Opt: A Domain Specific Language for Non-linear Least Squares Optimization in Graphics and Imaging

Many graphics and vision problems can be expressed as non-linear least squares optimizations of objective functions over visual data, such as images and meshes. The mathematical descriptions of these functions are extremely concise, but their implementation in real code is tedious, especially when optimized for real-time performance on modern GPUs in interactive applications. In this work, we propose a new language, Opt (available under http://optlang.org), for writing these objective functions over image- or graph-structured unknowns concisely and at a high level. Our compiler automatically transforms these specifications into state-of-the-art GPU solvers based on Gauss-Newton or Levenberg-Marquardt methods. Opt can generate different variations of the solver, so users can easily explore tradeoffs in numerical precision, matrix-free methods, and solver approaches. In our results, we implement a variety of real-world graphics and vision applications. Their energy functions are expressible in tens of lines of code, and produce highly-optimized GPU solver implementations. These solver have performance competitive with the best published hand-tuned, application-specific GPU solvers, and orders of magnitude beyond a general-purpose auto-generated solver

The Acute Effects of Whole-Body Corrective Exercise on Postural Alignment

International Journal of Exercise Science 8(3): 213-223, 2015. This study examined the acute effects of whole-body corrective exercise on postural alignment in a sample of 50 male participants (18-30 y) displaying asymmetrical postural deviations. All participants were randomly assigned to either a nonexercise control (n = 25) or corrective exercise treatment (n = 25) group. A three-dimensional motion analysis Vicon system was employed to quantify standing postural alignment at the beginning and end of a 6 d study. Postural misalignments were determined in degrees of symmetry (tilt) and rotation using horizontal and vertical virtual plumb lines for the following locations: hip (ASIS), leg (greater trochanter), shoulder (acromion process), and head (ear). The treatment group completed five corrective exercise sessions on separate days which included 11 exercises (requiring about 60 min per session to complete). The control group performed no intervention and maintained a normal lifestyle. At the commencement of the study there were no significant differences in the degree of postural misalignment between the control and treatment groups at any of the postural measurements. At the conclusion of the treatment period (following the five sessions of corrective exercise), there were no significant differences in any of the postural alignments of any of the postural measurements between the treatment and control groups. For example, all of the following postural measurements were not significantly different (critical F ≥ 4.24;df = 1,25) between groups: hip (ASIS) tilt (F = 0.05), hip (ASIS) rotation (F = 0.15), greater trochanter tilt (F = 1.58), greater trochanter rotation (F = 0.33), shoulder tilt (F = 2.63), shoulder rotation (F = 0.07), head tilt (F = 2.39), and head rotation (F = 2.79). The results of this study suggest that in this group of subjects, five sessions of corrective exercise were insufficient to significantly improve standing postural alignment. Although the results are non-significant, five sessions of corrective exercise were insufficient to measurably improve standing postural alignment. Although the results are non-significant, this study appears to be the first to use 3D video capture analysis to evaluate how corrective exercise might enhance standing whole-body postural alignment. Now, similar research methods can be employed to study a longer treatment period with the objective of identifying the minimal dose of corrective exercise necessary to improve postural alignment

Third molar development in a London population of White British and Black British or other Black ethnicity.

Funder: NIHR Cambridge Biomedical Research CentrePopulation differences in dental development between Black and White ethnic groups have been debated but not previously studied in the UK. Using inappropriate data for dental age estimation (DAE) could lead to erroneous results and injustice. Data were collected from dental panoramic radiographs of 5590 subjects aged 6-24 years in a teaching hospital archive. Demirjian stages were determined for left-sided teeth and third molars and data collected regarding hypodontia and third molar agenesis. Third molar development in self-assigned Black British, including other self-assigned Black ethnicity, was compared with that of self-assigned White British subjects. Data were compared for males and females in the two ethnic groups using T-tests for Demirjian Stages A-G of third molar development and Mann-Whitney tests for Stage H once a cut-off age at the maximum age for Stage G had been imposed. Third molar development occurred earlier in subjects of Black ancestry compared to those of White ancestry. While both ethnic groups showed large age ranges for every third molar stage, in female subjects these generally occurred at least 1.5 years earlier, and in males at least one year earlier. Hypodontia and third molar agenesis were more prevalent in White British, but the ethnic difference in third molar development persisted in subjects with complete dentitions. This is a large study that confirms ethnic differences in a London population, emphasises the difficulties of establishing the 18-year-old threshold using DAE, and confirms the risk of overestimating the age of individuals of Black ethnicity using White ethnic reference data

