Displaying 3D images: algorithms for single-image random-dot

A new, simple, and symmetric algorithm can be implemented that results in higher levels of detail in solid objects than previously possible with autostereograms. In a stereoscope, an optical instrument similar to binoculars, each eye views a different picture and thereby receives the specific image that would have arisen naturally. An early suggestion for a color stereo computer display involved a rotating filter wheel held in front of the eyes. In contrast, this article describes a method for viewing on paper or on an ordinary computer screen without special equipment, although it is limited to the display of 3D monochromatic objects. (The image can be colored, say, for artistic reasons, but the method we describe does not allow colors to be allocated in a way that corresponds to an arbitrary coloring of the solid object depicted.) The image can easily be constructed by computer from any 3D scene or solid object description

Jumble Java Byte Code to Measure the Effectiveness of Unit Tests

Jumble is a byte code level mutation testing tool for Java which inter-operates with JUnit. It has been designed to operate in an industrial setting with large projects. Heuristics have been included to speed the checking of mutations, for example, noting which test fails for each mutation and running this first in subsequent mutation checks. Significant effort has been put into ensuring that it can test code which uses custom class loading and reflection. This requires careful attention to class path handling and coexistence with foreign class-loaders. Jumble is currently used on a continuous basis within an agile programming environment with approximately 370,000 lines of Java code under source control. This checks out project code every fifteen minutes and runs an incremental set of unit tests and mutation tests for modified classes. Jumble is being made available as open source

Daughter-Specific Transcription Factors Regulate Cell Size Control in Budding Yeast

The asymmetric localization of cell fate determinants results in asymmetric cell cycle control in budding yeast

SunPy - Python for Solar Physics

This paper presents SunPy (version 0.5), a community-developed Python package for solar physics. Python, a free, cross-platform, general-purpose, high-level programming language, has seen widespread adoption among the scientific community, resulting in the availability of a large number of software packages, from numerical computation (NumPy, SciPy) and machine learning (scikit-learn) to visualisation and plotting (matplotlib). SunPy is a data-analysis environment specialising in providing the software necessary to analyse solar and heliospheric data in Python. SunPy is open-source software (BSD licence) and has an open and transparent development workflow that anyone can contribute to. SunPy provides access to solar data through integration with the Virtual Solar Observatory (VSO), the Heliophysics Event Knowledgebase (HEK), and the HELiophysics Integrated Observatory (HELIO) webservices. It currently supports image data from major solar missions (e.g., SDO, SOHO, STEREO, and IRIS), time-series data from missions such as GOES, SDO/EVE, and PROBA2/LYRA, and radio spectra from e-Callisto and STEREO/SWAVES. We describe SunPy's functionality, provide examples of solar data analysis in SunPy, and show how Python-based solar data-analysis can leverage the many existing tools already available in Python. We discuss the future goals of the project and encourage interested users to become involved in the planning and development of SunPy

Facies Distribution, Sequence Stratigraphy, Chemostratigraphy, and Diagenesis of the Middle-Late Triassic Al Aziziyah Formation, Jifarah Basin, NW Libya

This study presents the depositional facies, sequence stratigraphy, chemostratigraphy and diagenetic evolution of the Middle-Late Triassic Al Aziziyah Formation, Jifarah Basin northwest Libya. Eight measured sections were sampled and analyzed. High-resolution stable carbon isotope data were integrated with an outcrop-based sequence stratigraphic framework, to build the stratigraphic correlation, and to provide better age control of the Al Aziziyah Formation using thin section petrography, cathodoluminescence (CL) microscopy, stable isotope, and trace element analyses. The Al Aziziyah Formation was deposited on a gently sloping carbonate ramp and consists of gray limestone, dolomite, and dolomitic limestone interbedded with rare shale. The Al Aziziyah Formation is predominantly a 2nd-order sequence (5-20 m.y. duration), with shallow marine sandstone and peritidal carbonate facies restricted to southernmost sections. Seven 3rd-order sequences were identified (S1-S7) within the type section. North of the Ghryan Dome section are three mainly subtidal sequences (S8-S10) that do not correlate to the south. Shallowing upward trends define 4th-5th order parasequences, but correlating these parasequences between sections is difficult due to unconformities. The carbon isotope correlation between the Ghryan Dome and Kaf Bates sections indicates five units of δ13C depletion and enrichment (sequences 3-7). The enrichment of δ13C values in certain intervals most likely reflects local withdrawal of 12C from the ocean due to increased productivity, as indicated by the deposition of organic-rich sediment, and/or whole rock sediment composed of calcite admixed with aragonite. The depletion of δ13C is clearly associated with exposure surfaces and with shallow carbonate facies. Heavier δ18O values are related to evaporetic enrichment of 18O, whereas depletion of δ18O is related to diagenesis due to freshwater input. Al Aziziyah Formation diagenetic events indicate: 1) initial meteoric and shallow burial; 2) three types of dolomite D1, D2 and D3 were most likely formed by microbial, seepage reflux and burial processes, respectively; and 3) diagenetic cements cannot be related to the arid, mega-monsoonal climate of the Triassic and most likely formed subsequently in a humid, meteoric setting

