MapCap allows high-resolution detection and differential expression analysis of transcription start sites

The position, shape and number of transcription start sites (TSS) are critical determinants of gene regulation. Most methods developed to detect TSSs and study promoter usage are, however, of limited use in studies that demand quantification of expression changes between two or more groups. In this study, we combine high-resolution detection of transcription start sites and differential expression analysis using a simplified TSS quantification protocol, MAPCap (Multiplexed Affinity Purification of Capped RNA) along with the software icetea . Applying MAPCap on developing Drosophila melanogaster embryos and larvae, we detected stage and sex-specific promoter and enhancer activity and quantify the effect of mutants of maleless (MLE) helicase at X-chromosomal promoters. We observe that MLE mutation leads to a median 1.9 fold drop in expression of X-chromosome promoters and affects the expression of several TSSs with a sexually dimorphic expression on autosomes. Our results provide quantitative insights into promoter activity during dosage compensation

The Dipole Anisotropy of the 2mass Redshift Survey

We estimate the flux weighted acceleration on the Local Group (LG) from the near-infrared Two Micron All Sky Redshift Survey (2MRS). The near-infrared flux weighted dipoles are very robust because they closely approximate a mass weighted dipole, bypassing the effects of redshift distortions and require no preferred reference frame. We use this method with the redshift information to determine the change in dipole with distance. The LG dipole seemingly converges by 60 Mpc/h. Assuming convergence, the comparison of the 2MRS flux dipole and the CMB dipole provides a value for the combination of the mass density and luminosity bias parameters Omega_m^0.6/b_L= 0.40+/-0.09.Comment: 4 pages, 2 figures, Contribution to Rencontres de Moriond: Contents and Structures of the Universe, March 18-25, 2006, La Thuil

How COVID drove the evolution of fact-checking

With the outbreak of the coronavirus pandemic came a flood of novel misinformation. Ranging from harmless false cures to dangerous rhetoric targeting minorities, coronavirus-related misinformation spread quickly wherever the virus itself did. Fact-checking organizations around the world took up the charge against misinformation, essentially crowdsourcing the task of debunking false narratives. In many places, engagement with coronavirus-related content drove a large percentage of overall user engagement with fact-checking content, and the capacity organizations developed to address coronavirus-related misinformation was later deployed to debunk misinformation on other topics

Upper limits on neutrino masses from the 2dFGRS and WMAP: the role of priors

Solar, atmospheric, and reactor neutrino experiments have confirmed neutrino oscillations, implying that neutrinos have non-zero mass, but without pinning down their absolute masses. While it is established that the effect of neutrinos on the evolution of cosmic structure is small, the upper limits derived from large-scale structure data could help significantly to constrain the absolute scale of the neutrino masses. In a recent paper the 2dF Galaxy Redshift Survey (2dFGRS) team provided an upper limit m_nu,tot < 2.2 eV, i.e. approximately 0.7 eV for each of the three neutrino flavours, or phrased in terms of their contributioin to the matter density, Omega_nu/Omega_m < 0.16. Here we discuss this analysis in greater detail, considering issues of assumed 'priors' like the matter density Omega_m and the bias of the galaxy distribution with respect the dark matter distribution. As the suppression of the power spectrum depends on the ratio Omega_nu/Omega_m, we find that the out-of- fashion Mixed Dark Matter Model, with Omega_nu=0.2, Omega_m=1 and no cosmological constant, fits the 2dFGRS power spectrum and the CMB data reasonably well, but only for a Hubble constant H_0<50 km/s/Mpc. As a consequence, excluding low values of the Hubble constant, e.g. with the HST Key Project is important in order to get a strong constraint on the neutrino masses. We also comment on the improved limit by the WMAP team, and point out that the main neutrino signature comes from the 2dFGRS and the Lyman alpha forest.Comment: 24 pages, 12 figures Minor changes to matched version published in JCA

Modelling Processes and Products in the Cereal Chain

[EN] In recent years, modelling techniques have become more frequently adopted in the field of food processing, especially for cereal-based products, which are among the most consumed foods in the world. Predictive models and simulations make it possible to explore new approaches and optimize proceedings, potentially helping companies reduce costs and limit carbon emissions. Nevertheless, as the different phases of the food processing chain are highly specialized, advances in modelling are often unknown outside of a single domain, and models rarely take into account more than one step. This paper introduces the first high-level overview of modelling techniques employed in different parts of the cereal supply chain, from farming to storage, from drying to milling, from processing to consumption. This review, issued from a networking project including researchers from over 30 different countries, aims at presenting the current state of the art in each domain, showing common trends and synergies, to finally suggest promising future venues for research.The authors would like to acknowledge networking and article processing charge support by COST Action CA15118 (Mathematical and Computer Science Methods for Food Science and Industry).Carvalho, O.; Charalambides, MN.; Djekic, I.; Athanassiou, C.; Bakalis, S.; Benedito Fort, JJ.; Briffaz, A.... (2021). Modelling Processes and Products in the Cereal Chain. Foods. 10(1):1-18. https://doi.org/10.3390/foods10010082S11810

