Consistency tests of field level inference with the EFT likelihood

Analyzing the clustering of galaxies at the field level in principle promises access to all the cosmological information available. Given this incentive, in this paper we investigate the performance of field-based forward modeling approach to galaxy clustering using the effective field theory (EFT) framework of large-scale structure (LSS). We do so by applying this formalism to a set of consistency and convergence tests on synthetic datasets. We explore the high-dimensional joint posterior of LSS initial conditions by combining Hamiltonian Monte Carlo sampling for the field of initial conditions, and slice sampling for cosmology and model parameters. We adopt the Lagrangian perturbation theory forward model from [1], up to second order, for the forward model of biased tracers. We specifically include model mis-specifications in our synthetic datasets within the EFT framework. We achieve this by generating synthetic data at a higher cutoff scale $\Lambda_0$, which controls which Fourier modes enter the EFT likelihood evaluation, than the cutoff $\Lambda$ used in the inference. In the presence of model mis-specifications, we find that the EFT framework still allows for robust, unbiased joint inference of a) cosmological parameters - specifically, the scaling amplitude of the initial conditions - b) the initial conditions themselves, and c) the bias and noise parameters. In addition, we show that in the purely linear case, where the posterior is analytically tractable, our samplers fully explore the posterior surface. We also demonstrate convergence in the cases of nonlinear forward models. Our findings serve as a confirmation of the EFT field-based forward model framework developed in [2-7], and as another step towards field-level cosmological analyses of real galaxy surveys.Comment: 31 + 13 pages, 15 figures; Added 3 new figures, text cleanup and fix typos; matching the version to be published in JCA

Acute promyelocytic leukemia lacking t(15;17): Molecular evidence of atypical PML/RAR-α transcriptional variant by gene sequencing

Uvod. Precizno dijagnostikovanje akutne promijelocitne leukemije (APL), ne samo na osnovu morfoloških i kliničkih parametara, već i na molekularnom nivou, veoma je važno radi primene adekvatne ciljane terapije. Prikaz bolesnika. Prikazali smo bolesnicu, staru 62 godine, sa dijagnozom APL. Primenom standardne citogenetičke analize, kao i primenom fluorescentne in situ hibridizacije (FISH), nije bilo potvrđeno prisustvo t(15;17) kod opisane bolesnice. Primenom metode reverzna transkriptazalančana reakcija polimeraze (RT-PCR), identifikovana su dva atipična promyelotic leukemia/retinoic acid receptor alpha (PML/RAR-α) fuziona transkripta. Oba transkripta su predstavljala izoforme. Duži transkript je zadržao "okvir čitanja" i kodirao je funkcionalan PML/RAR-α aberantni protein, dok je kraći transkript bio van "okvira čitanja". Zaključak. Naša studija ukazuje na potrebu za primenom molekularne metodologije u svakodnevnoj kliničkoj praksi. Precizna karakterizacija PML/RAR-α fuzionih transkipta čini osnovu za identifikovanje retkih bolesnika čije lečenje zahteva dodatni oprez. Prema našim saznanjima, ovo je tek peti slučaj opisanog atipičnog PML/RAR-α transkripta koji u sebi sadrži celokupan PML egzon 7a, a među njima jedini koji se nije mogao detektovati primenom citogenetičke i FISH analize. Svi ovde predstavljeni slučajevi su imali smrtni ishod. Zbog toga, naši rezulatati, zajedno sa sličnim slučajevima opisanim u literaturi, naglašavaju značaj detaljne identifikacije atipičnih PML/RAR-α fuzija, ne samo u svrhu prepoznavanja njihove uloge u procesu leukemogeneze, veći i u smislu procene njihovog uticaja na ishod lečenja.Introduction. The accurate diagnosis of acute promyelocytic leukemia (APL), not only on the morphological and clinical, but also on the molecular level, is very important for application of targeted therapies. Case report. A 62year-old woman presented with APL. By using conventional cytogenetic analysis as well as applying the fluorescence in situ hybridization (FISH) analysis it has not been possible to confirm the presence of t(15;17) in the presented patient. Using reverse transcriptase polymerase chain reaction (RT-PCR) two atypical promyelotic leukemia/retinoic acid receptor alpha (PML/RAR-α) fusion transcripts were identified. Both detected transcripts were isoforms. The larger transcript was in-frame, coding for functional aberrant PML/RAR-α protein, while the shorter transcript was an out-of-frame. Conclusion. Our study highlights the need for the application of molecular methodology in daily clinical practice. Precise characterization of PML/RAR-α fusion transcript creates a basis for identifying rare individual cases that require special caution when treating such patients. To our knowledge this is only the fifth case of atypical PML/RAR-α transcript containing full PML exon 7a, and among them the only one that was cytogenetically cryptic and FISH negative. All of the herein presented cases had lethal outcome. Therefore, our findings with the additional review of the literature, emphasizes the importance of detailed identification of atypical PML/RAR-α fusions, not only for the purpose of knowing their role in leukemogenesis, but also for the assessment of the impact that they can have on the outcome of the treatment

