miRPlant : an integrated tool for identification of plant miRNA from RNA sequencing data

Background Small RNA sequencing is commonly used to identify novel miRNAs and to determine their expression levels in plants. There are several miRNA identification tools for animals such as miRDeep, miRDeep2 and miRDeep*. miRDeep-P was developed to identify plant miRNA using miRDeep’s probabilistic model of miRNA biogenesis, but it depends on several third party tools and lacks a user-friendly interface. The objective of our miRPlant program is to predict novel plant miRNA, while providing a user-friendly interface with improved accuracy of prediction. Result We have developed a user-friendly plant miRNA prediction tool called miRPlant. We show using 16 plant miRNA datasets from four different plant species that miRPlant has at least a 10% improvement in accuracy compared to miRDeep-P, which is the most popular plant miRNA prediction tool. Furthermore, miRPlant uses a Graphical User Interface for data input and output, and identified miRNA are shown with all RNAseq reads in a hairpin diagram. Conclusions We have developed miRPlant which extends miRDeep* to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants. miRPlant does not require any third party tools such as mapping or RNA secondary structure prediction tools. miRPlant is also the first plant miRNA prediction tool that dynamically plots miRNA hairpin structure with small reads for identified novel miRNAs. This feature will enable biologists to visualize novel pre-miRNA structure and the location of small RNA reads relative to the hairpin. Moreover, miRPlant can be easily used by biologists with limited bioinformatics skills

Ab initio structure prediction methods for battery materials a review of recent computational efforts to predict the atomic level structure and bonding in materials for rechargeable batteries

Portable electronic devices, electric vehicles and stationary energy storage applications, which encourage carbon-neutral energy alternatives, are driving demand for batteries that have concurrently higher energy densities, faster charging rates, safer operation and lower prices. These demands can no longer be met by incrementally improving existing technologies but require the discovery of new materials with exceptional properties. Experimental materials discovery is both expensive and time consuming: before the efficacy of a new battery material can be assessed, its synthesis and stability must be well-understood. Computational materials modelling can expedite this process by predicting novel materials, both in stand-alone theoretical calculations and in tandem with experiments. In this review, we describe a materials discovery framework based on density functional theory (DFT) to predict the properties of electrode and solid-electrolyte materials and validate these predictions experimentally. First, we discuss crystal structure prediction using the Ab initio random structure searching (AIRSS) method. Next, we describe how DFT results allow us to predict which phases form during electrode cycling, as well as the electrode voltage profile and maximum theoretical capacity. We go on to explain how DFT can be used to simulate experimentally measurable properties such as nuclear magnetic resonance (NMR) spectra and ionic conductivities. We illustrate the described workflow with multiple experimentally validated examples: materials for lithium-ion and sodium-ion anodes and lithium-ion solid electrolytes. These examples highlight the power of combining computation with experiment to advance battery materials research.(1) Gates Cambridge Trust, University of Cambridge, UK (2) EPSRC Centre for Doctoral Training in Computational Methods for Materials Science, UK, Grant No. EP/L015552/1. (3) Winton Programme for the Physics of Sustainability, University of Cambridge, UK (4) Sims Fund, University of Cambridge, UK (5) EPSRC Grant No. EP/P003532/1 (6) EPSRC Collaborative Computational Projects on the Electronic Structure of Condensed Matter (CCP9), Grant No. EP/M022595/1, and NMR crystallography, Grant No. EP/M022501/1 (7) Computing resources on the Tier 1 resource ARCHER were provided through the UKCP EPSRC High-End computational consortium (EP/P022561/1) and on the Tier 2 resources HPC Midlands+ (EP/P020232/1) and CSD3 (EP/P020259/1)

Mean-Payoff Optimization in Continuous-Time Markov Chains with Parametric Alarms

Continuous-time Markov chains with alarms (ACTMCs) allow for alarm events that can be non-exponentially distributed. Within parametric ACTMCs, the parameters of alarm-event distributions are not given explicitly and can be subject of parameter synthesis. An algorithm solving the $\varepsilon$-optimal parameter synthesis problem for parametric ACTMCs with long-run average optimization objectives is presented. Our approach is based on reduction of the problem to finding long-run average optimal strategies in semi-Markov decision processes (semi-MDPs) and sufficient discretization of parameter (i.e., action) space. Since the set of actions in the discretized semi-MDP can be very large, a straightforward approach based on explicit action-space construction fails to solve even simple instances of the problem. The presented algorithm uses an enhanced policy iteration on symbolic representations of the action space. The soundness of the algorithm is established for parametric ACTMCs with alarm-event distributions satisfying four mild assumptions that are shown to hold for uniform, Dirac and Weibull distributions in particular, but are satisfied for many other distributions as well. An experimental implementation shows that the symbolic technique substantially improves the efficiency of the synthesis algorithm and allows to solve instances of realistic size.Comment: This article is a full version of a paper accepted to the Conference on Quantitative Evaluation of SysTems (QEST) 201

