SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data

BACKGROUND: Next-generation parallel sequencing (NGS) allows the identification of viral pathogens by sequencing the small RNAs of infected hosts. Thus, viral genomes may be assembled from host immune response products without prior virus enrichment, amplification or purification. However, mapping of the vast information obtained presents a bioinformatics challenge. METHODS: In order to by pass the need of line command and basic bioinformatics knowledge, we develop a mapping software with a graphical interface to the assemblage of viral genomes from small RNA dataset obtained by NGS. SearchSmallRNA was developed in JAVA language version 7 using NetBeans IDE 7.1 software. The program also allows the analysis of the viral small interfering RNAs (vsRNAs) profile; providing an overview of the size distribution and other features of the vsRNAs produced in infected cells. RESULTS: The program performs comparisons between each read sequenced present in a library and a chosen reference genome. Reads showing Hamming distances smaller or equal to an allowed mismatched will be selected as positives and used to the assemblage of a long nucleotide genome sequence. In order to validate the software, distinct analysis using NGS dataset obtained from HIV and two plant viruses were used to reconstruct viral whole genomes. CONCLUSIONS: SearchSmallRNA program was able to reconstructed viral genomes using NGS of small RNA dataset with high degree of reliability so it will be a valuable tool for viruses sequencing and discovery. It is accessible and free to all research communities and has the advantage to have an easy-to-use graphical interface. AVAILABILITY AND IMPLEMENTATION: SearchSmallRNA was written in Java and is freely available at http://www.microbiologia.ufrj.br/ssrna/

Additive energy forward curves in a Heath-Jarrow-Morton framework

One of the peculiarities of power and gas markets is the delivery mechanism of forward contracts. The seller of a futures contract commits to deliver, say, power, over a certain period, while the classical forward is a financial agreement settled on a maturity date. Our purpose is to design a Heath-Jarrow-Morton framework for an additive, mean-reverting, multicommodity market consisting of forward contracts of any delivery period. The main assumption is that forward prices can be represented as affine functions of a universal source of randomness. This allows us to completely characterize the models which prevent arbitrage opportunities: this boils down to finding a density between a risk-neutral measure $\mathbb{Q}$, such that the prices of traded assets like forward contracts are true $\mathbb{Q}$-martingales, and the real world probability measure $\mathbb{P}$, under which forward prices are mean-reverting. The Girsanov kernel for such a transformation turns out to be stochastic and unbounded in the diffusion part, while in the jump part the Girsanov kernel must be deterministic and bounded: thus, in this respect, we prove two results on the martingale property of stochastic exponentials. The first allows to validate measure changes made of two components: an Esscher-type density and a Girsanov transform with stochastic and unbounded kernel. The second uses a different approach and works for the case of continuous density. We apply this framework to two models: a generalized Lucia-Schwartz model and a cross-commodity cointegrated market.Comment: 28 page

How cognitive enhancement can change our duties

This theoretical paper draws the scientific community's attention to how pharmacological cognitive enhancement may impact on society and law. Namely, if safe, reliable, and effective techniques to enhance mental performance are eventually developed, then this may under some circumstances impose new duties onto people in high-responsibility professions-e.g., surgeons or pilots-to use such substances to minimize risks of adverse outcomes or to increase the likelihood of good outcomes. By discussing this topic, we also hope to encourage scientists to bring their expertise to bear on this current public debate. © 2014 Santoni de Sio, Faulmüller and Vincent

Deformed wing virus prevalence and load in honeybees in South Africa

Deformed wing virus (DWV) is an emerging honeybee pathogen that has appeared across the globe in the past 40 years. When transmitted by the parasitic varroa mite, it has been associated with the collapse of millions of colonies throughout the Northern Hemisphere. However, despite the presence of the mite in the Southern Hemisphere, infested colonies survive. This study investigated the prevalence of DWV genotypes A, B and C along with their viral loads in South Africa and compared the fndings with recent data from Brazil, the UK and the USA. We found that DWV-B was the most prevalent genotype throughout South Africa, although the total DWV viral load was signifcantly lower (2.8E+07) than found in the Northern Hemisphere (2.8E+07 vs. 2.7E+10, p > 0.00001) and not signifcantly diferent to that found in Brazil (5E+06, p = 0.13). The diferences in viral load can be explained by the mite resistance in Brazil and South Africa, since mite-infested cells containing high viral loads are removed by the bees, thus lowering the colony’s viral burden. This behaviour is much less developed in the vast majority of honeybees in the Northern Hemisphere

Deadlock detection for actor-based coroutines

The actor-based language studied in this paper features asynchronous method calls and supports coroutines which allow for the cooperative scheduling of the method invocations belonging to an actor. We model the local behavior of an actor as a well-structured transition system by means of predicate abstraction and derive the decidability of the occurrence of deadlocks caused by the coroutine mode of method execution

Capgras-like syndrome in a patient with an acute urinary tract infection.

