Cosmological Fisher forecasts for next-generation spectroscopic surveys

Next-generation spectroscopic surveys such as the MegaMapper, MUltiplexed Survey Telescope (MUST), MaunaKea Spectroscopic Explorer (MSE), and Wide Spectroscopic Telescope (WST) are foreseen to increase the number of galaxy/quasar redshifts by an order of magnitude, with hundred millions of spectra that will be measured at $z>2$. We perform a Fisher matrix analysis for these surveys on the baryonic acoustic oscillation (BAO), the redshift-space distortion (RSD) measurement, the non-Gaussianity amplitude $f_{\rm NL}$, and the total neutrino mass $M_\nu$. For BAO and RSD parameters, these surveys may achieve precision at sub-percent level (<0.5 per cent), representing an improvement of factor 10 w.r.t. the latest database. For NG, these surveys may reach an accuracy of $\sigma(f_{\rm NL})\sim 1$. They can also put a tight constraint on $M_\nu$ with $\sigma(M_\nu) \sim 0.02\,\rm eV$ if we do joint analysis with Planck and even $0.01\,\rm eV$ if combined with other data. In addition, we introduce a general survey model, to derive the cosmic volume and number density of tracers, given instrumental facilities and survey strategy. Using our Fisher formalism, we can explore (continuously) a wide range of survey observational parameters, and propose different survey strategies that optimise the cosmological constraints. Fixing the fibre number and survey duration, we show that the best strategy for $f_{\rm NL}$ and $M_\nu$ measurement is to observe large volumes, despite the noise increase. However, the strategy differs for the apparent magnitude limit. Finally, we prove that increasing the fibre number improves $M_{\nu}$ measurement but not significantly $f_{\rm NL}$.Comment: 15 pages, 9 figure

Robust interlaboratory reproducibility of a gene expression signature measurement consistent with the needs of a new generation of diagnostic tools

The increasing use of DNA microarrays in biomedical research, toxicogenomics, pharmaceutical development, and diagnostics has focused attention on the reproducibility and reliability of microarray measurements. While the reproducibility of microarray gene expression measurements has been the subject of several recent reports, there is still a need for systematic investigation into what factors most contribute to variability of measured expression levels observed among different laboratories and different experimenters.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Validation and Clinical Utility of a 70-Gene Prognostic Signature for Women With Node-Negative Breast Cancer

Background: A 70-gene signature was previously shown to have prognostic value in patients with node-negative breast cancer. Our goal was to validate the signature in an independent group of patients. Methods: Patients (n = 307, with 137 events after a median follow-up of 13.6 years) from five European centers were divided into high- and low-risk groups based on the gene signature classification and on clinical risk classifications. Patients were assigned to the gene signature low-risk group if their 5-year distant metastasis-free survival probability as estimated by the gene signature was greater than 90%. Patients were assigned to the clinicopathologic low-risk group if their 10-year survival probability, as estimated by Adjuvant! software, was greater than 88% (for estrogen receptor [ER]-positive patients) or 92% (for ER-negative patients). Hazard ratios (HRs) were estimated to compare time to distant metastases, disease-free survival, and overall survival in high- versus low-risk groups. Results: The 70-gene signature outperformed the clinicopathologic risk assessment in predicting all endpoints. For time to distant metastases, the gene signature yielded HR = 2.32 (95% confidence interval [CI] = 1.35 to 4.00) without adjustment for clinical risk and hazard ratios ranging from 2.13 to 2.15 after adjustment for various estimates of clinical risk; clinicopathologic risk using Adjuvant! software yielded an unadjusted HR = 1.68 (95% CI = 0.92 to 3.07). For overall survival, the gene signature yielded an unadjusted HR = 2.79 (95% CI = 1.60 to 4.87) and adjusted hazard ratios ranging from 2.63 to 2.89; clinicopathologic risk yielded an unadjusted HR = 1.67 (95% CI = 0.93 to 2.98). For patients in the gene signature high-risk group, 10-year overall survival was 0.69 for patients in both the low- and high-clinical risk groups; for patients in the gene signature low-risk group, the 10-year survival rates were 0.88 and 0.89, respectively. Conclusions: The 70-gene signature adds independent prognostic information to clinicopathologic risk assessment for patients with early breast cance