Renal angiomyolipoma presenting with massive retroperitoneal haemorrhage due to deranged clotting factors: a case report

BACKGROUND: Angiomyolipomata of the kidney are unusual lesions composed of abnormal vasculature, smooth muscle, and adipose elements. They may be associated with tuberous sclerosis and occasionally present with flank pain, a palpable mass, and gross haematuria. As angiomyolipomata grow their risk of bleeding increases, with a greater than 50% chance of significant bleeding in lesions > 4 cm; anticoagulant therapy accentuates this risk. CASE PRESENTATION: A case of massive retroperitoneal haemorrhage in a patient on warfarin is presented. The underlying diagnosis of renal angiomyolipoma was diagnosed based on CT findings. Emergency resuscitation and selective interpolar arterial embolization was performed which saved the patient's life as well as his kidney. CONCLUSION: This case illustrates the clinical scenario of massive retroperitoneal haemorrhage in an anticoagulated patient with renal angiomyolipomata. In the emergent situation, adequate resuscitation along ABC principles, as well as control of haemorrhage with either nephrectomy (partial or radical), non-selective renal arterial embolization, or selective embolization of the feeding vessel(s), is necessary. For this to occur, it is imperative to consider the diagnosis early in warfarinized patients (and others at risk of bleeding) who present with abdominal pain. The authors hope this case report highlights to readers the clinical scenario of massive retroperitoneal haemorrhage in anticoagulated patients with renal angiomyolipomata so that they can deal appropriately with such presentations

Priming Analogical Reasoning with False Memories

Like true memories, false memories are capable of priming answers to insight-based problems. Recent research has attempted to extend this paradigm to more advanced problem-solving tasks, including those involving verbal analogical reasoning. However, these experiments are constrained inasmuch as problem solutions could be generated via spreading activation mechanisms (much like false memories themselves) rather than using complex reasoning processes. In three experiments we examined false memory priming of complex analogical reasoning tasks in the absence of simple semantic associations. In Experiment 1, we demonstrated the robustness of false memory priming in analogical reasoning when backward associative strength among the problem terms was eliminated. In Experiments 2a and 2b, we extended these findings by demonstrating priming on newly created homonym analogies that can only be solved by inhibiting semantic associations within the analogy. Overall, the findings of the present experiments provide evidence that the efficacy of false memory priming extends to complex analogical reasoning problems

Divergent mathematical treatments in utility theory

In this paper I study how divergent mathematical treatments affect mathematical modelling, with a special focus on utility theory. In particular I examine recent work on the ranking of information states and the discounting of future utilities, in order to show how, by replacing the standard analytical treatment of the models involved with one based on the framework of Nonstandard Analysis, diametrically opposite results are obtained. In both cases, the choice between the standard and nonstandard treatment amounts to a selection of set-theoretical parameters that cannot be made on purely empirical grounds. The analysis of this phenomenon gives rise to a simple logical account of the relativity of impossibility theorems in economic theory, which concludes the paper

Flavor in Minimal Conformal Technicolor

We construct a complete, realistic, and natural UV completion of minimal conformal technicolor that explains the origin of quark and lepton masses and mixing angles. As in "bosonic technicolor", we embed conformal technicolor in a supersymmetric theory, with supersymmetry broken at a high scale. The exchange of heavy scalar doublets generates higher-dimension interactions between technifermions and quarks and leptons that give rise to quark and lepton masses at the TeV scale. Obtaining a sufficiently large top quark mass requires strong dynamics at the supersymmetry breaking scale in both the top and technicolor sectors. This is natural if the theory above the supersymmetry breaking also has strong conformal dynamics. We present two models in which the strong top dynamics is realized in different ways. In both models, constraints from flavor-changing effects can be easily satisfied. The effective theory below the supersymmetry breaking scale is minimal conformal technicolor with an additional light technicolor gaugino. We argue that this light gaugino is a general consequence of conformal technicolor embedded into a supersymmetric theory. If the gaugino has mass below the TeV scale it will give rise to an additional pseudo Nambu-Goldstone boson that is observable at the LHC.Comment: 37 pages; references adde

Fistulotomy and drainage of deep postanal space abscess in the treatment of posterior horseshoe fistula

