Research papers

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin, Carrie Davis, Felix Schlesinger, Jörg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, T …

MOTIVATION: Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. RESULTS: To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. AVAILABILITY AND IMPLEMENTATION: STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.

Deep Neural Networks for Acoustic Modeling in Speech Recognition: The Shared Views of Four Research Groups

Geoffrey E. Hinton, Li Deng, Dong Yu, George E. Dahl, Abdelrahman Mohamed, Navdeep Jaitly, Andrew Senior, Vincent Vanhoucke,…

Most current speech recognition systems use hidden Markov models (HMMs) to deal with the temporal variability of speech and Gaussian mixture models (GMMs) to determine how well each state of each HMM fits a frame or a short window of frames of coefficients that represents the acoustic input. An alternative way to evaluate the fit is to use a feed-forward neural network that takes several frames of coefficients as input and produces posterior probabilities over HMM states as output. Deep neural networks (DNNs) that have many hidden layers and are trained using new methods have been shown to outperform GMMs on a variety of speech recognition benchmarks, sometimes by a large margin. This article provides an overview of this progress and represents the shared views of four research groups that have had recent successes in using DNNs for acoustic modeling in speech recognition.

MuJoCo: A physics engine for model-based control

Emanuel Todorov, Tom Erez, Yuval Tassa

We describe a new physics engine tailored to model-based control. Multi-joint dynamics are represented in generalized coordinates and computed via recursive algorithms. Contact responses are computed via efficient new algorithms we have developed, based on the modern velocity-stepping approach which avoids the difficulties with spring-dampers. Models are specified using either a high-level C++ API or an intuitive XML file format. A built-in compiler transforms the user model into an optimized data structure used for runtime computation. The engine can compute both forward and inverse dynamics. The latter are well-defined even in the presence of contacts and equality constraints. The model can include tendon wrapping as well as actuator activation states (e.g. pneumatic cylinders or muscles). To facilitate optimal control applications and in particular sampling and finite differencing, the dynamics can be evaluated for different states and controls in parallel. Around 400,000 dynamics evaluations per second are possible on a 12-core machine, for a 3D homanoid with 18 dofs and 6 active contacts. We have already used the engine in a number of control applications. It will soon be made publicly available.

The physics of wind-blown sand and dust

Jasper F. Kok, Eric J. R. Parteli, Timothy I. Michaels, Diana Bou Karam

The transport of sand and dust by wind is a potent erosional force, creates sand dunes and ripples, and loads the atmosphere with suspended dust aerosols. This paper presents an extensive review of the physics of wind-blown sand and dust on Earth and Mars. Specifically, we review the physics of aeolian saltation, the formation and development of sand dunes and ripples, the physics of dust aerosol emission, the weather phenomena that trigger dust storms, and the lifting of dust by dust devils and other small-scale vortices. We also discuss the physics of wind-blown sand and dune formation on Venus and Titan.

Making Physics Appealing to Female Students: Perspectives of Female Students and Physics Lecturers

Isaac Buabeng

This paper describes a qualitative study of how to improve females’ involvement in the learning of physics at the tertiary level. The study was conducted at the University of Cape Coast (UCC) and some select Senior High Schools (SHS) in the Cape Coast Metropolis, Ghana. Participants for the study were undergraduate female non-physics students, undergraduate female physics students, SHS final year female science students and physics lecturers and tutors. The study found that majority of female students do not pursue physics at higher levels of education because they perceived the subject as difficult, irrelevant, and one that has no or limited career opportunities. The participants, however, were optimistic that female participation in physics can be improved if necessary steps were taken to erase the widely held perceptions that have been associated with the study of the subject and its related career opportunities.

