The Configurable SAT Solver Challenge (CSSC)

It is well known that different solution strategies work well for different types of instances of hard combinatorial problems. As a consequence, most solvers for the propositional satisfiability problem (SAT) expose parameters that allow them to be customized to a particular family of instances. In the international SAT competition series, these parameters are ignored: solvers are run using a single default parameter setting (supplied by the authors) for all benchmark instances in a given track. While this competition format rewards solvers with robust default settings, it does not reflect the situation faced by a practitioner who only cares about performance on one particular application and can invest some time into tuning solver parameters for this application. The new Configurable SAT Solver Competition (CSSC) compares solvers in this latter setting, scoring each solver by the performance it achieved after a fully automated configuration step. This article describes the CSSC in more detail, and reports the results obtained in its two instantiations so far, CSSC 2013 and 2014

TRX SUSPENSION TRAINING METHOD AND STATIC BALANCE IN JUNIOR BASKETBALL PLAYERS

Introduction: Described as an ingenious physical preparation method, suspension training was developed based on the concept of instability. This study was aimed at finding out if three weeks of TRX suspension training were enough to enhance static balance in junior basketball players. Materials and methods: Twelve male junior basketball players from the “U” Mobitelco club of Cluj-Napoca participated in this research. The subjects were randomly divided into two groups: Experimental (n=6) and Control (n=6). For three weeks, three TRX suspension training sessions per week were performed by all athletes from the Experimental group. Anthropometric measures (weight, height and arm span) were performed on all participants prior to suspension training. Static balance, assessed as the excursion of the center of pressure (COP), was measured with an AMTI® force platform (model BP400600, Advanced Mechanical Technology Inc., Watertown, MA, USA) on both legs, before and after the training period. Results: Mean age of participants was 13.33 ± 0.49 years, mean height was 173.05 ± 6.56 cm, mean weight was 59.14 ± 24.38 kg, and mean arm span was 171.58 ± 8.85 cm. No significant changes were found between the mean values of chosen COP parameters corresponding to the Experimental and to the Control group, respectively. Conclusions: Three weeks of TRX suspension training seem to be insufficient for modifications to occur in the static balance of junior basketball players. For future studies, a longer training period should be considered in order to see if there are any ways in which the TRX method affects static balance in junior athletes. Metoda de antrenament TRX și echilibrul static la baschetbaliști juniori. Introducere: Descrisă ca o metodă ingenioasă de pregătire fizică, antrenamentul realizat prin suspensie a fost dezvoltat pe baza conceptului de instabilitate. Acest studiu a avut ca scop investigarea rezultatelor unui program de antrenament cu durata de trei săptămâni obținut cu ajutorul sistemului TRX asupra echilibrului static al baschetbaliștilor juniori. Materiale și metode: La acest studiu au participat doisprezece baschetbaliști juniori din cadrul clubului “U” Mobitelco din Cluj-Napoca. Participanții au fost împărțiți aleatoriu în două grupe: Experimentală (n=6) și de Control (n=6). Timp de trei săptămâni, sportivii din grupa Experimentală au efectuat câte trei antrenamente pe săptămână utilizând TRX-ul. Înainte de perioada de antrenamente, toții subiecții studiului au participat la măsurători antropometrice (înălțime, greutate, anvergura brațelor). Echilibrul static, evaluat ca excursia centrului de presiune (CDP), a fost măsurat cu o platformă AMTI® (model BP400600, Advanced Mechanical Technology Inc., Watertown, MA, USA) în cazul ambelor membre inferioare, atât înainte cât și după perioada de antrenamente. Rezultate: Vârsta medie a participanților a fost de 13.33 ± 0.49 ani, înălțimea medie a fost de 173.05 ± 6.56 cm, greutatea medie a fost de 59.14 ± 24.38 kg și anvergura medie a brațelor a fost de 171.58 ± 8.85 cm. Nu s-au observat diferențe semnificative din punct de vedere statistic între valorile medii ale parametrilor centrului de presiune corespunzători valorilor măsurate în cazul grupelor Experimentală și, respectiv, de Control. Concluzii: Trei săptămâni de antrenament cu metoda TRX par a fi insuficiente pentru a fi observate modificări în ceea ce privește echilibrul static al baschetbaliștilor juniori. Pe viitor, ar trebui luată în calcul o perioadă de antrenament mai lungă pentru a investiga dacă există vreo modalitate în care antrenamentul cu TRX afectează echilibrul static al sportivilor juniori. Cuvinte cheie: echilibru static, centru de presiune, metoda de antrenament TRX, jucători de baschet junior

