BayMiR: inferring evidence for endogenous miRNA-induced gene repression from mRNA expression profiles

BACKGROUND: Popular miRNA target prediction techniques use sequence features to determine the functional miRNA target sites. These techniques commonly ignore the cellular conditions in which miRNAs interact with their targets in vivo. Gene expression data are rich resources that can complement sequence features to take into account the context dependency of miRNAs. RESULTS: We introduce BayMiR, a new computational method, that predicts the functionality of potential miRNA target sites using the activity level of the miRNAs inferred from genome-wide mRNA expression profiles. We also found that mRNA expression variation can be used as another predictor of functional miRNA targets. We benchmarked BayMiR, the expression variation, Cometa, and the TargetScan “context scores” on two tasks: predicting independently validated miRNA targets and predicting the decrease in mRNA abundance in miRNA overexpression assays. BayMiR performed better than all other methods in both benchmarks and, surprisingly, the variation index performed better than Cometa and some individual determinants of the TargetScan context scores. Furthermore, BayMiR predicted miRNA target sets are more consistently annotated with GO and KEGG terms than similar sized random subsets of genes with conserved miRNA seed regions. BayMiR gives higher scores to target sites residing near the poly(A) tail which strongly favors mRNA degradation using poly(A) shortening. Our work also suggests that modeling multiplicative interactions among miRNAs is important to predict endogenous mRNA targets. CONCLUSIONS: We develop a new computational method for predicting the target mRNAs of miRNAs. BayMiR applies a large number of mRNA expression profiles and successfully identifies the mRNA targets and miRNA activities without using miRNA expression data. The BayMiR package is publicly available and can be readily applied to any mRNA expression data sets

Basics of Biosafety

This slide presentation reviews the basics of biosafety and the importance of assuring proper biosafety practices. The objectives of the presentation are to review regulations about biosafety, and the different biosafety levels; the biosafety facilities at Johnson Space Center; the usage and maintenance of the biosafety cabinet, the proper methods to handle biologically hazardous materials upon exposure, and the methods of cleanup in the event of a spill, and the training requirements that are mandated for personnel handling biologically hazardous materials

Modelling the visual response to an OUReP retinal prosthesis with photoelectric dye coupled to polyethylene film

Objective. Retinal prostheses have been developed to restore vision in blind patients suffering from diseases like retinitis pigmentosa. Approach. A new type of retinal prosthesis called the Okayama University-type retinal prosthesis (OUReP) was developed by chemically coupling photoelectric dyes to a polyethylene film surface. The prosthesis works by passively generating an electric potential when stimulated by light. However, the neurophysiological mechanism of how OUReP stimulates the degenerated retina is unknown. Main results. Here, we explore how the OUReP affects retinal tissues using a finite element model to solve for the potential inside the tissue and an active Hodgkin-Huxley model based on rat vision to predict the corresponding retinal bipolar response. Significance. We show that the OUReP is likely capable of eliciting responses in retinal bipolar cells necessary to generate vision under most ambient conditions

Broadcast encryption with dealership

In this paper, we introduce a new cryptographic primitive called broadcast encryption with dealership. This notion, which has never been discussed in the cryptography literature, is applicable to many realistic broadcast services, for example subscription-based television service. Specifically, the new primitive enables a dealer to bulk buy the access to some products (e.g., TV channels) from the broadcaster, and hence, it will enable the dealer to resell the contents to the subscribers with a cheaper rate. Therefore, this creates business opportunity model for the dealer. We highlight the security consideration in such a scenario and capture the security requirements in the security model. Subsequently, we present a concrete scheme, which is proven secure under the decisional bilinear Diffie-Hellman exponent and the Diffie-Hellman exponent assumptions

