Automatic improvement of apache spark queries using semantics-preserving program reduction

© 2016 ACM. Apache Spark is a popular framework for large-scale data analytics. Unfortunately, Spark's performance can be difficult to optimise, since queries freely expressed in source code are not amenable to traditional optimisation techniques. This article describes Hylas, a tool for automatically optimising Spark queries embedded in source code via the application of semantics-preserving transformations. The transformation method is inspired by functional programming techniques of "deforestation", which eliminate intermediate data structures from a computation. This contrasts with approaches defined entirely within structured query formats such as Spark SQL. Hylas can identify certain computationally expensive operations and ensure that performing them creates no superfluous data structures. This optimisation leads to significant improvements in execution time, with over 10,000 times improvement observed in some cases

RNA-Seq identifies SPGs as a ventral skeletal patterning cue in sea urchins

The sea urchin larval skeleton offers a simple model for formation of developmental patterns. The calcium carbonate skeleton is secreted by primary mesenchyme cells (PMCs) in response to largely unknown patterning cues expressed by the ectoderm. To discover novel ectodermal cues, we performed an unbiased RNA-Seq-based screen and functionally tested candidates; we thereby identified several novel skeletal patterning cues. Among these, we show that SLC26a2/7 is a ventrally expressed sulfate transporter that promotes a ventral accumulation of sulfated proteoglycans, which is required for ventral PMC positioning and skeletal patterning. We show that the effects of SLC perturbation are mimicked by manipulation of either external sulfate levels or proteoglycan sulfation. These results identify novel skeletal patterning genes and demonstrate that ventral proteoglycan sulfation serves as a positional cue for sea urchin skeletal patterning

Electron energy loss and induced photon emission in photonic crystals

The interaction of a fast electron with a photonic crystal is investigated by solving the Maxwell equations exactly for the external field provided by the electron in the presence of the crystal. The energy loss is obtained from the retarding force exerted on the electron by the induced electric field. The features of the energy loss spectra are shown to be related to the photonic band structure of the crystal. Two different regimes are discussed: for small lattice constants $a$ relative to the wavelength of the associated electron excitations $\lambda$, an effective medium theory can be used to describe the material; however, for $a\sim\lambda$ the photonic band structure plays an important role. Special attention is paid to the frequency gap regions in the latter case.Comment: 12 pages, 7 figure

Audible Image Description as an Accommodation in Statewide Assessments for Students with Visual and Print Disabilities.

Introduction:Although image description has been identified as an accommodation for presentations conducted in the classroom, only a few U.S. states have approved it for use in high-stakes assessments. This study examined the use of audible image description as an assessment accommodation for students with visual and print disabilities by investigating student comprehension under multiple conditions. Methods: Students in three western states in grades three through eight who had visual (n= 117) or print (n= 178) disabilities participated in an abbreviated test constructed of retired assessment questions in English language arts, mathematics, and science, that were aligned with each state's instructional standards, under conditions with and without standardized description of graphic images. The study used a within-subjects block design to collect and compare comprehension data under conditions where audible image description was both used and not used in an abbreviated test. Results: Results indicated that students who read braille were more likely to respond correctly under the audible image description condition, and students with visual and print disabilities who used print were equally likely to respond correctly regardless of condition. Discussion: Braille readers were more likely to obtain a correct answer when audible image description accompanied the question. Audible image description did not affect the likelihood of a correct response from students with print disabilities or students with visual disabilities who read print. Implications for practitioners: Audible image description is an accommodation that may help braille readers perform better on tests. Although the Partnership for Assessment of Readiness for College and Careers (PARCC) and Smarter Balanced consortia are taking steps to include image (or picture) descriptions in their assessment accommodations, teachers may want to develop a standard method for describing images and familiarize their braille readers to the strategy by including it in instruction and in classroom tests. Readers are referred to the National Center on Accessible Media’s online guidelines for image description

Kinome rewiring reveals AURKA limits PI3K-pathway inhibitor efficacy in breast cancer.

Dysregulation of the PI3K-AKT-mTOR signaling network is a prominent feature of breast cancers. However, clinical responses to drugs targeting this pathway have been modest, possibly because of dynamic changes in cellular signaling that drive resistance and limit drug efficacy. Using a quantitative chemoproteomics approach, we mapped kinome dynamics in response to inhibitors of this pathway and identified signaling changes that correlate with drug sensitivity. Maintenance of AURKA after drug treatment was associated with resistance in breast cancer models. Incomplete inhibition of AURKA was a common source of therapy failure, and combinations of PI3K, AKT or mTOR inhibitors with the AURKA inhibitor MLN8237 were highly synergistic and durably suppressed mTOR signaling, resulting in apoptosis and tumor regression in vivo. This signaling map identifies survival factors whose presence limits the efficacy of targeted therapies and reveals new drug combinations that may unlock the full potential of PI3K-AKT-mTOR pathway inhibitors in breast cancer