Observation of a new particle in the search for the Standard Model Higgs boson with the ATLAS detector at the LHC

G. Aad, T. Abajyan, B. Abbott, J. Abdallah, S. Abdel Khalek, A. A. Abdelalim, O. Abdinov, R. Aben, B. Abi, M. Abolins, O. S.…

Nursing documentation: Experience of the use of the nursing process model in selected hospitals in<scp>I</scp>badan,<scp>O</scp>yo<scp>S</scp>tate,<scp>N</scp>igeria

Bola Abosede Ofi, Olanrewaju Sowunmi

The descriptive study was conducted to determine the extent of utilization of the nursing process for documentation of nursing care in three selected hospitals, Ibadan, Nigeria. One hundred fifty nurses and 115 discharged clients' records were selected from the hospitals. Questionnaires and checklists were used to collect data. Utilization of nursing process for care was 100%, 73.6% and 34.8% in the three hospitals. Nurses encountered difficulties in history taking, formulation of nursing diagnoses, objectives, nursing orders and evaluation. Most nurses disagreed or were undecided with the use of authorized abbreviations and symbols (34.3%, 40.3% and 69.5%), recording errors that occurred during care (37.1%, 56.1% and 52.2%) and inclusion of change in clients' condition (54.3%, 56.1% and 73.8%). Most nurses appreciated the significance of documentation. Lack of time, knowledge and need for extensive writing are the major barriers against documentation. Seventy-seven point four per cent of the 115 clients' records from one hospital showed evidence of documentation, no evidence from the other two. Study findings have implications for continuing professional education, practice and supervision.

Review of Particle Physics

J. Beringer, J-F. Arguin, R. M. Barnett, K. Copic, O. I. Dahl, D. E. Groom, C.-J. Lin, J. Lys, H. Murayama, C.G. Wohl, W.-M.…

This biennial Review summarizes much of particle physics. Using data from previous editions, plus 2658 new measurements from 644 papers, we list, evaluate, and average measured properties of gauge bosons, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as Higgs bosons, heavy neutrinos, and supersymmetric particles. All the particle properties and search limits are listed in Summary Tables. We also give numerous tables, figures, formulae, and reviews of topics such as the Standard Model, particle detectors, probability, and statistics. Among the 112 reviews are many that are new or heavily revised including those on Heavy-Quark and Soft-Collinear Effective Theory, Neutrino Cross Section Measurements, Monte Carlo Event Generators, Lattice QCD, Heavy Quarkonium Spectroscopy, Top Quark, Dark Matter, ${V}_{\mathit{cb}}$ ${V}_{\mathit{ub}}$, Quantum Chromodynamics, High-Energy Collider Parameters, Astrophysical Constants, Cosmological Parameters, and Dark Matter.A booklet is available containing the Summary Tables and abbreviated versions of some of the other sections of this full Review. All tables, listings, and reviews (and errata) are also available on the Particle Data Group website: http://pdg.lbl.gov/.The 2012 edition of Review of Particle Physics is published for the Particle Data Group as article 010001 in volume 86 of Physical Review D.This edition should be cited as: J. Beringer et al. (Particle Data Group), Phys. Rev. D 86, 010001 (2012).

