Bayesian evidence for two companions orbiting HIP 5158

We present results of a Bayesian analysis of radial velocity (RV) data for the star HIP 5158, confirming the presence of two companions and also constraining their orbital parameters. Assuming Keplerian orbits, the two-companion model is found to be e^{48} times more probable than the one-planet model, although the orbital parameters of the second companion are only weakly constrained. The derived orbital periods are 345.6 +/- 2.0 d and 9017.8 +/- 3180.7 d respectively, and the corresponding eccentricities are 0.54 +/- 0.04 and 0.14 +/- 0.10. The limits on planetary mass (m \sin i) and semimajor axis are (1.44 +/- 0.14 M_{J}, 0.89 +/- 0.01 AU) and (15.04 +/- 10.55 M_{J}, 7.70 +/- 1.88 AU) respectively. Owing to large uncertainty on the mass of the second companion, we are unable to determine whether it is a planet or a brown dwarf. The remaining `noise' (stellar jitter) unaccounted for by the model is 2.28 +/- 0.31 m/s. We also analysed a three-companion model, but found it to be e^{8} times less probable than the two-companion model.Comment: 5 pages, 4 figures, 3 tables. Added a couple of figures showing the residuals after one and two companion fits. Accepted for publication in MNRAS Letter

Frequent expansion of Plasmodium vivax Duffy Binding Protein in Ethiopia and its epidemiological significance.

Plasmodium vivax invasion of human erythrocytes depends on the Duffy Binding Protein (PvDBP) which interacts with the Duffy antigen. PvDBP copy number has been recently shown to vary between P. vivax isolates in Sub-Saharan Africa. However, the extent of PvDBP copy number variation, the type of PvDBP multiplications, as well as its significance across broad samples are still unclear. We determined the prevalence and type of PvDBP duplications, as well as PvDBP copy number variation among 178 Ethiopian P. vivax isolates using a PCR-based diagnostic method, a novel quantitative real-time PCR assay and whole genome sequencing. For the 145 symptomatic samples, PvDBP duplications were detected in 95 isolates, of which 81 had the Cambodian and 14 Malagasy-type PvDBP duplications. PvDBP varied from 1 to >4 copies. Isolates with multiple PvDBP copies were found to be higher in symptomatic than asymptomatic infections. For the 33 asymptomatic samples, PvDBP was detected with two copies in two of the isolates, and both were the Cambodian-type PvDBP duplication. PvDBP copy number in Duffy-negative heterozygotes was not significantly different from that in Duffy-positives, providing no support for the hypothesis that increased copy number is a specific association with Duffy-negativity, although the number of Duffy-negatives was small and further sampling is required to test this association thoroughly

Including Everyone, Everywhere:Understanding Opportunities and Challenges of Geographic Gender-Inclusion in OSS

The gender gap is a significant concern facing the software industry as the development becomes more geographically distributed. Widely shared reports indicate that gender differences may be specific to each region. However, how complete can these reports be with little to no research reflective of the Open Source Software (OSS) process and communities software is now commonly developed in? Our study presents a multi-region geographical analysis of gender inclusion on GitHub. This mixed-methods approach includes quantitatively investigating differences in gender inclusion in projects across geographic regions and investigate these trends over time using data from contributions to 21,456 project repositories. We also qualitatively understand the unique experiences of developers contributing to these projects through a survey that is strategically targeted to developers in various regions worldwide. Our findings indicate that gender diversity is low across all parts of the world, with no substantial difference across regions. However, there has been statistically significant improvement in diversity worldwide since 2014, with certain regions such as Africa improving at faster pace. We also find that most motivations and barriers to contributions (e.g., lack of resources to contribute and poor working environment) were shared across regions, however, some insightful differences, such as how to make projects more inclusive, did arise. From these findings, we derive and present implications for tools that can foster inclusion in open source software communities and empower contributions from everyone, everywhere

Directed follow-up strategy of low-cadence photometric surveys in Search of transiting exoplanets - I. Bayesian approach for adaptive scheduling

