This mechanism of action highlights an important paradigm for the role of a nuclear-retained stable RNA transcript in regulating gene expression

Repowering with clean coal technologies

Repowering with clean coal technology can offer significant advantages, including lower heat rates and production costs, environmental compliance, incremental capacity increases, and life extension of existing facilities. Significant savings of capital costs can result by refurbishing and reusing existing sites and infrastructure relative to a greenfield siting approach. This paper summarizes some key results of a study performed by Parsons Power Group, Inc., under a contract with DOE/METC, which investigates many of the promising advanced power generation technologies in a repowering application. The purpose of this study was to evaluate the technical and economic results of applying each of a menu of Clean Coal Technologies in a repowering of a hypothetical representative fossil fueled power station. Pittsburgh No. 8 coal is used as the fuel for most of the cases evaluated herein, as well as serving as the fuel for the original unrepowered station. The steam turbine-generator, condenser, and circulating water system are refurbished and reused in this study, as is most of the existing site infrastructure such as transmission lines, railroad, coal yard and coal handling equipment, etc. The technologies evaluated in this study consisted of an atmospheric fluidized bed combustor, several varieties of pressurized fluid bed combustors, several types of gasifiers, a refueling with a process derived fuel, and, for reference, a natural gas fired combustion turbine-combined cycle

Developing Healthy Kids in Healthy Communities: Eight Evidence-based Strategies for Preventing High-risk Behaviour.

Australian youth engage in behaviour that threatens their health and wellbeing. National surveys report that about a third of young Australians have tried an illicit drug. High rates of substance use and risky sexual behaviour among young Australians suggest that effective prevention efforts based on empirical evidence need to be expanded. Church-associated organisations are an untapped resource that could be used to improve the health and welfare of young people. We describe eight evidence-based elements to consider in designing strategies to prevent high-risk behaviour in young people

Investigation of cell adhesion in chitosan membranes for peripheral nerve regeneration

Peripheral nerve injuries have produced major concerns in regenerative medicine for several years, as the recovery of normal nerve function continues to be a significant clinical challenge. Chitosan (CHT), because of its good biocompatibility, biodegradability and physicochemical properties, has been widely used as a biomaterial in tissue engineering scaffolding. In this study, CHT membranes were produced with three different Degrees of Acetylation (DA), envisioning its application in peripheral nerve regeneration. The three CHT membranes (DA I: 1%, DA II: 2%, DA III: 5%) were extensively characterized and were found to have a smooth and flat surface, with DA III membrane having slightly higher roughness and surface energy. All the membranes presented suitable mechanical properties and did not show any signs of calcification after SBF test. Biodegradability was similar for all samples, and adequate to physically support neurite outgrowth. The in vitro cell culture results indicate selective cell adhesion. The CHT membranes favoured Schwann cells invasion and proliferation, with a display of appropriate cytoskeletal morphology. At the same time they presented low fibroblast infiltration. This fact may be greatly beneficial for the prevention of fibrotic tissue formation, a common phenomenon impairing peripheral nerve regeneration. The great deal of results obtained during this work permitted to select the formulation with the greatest potential for further biological tests.This work has received funding from the European Community's Seventh Framework Programme (FP7-HEALTH-2011) under grant agreement no 278612 (BIOHYBRID). This study was also funded by European Union's FP7 Programme under grant agreement no REGPOT-CT2012-316331-POLARIS.The authors thank the chitosan raw material provided by Altakitin S.A., (Lisboa, Portugal). We are further thankful to Silke Fischer, Natascha Heidrich, Kerstin Kuhlemann, Jennifer Metzen, Hildegard Streich and Maike Wesemann (all from the Institute of Neuroanatomy, Hannover Medical School) for their technical support