Type 2 Diabetes Mellitus: A Review of Current Trends

A B Olokoba, O.A. Obateru, Lateefat B. Olokoba

Type 2 diabetes mellitus (DM) is a chronic metabolic disorder in which prevalence has been increasing steadily all over the world. As a result of this trend, it is fast becoming an epidemic in some countries of the world with the number of people affected expected to double in the next decade due to increase in ageing population, thereby adding to the already existing burden for healthcare providers, especially in poorly developed countries. This review is based on a search of Medline, the Cochrane Database of Systemic Reviews, and citation lists of relevant publications. Subject heading and key words used include type 2 diabetes mellitus, prevalence, current diagnosis, and current treatment. Only articles in English were included. Screening and diagnosis is still based on World Health Organization (WHO) and American Diabetes Association (ADA) criteria which include both clinical and laboratory parameters. No cure has yet been found for the disease; however, treatment modalities include lifestyle modifications, treatment of obesity, oral hypoglycemic agents, and insulin sensitizers like metformin, a biguanide that reduces insulin resistance, is still the recommended first line medication especially for obese patients. Other effective medications include non-sulfonylurea secretagogues, thiazolidinediones, alpha glucosidase inhibitors, and insulin. Recent research into the pathophysiology of type 2 DM has led to the introduction of new medications like glucagon-like peptide 1 analogoues: dipeptidyl peptidase-IV inhibitors, inhibitors of the sodium-glucose cotransporter 2 and 11ß-hydroxysteroid dehydrogenase 1, insulin-releasing glucokinase activators and pancreatic-G-protein-coupled fatty-acid-receptor agonists, glucagon-receptor antagonists, metabolic inhibitors of hepatic glucose output and quick-release bromocriptine. Inhaled insulin was licensed for use in 2006 but has been withdrawn from the market because of low patronage.

Principles and Practice of Structural Equation Modeling

Nassim Tabri, Corinna M. Elliott

Amyloid Oligomers Exacerbate Tau Pathology in a Mouse Model of Tauopathy

Maj-Linda B. Selenica, Milene L. Brownlow, Jeffy P. Jimenez, Daniel C. Lee, Gabriela Peña, Chad A. Dickey, Marcia N. Gordon,…

BACKGROUND: We aimed to investigate the influence of oligomeric forms of β-amyloid (Aβ) and the influence of the duration of exposure on the development of tau phosphorylation. METHODS: Aβ oligomers were injected intracranially either acutely into 5-month-old rTg4510 mice and tissue was collected 3 days later, or chronically into 3-month-old mice and tissue was collected 2 months later. Several forms of phosphorylated tau (p-tau), GSK3 (glycogen synthase kinase-3) and microglial and astrocyte activation were measured. RESULTS: Acute injections of Aβ oligomers had no effect on p-tau epitopes but did result in elevation of phosphorylated/activated GSK3 (pGSK3). Chronic infusion of Aβ oligomers into the right hippocampus resulted in 3- to 4-fold elevations in several p-tau isoforms with no changes in total tau levels. A significant elevation in pGSK3 accompanied these changes. Microglial staining with CD68 paralleled the increase in tau phosphorylation, however, CD45 staining was unaffected by Aβ. Control experiments revealed that the infusion of Aβ from the minipumps was largely complete by 10 days after implantation. Thus, the elevation in p-tau 2 months after implantation implies that the changes are quite persistent. CONCLUSION: Soluble Aβ(1-42) oligomers have long-lasting effects on tau phosphorylation in the rTg4510 model, possibly due to elevations in GSK3. These data suggest that even brief elevations in Aβ production, may have enduring impact on the risk for tauopathy.

NIH Image to ImageJ: 25 years of image analysis

Caroline A Schneider, Wayne Rasband, Kevin W. Eliceiri

Fiji: an open-source platform for biological-image analysis

Johannes Schindelin, Ignacio Arganda‐Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch,…

Creating a Caring Science Curriculum: An Emancipatory Pedagogy for Nursing

Afam Ndu

ZINC: A Free Tool to Discover Chemistry for Biology

John J. Irwin, Teague Sterling, Michael M. Mysinger, Erin S. D. Bolstad, Ryan G. Coleman

ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site also enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number. Small custom subsets may be created, edited, shared, docked, downloaded, and conveyed to a vendor for purchase. The database is maintained and curated for a high purchasing success rate and is freely available at zinc.docking.org.

