Structural features of geostrophic circulation in open region of the South China Sea

On the basis of observation data of water temperature and salinity the mean seasonal geostrophic circulation in open region of the South China Sea (SCS) was computed by the dynamic method relative to the 800 decibar reference surface. The results of computation let go to following notices: In both main monsoons (winter and summer) there are two main geostrophic eddies: the anticlockwise eddy in the northern and northwestern part, and the clockwise eddy in the southern part of the SCS with corresponding divergent and convergent zones. The main frontal zones go along the middle latitudes of the sea from the southern continental shelf of Vietnam to the area west of Luzon Island. The strength and stability of the current in winter are higher than in summer. The Kuroshio has an enough strong branch intruding into the SCS through Bashi Strait in winter creating in the sea the water structure similar to that of the Northwest Pacific subtropical and tropical regions. In summer the Kuroshio water can intrude directly only into the area southwest of Taiwan.

Analytical intercomparison results from the 1990 Intergovernmental Oceanographic Commission open-ocean baseline survey for trace metals: Atlantic Ocean

“Dissolved” (< 0.4 μm filtered) and “total dissolvable” (unfiltered) trace element samples were collected using “clean” sampling techniques from four vertical profiles in the eastern Atlantic Ocean on the first IOC Trace Metals Baseline expedition. The analytical results obtained by 9 participating laboratories for Mn, Fe, Co, Ni, Cu, Zn, Cd, Pb, and Se on samples from station 4 in the northeast Atlantic have been evaluated with respect to accuracy and precision (intercomparability). The data variability among the reporting laboratories was expressed as 2 × SD for a given element and depth, and was comparable to the 95% confidence interval reported for the NASS seawater reference standards (representing analytical variability only). The discrepancies between reporting laboratories appear to be due to inaccuracies in standardization (analytical calibration), blank correction, and/or extraction efficiency corrections.Several of the sampling bottles used at this station were not adequately pre-cleaned (anomalous Pb results). The sample filtration process did not appear to have been a source of contamination for either dissolved or particulate trace elements. The trace metal profiles agree in general with previously reported profiles from the Atlantic Ocean. We conclude that the sampling and analytical methods we have employed for this effort, while still in need of improvement, are sufficient for obtaining accurate concentration data on most trace metals in the major water masses of the oceans, and to enable some evaluation of the biogeochemical cycling of the metals.

data transformation and attribute subset selection: do they help make differences in software failure prediction?

IEEE, IEEE Comp Soc, Tech Council Software Engn

an empirical study on bug assignment automation using chinese bug data

Univ SE Calif, Ctr Syst & Software Engn, ABB, Microsoft Res, IEEE, ACMSIGSOFT, N Carolina State Univ Comp Sci

Orthodontic and orthopaedic treatment for anterior open bite in children

BackgroundAnterior open bite occurs when there is a lack of vertical overlap of the upper and lower incisors. the aetiology is multifactorial including: oral habits, unfavourable growth patterns, enlarged lymphatic tissue with mouth breathing. Several treatments have been proposed to correct this malocclusion, but interventions are not supported by strong scientific evidence.ObjectivesThe aim of this systematic review was to evaluate orthodontic and orthopaedic treatments to correct anterior open bite in children.Search methodsThe following databases were searched: the Cochrane Oral Health Group's Trials Register (to 14 February 2014); the Cochrane Central Register of Controlled Trials (CENTRAL)(The Cochrane Library 2014, Issue 1); MEDLINE via OVID (1946 to 14 February 2014); EMBASE via OVID (1980 to 14 February 2014); LILACS via BIREME Virtual Health Library (1982 to 14 February 2014); BBO via BIREME Virtual Health Library (1980 to 14 February 2014); and SciELO (1997 to 14 February 2014). We searched for ongoing trials via ClinicalTrials.gov (to 14 February 2014). Chinese journals were handsearched and the bibliographies of papers were retrieved.Selection criteriaAll randomised or quasi-randomised controlled trials of orthodontic or orthopaedic treatments or both to correct anterior open bite in children.Data collection and analysisTwo review authors independently assessed the eligibility of all reports identified.Risk ratios (RRs) and corresponding 95% confidence intervals (CIs) were calculated for dichotomous data. the continuous data were expressed as described by the author.Main resultsThree randomised controlled trials were included comparing: effects of Frankel's function regulator-4 (FR-4) with lip-seal training versus no treatment; repelling-magnet splints versus bite-blocks; and palatal crib associated with high-pull chincup versus no treatment.The study comparing repelling-magnet splints versus bite-blocks could not be analysed because the authors interrupted the treatment earlier than planned due to side effects in four of ten patients.FR-4 associated with lip-seal training (RR = 0.02 (95% CI 0.00 to 0.38)) and removable palatal crib associated with high-pull chincup (RR = 0.23 (95% CI 0.11 to 0.48)) were able to correct anterior open bite.No study described: randomisation process, sample size calculation, there was not blinding in the cephalometric analysis and the two studies evaluated two interventions at the same time. These results should be therefore viewed with caution.Authors' conclusionsThere is weak evidence that the interventions FR-4 with lip-seal training and palatal crib associated with high-pull chincup are able to correct anterior open bite. Given that the trials included have potential bias, these results must be viewed with caution. Recommendations for clinical practice cannot be made based only on the results of these trials. More randomised controlled trials are needed to elucidate the interventions for treating anterior open bite.

