Prider: multiplexed primer design using linearly scaling approximation of set coverage

BackgroundDesigning oligonucleotide primers and probes is one of the key steps of various laboratory experiments such as multiplexed PCR or digital multiplexed ligation assays. When designing multiplexed primers and probes to complex, heterogeneous DNA data sets, an optimization problem can arise where the smallest number of oligonucleotides covering the largest diversity of the input dataset needs to be identified. Tools that provide this optimization in an efficient manner for large input data are currently lacking.ResultsHere we present Prider, an R package for designing primers and probes with a nearly optimal coverage for complex and large sequence sets. Prider initially prepares a full primer coverage of the input sequences, the complexity of which is subsequently reduced by removing components of high redundancy or narrow coverage. The primers from the resulting near-optimal coverage are easily accessible as data frames and their coverage across the input sequences can be visualised as heatmaps using Prider’s plotting function. Prider permits efficient design of primers to large DNA datasets by scaling linearly to increasing sequence data, regardless of the diversity of the dataset.ConclusionsPrider solves a recalcitrant problem in molecular diagnostics: how to cover a maximal sequence diversity with a minimal number of oligonucleotide primers or probes. The combination of Prider with highly scalable molecular quantification techniques will permit an unprecedented molecular screening capability with immediate applicability in fields such as clinical microbiology, epidemic virus surveillance or antimicrobial resistance surveillance.</p

Digital multiplex ligation assay for highly multiplexed screening of β-lactamase-encoding genes in bacterial isolates

Increasing incidence of antibiotic resistance in clinical and environmental settings calls for increased scalability in their surveillance. Current screening technologies are limited by the number of samples and genes that can easily be screened. We demonstrate here digital multiplex ligation assay (dMLA) as a low-cost targeted genomic detection workflow capable of highly-parallel screening of bacterial isolates for multiple target gene regions simultaneously. Here, dMLA is used for simultaneous detection of 1187 β-lactamase-encoding genes, including extended spectrum β-lactamase (ESBL) genes, in 74 bacterial isolates. We demonstrate dMLA as a light-weight and cost-efficient workflow which provides a highly scalable tool for antimicrobial resistance surveillance and is also adaptable to genetic screening applications beyond antibiotic resistance

Forest soil carbon stock estimates in a nationwide inventory: evaluating performance of the ROMULv and Yasso07 models in Finland

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The impact of music on learning and consolidation of novel words

Music can be a powerful mnemonic device, as shown by a body of literature demonstrating that listening to text sung to a familiar melody results in better memory for the words compared to conditions where they are spoken. Furthermore, patients with a range of memory impairments appear to be able to form new declarative memories when they are encoded in the form of lyrics in a song, while unable to remember similar materials after hearing them in the spoken modality. Whether music facilitates the acquisition of completely new information, such as new vocabulary, remains unknown. Here we report three experiments in which adult participants learned novel words in the spoken or sung modality. While we found no benefit of musical presentation on free recall or recognition memory of novel words, novel words learned in the sung modality were more strongly integrated in the mental lexicon compared to words learned in the spoken modality. This advantage for the sung words was only present when the training melody was familiar. The impact of musical presentation on learning therefore appears to extend beyond episodic memory and can be reflected in the emergence and properties of new lexical representations

Construction and Characterization of Synthetic Bacterial Community for Experimental Ecology and Evolution

Experimental microbial ecology and evolution have yielded foundational insights into ecological and evolutionary processes using simple microcosm setups and phenotypic assays with one- or two-species model systems. The fields are now increasingly incorporating more complex systems and exploration of the molecular basis of observations. For this purpose, simplified, manageable and well-defined multispecies model systems are required that can be easily investigated using culturing and high-throughput sequencing approaches, bridging the gap between simpler and more complex synthetic or natural systems. Here we address this need by constructing a completely synthetic 33 bacterial strain community that can be cultured in simple laboratory conditions. We provide whole-genome data for all the strains as well as metadata about genomic features and phenotypic traits that allow resolving individual strains by amplicon sequencing and facilitate a variety of envisioned mechanistic studies. We further show that a large proportion of the strains exhibit coexistence in co-culture over serial transfer for 48 days in the absence of any experimental manipulation to maintain diversity. The constructed bacterial community can be a valuable resource in future experimental work

Eye-tracking the time‐course of novel word learning and lexical competition in adults and children