BACKGROUND: Posterior horseshoe fistula with deep postanal space abscess is a complex disease. Most patients have a history of anorectal abscess drainage or surgery for fistula-in-ano. METHODS: Twenty-five patients who underwent surgery for posterior horseshoe fistula with deep postanal space abscess were analyzed retrospectively with respect to age, gender, previous surgery for fistula-in-ano, number of external openings, diagnostic studies, concordance between preoperative studies and operative findings for the extent of disease, operating time, healing time, complications, and recurrence. RESULTS: There were 22 (88%) men and 3 (12%) women with a median age of 37 (range, 25–58) years. The median duration of disease was 13 (range, 3–96) months. There was one external opening in 12 (48%) patients, 2 in 8 (32%), 3 in 4 (16%), and 4 in 1 (4%). Preoperative diagnosis of horseshoe fistula was made by contrast fistulography in 4 (16%) patients, by ultrasound in 3 (12%), by magnetic resonance imaging in 6 (24%), and by physical examination only in the remainder (48%). The mean ± SD operating time was 47 ± 10 min. The mean ± SD healing time was 12 ± 3 weeks. Three of the 25 patients (12%) had diabetes mellitus type II. Nineteen (76%) patients had undergone previous surgery for fistula-in-ano, while five (20%) had only perianal abscess drainage. Neither morbidity nor mortality developed. All patients were followed up for a median of 35 (range, 6–78) months and no recurrence was observed. CONCLUSIONS: Fistulotomy of the tracts along the arms of horseshoe fistula and drainage of the deep postanal space abscess with posterior midline incision that severs both the lower edge of the internal sphincter and the subcutaneous external sphincter and divides the superficial external sphincter into halves gives excellent results with no recurrence. When it is necessary, severing the halves of the superficial external sphincter unilaterally or even bilaterally in the same session does not result in anal incontinence. Close follow-up of patients until the wounds completely healed is essential in the prevention of premature wound closure and recurrence

Comparison of the CDC Backpack aspirator and the Prokopack aspirator for sampling indoor- and outdoor-resting mosquitoes in southern Tanzania.

BACKGROUND\ud \ud Resting mosquitoes can easily be collected using an aspirating device. The most commonly used mechanical aspirator is the CDC Backpack aspirator. Recently, a simple, and low-cost aspirator called the Prokopack has been devised and proved to have comparable performance. The following study evaluates the Prokopack aspirator compared to the CDC backpack aspirator when sampling resting mosquitoes in rural Tanzania.\ud \ud METHODS\ud \ud Mosquitoes were sampled in- and outdoors of 48 typical rural African households using both aspirators. The aspirators were rotated between collectors and households in a randomized, Latin Square design. Outdoor collections were performed using artificial resting places (large barrel and car tyre), underneath the outdoor kitchen (kibanda) roof and from a drop-net. Data were analysed with generalized linear models.\ud \ud RESULTS\ud \ud The number of mosquitoes collected using the CDC Backpack and the Prokopack aspirator were not significantly different both in- and outdoors (indoors p = 0.735; large barrel p = 0.867; car tyre p = 0.418; kibanda p = 0.519). The Prokopack was superior for sampling of drop-nets due to its smaller size. The number mosquitoes collected per technician was more consistent when using the Prokopack aspirator. The Prokopack was more user-friendly: technicians preferred using the it over the CDC backpack aspirator as it weighs considerably less, retains its charge for longer and is easier to manoeuvre.\ud \ud CONCLUSIONS\ud \ud The Prokopack proved in the field to be more advantageous than the CDC Backpack aspirator. It can be self assembled using simple, low-cost and easily attainable materials. This device is a useful tool for researchers or vector-control surveillance programs operating in rural Africa, as it is far simpler and quicker than traditional means of sampling resting mosquitoes. Further longitudinal evaluations of the Prokopack aspirator versus the gold standard pyrethrum spray catch for indoor resting catches are recommended

Quality of Life Changes Following Peripheral Blood Stem Cell Transplantation and Participation in a Mixed-Type, Moderate-intensity, Exercise Program

Summary:The purpose of this investigation was to evaluate the impact of undertaking peripheral blood stem cell transplantation (PBST) on quality of life (QoL), and to determine the effect of participating in a mixed-type, moderate-intensity exercise program on QoL. It was also an objective to determine the relationship between peak aerobic capacity and QoL in PBST patients. QoL was assessed via the CARES questionnaire and peak aerobic capacity by a maximal graded treadmill test, pretransplant (PI), post transplant (PII) and following a 12-week intervention period (PIII). At PII, 12 patients were divided equally into a control or exercise intervention group. Undergoing a PBST was associated with a statistically but not clinically significant decline in QoL (P<0.05). Following the intervention, exercising patients demonstrated an improved QoL when compared with pretransplant ratings (P<0.01) and nonexercising transplant patients (P<0.05). Moreover, peak aerobic capacity and QoL were correlated (P<0.05). The findings demonstrated that exercise participation following oncology treatment is associated with a reduction in the number and severity of endorsed problems, which in turn leads to improvements in global, physical and psychosocial QoL. Furthermore, a relationship between fitness and QoL exists, with those experiencing higher levels of fitness also demonstrating higher QoL.Bone Marrow Transplantation (2004) 33, 553-558. doi:10.1038/sj.bmt.1704378 Published online 12 January 200