Stereological analysis of liver biopsy histology sections as a reference standard for validating non-invasive liver fat fraction measurements by MRI

© 2016 St. Pierre et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Background and Aims: Validation of non-invasive methods of liver fat quantification requires a reference standard. However, using standard histopathology assessment of liver biopsies is problematical because of poor repeatability. We aimed to assess a stereological method of measuring volumetric liver fat fraction (VLFF) in liver biopsies and to use the method to validate a magnetic resonance imaging method for measurement of VLFF. Methods: VLFFs were measured in 59 subjects (1) by three independent analysts using a stereological point counting technique combined with the Delesse principle on liver biopsy histological sections and (2) by three independent analysts using the HepaFat-Scan® technique on magnetic resonance images of the liver. Bland Altman statistics and intraclass correlation (IC) were used to assess the repeatability of each method and the bias between the methods of liver fat fraction measurement. Results: Inter-analyst repeatability coefficients for the stereology and HepaFat-Scan® methods were 8.2 (95% CI 7.7-8.8)% and 2.4 (95% CI 2.2-2.5)% VLFF respectively. IC coefficients were 0.86 (95% CI 0.69-0.93) and 0.990 (95% CI 0.985-0.994) respectively. Small biases (=3.4%) were observable between two pairs of analysts using stereology while no significant biases were observable between any of the three pairs of analysts using Hepa-Fat-Scan®. A bias of 1.4±0.5% VLFF was observed between the HepaFat-Scan® method and the stereological method. Conclusions: Repeatability of the stereological method is superior to the previously reported performance of assessment of hepatic steatosis by histopathologists and is a suitable reference standard for validating non-invasive methods of measurement of VLFF

Parameters affecting the enhanced permeability and retention effect: the need for patient selection

The enhanced permeability and retention (EPR) effect constitutes the rationale by which nanotechnologies selectively target drugs to tumors. Despite promising pre-clinical and clinical results, these technologies have, in our view, underachieved compared to their potential, possibly due to a suboptimal exploitation of the EPR effect. Here, we have systematically analyzed clinical data to identify key parameters affecting the extent of the EPR effect. An analysis of 17 clinical studies showed that the magnitude of the EPR effect was varied and was influenced by tumor type and size. Pancreatic, colon, breast, and stomach cancers showed the highest levels of accumulation of nanomedicines. Tumor size also had an effect on the accumulation of nanomedicines, with large size tumors having higher accumulation than both medium- and very large- sized tumors. However, medium tumors had the highest percentage of cases (100% of patients) with evidence of the EPR effect. Moreover, tumor perfusion, angiogenesis, inflammation in tumor tissues, and other factors also emerged as additional parameters that might affect the accumulation of nanomedicines into tumors. At the end of the commentary, we propose two strategies for identification of suitable patient sub-populations, with respect to the EPR effect, in order to maximize therapeutic outcome

Cosmological Fisher forecasts for next-generation spectroscopic surveys

Next-generation spectroscopic surveys such as the MegaMapper, MUltiplexed Survey Telescope (MUST), MaunaKea Spectroscopic Explorer (MSE), and Wide Spectroscopic Telescope (WST) are foreseen to increase the number of galaxy/quasar redshifts by an order of magnitude, with hundred millions of spectra that will be measured at $z>2$. We perform a Fisher matrix analysis for these surveys on the baryonic acoustic oscillation (BAO), the redshift-space distortion (RSD) measurement, the non-Gaussianity amplitude $f_{\rm NL}$, and the total neutrino mass $M_\nu$. For BAO and RSD parameters, these surveys may achieve precision at sub-percent level (<0.5 per cent), representing an improvement of factor 10 w.r.t. the latest database. For NG, these surveys may reach an accuracy of $\sigma(f_{\rm NL})\sim 1$. They can also put a tight constraint on $M_\nu$ with $\sigma(M_\nu) \sim 0.02\,\rm eV$ if we do joint analysis with Planck and even $0.01\,\rm eV$ if combined with other data. In addition, we introduce a general survey model, to derive the cosmic volume and number density of tracers, given instrumental facilities and survey strategy. Using our Fisher formalism, we can explore (continuously) a wide range of survey observational parameters, and propose different survey strategies that optimise the cosmological constraints. Fixing the fibre number and survey duration, we show that the best strategy for $f_{\rm NL}$ and $M_\nu$ measurement is to observe large volumes, despite the noise increase. However, the strategy differs for the apparent magnitude limit. Finally, we prove that increasing the fibre number improves $M_{\nu}$ measurement but not significantly $f_{\rm NL}$