Lexical competition is a hallmark of proficient, automatic word recognition. Previous research suggests that there is a delay before a new spoken word becomes engaged in this process, with sleep playing an important role. However, data from one method--the visual world paradigm--consistently show competition without a delay. We trained 42 adults and 40 children (aged 7-8) on novel word-object pairings, and employed this paradigm to measure the time-course of lexical competition. Fixations to novel objects upon hearing existing words (e.g., looks to the novel object biscal upon hearing “click on the biscuit”) were compared to fixations on untrained objects. Novel word-object pairings learned immediately before testing and those learned the previous day exhibited significant competition effects, with stronger competition for the previous day pairings for children but not adults. Crucially, this competition effect was significantly smaller for novel than existing competitors (e.g., looks to candy upon hearing “click on the candle”), suggesting that novel items may not compete for recognition like fully-fledged lexical items, even after 24 hours. Explicit memory (cued recall) was superior for words learned the day before testing, particularly for children; this effect (but not the lexical competition effects) correlated with sleep-spindle density. Together, the results suggest that different aspects of new word learning follow different time courses: visual world competition effects can emerge swiftly, but are qualitatively different from those observed with established words, and are less reliant upon sleep. Furthermore, the findings fit with the view that word learning earlier in development is boosted by sleep to a greater degree

Harmonized Dataset of Ozone Profiles from Satellite Limb and Occultation Measurements

In this paper, we present a HARMonized dataset of OZone profiles (HARMOZ) based on limb and occultation measurements from Envisat (GOMOS, MIPAS and SCIAMACHY), Odin (OSIRIS, SMR) and SCISAT (ACE-FTS) satellite instruments. These measurements provide high-vertical-resolution ozone profiles covering the altitude range from the upper troposphere up to the mesosphere in years 2001-2012. HARMOZ has been created in the framework of the European Space Agency Climate Change Initiative project. The harmonized dataset consists of original retrieved ozone profiles from each instrument, which are screened for invalid data by the instrument teams. While the original ozone profiles are presented in different units and on different vertical grids, the harmonized dataset is given on a common pressure grid in netCDF (network common data form)-4 format. The pressure grid corresponds to vertical sampling of similar to 1 km below 20 km and 2-3 km above 20 km. The vertical range of the ozone profiles is specific for each instrument, thus all information contained in the original data is preserved. Provided altitude and temperature profiles allow the representation of ozone profiles in number density or mixing ratio on a pressure or altitude vertical grid. Geolocation, uncertainty estimates and vertical resolution are provided for each profile. For each instrument, optional parameters, which are related to the data quality, are also included. For convenience of users, tables of biases between each pair of instruments for each month, as well as bias uncertainties, are provided. These tables characterize the data consistency and can be used in various bias and drift analyses, which are needed, for instance, for combining several datasets to obtain a long-term climate dataset. This user-friendly dataset can be interesting and useful for various analyses and applications, such as data merging, data validation, assimilation and scientific research. The dataset is available at http://www.esa-ozone-cci.org/?q=node/161 or at doi: 10.5270/esa-ozone_cci-limb_occultation_profiles-2001_2012-v_1-201308

Interpersonal emotion regulation in team sport: mechanisms and reasons to regulate teammates' emotions examined

The interpersonal dimension of emotion regulation in the field of sport has lately received a burgeoning interest. Nevertheless, how and why athletes regulate their teammates' emotions in competitive setting remains unclear. Across two studies within a team sport context, we uncovered athletes' mechanisms for, and reasons to regulate teammates' emotions during competition. In Study 1, we investigated how rugby (N = 22 males) players' emotions were self- and interpersonally regulated during games. Findings revealed the emergence of a continuum of self-involvement in the regulatory processes, wherein two forms of emotion regulation co-existed: self-regulation (total self-involvement) and interpersonal regulation, which included co-regulation (partial self-involvement; regulation with others) and extrinsic regulation (no self-involvement; regulation by/of others). In Study 2, we examined the motives that lead rugby (n = 30 males) players to use interpersonal extrinsic regulation strategies during games. Interview data indicated that players regulated teammates' emotions for altruistic reasons (to help a teammate), egoistic reasons (for one's own benefits), or both. Overall, our findings further knowledge to better understand interpersonal emotion regulation within competitive team sport contexts. From an applied perspective, findings highlight the role that both individual goals and ego involvement may play in optimising efficient interpersonal regulation during competition at team level

Positive youth development in swimming: clarification and consensus of key psychosocial assets

The purpose of this study was to gain a more cohesive understanding of the assets considered necessary to develop in young swimmers to ensure both individual and sport specific development. This two stage study involved (a) a content analysis of key papers to develop a list of both psychosocial skills for performance enhancement and assets associated with positive youth development, and (b) in-depth interviews involving ten expert swim coaches, practitioners and youth sport scholars. Five higher order categories containing seventeen individual assets emerged. These results are discussed in relation to both existing models of positive youth development and implications for coaches, practitioners and parents when considering the psychosocial development of young British swimmers