Simplifying Dependent Reductions in the Polyhedral Model

A Reduction -- an accumulation over a set of values, using an associative and commutative operator -- is a common computation in many numerical computations, including scientific computations, machine learning, computer vision, and financial analytics. Contemporary polyhedral-based compilation techniques make it possible to optimize reductions, such as prefix sums, in which each component of the reduction's output potentially shares computation with another component in the reduction. Therefore an optimizing compiler can identify the computation shared between multiple components and generate code that computes the shared computation only once. These techniques, however, do not support reductions that -- when phrased in the language of the polyhedral model -- span multiple dependent statements. In such cases, existing approaches can generate incorrect code that violates the data dependences of the original, unoptimized program. In this work, we identify and formalize the optimization of dependent reductions as an integer bilinear program. We present a heuristic optimization algorithm that uses an affine sequential schedule of the program to determine how to simplfy reductions yet still preserve the program's dependences. We demonstrate that the algorithm provides optimal complexity for a set of benchmark programs from the literature on probabilistic inference algorithms, whose performance critically relies on simplifying these reductions. The complexities for 10 of the 11 programs improve siginifcantly by factors at least of the sizes of the input data, which are in the range of $10^4$ to $10^6$ for typical real application inputs. We also confirm the significance of the improvement by showing speedups in wall-clock time that range from $1.1\text{x}$ to over $10^6\text{x}$

Xenopus: An ideal system for chemical genetics

Chemical genetics, or chemical biology, has become an increasingly powerful method for studying biological processes. The main objective of chemical genetics is the identification and use of small molecules that act directly on proteins, allowing rapid and reversible control of activity. These compounds are extremely powerful tools for researchers, particularly in biological systems that are not amenable to genetic methods. In addition, identification of small molecule interactions is an important step in the drug discovery process. Increasingly, the African frog Xenopus is being used for chemical genetic approaches. Here, we highlight the advantages of Xenopus as a first-line in vivo model for chemical screening as well as for testing reverse engineering approaches. genesis 50:207–218, 2012. © 2012 Wiley Periodicals, Inc

System wide analyses have underestimated protein abundances and the importance of transcription in mammals

Large scale surveys in mammalian tissue culture cells suggest that the protein expressed at the median abundance is present at 8,000–16,000 molecules per cell and that differences in mRNA expression between genes explain only 10–40% of the differences in protein levels. We find, however, that these surveys have significantly underestimated protein abundances and the relative importance of transcription. Using individual measurements for 61 housekeeping proteins to rescale whole proteome data from Schwanhausser et al. (2011), we find that the median protein detected is expressed at 170,000 molecules per cell and that our corrected protein abundance estimates show a higher correlation with mRNA abundances than do the uncorrected protein data. In addition, we estimated the impact of further errors in mRNA and protein abundances using direct experimental measurements of these errors. The resulting analysis suggests that mRNA levels explain at least 56% of the differences in protein abundance for the 4,212 genes detected by Schwanhausser et al. (2011), though because one major source of error could not be estimated the true percent contribution should be higher. We also employed a second, independent strategy to determine the contribution of mRNA levels to protein expression. We show that the variance in translation rates directly measured by ribosome profiling is only 9% of that inferred by Schwanhausser et al. (2011), and that the measured and inferred translation rates correlate poorly (R2 = 0.14). Based on this, our second strategy suggests that mRNA levels explain ∼84% of the variance in protein levels. We also determined the percent contributions of transcription, RNA degradation, translation and protein degradation to the variance in protein abundances using both of our strategies. While the magnitudes of the two estimates vary, they both suggest that transcription plays a more important role than the earlier studies implied and translation a much smaller role. Finally, the above estimates apply to those genes whose mRNA and protein expression was detected. Based on a detailed analysis by Hebenstreit et al. (2012), we estimate that approximately 40% of genes in a given cell within a population express no mRNA. Since there can be no translation in the absence of mRNA, we argue that differences in translation rates can play no role in determining the expression levels for the ∼40% of genes that are non-expressed

Surgical complications in neuromuscular scoliosis operated with posterior- only approach using pedicle screw fixation