Intrinsic alignments of galaxies around cosmic voids

The intrinsic alignments of galaxies, i.e. the correlation between galaxy shapes and their environment, are a major source of contamination for weak gravitational lensing surveys. Most studies of intrinsic alignments have so far focused on measuring and modelling the correlations of luminous red galaxies with galaxy positions or the filaments of the cosmic web. In this work, we investigate alignments around cosmic voids. We measure the intrinsic alignments of luminous red galaxies detected by the Sloan Digital Sky Survey around a sample of voids constructed from those same tracers and with radii in the ranges: [20-30; 30-40; 40-50] h-1 Mpc and in the redshift range z = 0.4-0.8. We present fits to the measurements based on a linear model at large scales, and on a new model based on the void density profile inside the void and in its neighbourhood. We constrain the free scaling amplitude of our model at small scales, finding no significant alignment at 1σ for either sample. We observe a deviation from the null hypothesis, at large scales, of 2σ for voids with radii between 20 and 30 h-1 Mpc, and 1.5σ for voids with radii between 30 and 40 h-1 Mpc and constrain the amplitude of the model on these scales. We find no significant deviation at 1σ for larger voids. Our work is a first attempt at detecting intrinsic alignments of galaxy shapes around voids and provides a useful framework for their mitigation in future void lensing studies

Intrinsic alignments of galaxies around cosmic voids

International audienceThe intrinsic alignments of galaxies, i.e. the correlation between galaxy shapes and their environment, are a major source of contamination for weak gravitational lensing surveys. Most studies of intrinsic alignments have so far focused on measuring and modelling the correlations of luminous red galaxies with galaxy positions or the filaments of the cosmic web. In this work, we investigate alignments around cosmic voids. We measure the intrinsic alignments of luminous red galaxies detected by the Sloan Digital Sky Survey around a sample of voids constructed from those same tracers and with radii in the ranges: [20–30; 30–40; 40–50] h^−1 Mpc and in the redshift range z = 0.4−0.8. We present fits to the measurements based on a linear model at large scales, and on a new model based on the void density profile inside the void and in its neighbourhood. We constrain the free scaling amplitude of our model at small scales, finding no significant alignment at 1σ for either sample. We observe a deviation from the null hypothesis, at large scales, of 2σ for voids with radii between 20 and 30 h^−1 Mpc, and 1.5σ for voids with radii between 30 and 40 h^−1 Mpc and constrain the amplitude of the model on these scales. We find no significant deviation at 1σ for larger voids. Our work is a first attempt at detecting intrinsic alignments of galaxy shapes around voids and provides a useful framework for their mitigation in future void lensing studies

Intrinsic alignments of galaxies around cosmic voids

The intrinsic alignments of galaxies, i.e. the correlation between galaxy shapes and their environment, are a major source of contamination for weak gravitational lensing surveys. Most studies of intrinsic alignments have so far focused on measuring and modelling the correlations of luminous red galaxies with galaxy positions or the filaments of the cosmic web. In this work, we investigate alignments around cosmic voids. We measure the intrinsic alignments of luminous red galaxies detected by the Sloan Digital Sky Survey around a sample of voids constructed from those same tracers and with radii in the ranges: [20-30; 30-40; 40-50] h-1 Mpc and in the redshift range z = 0.4-0.8. We present fits to the measurements based on a linear model at large scales, and on a new model based on the void density profile inside the void and in its neighbourhood. We constrain the free scaling amplitude of our model at small scales, finding no significant alignment at 1σ for either sample. We observe a deviation from the null hypothesis, at large scales, of 2σ for voids with radii between 20 and 30 h-1 Mpc, and 1.5σ for voids with radii between 30 and 40 h-1 Mpc and constrain the amplitude of the model on these scales. We find no significant deviation at 1σ for larger voids. Our work is a first attempt at detecting intrinsic alignments of galaxy shapes around voids and provides a useful framework for their mitigation in future void lensing studies