Delusional misidentification syndromes are a group of delusional phenomena in which patients misidentify familiar persons, objects, or themselves, believing that they have been replaced or transformed. In 25%-40% of cases, misidentification syndromes have been reported in association with organic illness. We report an acute episode of Capgras-like delusion lasting 8 days, focused on the idea that people were robots with human bodies, in association with an acute urinary infection. To our knowledge, this is the first case report associating urinary tract infection with Capgras-like syndrome. Awareness of the prevalence of delusional misidentification syndromes associated with acute medical illness should promote diligence on the part of clinicians in recognizing this disorder

Occurrence of deformed wing virus variants in the stingless Melipona subnitida and honey Apis mellifera bee populations in North Eastern Brazil

Deformed wing virus (DWV) is now a global insect pathogen. Brazilian stingless bees are a diverse group often managed in close proximity to honey bees. We investigated the prevalence and load of DWV in 33 stingless bees (Melipona subnitida) and 12 honey bees (Apis mellifera) colonies from NE Brazil. DWV was detected in all colonies with the A and C-variants dominating M. subnitida and A-variant in A. mellifera. Viral loads were 8.83E+07 and 7.19E+07 in M. subnitida and A. mellifera, respectively. On Fernando de Noronha island DWV is low (<1E+03) in honey bees, but we detected high loads (1.6E+08) in nine island M. subnitida colonies, indicating no viral spill-over of DWV has occurred during the past 34 years. Furthermore, the ubiquitous presence of the DWV-C variant in M. subnitida colonies, and rarity in A. mellifera, may suggest limited viral exchange between these two species

The surgical treatment of pituitary adenomas in the eighth decade

BACKGROUND The surgical treatment of pituitary adenomas in elderly patients (i.e., over 70 years of age) is a special problem because of the increased rate of perioperative complications and the reduced tolerance of postoperative fluid and electrolyte imbalance. Therefore, the unquestionable progress in the pharmacological and radiotherapy may not allow these patients the option of radical surgical treatment, We report our experience with the transsphenoidal procedure for pituitary adenomas in aged patients in an attempt to contribute to a better definition of the actual role of surgery. METHODS Transsphenoidal surgery was performed in 11 patients over 70 years of age affected by various histological types of pituitary micro- and macroadenomas, ranging from Hardy Grade I through IIIc, Special care was dedicated to the postoperative treatment, in particular to water and electrolyte balances, and to the immediate treatment of any pathological variation of these parameters. RESULTS We had no mortality and no postoperative adjunctive morbidity, All the patients recovered well from the operation with an average hospital stay of 20 days. The tumor removal was complete in six cases and partial in the remaining five. With an average follow-up of 2 years, we did observe only one case of symptomatic recurrence of the disease. CONCLUSIONS Transsphenoidal surgery in the elderly is feasible and quite safe in the hands of an experienced team, if special care is devoted to the preoperative selection of patients and to the postoperative treatment of fluid and electrolyte imbalanc

Combined Inflammatory and Metabolic Defects Reflected by Reduced Serum Protein Levels in Patients with Buruli Ulcer Disease

Buruli ulcer is a skin disease caused by Mycobacterium ulcerans that is spreading in tropical countries, with major public health and economic implications in West Africa. Multi-analyte profiling of serum proteins in patients and endemic controls revealed that Buruli ulcer disease down-regulates the circulating levels of a large array of inflammatory mediators, without impacting on the leukocyte composition of peripheral blood. Notably, several proteins contributing to acute phase reaction, lipid metabolism, coagulation and tissue remodelling were also impacted. Their down-regulation was selective and persisted after the elimination of bacteria with antibiotic therapy. It involved proteins with various functions and origins, suggesting that M. ulcerans infection causes global and chronic defects in the host’s protein metabolism. Accordingly, patients had reduced levels of total serum proteins and blood urea, in the absence of signs of malnutrition, or functional failure of liver or kidney. Interestingly, slow healers had deeper metabolic and coagulation defects at the start of antibiotic therapy. In addition to providing novel insight into Buruli ulcer pathogenesis, our study therefore identifies a unique proteomic signature for this disease