Confirmation of Data Mining Based Predictions of Protein Function

King, R. D. and Wise, P. H. and Clare, A. (2004) Confirmation of Data Mining Based Predictions of Protein Function. Bioinformatics 20(7), 1110-1118

WriteSim TCExam--an open source text simulation environment for training novice researchers in scientific writing.

BACKGROUND: The ability to write clearly and effectively is of central importance to the scientific enterprise. Encouraged by the success of simulation environments in other biomedical sciences, we developed WriteSim TCExam, an open-source, Web-based, textual simulation environment for teaching effective writing techniques to novice researchers. We shortlisted and modified an existing open source application - TCExam to serve as a textual simulation environment. After testing usability internally in our team, we conducted formal field usability studies with novice researchers. These were followed by formal surveys with researchers fitting the role of administrators and users (novice researchers) RESULTS: The development process was guided by feedback from usability tests within our research team. Online surveys and formal studies, involving members of the Research on Research group and selected novice researchers, show that the application is user-friendly. Additionally it has been used to train 25 novice researchers in scientific writing to date and has generated encouraging results. CONCLUSION: WriteSim TCExam is the first Web-based, open-source textual simulation environment designed to complement traditional scientific writing instruction. While initial reviews by students and educators have been positive, a formal study is needed to measure its benefits in comparison to standard instructional methods.

Computational Inference of Genome-Wide Protein-DNA Interactions Using High-Throughput Genomic Data

Transcriptional regulation has been studied intensively in recent decades. One important aspect of this regulation is the interaction between regulatory proteins, such as transcription factors (TF) and nucleosomes, and the genome. Different high-throughput techniques have been invented to map these interactions genome-wide, including ChIP-based methods (ChIP-chip, ChIP-seq, etc.), nuclease digestion methods (DNase-seq, MNase-seq, etc.), and others. However, a single experimental technique often only provides partial and noisy information about the whole picture of protein-DNA interactions. Therefore, the overarching goal of this dissertation is to provide computational developments for jointly modeling different experimental datasets to achieve a holistic inference on the protein-DNA interaction landscape.

We first present a computational framework that can incorporate the protein binding information in MNase-seq data into a thermodynamic model of protein-DNA interaction. We use a correlation-based objective function to model the MNase-seq data and a Markov chain Monte Carlo method to maximize the function. Our results show that the inferred protein-DNA interaction landscape is concordant with the MNase-seq data and provides a mechanistic explanation for the experimentally collected MNase-seq fragments. Our framework is flexible and can easily incorporate other data sources. To demonstrate this flexibility, we use prior distributions to integrate experimentally measured protein concentrations.

We also study the ability of DNase-seq data to position nucleosomes. Traditionally, DNase-seq has only been widely used to identify DNase hypersensitive sites, which tend to be open chromatin regulatory regions devoid of nucleosomes. We reveal for the first time that DNase-seq datasets also contain substantial information about nucleosome translational positioning, and that existing DNase-seq data can be used to infer nucleosome positions with high accuracy. We develop a Bayes-factor-based nucleosome scoring method to position nucleosomes using DNase-seq data. Our approach utilizes several effective strategies to extract nucleosome positioning signals from the noisy DNase-seq data, including jointly modeling data points across the nucleosome body and explicitly modeling the quadratic and oscillatory DNase I digestion pattern on nucleosomes. We show that our DNase-seq-based nucleosome map is highly consistent with previous high-resolution maps. We also show that the oscillatory DNase I digestion pattern is useful in revealing the nucleosome rotational context around TF binding sites.

Finally, we present a state-space model (SSM) for jointly modeling different kinds of genomic data to provide an accurate view of the protein-DNA interaction landscape. We also provide an efficient expectation-maximization algorithm to learn model parameters from data. We first show in simulation studies that the SSM can effectively recover underlying true protein binding configurations. We then apply the SSM to model real genomic data (both DNase-seq and MNase-seq data). Through incrementally increasing the types of genomic data in the SSM, we show that different data types can contribute complementary information for the inference of protein binding landscape and that the most accurate inference comes from modeling all available datasets.