We propose a novel approach to utilize low-cadence photometric surveys for exoplanetary transit search. Even if transits are undetectable in the survey database alone, it can still be useful for finding preferred times for directed follow-up observations that will maximize the chances to detect transits. We demonstrate the approach through a few simulated cases. These simulations are based on the Hipparcos Epoch Photometry data base, and the transiting planets whose transits were already detected there. In principle, the approach we propose will be suitable for the directed follow-up of the photometry from the planned Gaia mission, and it can hopefully significantly increase the yield of exoplanetary transits detected, thanks to Gaia.Comment: 11 pages, 11 figures,accepted for publication in MNRA

Rapid detection of BRCA1/2 recurrent mutations in Chinese breast and ovarian cancer patients with multiplex SNaPshot genotyping panels.

BRCA1/2 mutations are significant risk factors for hereditary breast and ovarian cancer (HBOC), its mutation frequency in HBOC of Chinese ethnicity is around 9%, in which nearly half are recurrent mutations. In Hong Kong and China, genetic testing and counseling are not as common as in the West. To reduce the barrier of testing, a multiplex SNaPshot genotyping panel that targeted 25 Chinese BRCA1/2 mutation hotspots was developed, and its feasibility was evaluated in a local cohort of 441 breast and 155 ovarian cancer patients. For those who tested negative, they were then subjected to full-gene testing with next-generation sequencing (NGS). BRCA mutation prevalence in this cohort was 8.05% and the yield of the recurrent panel was 3.52%, identifying over 40% of the mutation carriers. Moreover, from 79 Chinese breast cancer cases recruited overseas, 2 recurrent mutations and one novel BRCA2 mutation were detected by the panel and NGS respectively. The developed genotyping panel showed to be an easy-to-perform and more affordable testing tool that can provide important contributions to improve the healthcare of Chinese women with cancer as well as family members that harbor high risk mutations for HBOC

On the Eccentricity Distribution of Short-Period Single-Planet Systems

We apply standard Markov chain Monte Carlo (MCMC) analysis techniques for 50 short- period, single-planet systems discovered with radial velocity technique. We develop a new method for accessing the significance of a non-zero orbital eccentricity, namely {\Gamma} analysis, which combines frequentist bootstrap approach with Bayesian analysis of each simulated data set. We find the eccentricity estimations from {\Gamma} analysis are generally consistent with results from both standard MCMC analysis and previous references. The {\Gamma} method is particular useful for assessing the significance of small eccentricities. Our results suggest that the current sample size is insufficient to draw robust conclusions about the roles of tidal interaction and perturbations in shaping the eccentricity distribution of short-period single-planet systems. We use a Bayesian population analysis to show that a mixture of analytical distributions is a good approximation of the underlying eccentricity distribution. For short-period planets, we find the most probable values of parameters in the analytical functions given the observed eccentricities. These analytical functions can be used in theoretical investigations or as priors for the eccentricity distribution when analyzing short-period planets. As the measurement precision improves and sample size increases, the method can be applied to more complex parametrizations for the underlying distribution of eccentricity for extrasolar planetary systems.Comment: 13 pages, 11 figures, 4 tables, accepted by MNRA

6.7 GHz methanol absorption toward the Seyfert 2 galaxy NGC 3079

The detection of the 6.7 GHz line of methanol (CH3OH) is reported for the first time toward an object beyond the Magellanic Clouds. Using the Effelsberg 100 m telescope, two absorption features were identified toward the Seyfert 2 galaxy NGC 3079. Both components probably originated on lines-of-sight toward the central region, presumably absorbing the radio continuum of the nuclear sources A, B, and E of NGC 3079. One absorption feature, at the systemic velocity, is narrow and may arise from gas not related to the nuclear environment of the galaxy. The weaker blue-shifted component is wider and may trace outflowing gas. Total A-type CH3OH column densities are estimated to be between a few times 10^13 and a few times 10^15 cm^-2. Because of a highly frequency-dependent continuum background, the overall similarity of HI, OH, and CH3OH absorption profiles hints at molecular clouds that cover the entire area occupied by the nuclear radio continuum sources ~ 4 pc.Comment: 4 pages, 1 figure, accepted for publication in A&A Letter

Whole genome sequencing of Plasmodium vivax isolates reveals frequent sequence and structural polymorphisms in erythrocyte binding genes.

Plasmodium vivax malaria is much less common in Africa than the rest of the world because the parasite relies primarily on the Duffy antigen/chemokine receptor (DARC) to invade human erythrocytes, and the majority of Africans are Duffy negative. Recently, there has been a dramatic increase in the reporting of P. vivax cases in Africa, with a high number of them being in Duffy negative individuals, potentially indicating P. vivax has evolved an alternative invasion mechanism that can overcome Duffy negativity. Here, we analyzed single nucleotide polymorphism (SNP) and copy number variation (CNV) in Whole Genome Sequence (WGS) data from 44 P. vivax samples isolated from symptomatic malaria patients in southwestern Ethiopia, where both Duffy positive and Duffy negative individuals are found. A total of 123,711 SNPs were detected, of which 22.7% were nonsynonymous and 77.3% were synonymous mutations. The largest number of SNPs were detected on chromosomes 9 (24,007 SNPs; 19.4% of total) and 10 (16,852 SNPs, 13.6% of total). There were particularly high levels of polymorphism in erythrocyte binding gene candidates including merozoite surface protein 1 (MSP1) and merozoite surface protein 3 (MSP3.5, MSP3.85 and MSP3.9). Two genes, MAEBL and MSP3.8 related to immunogenicity and erythrocyte binding function were detected with significant signals of positive selection. Variation in gene copy number was also concentrated in genes involved in host-parasite interactions, including the expansion of the Duffy binding protein gene (PvDBP) on chromosome 6 and MSP3.11 on chromosome 10. Based on the phylogeny constructed from the whole genome sequences, the expansion of these genes was an independent process among the P. vivax lineages in Ethiopia. We further inferred transmission patterns of P. vivax infections among study sites and showed various levels of gene flow at a small geographical scale. The genomic features of P. vivax provided baseline data for future comparison with those in Duffy-negative individuals and allowed us to develop a panel of informative Single Nucleotide Polymorphic markers diagnostic at a micro-geographical scale

Distinct Streptococcus pneumoniae cause invasive disease in Papua New Guinea

Streptococcus pneumoniae is a key contributor to childhood morbidity and mortality in Papua New Guinea (PNG). For the first time, whole genome sequencing of 174 isolates has enabled detailed characterisation of diverse S. pneumoniae causing invasive disease in young children in PNG, 1989-2014. This study captures the baseline S. pneumoniae population prior to the introduction of 13-valent pneumococcal conjugate vaccine (PCV13) into the national childhood immunisation programme in 2014. Relationships amongst lineages, serotypes and antimicrobial resistance traits were characterised, and the population was viewed in the context of a global collection of isolates. The analyses highlighted adiverse S. pneumoniae population associated with invasive disease in PNG, with 45 unique Global Pneumococcal Sequence Clusters (GPSCs) observed amongst the 174 isolates reflecting multiple lineages observed in PNG that have not been identified in other geographic locations. The majority of isolates were from children with meningitis, of which 52% (n=72) expressed non-PCV13 serotypes. Over a third of isolates were predicted to be resistant to at least one antimicrobial. PCV13 serotype isolates had 10.1 times the odds of being multidrug-resistant (MDR) compared to non-vaccine serotype isolates, and no isolates with GPSCs unique to PNG were MDR. Serotype 2 was the most commonly identified serotype; we identified a highly clonal cluster of serotype 2 isolates unique to PNG, and a distinct second cluster indicative of long-distance transmission. Ongoing surveillance, including whole-genome sequencing, is needed to ascertain the impact of the national PCV13 programme upon the S. pneumoniae population, including serotype replacement and antimicrobial resistance traits. © 2022 The Authors