The genetic architecture underlying prey-dependent performance in a microbial predator

Natural selection should favour generalist predators that outperform specialists across all prey types. Two genetic solutions could explain why intraspecific variation in predatory performance is, nonetheless, widespread: mutations beneficial on one prey type are costly on another (antagonistic pleiotropy), or mutational effects are prey-specific, which weakens selection, allowing variation to persist (relaxed selection). To understand the relative importance of these alternatives, we characterised natural variation in predatory performance in the microbial predator Dictyostelium discoideum. We found widespread nontransitive differences among strains in predatory success across different bacterial prey, which can facilitate stain coexistence in multi-prey environments. To understand the genetic basis, we developed methods for high throughput experimental evolution on different prey (REMI-seq). Most mutations (~77%) had prey-specific effects, with very few (~4%) showing antagonistic pleiotropy. This highlights the potential for prey-specific effects to dilute selection, which would inhibit the purging of variation and prevent the emergence of an optimal generalist predator

Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology

Background Genomes can be sequenced with relative ease, but ascribing gene function remains a major challenge. Genetically tractable model systems are crucial to meet this challenge. One powerful model is the social amoeba Dictyostelium discoideum, a eukaryotic microbe widely used to study diverse questions in the cell, developmental and evolutionary biology. Results We describe REMI-seq, an adaptation of Tn-seq, which allows high throughput, en masse, and quantitative identification of the genomic site of insertion of a drug resistance marker after restriction enzyme-mediated integration. We use REMI-seq to develop tools which greatly enhance the efficiency with which the sequence, transcriptome or proteome variation can be linked to phenotype in D. discoideum. These comprise (1) a near genome-wide resource of individual mutants and (2) a defined pool of ‘barcoded’ mutants to allow large-scale parallel phenotypic analyses. These resources are freely available and easily accessible through the REMI-seq website that also provides comprehensive guidance and pipelines for data analysis. We demonstrate that integrating these resources allows novel regulators of cell migration, phagocytosis and macropinocytosis to be rapidly identified. Conclusions We present methods and resources, generated using REMI-seq, for high throughput gene function analysis in a key model system

A new mechanism for Cannabidiol in regulating the one-carbon cycle and methionine levels in Dictyostelium and in mammalian epilepsy models

Background and Purpose: Epidiolex, a form of highly purified cannabidiol (CBD) derived from Cannabis plants has demonstrated seizure control activity in patients with Dravet syndrome, without a fully elucidated mechanism of action. We have employed an unbiased approach to investigate this mechanism at a cellular level. Experimental Approach: We use a tractable biomedical model organism, Dictyostelium, to identify protein controlling the effect of CBD and characterize this mechanism. We then translate these results to a Dravet Syndrome mouse model and an acute in vitro seizure model. Key Results: CBD activity is partially dependent upon the mitochondrial glycine cleavage system component, GcvH1 in Dictyostelium, orthologous to the human GCSH protein, which is functionally linked to folate one-carbon metabolism (FOCM). Analysis of FOCM components identified a mechanism for CBD in directly inhibiting methionine synthesis. Analysis of brain tissue from a Dravet syndrome mouse model also showed drastically altered levels of one-carbon components including methionine, and an in vitro rat seizure model showed an elevated level of methionine that is attenuated following CBD treatment. Conclusions and Implications: Our results suggest a novel mechanism for CBD in the regulating methionine levels, and identify altered one-carbon metabolism in Dravet syndrome and seizure activity. voltage-dependent anion selective channel proteins, VDAC1

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. Conclusion We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.Peer reviewe