Causal Inference When Counterfactuals Depend on the Proportion of All Subjects Exposed

The assumption that no subject's exposure affects another subject's outcome, known as the no-interference assumption, has long held a foundational position in the study of causal inference. However, this assumption may be violated in many settings, and in recent years has been relaxed considerably. Often this has been achieved with either the aid of a known underlying network, or the assumption that the population can be partitioned into separate groups, between which there is no interference, and within which each subject's outcome may be affected by all the other subjects in the group via the proportion exposed (the stratified interference assumption). In this paper, we instead consider a complete interference setting, in which each subject affects every other subject's outcome. In particular, we make the stratified interference assumption for a single group consisting of the entire sample. This can occur when the exposure is a shared resource whose efficacy is modified by the number of subjects among whom it is shared. We show that a targeted maximum likelihood estimator for the i.i.d.~setting can be used to estimate a class of causal parameters that includes direct effects and overall effects under certain interventions. This estimator remains doubly-robust, semiparametric efficient, and continues to allow for incorporation of machine learning under our model. We conduct a simulation study, and present results from a data application where we study the effect of a nurse-based triage system on the outcomes of patients receiving HIV care in Kenyan health clinics.Comment: 23 pages main article, 23 pages supplementary materials + references, 4 tables, 1 figur

A study of multiscale density fluctuation measurements

Intriguing parallels between density fluctuation power versus wavenumber on small (mm) and large (Mpc) scales are presented. The comparative study is carried out between fusion plasma measurements and cosmological data. Based on predictions from classical fluid turbulence theory, we argue that our observations are consistent with 2D turbulence. The similar dependencies of density fluctuations on these disparate scales might indicate that primordial turbulence has been expanded to cosmological proportions.Comment: Four pages, three figures. Accepted for publication in IEEE Transactions on Plasma Scienc

Analisa Pengaruh Kualitas Aset, Likuiditas, Efensiensi Usaha dan Profitabilitas terhadap Rasio Kecukupan Modal pada Umum Syariah Periode 2012-2015

The aim of this study is to examine the influence of effect of Asset Quality (NPF), Liquidity Level (FDR), Operating Efficiency (BOPO) and Return On Asset (ROA) on the Capital Adequacy Level by Capital Adequacy (CAR) on the general Islamic Bank listed on the Indonesian Bank in period 2012-2015. There are 11 samples in this research that is sharia BCA Bank, Muamalat Bank, Bukopin Bank, BRI Bank, Mega Bank, BNI Bank, BJB Bank, Mandiri Bank, Victoria Bank, Panin Bank and Maybank Bank. Hypotheses test used is panel data regression by carry out F Test and T test with value significant 5%. The result of F test, shows that simultaneously the NPF, FDR, BOPO and ROA have a influence on Capital Adequacy Ratio (CAR). The result of t-test,shows that ROA, FDR and BOPO are have negative influence on Capital Adequacy (CAR) and NPF have no effect towards Capital Adequacy (CAR) at Sharia Bank period 2010-2015

Spherical collapse of dark energy with an arbitrary sound speed

We consider a generic type of dark energy fluid, characterised by a constant equation of state parameter w and sound speed c_s, and investigate the impact of dark energy clustering on cosmic structure formation using the spherical collapse model. Along the way, we also discuss in detail the evolution of dark energy perturbations in the linear regime. We find that the introduction of a finite sound speed into the picture necessarily induces a scale-dependence in the dark energy clustering, which in turn affects the dynamics of the spherical collapse in a scale-dependent way. As with other, more conventional fluids, we can define a Jeans scale for the dark energy clustering, and hence a Jeans mass M_J for the dark matter which feels the effect of dark energy clustering via gravitational interactions. For bound objects (halos) with masses M >> M_J, the effect of dark energy clustering is maximal. For those with M << M_J, the dark energy component is effectively homogeneous, and its role in the formation of these structures is reduced to its effects on the Hubble expansion rate. To compute quantitatively the virial density and the linearly extrapolated threshold density, we use a quasi-linear approach which is expected to be valid up to around the Jeans mass. We find an interesting dependence of these quantities on the halo mass M, given some w and c_s. The dependence is the strongest for masses lying in the vicinity of M ~ M_J. Observing this M-dependence will be a tell-tale sign that dark energy is dynamic, and a great leap towards pinning down its clustering properties.Comment: 25 pages, 6 figures, matches version published in JCA