No evidence for p- or d-wave dark matter annihilation from local large-scale structure

International audienceIf dark matter annihilates into standard model particles with a cross-section which is velocity dependent, then Local Group dwarf galaxies will not be the best place to search for the resulting gamma ray emission. A greater flux would be produced by more distant and massive halos, with larger velocity dispersions. We construct full-sky predictions for the gamma-ray emission from galaxy- and cluster-mass halos within $\sim 200 \, {\mathrm{Mpc}}$ using a suite of constrained $N$-body simulations (CSiBORG) based on the Bayesian Origin Reconstruction from Galaxies algorithm. Comparing to observations from the Fermi Large Area Telescope and marginalising over reconstruction uncertainties and other astrophysical contributions to the flux, we obtain constraints on the cross-section which are two (seven) orders of magnitude tighter than those obtained from dwarf spheroidals for $p$-wave ($d$-wave) annihilation. We find no evidence for either type of annihilation from dark matter particles with masses in the range $m_\chi = 2-500 \, {\mathrm{GeV}}/c^2$, for any channel. As an example, for annihilations producing bottom quarks with $m_\chi = 10 \, {\mathrm{GeV}}/c^2$, we find $a_{1} < 2.4 \times 10^{-21} \, {\mathrm{cm^3 s^{-1}}}$ and $a_{2} < 3.0 \times 10^{-18} \, {\mathrm{cm^3 s^{-1}}}$ at 95% confidence, where the product of the cross-section, $\sigma$, and relative particle velocity, $v$, is given by $\sigma v = a_\ell (v/c)^{2\ell}$ and $\ell=1, 2$ for $p$-, $d$-wave annihilation, respectively. Our bounds, although failing to exclude the thermal relic cross-section for velocity-dependent annihilation channels, are among the tightest to date

Optimal machine-driven acquisition of future cosmological data

International audienceWe present a set of maps classifying regions of the sky according to their information gain potential as quantified by Fisher information. These maps can guide the optimal retrieval of relevant physical information with targeted cosmological searches. Specifically, we calculated the response of observed cosmic structures to perturbative changes in the cosmological model and we charted their respective contributions to Fisher information. Our physical forward-modeling machinery transcends the limitations of contemporary analyses based on statistical summaries to yield detailed characterizations of individual 3D structures. We demonstrate this advantage using galaxy counts data and we showcase the potential of our approach by studying the information gain of the Coma cluster. We find that regions in the vicinity of the filaments and cluster core, where mass accretion ensues from gravitational infall, are the most informative with regard to our physical model of structure formation in the Universe. Hence, collecting data in those regions would be most optimal for testing our model predictions. The results presented in this work are the first of their kind to elucidate the inhomogeneous distribution of cosmological information in the Universe. This study paves a new way forward for the performance of efficient targeted searches for the fundamental physics of the Universe, where search strategies are progressively refined with new cosmological data sets within an active learning framework.Key words: galaxies: statistics / cosmology: observations / methods: data analysis / methods: statistical / large-scale structure of Univers

Constraints on dark matter annihilation and decay from the large-scale structure of the nearby universe