This dissertation provides a foundation for future research by taking a step toward the genome-wide inference of protein-DNA interaction landscape through data integration.

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

Bayesian Model Averaging in the M-Open Framework

This chapter presents a model averaging approach in the M-open setting using sample re-use methods to approximate the predictive distribution of future observations. It first reviews the standard M-closed Bayesian Model Averaging approach and decision-theoretic methods for producing inferences and decisions. It then reviews model selection from the M-complete and M-open perspectives, before formulating a Bayesian solution to model averaging in the M-open perspective. It constructs optimal weights for MOMA:M-open Model Averaging using a decision-theoretic framework, where models are treated as part of the ‘action space’ rather than unknown states of nature. Using ‘incompatible’ retrospective and prospective models for data from a case-control study, the chapter demonstrates that MOMA gives better predictive accuracy than the proxy models. It concludes with open questions and future directions.

Community-based Data Validation Practices in Citizen Science

Technology-supported citizen science has created huge volumes of data with increasing potential to facilitate scientific progress, however, verifying data quality is still a substantial hurdle due to the limitations of existing data quality mechanisms. In this study, we adopted a mixed methods approach to investigate community-based data validation practices and the characteristics of records of wildlife species observations that affected the outcomes of collaborative data quality management in an online community where people record what they see in the nature. The findings describe the processes that both relied upon and added to information provenance through information stewardship behaviors, which led to improved reliability and informativity. The likelihood of community-based validation interactions were predicted by several factors, including the types of organisms observed and whether the data were submitted from a mobile device. We conclude with implications for technology design, citizen science practices, and research.

Model-based pilot and data power adaptation in psam with periodic delayed feedback

We consider the optimum design of pilot-symbol-assisted modulation (PSAM) schemes with feedback. The received signal is periodically fed back to the transmitter through a noiseless delayed link and the time-varying channel is modeled as a Gauss-Markov process. We optimize a lower bound on the channel capacity which incorporates the PSAM parameters and Kalman-based channel estimation and prediction. The parameters available for the capacity optimization are the data power adaptation strategy, pilot spacing and pilot power ratio, subject to an average power constraint. Compared to the optimized open-loop PSAM (i.e., the case where no feedback is provided from the receiver), our results show that even in the presence of feedback delay, the optimized power adaptation provides higher information rates at low signal-to-noise ratios (SNR) in medium-rate fading channels. However, in fast fading channels, even the presence of modest feedback delay dissipates the advantages of power adaptation.

Association for Learning Technology Annual Survey 2014 Data and Report

This is the first report from ALT’s new Annual Survey launched in December 2014. This survey was primarily for ALT members (individual or at an organisation which is an organisational member) it could however also be filled in by others, perhaps those interested in taking out membership. The report and data highlight emerging work areas that are important to the survey respondents. Analysis of the survey responses indicates a number of areas ALT should continue to support and develop. Priorities for the membership are ‘Intelligent use of learning technology’ and ‘Research and practice’, aligned to this is the value placed by respondent’s on by communication via the ALT Newsletter/News, social media and Research in Learning Technology. The survey also reveals ‘Data and Analytics’ and ‘Open Education’ are areas where the majority of respondents are finding are becoming increasingly important. As such our community may benefit from development opportunities ALT can provide. The survey is also a reminder that ALT has an essential role in enabling members to develop research and practice in areas which might be considered as minority interest. For example whilst the majority of respondents didn't indicate areas such as ‘Digital and Open Badges’, and ‘Game Based Learning’ as important there are still members who consider these areas are very significant and becoming increasingly valuable and as such ALT will continue to better support these groups within our community. Whilst ALT has conducted previous surveys of ALT membership this is the first iteration in this form. ALT has committed to surveying the sector on an annual basis, refining the core question set but trying to preserve an opportunity for longitudinal analysis.

Association for Learning Technology Annual Survey 2015 Data and Report.

This is the second report of the ALT’s Annual Survey which was open for responses between the 1st December 2015 and 17th January 2016. In total 196 responses have been analysed as part of this report. Given a number of core questions remain unchanged between this and the 2014 edition of the survey analysis includes data from the previous survey.

Towards Data Management Planning Support for Research Data

Görzig, H., Engel, F., Brocks, H., Vogel, T. & Hemmje, M. (2015, August). Towards Data Management Planning Support for Research Data. Paper presented at the ASE International Conference on Data Science, Stanford, United States of America.