<p>Abstract</p> <p>Background</p> <p>There are no reports describing complications with posterior spinal fusion (PSF) with segmental spinal instrumentation (SSI) using pedicle screw fixation in patients with neuromuscular scoliosis.</p> <p>Methods</p> <p>Fifty neuromuscular patients (18 cerebral palsy, 18 Duchenne muscular dystrophy, 8 spinal muscular atrophy and 6 others) were divided in two groups according to severity of curves; group I (< 90°) and group II (> 90°). All underwent PSF and SSI with pedicle screw fixation. There were no anterior procedures. Perioperative (within three months of surgery) and postoperative (after three months of surgery) complications were retrospectively reviewed.</p> <p>Results</p> <p>There were fifty (37 perioperative, 13 postoperative) complications. Hemo/pneumothorax, pleural effusion, pulmonary edema requiring ICU care, complete spinal cord injury, deep wound infection and death were major complications; while atelectesis, pneumonia, mild pleural effusion, UTI, ileus, vomiting, gastritis, tingling sensation or radiating pain in lower limb, superficial infection and wound dehiscence were minor complications. Regarding perioperative complications, 34(68%) patients had at least one major or one minor complication. There were 16 patients with pulmonary, 14 with abdominal, 3 with wound related, 2 with neurological and 1 cardiovascular complications, respectively. There were two deaths, one due to cardiac arrest and other due to hypovolemic shock. Regarding postoperative complications 7 patients had coccygodynia, 3 had screw head prominence, 2 had bed sore and 1 had implant loosening, respectively. There was a significant relationship between age and increased intraoperative blood loss (p = 0.024). However it did not increased complications or need for ICU care. Similarly intraoperative blood loss > 3500 ml, severity of curve or need of pelvic fixation did not increase the complication rate or need for ICU. DMD patients had higher chances of coccygodynia postoperatively.</p> <p>Conclusion</p> <p>Although posterior-only approach using pedicle screw fixation had good correction rate, complications were similar to previous reports. There were few unusual complications like coccygodynia.</p

Anti-neutrophil cytoplasmic antibodies:Current diagnostic and pathophysiological potential

Rapidly progressive glomerulonephritis (RPGN) is a clinical syndrome characterized by rapid deterioration of renal function occurring within days or weeks together with signs of glomerulonephritis, that is, proteinuria and hematuria with cellular casts. The syndrome is, in many cases, histopathologically manifested as fibrinoid necrosis of the capillary wall with extracapillary proliferation and crescent formation [1]. This so-called necrotizing crescentic glomerulonephritis (NCGN) is seen in 5 to 15% of renal biopsies in most series [1–3]. Although it is infrequent, the importance of the condition is illustrated by the fact that most cases of NCGN, if left untreated, develop renal failure within days or weeks [1]. Based on immunohistopathology NCGN can be subdivided into three distinct categories. The first one, occurring in 2 to 20% of the cases and characterized by linear staining of the glomerular capillary wall for immunoglobulin and complement, has classically been described as anti-glomerular basement membrane (GBM) disease. It is associated with autoantibodies to structural antigens of the GBM, in particular to the first globular noncollagen domain of collagen type IV [4]. The antibodies are considered of pathogenetic significance. The second category, comprising 15 to 50% of cases, is characterized by granular deposits of immunoglobulin and complement suggesting that immune complexes are pathogenetically involved. This type occurs in conjunction with systemic autoimmune diseases such as lupus erythematosus, in cases of post-infectious glomerulonephritis, IgA nephropathy or Henoch-Schönlein purpura, or as an idiopathic variety. The third group of NCGN, occurring in 40 to 80%, demonstrates only a few or no immune deposits and is designated as pauci-immune NCGN [1–3, 5, 6]. Pauci-immune NCGN occurs as part of Wegener's granulomatosis (WG) or related conditions, or without systemic vasculitis (idiopathic NCGN). The pathophysiology of this pauci-immune type of NCGN has not been elucidated. Within the last decade, however, it has been recognized that the condition is associated with autoantibodies to cytoplasmic components of neutrophils (anti-neutrophil cytoplasmic antibodies or ANCA).ANCA were first described in 1982 by Davies et al in a few patients with segmental necrotizing glomerulonephritis [7]. Only in 1985 did it become apparent that ANCA are a sensitive and specific marker for Wegener's granulomatosis (WG) [8]. Later on, ANCA were described in patients with microscopic polyarteritis [9]. Falk and Jennette, in 1988, showed that ANCA are also associated with the idiopathic form of pauci-immune NCGN [10]. These data have now been confirmed by many groups and support the view that ANCA-associated glomerulonephritis and vasculitis is, indeed, a distinct disease category. A number of studies, in addition, have suggested that ANCA are involved in the pathophysiology of the aforementioned disorders. As ANCA, however, have recently also been detected in a wide range of inflammatory and infectious conditions, a critical reappraisal of the diagnostic significance of ANCA-testing seems justified.In this review we will evaluate the current state of ANCA-testing as well as elaborate on the pathophysiological role of the autoantibodies in necrotizing glomerulonephritis and vasculitis. Data presented recently at the Fifth International Workshop on ANCA, held in Cambridge, United Kingdom, will be included [11]. As such, it adds to previous reviews on ANCA that were published following the Second [12], Third [13], and Fourth [14] Workshops on ANCA