Decaying or annihilating dark matter particles could be detected through gamma-ray emission from the species they decay or annihilate into. This is usually done by modelling the flux from specific dark matter-rich objects such as the Milky Way halo, Local Group dwarfs and nearby groups. However, these objects are expected to have significant emission from baryonic processes as well, and the analyses discard gamma-ray data over most of the sky. Here we construct full-sky templates for gamma-ray flux from the large-scale structure within $\sim$200 Mpc by means of a suite of constrained $N$-body simulations (CSiBORG) produced using the Bayesian Origin Reconstruction from Galaxies algorithm. Marginalising over uncertainties in this reconstruction, small-scale structure and parameters describing astrophysical contributions to the observed gamma ray sky, we compare to observations from the Fermi Large Area Telescope to constrain dark matter annihilation cross-sections and decay rates through a Markov Chain Monte Carlo analysis. We rule out the thermal relic cross-section for $s$-wave annihilation for all $m_\chi \lesssim 7 {\rm \, GeV}/c^2$ at 95% confidence if the annihilation produces $Z$ bosons, gluons or quarks less massive than the bottom quark. We infer a contribution to the gamma ray sky with the same spatial distribution as dark matter decay at $3.3\sigma$. Although this could be due to dark matter decay via these channels with a decay rate $\Gamma \approx 3 \times 10^{-28} {\rm \, s^{-1}}$, we find that a power-law spectrum of index $p=-2.75^{+0.71}_{-0.46}$, likely of baryonic origin, is preferred by the data.Comment: 23 pages, 9 figures, 1 table. Submitted to Physical Review

Constraints on dark matter annihilation and decay from the large-scale structure of the nearby universe

Decaying or annihilating dark matter particles could be detected through gamma-ray emission from the species they decay or annihilate into. This is usually done by modelling the flux from specific dark matter-rich objects such as the Milky Way halo, Local Group dwarfs and nearby groups. However, these objects are expected to have significant emission from baryonic processes as well, and the analyses discard gamma-ray data over most of the sky. Here we construct full-sky templates for gamma-ray flux from the large-scale structure within $\sim$200 Mpc by means of a suite of constrained $N$-body simulations (CSiBORG) produced using the Bayesian Origin Reconstruction from Galaxies algorithm. Marginalising over uncertainties in this reconstruction, small-scale structure and parameters describing astrophysical contributions to the observed gamma ray sky, we compare to observations from the Fermi Large Area Telescope to constrain dark matter annihilation cross-sections and decay rates through a Markov Chain Monte Carlo analysis. We rule out the thermal relic cross-section for $s$-wave annihilation for all $m_\chi \lesssim 7 {\rm \, GeV}/c^2$ at 95% confidence if the annihilation produces $Z$ bosons, gluons or quarks less massive than the bottom quark. We infer a contribution to the gamma ray sky with the same spatial distribution as dark matter decay at $3.3\sigma$. Although this could be due to dark matter decay via these channels with a decay rate $\Gamma \approx 3 \times 10^{-28} {\rm \, s^{-1}}$, we find that a power-law spectrum of index $p=-2.75^{+0.71}_{-0.46}$, likely of baryonic origin, is preferred by the data

Non-parametric Bayesian Causal Modeling of the SARS-CoV-2 Viral Load Distribution vs. Patient's Age

The viral load of patients infected with SARS-CoV-2 varies on logarithmic scales and possibly with age. Controversial claims have been made in the literature regarding whether the viral load distribution actually depends on the age of the patients. Such a dependence would have implications for the COVID-19 spreading mechanism, the age-dependent immune system reaction, and thus for policymaking. We hereby develop a method to analyze viral-load distribution data as a function of the patients' age within a flexible, non-parametric, hierarchical, Bayesian, and causal model. This method can be applied to other contexts as well, and for this purpose, it is made freely available. The developed reconstruction method also allows testing for bias in the data. This could be due to, e.g., bias in patient-testing and data collection or systematic errors in the measurement of the viral load. We perform these tests by calculating the Bayesian evidence for each implied possible causal direction. When applying these tests to publicly available age and SARS-CoV-2 viral load data, we find a statistically significant increase in the viral load with age, but only for one of the two analyzed datasets. If we consider this dataset, and based on the current understanding of viral load's impact on patients' infectivity, we expect a non-negligible difference in the infectivity of different age groups. This difference is nonetheless too small to justify considering any age group as noninfectious