Reconstructed Density and Velocity Fields from the 2MASS Redshift Survey

We present the reconstructed real-space density and the predicted velocity fields from the Two Mass Redshift Survey (2MRS). The 2MRS is the densest all-sky redshift survey to date and includes about 23,200 galaxies with extinction corrected magnitudes brighter than K = 11.25. Our method is based on the expansion of these fields in Fourier-Bessel functions. Within this framework, the linear redshift distortions only affect the density field in the radial direction and can easily be deconvolved using a distortion matrix. Moreover, in this coordinate system, the velocity field is related to the density field by a simple linear transformation. The shot noise errors in the reconstructions are suppressed by means of a Wiener filter which yields a minimum variance estimate of the density and velocity fields. Using the reconstructed real-space density fields, we identify all major superclusters and voids. At 50 Mpc/h, our reconstructed velocity field indicates a back-side infall to the Great Attractor region of vi = (491 +/- 200)(beta/0.5) km/sec in the Local Group frame and v = (64 +/- 205)(beta/0.5) km/sec in the cosmic microwave background (CMB) frame and beta is the redshift distortion parameter. The direction of the reconstructed dipole agrees well with the dipole derived by Erdogdu et al. (2006). The misalignment between the reconstructed 2MRS and the CMB dipoles drops to 13 degrees at around 5000 km/sec but then increases at larger distances. A version of this paper with high resolution figures can be obtained from http://www.nottingham.ac.uk/~ppzzpeComment: 21 pages. 22 figures, accepted for publication in MNRAS. The figures are coarsely resolved, a version of this paper with high resolution figures can be obtained from http://www.nottingham.ac.uk/~ppzzp

Modelling Processes and Products in the Cereal Chain

ReviewIn recent years, modelling techniques have become more frequently adopted in the field of food processing, especially for cereal-based products, which are among the most consumed foods in the world. Predictive models and simulations make it possible to explore new approaches and optimize proceedings, potentially helping companies reduce costs and limit carbon emissions. Nevertheless, as the different phases of the food processing chain are highly specialized, advances in modelling are often unknown outside of a single domain, and models rarely take into account more than one step. This paper introduces the first high-level overview of modelling techniques employed in different parts of the cereal supply chain, from farming to storage, from drying to milling, from processing to consumption. This review, issued from a networking project including researchers from over 30 different countries, aims at presenting the current state of the art in each domain, showing common trends and synergies, to finally suggest promising future venues for researchinfo:eu-repo/semantics/publishedVersio

NF-KappaB expression correlates with apoptosis and angiogenesis in clear cell renal cell carcinoma tissues

<p>Abstract</p> <p>Background</p> <p>Clear cell renal cell carcinoma (ccRCC) is the most frequently encountered tumor in the adult kidney. Many factors are known to take part in the development and progression of this tumor. Nuclear factor kappa B (NF-κB) is a family of the genes that includes five members acting in events such as inflammation and apoptosis. In this study, the role of NF-κB (p50 subunit) in ccRCC and its relation to angiogenesis and apoptosis were investigated.</p> <p>Methods</p> <p>Formalin-fixed and paraffin embedded tissue blocks from 40 patients with ccRCC were studied. Expressions of NF-κB (p50), VEGF, EGFR, bc1-2 and p53 were detected immunohistochemically. The relationship of NF-κB with these markers and clinicopathological findings were evaluated.</p> <p>Results</p> <p>The expression of NF-κB was detected in 35 (85%), VEGF in 37 (92.5%), EGFR in 38 (95%), bc1-2 in 33 (82.5%) and p53 in 13 (32.5%) of 40 ccRCC patients. Statistical analyses revealed a significant relation between NF-κB expression and VEGF (p = 0.001), EGFR (p = 0.004), bc1-2 (p = 0.010) and p53 (p = 0.037). There was no significant correlation between NF-κB and such parameters as tumor grade, stage, age and sex.</p> <p>Conclusion</p> <p>The results of this study indicated that in ccRCC cases NF-κB was associated with markers of angiogenesis and apoptosis such as VEGF, EGFR, bc1-2 and p53. In addition, the results did not only suggest a close relationship between NF-κB and VEGF, EGFR, bc1-2 and p53 in ccRCC, but also indicate that NF-κB was a potential therapeutic target in the treatment of ccRCC resistant to chemotherapy.</p