Significance of Pelvic Fluid Observed during Ovarian Cancer Screening with Transvaginal Sonogram

The primary objective was to examine the role of pelvic fluid observed during transvaginal ultrasonography (TVS) in identifying ovarian malignancy. A single-institution, observational study was conducted within the University of Kentucky Ovarian Cancer Screening trial from January 1987 to September 2019. We analyzed true-positive (TP), false-positive (FP), true-negative (TN), and false-negative (FN) groups for the presence of pelvic fluid during screening encounters. Measured outcomes were the presence and duration of fluid over successive screening encounters. Of the 48,925 women surveyed, 2001 (4.1%) had pelvic fluid present during a TVS exam. The odds ratio (OR) of detecting fluid in the comparison group (TN screen; OR = 1) significantly differed from that of the FP cases (benign pathology; OR: 13.4; 95% confidence interval (CI): 9.1–19.8), the TP cases with a low malignant potential (LMP; OR: 28; 95% CI: 26.5–29.5), TP ovarian cancer cases (OR: 50.4; 95% CI: 27.2–93.2), and FN ovarian cancer cases (OR: 59.3; 95% CI: 19.7–178.1). The mean duration that pelvic fluid was present for women with TN screens was 2.2 ± 0.05 encounters, lasting 38.7 ± 1.3 months. In an asymptomatic screening population, free fluid identified in TVS exams was more associated with ovarian malignancy than in the control group or benign ovarian tumors. While pelvic free fluid may not solely discriminate malignancy from non-malignancy, it appears to be clinically relevant and warrants thoughtful consideration

Affecting qualitative health psychology

The ‘affective turn’ is a contemporary movement within the humanities, social science and psychology to investigate affect, emotion and feeling as hybrid phenomena jointly constituted from both biological and social influences. Health and illness are themselves jointly constituted in this way, and many of the topics, concerns and methods of health psychology are strongly permeated by affective phenomena. Qualitative research in health psychology might therefore benefit by engaging with this work. This paper describes some features of the affective turn, and suggests theories, terminology and methods that might be useful

Osteoarthritis: 119. The Effectiveness of Exercise Therapy with and without Manual Therapy for Hip Osteoarthritis: A Multicentre Randomised Controlled Trial

Background: Current evidence indicates that exercise therapy (ET) has a short and medium-term benefit for hip osteoarthritis (OA), but evidence is inconclusive regarding the effect of manual therapy (MT). The primary aim of this randomised controlled trial was to determine the effectiveness of ET with and without MT on clinical outcomes for individuals with hip OA. A secondary aim was to ascertain the effect of an 8-week waiting period on outcomes. Methods: 131 men and women with hip OA recruited in four hospitals were initially randomised to one of three groups: ET (n = 45), a combination of ET and MT (n = 43) and wait-list control (n = 43). The two intervention groups underwent individualised ET or ET/MT for 8 weeks. Patients in the control group waited 8 weeks and were randomised to receive either ET or ET/MT after 9 week follow-up, and pooled with original treatment group data: ET (n = 66) and ET/ MT (n = 65). All participants were followed up at 9 and 18 weeks and the control group was reassessed at 27 weeks (18 weeks post-treatment) by the same blinded assessor. The primary outcome measure was the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC). Other outcomes included sit-to-stand, 50-foot walk test, pain severity, hip range of motion (ROM), anxiety, depression, quality of life (QOL), analgesic usage, physical activity, patient-perceived change and patient satisfaction. Intention-to-treat analysis was performed to determine within-group change and between-group differences for the three groups at baseline and 9 weeks, and the two treatment groups at baseline, 9 and 18 weeks. Results: Eight patients (6.1%) were lost to follow-up at 9 weeks and 19 (14.5%) were lost to follow-up by 18 weeks. Both ET (n = 66) and ET/MT groups (n = 65) showed significant within-group improvements in WOMAC, pain severity, sit-to-stand and HROM measures at 9 weeks, which were still evident at 18 weeks. There was no significant within-group change in anxiety, depression, QOL, analgesic usage, 50-foot walk test or physical activity. There was no significant difference between the two intervention groups for any of the outcomes. Regarding the results of the original ET, ET/MT and control group allocation, there was a significant improvement in one or both ET and ET/MT groups compared with the control group in the same outcomes, as well as patient perceived improvement at 9 weeks. There was no significant difference between the three groups in analgesic usage, WOMAC stiffness subscale, sit-to-stand and 50 foot walk tests, QOL and physical activity. There was an overall deterioration in anxiety and depression scores. Conclusions: The addition of MT to an 8 week programme of ET for hip OA resulted in similar improvements in pain, function and ROM at 9 and 18 weeks. The significant improvement which occurred in the same outcomes in the two treatment groups compared with a wait-list control of 8 weeks has implications for waiting list management Disclosure statement: The authors have declared no conflicts of interes