Global gene expression profiling of brown to white adipose tissue transformation in sheep reveals novel transcriptional components linked to adipose remodeling

BACKGROUND: Large mammals are capable of thermoregulation shortly after birth due to the presence of brown adipose tissue (BAT). The majority of BAT disappears after birth and is replaced by white adipose tissue (WAT). RESULTS: We analyzed the postnatal transformation of adipose in sheep with a time course study of the perirenal adipose depot. We observed changes in tissue morphology, gene expression and metabolism within the first two weeks of postnatal life consistent with the expected transition from BAT to WAT. The transformation was characterized by massively decreased mitochondrial abundance and down-regulation of gene expression related to mitochondrial function and oxidative phosphorylation. Global gene expression profiling demonstrated that the time points grouped into three phases: a brown adipose phase, a transition phase and a white adipose phase. Between the brown adipose and the transition phase 170 genes were differentially expressed, and 717 genes were differentially expressed between the transition and the white adipose phase. Thirty-eight genes were shared among the two sets of differentially expressed genes. We identified a number of regulated transcription factors, including NR1H3, MYC, KLF4, ESR1, RELA and BCL6, which were linked to the overall changes in gene expression during the adipose tissue remodeling. Finally, the perirenal adipose tissue expressed both brown and brite/beige adipocyte marker genes at birth, the expression of which changed substantially over time. CONCLUSIONS: Using global gene expression profiling of the postnatal BAT to WAT transformation in sheep, we provide novel insight into adipose tissue plasticity in a large mammal, including identification of novel transcriptional components linked to adipose tissue remodeling. Moreover, our data set provides a useful resource for further studies in adipose tissue plasticity. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1405-8) contains supplementary material, which is available to authorized users

Modelling radiation-induced cell cycle delays

Ionizing radiation is known to delay the cell cycle progression. In particular after particle exposure significant delays have been observed and it has been shown that the extent of delay affects the expression of damage such as chromosome aberrations. Thus, to predict how cells respond to ionizing radiation and to derive reliable estimates of radiation risks, information about radiation-induced cell cycle perturbations is required. In the present study we describe and apply a method for retrieval of information about the time-course of all cell cycle phases from experimental data on the mitotic index only. We study the progression of mammalian cells through the cell cycle after exposure. The analysis reveals a prolonged block of damaged cells in the G2 phase. Furthermore, by performing an error analysis on simulated data valuable information for the design of experimental studies has been obtained. The analysis showed that the number of cells analyzed in an experimental sample should be at least 100 to obtain a relative error less than 20%.Comment: 19 pages, 11 figures, accepted for publication in Radiation and Environmental Biophysic

Cell cycle times of short-term cultures of brain cancers as predictors of survival

Tumour cytokinetics estimated in vivo as potential doubling times (Tpot values) have been found to range in a variety of human cancers from 2 days to several weeks and are often related to clinical outcome. We have previously developed a method to estimate culture cycle times of short-term cultures of surgical material for several tumour types and found, surprisingly, that their range was similar to that reported for Tpot values. As Tpot is recognised as important prognostic variable in cancer, we wished to determine whether culture cycle times had clinical significance. Brain tumour material obtained at surgery from 70 patients with glioblastoma, medulloblastoma, astrocytoma, oligodendroglioma and metastatic melanoma was cultured for 7 days on 96-well plates, coated with agarose to prevent proliferation of fibroblasts. Culture cycle times were estimated from relative 3H-thymidine incorporation in the presence and absence of cell division. Patients were divided into two groups on the basis of culture cycle times of ⩽10 days and >10 days and patient survival was compared. For patients with brain cancers of all types, median survival for the ⩽10-day and >10-day groups were 5.1 and 12.5 months, respectively (P=0.0009). For 42 patients with glioblastoma, the corresponding values were 6.5 and 9.0 months, respectively (P=0.03). Lower grade gliomas had longer median culture cycle times (16 days) than those of medulloblastomas (9.9 days), glioblastomas (9.8 days) or melanomas (6.7 days). We conclude that culture cycle times determined using short-term cultures of surgical material from brain tumours correlate with patient survival. Tumour cells thus appear to preserve important cytokinetic characteristics when transferred to culture