Lactate, a product of glycolytic metabolism, inhibits histone deacetylase activity and promotes changes in gene expression

Chemical inhibitors of histone deacetylase (HDAC) activity are used as experimental tools to induce histone hyperacetylation and deregulate gene transcription, but it is not known whether the inhibition of HDACs plays any part in the normal physiological regulation of transcription. Using both in vitro and in vivo assays, we show that lactate, which accumulates when glycolysis exceeds the cell’s aerobic metabolic capacity, is an endogenous HDAC inhibitor, deregulating transcription in an HDAC-dependent manner. Lactate is a relatively weak inhibitor (IC(50) 40 mM) compared to the established inhibitors trichostatin A and butyrate, but the genes deregulated overlap significantly with those affected by low concentrations of the more potent inhibitors. HDAC inhibition causes significant up and downregulation of genes, but genes that are associated with HDAC proteins are more likely to be upregulated and less likely to be downregulated than would be expected. Our results suggest that the primary effect of HDAC inhibition by endogenous short-chain fatty acids like lactate is to promote gene expression at genes associated with HDAC proteins. Therefore, we propose that lactate may be an important transcriptional regulator, linking the metabolic state of the cell to gene transcription

Participation of Multifunctional RNA in Replication, Recombination and Regulation of Endogenous Plant Pararetroviruses (EPRVs)

Pararetroviruses, taxon Caulimoviridae, are typical of retroelements with reverse transcriptase and share a common origin with retroviruses and LTR retrotransposons, presumably dating back 1.6 billion years and illustrating the transition from an RNA to a DNA world. After transcription of the viral genome in the host nucleus, viral DNA synthesis occurs in the cytoplasm on the generated terminally redundant RNA including inter- and intra-molecule recombination steps rather than relying on nuclear DNA replication. RNA recombination events between an ancestral genomic retroelement with exogenous RNA viruses were seminal in pararetrovirus evolution resulting in horizontal transmission and episomal replication. Instead of active integration, pararetroviruses use the host DNA repair machinery to prevail in genomes of angiosperms, gymnosperms and ferns. Pararetrovirus integration – leading to Endogenous ParaRetroViruses, EPRVs – by illegitimate recombination can happen if their sequences instead of homologous host genomic sequences on the sister chromatid (during mitosis) or homologous chromosome (during meiosis) are used as template. Multiple layers of RNA interference exist regulating episomal and chromosomal forms of the pararetrovirus. Pararetroviruses have evolved suppressors against this plant defense in the arms race during co-evolution which can result in deregulation of plant genes. Small RNAs serve as signaling molecules for Transcriptional and Post-Transcriptional Gene Silencing (TGS, PTGS) pathways. Different populations of small RNAs comprising 21–24 nt and 18–30 nt in length have been reported for Citrus, Fritillaria, Musa, Petunia, Solanum and Beta. Recombination and RNA interference are driving forces for evolution and regulation of EPRVs

The psychological foundations of reputation-based cooperation

Humans care about having a positive reputation, which may prompt them to help in scenarios where the return benefits are not obvious. Various game-theoretical models support the hypothesis that concern for reputation may stabilize cooperation beyond kin, pairs or small groups. However, such models are not explicit about the underlying psychological mechanisms that support reputation-based cooperation. These models therefore cannot account for the apparent rarity of reputation-based cooperation in other species. Here, we identify the cognitive mechanisms that may support reputation-based cooperation in the absence of language. We argue that a large working memory enhances the ability to delay gratification, to understand others' mental states (which allows for perspective-taking and attribution of intentions) and to create and follow norms, which are key building blocks for increasingly complex reputation-based cooperation. We review the existing evidence for the appearance of these processes during human ontogeny as well as their presence in non-human apes and other vertebrates. Based on this review, we predict that most non-human species are cognitively constrained to show only simple forms of reputation-based cooperation. This article is part of the theme issue ‘The language of cooperation: reputation and honest signalling’

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN