A NEAT Way to do Network Programming

This work has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 644334 (NEAT). The views expressed are solely those of the author(s)Peer reviewedPreprin

Detecting binary compact-object mergers with gravitational waves: Understanding and Improving the sensitivity of the PyCBC search

We present an improved search for binary compact-object mergers using a network of ground-based gravitational-wave detectors. We model a volumetric, isotropic source population and incorporate the resulting distribution over signal amplitude, time delay, and coalescence phase into the ranking of candidate events. We describe an improved modeling of the background distribution, and demonstrate incorporating a prior model of the binary mass distribution in the ranking of candidate events. We find a $\sim 10\%$ and $\sim 20\%$ increase in detection volume for simulated binary neutron star and neutron star--binary black hole systems, respectively, corresponding to a reduction of the false alarm rates assigned to signals by between one and two orders of magnitude.Comment: 7 pages, 3 figures, as accepted by Ap

Handbook for integrated soil fertility management

This handbook presents Integrated Soil Fertility Management, commonly known as ISFM, as a key contributor to improving Africa’s soil and crop productivity, especially for the key staples in the continent that include maize, legumes, rice, cassava, bananas, sorghum, millet and coffee. It is meant for training of extension workers on soil fertility management techniques in sub-Saharan Africa and for workers involved in rural development that would like to learn more about the principles of ISFM. The handbook is also a useful primer on ISFM for educational organizations such as universities and technical colleges, and organizations involved in the development of policy on agriculture and rural development that need reference materials on ISFM techniques

Manuel de gestion intégrée de la fertilité des sols

Ce manuel présente la gestion intégrée de la fertilité des sols, communément appelée GIFS, comme un facteur clé de l’amélioration de la faible productivité des sols et des cultures en Afrique, surtout pour les principales cultures vivrières de base, à savoir : le maïs, le haricot, le riz, le manioc, les bananes, le sorgho, le millet et les autres cultures. Il est destiné à la formation des vulgarisateurs sur les techniques de gestion intégrée de la fertilité des sols en Afrique Sub-saharienne, et des agents impliqués dans le développement rural qui souhaiteraient en savoir plus sur les principes et pratiques GIFS. Le présent manuel se veut également une introduction pratique à la GIFS pour les institutions d’enseignement, telles que les universités et les collèges techniques, les organisations impliquées dans l’élaboration des politiques agricoles et de développement rural qui ont besoin de ces documents de référence sur les techniques GIFS, ainsi que d’autres organisations gouvernementales et non gouvernementales (ONG) qui cherchent à mettre en œuvre la GIFS

Nebular Line Emission During the Epoch of Reionization

Nebular emission lines associated with galactic HII regions carry information about both physical properties of the ionised gas and the source of ionising photons as well as providing the opportunity of measuring accurate redshifts and thus distances once a cosmological model is assumed. While nebular line emission has been extensively studied at lower redshift there are currently only few constraints within the epoch of reionisation (EoR, $z>6$), chiefly due to the lack of sensitive near-IR spectrographs. However, this will soon change with the arrival of the Webb Telescope providing sensitive near-IR spectroscopy covering the rest-frame UV and optical emission of galaxies in the EoR. In anticipation of Webb we combine the large cosmological hydrodynamical simulation Bluetides with photoionisation modelling to predict the nebular emission line properties of galaxies at $z=8\to 13$. We find good agreement with the, albeit limited, existing direct and indirect observational constraints on equivalent widths though poorer agreement with luminosity function constraints.Comment: 17 pages, accepted to MNRAS, significant modification from v1.0 data available at https://stephenmwilkins.github.io/BluetidesEmissionLines_Public

Deeper, Wider, Sharper: Next-Generation Ground-Based Gravitational-Wave Observations of Binary Black Holes

Next-generation observations will revolutionize our understanding of binary black holes and will detect new sources, such as intermediate-mass black holes. Primary science goals include: Discover binary black holes throughout the observable Universe; Reveal the fundamental properties of black holes; Uncover the seeds of supermassive black holes.Comment: 14 pages, 3 figures, White Paper Submitted to Astro2020 (2020 Astronomy and Astrophysics Decadal Survey) by GWIC 3G Science Case Team (GWIC: Gravitational Wave International Committee

Extreme mutation bias and high AT content in Plasmodium falciparum.