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Effectiveness of a national quality improvement programme to improve survival after emergency abdominal surgery (EPOCH): a stepped-wedge cluster-randomised trial

Background: Emergency abdominal surgery is associated with poor patient outcomes. We studied the effectiveness of a national quality improvement (QI) programme to implement a care pathway to improve survival for these patients. Methods: We did a stepped-wedge cluster-randomised trial of patients aged 40 years or older undergoing emergency open major abdominal surgery. Eligible UK National Health Service (NHS) hospitals (those that had an emergency general surgical service, a substantial volume of emergency abdominal surgery cases, and contributed data to the National Emergency Laparotomy Audit) were organised into 15 geographical clusters and commenced the QI programme in a random order, based on a computer-generated random sequence, over an 85-week period with one geographical cluster commencing the intervention every 5 weeks from the second to the 16th time period. Patients were masked to the study group, but it was not possible to mask hospital staff or investigators. The primary outcome measure was mortality within 90 days of surgery. Analyses were done on an intention-to-treat basis. This study is registered with the ISRCTN registry, number ISRCTN80682973. Findings: Treatment took place between March 3, 2014, and Oct 19, 2015. 22 754 patients were assessed for elegibility. Of 15 873 eligible patients from 93 NHS hospitals, primary outcome data were analysed for 8482 patients in the usual care group and 7374 in the QI group. Eight patients in the usual care group and nine patients in the QI group were not included in the analysis because of missing primary outcome data. The primary outcome of 90-day mortality occurred in 1210 (16%) patients in the QI group compared with 1393 (16%) patients in the usual care group (HR 1·11, 0·96–1·28). Interpretation: No survival benefit was observed from this QI programme to implement a care pathway for patients undergoing emergency abdominal surgery. Future QI programmes should ensure that teams have both the time and resources needed to improve patient care. Funding: National Institute for Health Research Health Services and Delivery Research Programme

Effectiveness of a national quality improvement programme to improve survival after emergency abdominal surgery (EPOCH): a stepped-wedge cluster-randomised trial

BACKGROUND: Emergency abdominal surgery is associated with poor patient outcomes. We studied the effectiveness of a national quality improvement (QI) programme to implement a care pathway to improve survival for these patients. METHODS: We did a stepped-wedge cluster-randomised trial of patients aged 40 years or older undergoing emergency open major abdominal surgery. Eligible UK National Health Service (NHS) hospitals (those that had an emergency general surgical service, a substantial volume of emergency abdominal surgery cases, and contributed data to the National Emergency Laparotomy Audit) were organised into 15 geographical clusters and commenced the QI programme in a random order, based on a computer-generated random sequence, over an 85-week period with one geographical cluster commencing the intervention every 5 weeks from the second to the 16th time period. Patients were masked to the study group, but it was not possible to mask hospital staff or investigators. The primary outcome measure was mortality within 90 days of surgery. Analyses were done on an intention-to-treat basis. This study is registered with the ISRCTN registry, number ISRCTN80682973. FINDINGS: Treatment took place between March 3, 2014, and Oct 19, 2015. 22 754 patients were assessed for elegibility. Of 15 873 eligible patients from 93 NHS hospitals, primary outcome data were analysed for 8482 patients in the usual care group and 7374 in the QI group. Eight patients in the usual care group and nine patients in the QI group were not included in the analysis because of missing primary outcome data. The primary outcome of 90-day mortality occurred in 1210 (16%) patients in the QI group compared with 1393 (16%) patients in the usual care group (HR 1·11, 0·96-1·28). INTERPRETATION: No survival benefit was observed from this QI programme to implement a care pathway for patients undergoing emergency abdominal surgery. Future QI programmes should ensure that teams have both the time and resources needed to improve patient care. FUNDING: National Institute for Health Research Health Services and Delivery Research Programme

Musical image compression

Optical music recognition aims to convert the vast repositories of sheet music in the world into an on-line digital format [Bai97]. In the near future it will be possible to assimilate music into digital libraries and users will be able to perform searches based on a sung melody in addition to typical text-based searching [MSW+96]. An important requirement for such a system is the ability to reproduce the original score as accurately as possible. Due to the huge amount of sheet music available, the efficient storage of musical images is an important topic of study. This paper investigates whether the “knowledge” extracted from the optical music recognition (OMR) process can be exploited to gain higher compression than the JBIG international standard for bi-level image compression. We present a hybrid approach where the primitive shapes of music extracted by the optical music recognition process-note heads, note stems, staff lines and so forth-are fed into a graphical symbol based compression scheme originally designed for images containing mainly printed text. Using this hybrid approach the average compression rate for a single page is improved by 3.5% over JBIG. When multiple pages with similar typography are processed in sequence, the file size is decreased by 4-8%. Section 2 presents the relevant background to both optical music recognition and textual image compression. Section 3 describes the experiments performed on 66 test images, outlining the combinations of parameters that were examined to give the best results. The initial results and refinements are presented in Section 4, and we conclude in the last section by summarizing the findings of this work