Cognitive-behavioural therapy and short-term psychoanalytic psychotherapy versus brief psychosocial intervention in adolescents with unipolar major depression (IMPACT): a multicentre, pragmatic, observer-blind, randomised controlled trial.

Although there are effective psychological treatments for unipolar major depression in adolescents, whether or not one or more of the available therapies maintain reduced depressive symptoms 1 year after the end of treatment is not known. This is a non-trivial issue because maintaining lowered depressive symptoms below a clinical threshold level reduces the risk for diagnostic relapse into the adult years. To determine whether or not either of two specialist psychological treatments, cognitive-behavioural therapy (CBT) or short-term psychoanalytic psychotherapy (STPP), is more effective than a reference brief psychosocial intervention (BPI) in maintaining reduction of depression symptoms in the year after treatment. Observer-blind, parallel-group, pragmatic superiority randomised controlled trial. A total of 15 outpatient NHS clinics in the UK from East Anglia, north-west England and North London. Adolescents aged 11-17 years with Diagnostic and Statistical Manual of Mental Disorders-Fourth Edition major depression including those with suicidality, depressive psychosis and conduct disorder. Patients were randomised using stochastic minimisation controlling for age, sex and self-reported depression sum score; 470 patients were randomised and 465 were included in the analyses. In total, 154 adolescents received CBT, 156 received STPP and 155 received BPI. The trial lasted 86 weeks and study treatments were delivered in the first 36 weeks, with 52 weeks of follow-up. Mean sum score on self-reported depressive symptoms (primary outcome) at final study assessment (nominally 86 weeks, at least 52 weeks after end of treatment). Secondary measures were change in mean sum scores on self-reported anxiety symptoms and researcher-rated Health of the Nation scales for children and adolescents measuring psychosocial function. Following baseline assessment, there were a further five planned follow-up reassessments at nominal time points of 6, 12, 52 and 86 weeks post randomisation. There were non-inferiority effects of CBT compared with STPP [treatment effect by final follow-up = -0.578, 95% confidence interval (CI) -2.948 to 4.104; p = 0.748]. There were no superiority effects for the two specialist treatments (CBT + STPP) compared with BPI (treatment effect by final follow-up = -1.898, 95% CI -4.922 to 1.126; p = 0.219). At final assessment there was no significant difference in the mean depressive symptom score between treatment groups. There was an average 49-52% reduction in depression symptoms by the end of the study. There were no differences in total costs or quality-of-life scores between treatment groups and prescribing a selective serotonin reuptake inhibitor (SSRI) during treatment or follow-up did not differ between the therapy arms and, therefore, did not mediate the outcome. The three psychological treatments differed markedly in theoretical and clinical approach and are associated with a similar degree of clinical improvement, cost-effectiveness and subsequent maintenance of lowered depressive symptoms. Both STPP and BPI offer an additional patient treatment choice, alongside CBT, for depressed adolescents attending specialist Child and Adolescent Mental Health Services. Further research should focus on psychological mechanisms that are associated with treatment response, the maintenance of positive effects, determinants of non-response and whether or not brief psychotherapies are of use in primary care and community settings. Neither reason for SSRI prescribing or monitoring of medication compliance was controlled for over the course of the study, and the economic results were limited by missing data. Current Controlled Trials ISRCTN83033550. This project was funded by the National Institute for Heath Research Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 21, No. 12. See the National Institute for Heath Research Journals Library website for further project information. Funding was also provided by the Department of Health. The funders had no role in the study design, patient recruitment, data collection, analysis or writing of the study, any aspect pertinent to the study or the decision to submit to The Lancet