For reasons that remain unknown, the Plasmodium falciparum genome has an exceptionally high AT content compared to other Plasmodium species and eukaryotes in general - nearly 80% in coding regions and approaching 90% in non-coding regions. Here, we examine how this phenomenon relates to genome-wide patterns of de novo mutation. Mutation accumulation experiments were performed by sequential cloning of six P. falciparum isolates growing in human erythrocytes in vitro for 4 years, with 279 clones sampled for whole genome sequencing at different time points. Genome sequence analysis of these samples revealed a significant excess of G:C to A:T transitions compared to other types of nucleotide substitution, which would naturally cause AT content to equilibrate close to the level seen across the P. falciparum reference genome (80.6% AT). These data also uncover an extremely high rate of small indel mutation relative to other species, primarily associated with repetitive AT-rich sequences, in addition to larger-scale structural rearrangements focused in antigen-coding var genes. In conclusion, high AT content in P. falciparum is driven by a systematic mutational bias and ultimately leads to an unusual level of microstructural plasticity, raising the question of whether this contributes to adaptive evolution

No difference found in time to publication by statistical significance of trial results: a methodological review

Objective: Time-lag from study completion to publication is a potential source of publication bias in randomised controlled trials. This study sought to update the evidence base by identifying the effect of the statistical significance of research findings on time to publication of trial results.Design: Literature searches were carried out in four general medical journals from June 2013 to June 2014 inclusive (BMJ, JAMA, the Lancet and the New England Journal of Medicine). Setting: Methodological review of four general medical journals. Participants: Original research articles presenting the primary analyses from phase 2, 3 and 4 parallel-group randomised controlled trials were included. Main outcome measures: Time from trial completion to publication.Results: The median time from trial completion to publication was 431 days (n ¼ 208, interquartile range 278–618). A multivariable adjusted Cox model found no statistically significant difference in time to publication for trials reporting positive or negative results (hazard ratio: 0.86, 95% CI 0.64 to 1.16, p ¼ 0.32). Conclusion: In contrast to previous studies, this review did not demonstrate the presence of time-lag bias in time to publication. This may be a result of these articles being published in four high-impact general medical journals that may be more inclined to publish rapidly, whatever the findings. Further research is needed to explore the presence of time-lag bias in lower quality studies and lower impact journals

X-Linked G6PD Deficiency Protects Hemizygous Males but Not Heterozygous Females against Severe Malaria

BACKGROUND: Glucose-6-phosphate dehydrogenase (G6PD) is important in the control of oxidant stress in erythrocytes, the host cells for Plasmodium falciparum. Mutations in this enzyme produce X-linked deficiency states associated with protection against malaria, notably in Africa where the A− form of G6PD deficiency is widespread. Some reports have proposed that heterozygous females with mosaic populations of normal and deficient erythrocytes (due to random X chromosome inactivation) have malaria resistance similar to or greater than hemizygous males with populations of uniformly deficient erythrocytes. These proposals are paradoxical, and they are not consistent with currently hypothesized mechanisms of protection. METHODS AND FINDINGS: We conducted large case-control studies of the A− form of G6PD deficiency in cases of severe or uncomplicated malaria among two ethnic populations of rural Mali, West Africa, where malaria is hyperendemic. Our results indicate that the uniform state of G6PD deficiency in hemizygous male children conferred significant protection against severe, life-threatening malaria, and that it may have likewise protected homozygous female children. No such protection was evident from the mosaic state of G6PD deficiency in heterozygous females. We also found no significant differences in the parasite densities of males and females with differences in G6PD status. Pooled odds ratios from meta-analysis of our data and data from a previous study confirmed highly significant protection against severe malaria in hemizygous males but not in heterozygous females. Among the different forms of severe malaria, protection was principally evident against cerebral malaria, the most frequent form of life-threatening malaria in these studies. CONCLUSIONS: The A− form of G6PD deficiency in Africa is under strong natural selection from the preferential protection it provides to hemizygous males against life-threatening malaria. Little or no such protection is present among heterozygous females. Although these conclusions are consistent with data from at least one previous study, they have not heretofore been realized to our knowledge, and they therefore give fresh perspectives on malaria protection by G6PD deficiency as an X-linked trait