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/

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

Agent Programming with Declarative Goals

A long and lasting problem in agent research has been to close the gap between agent logics and agent programming frameworks. The main reason for this problem of establishing a link between agent logics and agent programming frameworks is identified and explained by the fact that agent programming frameworks have not incorporated the concept of a `declarative goal'. Instead, such frameworks have focused mainly on plans or `goals-to-do' instead of the end goals to be realised which are also called `goals-to-be'. In this paper, a new programming language called GOAL is introduced which incorporates such declarative goals. The notion of a `commitment strategy' - one of the main theoretical insights due to agent logics, which explains the relation between beliefs and goals - is used to construct a computational semantics for GOAL. Finally, a proof theory for proving properties of GOAL agents is introduced. Thus, we offer a complete theory of agent programming in the sense that our theory provides both for a programming framework and a programming logic for such agents. An example program is proven correct by using this programming logic

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

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

A habituation account of change detection in same/different judgments

We investigated the basis of change detection in a short-term priming task. In two experiments, participants were asked to indicate whether or not a target word was the same as a previously presented cue. Data from an experiment measuring magnetoencephalography failed to find different patterns for “same” and “different” responses, consistent with the claim that both arise from a common neural source, with response magnitude defining the difference between immediate novelty versus familiarity. In a behavioral experiment, we tested and confirmed the predictions of a habituation account of these judgments by comparing conditions in which the target, the cue, or neither was primed by its presentation in the previous trial. As predicted, cue-primed trials had faster response times, and target-primed trials had slower response times relative to the neither-primed baseline. These results were obtained irrespective of response repetition and stimulus–response contingencies. The behavioral and brain activity data support the view that detection of change drives performance in these tasks and that the underlying mechanism is neuronal habituation

Challenges of Profile Likelihood Evaluation in Multi-Dimensional SUSY Scans

Statistical inference of the fundamental parameters of supersymmetric theories is a challenging and active endeavor. Several sophisticated algorithms have been employed to this end. While Markov-Chain Monte Carlo (MCMC) and nested sampling techniques are geared towards Bayesian inference, they have also been used to estimate frequentist confidence intervals based on the profile likelihood ratio. We investigate the performance and appropriate configuration of MultiNest, a nested sampling based algorithm, when used for profile likelihood-based analyses both on toy models and on the parameter space of the Constrained MSSM. We find that while the standard configuration is appropriate for an accurate reconstruction of the Bayesian posterior, the profile likelihood is poorly approximated. We identify a more appropriate MultiNest configuration for profile likelihood analyses, which gives an excellent exploration of the profile likelihood (albeit at a larger computational cost), including the identification of the global maximum likelihood value. We conclude that with the appropriate configuration MultiNest is a suitable tool for profile likelihood studies, indicating previous claims to the contrary are not well founded.Comment: 21 pages, 9 figures, 1 table; minor changes following referee report. Matches version accepted by JHE

Phase-slip induced dissipation in an atomic Bose-Hubbard system

Phase slips play a primary role in dissipation across a wide spectrum of bosonic systems, from determining the critical velocity of superfluid helium to generating resistance in thin superconducting wires. This subject has also inspired much technological interest, largely motivated by applications involving nanoscale superconducting circuit elements, e.g., standards based on quantum phase-slip junctions. While phase slips caused by thermal fluctuations at high temperatures are well understood, controversy remains over the role of phase slips in small-scale superconductors. In solids, problems such as uncontrolled noise sources and disorder complicate the study and application of phase slips. Here we show that phase slips can lead to dissipation for a clean and well-characterized Bose-Hubbard (BH) system by experimentally studying transport using ultra-cold atoms trapped in an optical lattice. In contrast to previous work, we explore a low velocity regime described by the 3D BH model which is not affected by instabilities, and we measure the effect of temperature on the dissipation strength. We show that the damping rate of atomic motion-the analogue of electrical resistance in a solid-in the confining parabolic potential fits well to a model that includes finite damping at zero temperature. The low-temperature behaviour is consistent with the theory of quantum tunnelling of phase slips, while at higher temperatures a cross-over consistent with the transition to thermal activation of phase slips is evident. Motion-induced features reminiscent of vortices and vortex rings associated with phase slips are also observed in time-of-flight imaging.Comment: published in Nature 453, 76 (2008

Demography and disorders of the French Bulldog population under primary veterinary care in the UK in 2013

Abstract Background Despite its Gallic name, the French Bulldog is a breed of both British and French origin that was first recognised by The Kennel Club in 1906. The French Bulldog has demonstrated recent rapid rises in Kennel Club registrations and is now (2017) the second most commonly registered pedigree breed in the UK. However, the breed has been reported to be predisposed to several disorders including ocular, respiratory, neurological and dermatological problems. The VetCompass™ Programme collates de-identified clinical data from primary-care veterinary practices in the UK for epidemiological research. Using VetCompass™ clinical data, this study aimed to characterise the demography and common disorders of the general population of French Bulldogs under veterinary care in the UK. Results French Bulldogs comprised 2228 (0.49%) of 445,557 study dogs under veterinary care during 2013. Annual proportional birth rates showed that the proportional ownership of French Bulldog puppies rose steeply from 0.02% of the annual birth cohort attending VetCompass™ practices in 2003 to 1.46% in 2013. The median age of the French Bulldogs overall was 1.3 years (IQR 0.6–2.5, range 0.0–13.0). The most common colours of French Bulldogs were brindle (solid or main) (32.36%) and fawn (solid or main) (29.9%). Of the 2228 French Bulldogs under veterinary care during 2013, 1612 (72.4%) had at least one disorder recorded. The most prevalent fine-level precision disorders recorded were otitis externa (14.0%, 95% CI: 12.6–15.5), diarrhoea (7.5%, 95% CI: 6.4–8.7), conjunctivitis (3.2%, 95% CI: 2.5–4.0), nails overlong (3.1%, 95% CI% 2.4–3.9) and skin fold dermatitis (3.0%, 95% CI% 2.3–3.8). The most prevalent disorder groups were cutaneous (17.9%, 95% CI: 16.3–19.6), enteropathy (16.7%, 95% CI: 15.2–18.3), aural (16.3%, 95% CI: 14.8–17.9), upper respiratory tract (12.7%, 95% CI: 11.3–14.1) and ophthalmological (10.5%, 95% CI: 9.3–11.9). Conclusions Ownership of French Bulldogs in the UK is rising steeply. This means that the disorder profiles reported in this study reflect a current young UK population and are likely to shift as this cohort ages. Otitis externa, diarrhoea and conjunctivitis were the most common disorders in French Bulldogs. Identification of health priorities based on VetCompass™ data can support evidence–based reforms to improve health and welfare within the breed