Advances in modern mental chronometry

Mental chronometry encompasses all aspects of time processing in the nervous system and constitutes a standard tool in many disciplines including theoretical and experimental psychology and human neuroscience. Mental chronometry has represented a fundamental approach to elucidate the time course of many cognitive phenomena and their underlying neural circuits over more than a century. Nowadays, mental chronometry continues evolving and expanding our knowledge, and our understanding of the temporal organization of the brain in combination with different neuroscience techniques and advanced methods in mathematical analysis. In research on mental chronometry, human reaction/responses times (RT) play a central role. Together with RTs, other topics in mental chronometry include vocal, manual and saccadic latencies, subjective time, psychological time, interval timing, time perception, internal clock, time production, time representation, time discrimination, time illusion, temporal summation, temporal integration, temporal judgment, redundant signals effect, perceptual, decision and motor time, etc. It is worth noting that there have been well over 37,000 full-length journal papers published in the last decade on a variety of topics related to simple and choice RTs, etc. This amounts to approximately 3800 papers per year, or roughly 10 papers per day (source: PubMed, similarly Thomson Reuters Web of Science). There are comprehensive reviews that deal extensively with the history of mental chronometry, experimental methods and paradigms, stochastic models, etc. as well as its relationship to other psychological and physiological variables, neuroscience methods and clinical applications

A case study of long-term CCA preservative leaching from treated hardwood poles in a humid tropical condition

Chromated copper arsenate (CCA)-treated Malaysian hardwoods have long been used as utility poles, posts, construction piles and motorway fencing in soil contact exposed to the threats of decay fungi and termites. Despite global concerns citing predominantly temperate conditions of long-term leaching of CCA toxic heavy metals from wood into surrounding soils and groundwater since the 1990’s, the preservative leaching severity in the tropics has been far less appreciated due to dearth of work in this area. In 2013 (after 30 years exposure), levels of total copper, chromium and arsenic within 20 treated hardwood poles of Sarawak and in soils surrounding these poles, installed in 1980 and 1981 at a plot located in Timber Research and Technical Training Centre, Kuching, Sarawak, Malaysia, were sampled. The ground is waterlogged after heavy rainfall. It is shown that there is insignificant variations of CCA salt retention in wood between 1300 cm above ground and 0-20 cm below ground (P<0.05). Nevertheless levels of these elements are significantly (P<0.05) elevated in soils surrounding, especially up to 25 mm away from, the poles than at distant sampling points (150 – 300 mm) from poles as well as at sites well away from the poles containing very low levels (<6 – 13.4 ppm) of such heavy metals. Metal levels were also highest at the soil surface directly in contact with the poles (0 – 50 mm soil depth position) and decreased with remaining 2 soil depth positions 150 – 200 mm and 300 – 350 mm. Mean extractable arsenic levels ranged from 14.5 to 100.1 ppm, chromium levels from 23.3 to 148.3 ppm and copper from 21.8 to 104.7 ppm. Results, rather than indicating relatively higher CCA leaching, concurred with that reported temperate experience and showed that soil closest to the treated poles are most contaminated, albeit slightly, after 30 years of in-ground exposure

Group-Oriented Fair Exchange of Signatures

In an Optimistic Fair Exchange (OFE) for digital signatures, two parties exchange their signatures fairly without requiring any online trusted third party. The third party is only involved when a dispute occurs. In all the previous work, OFE has been considered only in a setting where both of the communicating parties are individuals. There is little work discussing about the fair exchange between two \emph{groups} of users, though we can see that this is actually a common scenario in actual OFE applications. In this paper, we introduce a new variant of OFE, called \emph{Group-Oriented Optimistic Fair Exchange} (GOFE). A GOFE allows two users from two different groups to exchange signatures on behalf of their groups in a fair and anonymous manner. Although GOFE may be considered as a fair exchange for group signatures, it might be inefficient if it is constructed generically from a group signature scheme. Instead, we show that GOFE is \emph{backward compatible} to the Ambiguous OFE (AOFE). Also, we propose an efficient and concrete construction of GOFE, and prove its security under the security models we propose in this model. The security of the scheme relies on the decision linear assumption and strong Diffie-Hellman assumption under the random oracle model

Non-delegatable Identity-based Designated Verifier Signature

Designated verifier signature is a cryptographic primitive which allows a signer to convince a designated verifier of the validity of a statement but in the meanwhile prevents the verifier from transferring this conviction to any third party. In this work we present the \emph{first} identity-based designated verifier signature scheme that supports non-delegatability, and prove its security in the random oracle model, based on computational Diffie-Hellman assumption. Our scheme is perfectly non-transferable, and its non-delegatability follows the original definition proposed by Lipmaa et al. \cite{LipmaaWaBa05}