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Serge…

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Adolescence and the social determinants of health

Russell Viner, Elizabeth M. Ozer, Simon Denny, Michael Marmot, Michael D. Resnick, Adesegun Fatusi, Candace Currie

The effect of concept mapping instructional strategy on the biology achievement of senior secondary school slow learners

Uchenna Udeani, Philomena N. Okafor

The study investigated the comparative effectiveness of the expository and concept mapping instructional strategy of presenting secondary school biology concepts to slow learners. One hundred and twenty four biology slow learners were identified and randomly assigned to the expository group (n=62) and concept mapping group (n=62) and respectively taught the concept of photosynthesis. The groups were post-tested after two weeks of teaching for any significant differences in their biology achievement. Analysis of post-test scores indicated that the group taught by the concept mapping instructional strategy performed significantly (p&amp;lt;0.05) better than their expository group counterparts. Specifically, female slow learners taught with the concept mapping instructional strategy performed significantly (p&amp;lt;0.05) better than their male counterparts taught by the same method. These results have implications for biology teacher preparation, especially in the areas of teaching females and identifying slow learners and adopting effective methods of tackling their problems

Biology of Malaria Parasites

Chandy C. John

The organism itself was first seen by Lavern on November 6, 1880 at a military hospital in Constantine, Algeria, when he discovered a microgametocyte exflagellating. In 1885, similar organisms were discovered within the blood of birds in Russia. There was brief speculation that birds might be involved in the transmission of malaria; in 1894 Patrick Manson hypothesized that mosquito could transmit malaria. This hypothesis was independently confirmed by the Italian physician Giovanni Battista Grassi working in Italy and the British physician Ronald Ross working in India, both in 1898. [3] Ross demonstrated the existence of Plasmodium in the wall of the midgut and salivary glands of a Culex mosquito using bird species as the vertebrate host. For this discovery he won the Noble Prize in 1902. Grassi showed that human malaria could only be transmitted by Anopheles mosquito. It is worth noting, however, that for some species the vector may not be mosquito.[4]

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

Jordi Barretina, Giordano Caponigro, Nicolas Stransky, K. Venkatesan, Adam A. Margolin, Sung Joon Kim, Christopher J. Wilson…

Probabilistic topic models

David M. Blei

Surveying a suite of algorithms that offer a solution to managing large document archives.

Chemistry and Biology Of Multicomponent Reactions

Alexander Dömlingꝉ, Wei Wang, Kan Wang

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTChemistry and Biology Of Multicomponent ReactionsAlexander Dömling*†‡, Wei Wang†§, and Kan Wang†View Author Information† Department of Pharmaceutical Sciences, University of Pittsburgh, Biomedical Science Tower 3, Suite 10019, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States‡ Chair of Drug Design, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands§ Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, P. R. China*E-mail: [email protected]. Fax: (+)412-383-5298.Cite this: Chem. Rev. 2012, 112, 6, 3083–3135Publication Date (Web):March 22, 2012Publication History Received23 July 2010Published online22 March 2012Published inissue 13 June 2012https://pubs.acs.org/doi/10.1021/cr100233rhttps://doi.org/10.1021/cr100233rreview-articleACS PublicationsCopyright © 2012 American Chemical SocietyRequest reuse permissionsArticle Views31588Altmetric-Citations1987LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Inhibitors,Peptides and proteins,Reaction products,Receptors,Scaffolds Get e-Alerts

Unitary Qubit Lattice Gas Representation of 2D and 3D Quantum Turbulence

George Vahala, Bo Zhang, Jeffrey Yepez, Linda Vahala, Min Soe

Turbulence is of vital interest and importance to the study of fluid dynamics Pope (1990). In classical physics, turbulence was first studied carefully for incompressible flows whose evolution was given by the Navier-Stokes equations. One of the most celebrated results of incompressible classical turbulence (CT) is the existence of an inertial range with the cascade of kinetic energy from large to small spatial scales until one reaches scale lengths on the order of the dissipationwave length and the eddies/vortices are destroyed. The Kolmogorov kinetic energy spectrum in this inertial range follows the power law in wave number space.

Monte Carlo simulation of additional safety control rod for commercial MNSR to enhance safety

Y.V. Ibrahim, H.C. Odoi, Raymond L. Njinga, M.O. Adeleye, S.A. Jonah