MCPtaggR: R package for accurate genotype calling in reduced representation sequencing data by eliminating error-prone markers based on genome comparison

Reduced representation sequencing (RRS) offers cost-effective, high-throughput genotyping platforms such as genotyping-by-sequencing (GBS). RRS reads are typically mapped onto a reference genome. However, mapping reads harbouring mismatches against the reference can potentially result in mismapping and biased mapping, leading to the detection of error-prone markers that provide incorrect genotype information. We established a genotype-calling pipeline named mappable collinear polymorphic tag genotyping (MCPtagg) to achieve accurate genotyping by eliminating error-prone markers. MCPtagg was designed for the RRS-based genotyping of a population derived from a biparental cross. The MCPtagg pipeline filters out error-prone markers prior to genotype calling based on marker collinearity information obtained by comparing the genome sequences of the parents of a population to be genotyped. A performance evaluation on real GBS data from a rice F2 population confirmed its effectiveness. Furthermore, our performance test using a genome assembly that was obtained by genome sequence polishing on an available genome assembly suggests that our pipeline performs well with converted genomes, rather than necessitating de novo assembly. This demonstrates its flexibility and scalability. The R package, MCPtaggR, was developed to provide functions for the pipeline and is available at https://github.com/tomoyukif/MCPtaggR

A New Method for Sex Determination Based on Detection of SRY, STS and Amelogenin Gene Regions with Simultaneous Amplification of Their Homologous Sequences by a Multiplex PCR

We have developed a new method for sex determination based on simultaneous detection of the SRY (sex-determining region Y), STS (steroid sulfatase) and amelogenin (AMELX and AMELY) gene regions and their homologous sequences. The sex of 246 blood samples was correctly determined by this method. An AMELY-deleted male sample, which would have been erroneously considered female based solely on analysis of the amelogenin locus, was successfully identified as male by the present method. The detection limit of this method was 63 pg of genomic DNA, and the male DNA component could be detected from mixed samples having a male:female ratio as low as 1:10. This method was useful for degraded DNA and possessed the human specificity. Practical application to 35 autopsy cases is described

Direct search for solar axions by using strong magnetic field and X-ray detectors

We have searched for axions which could be produced in the solar core by exploiting their conversion to X rays in a strong laboratory magnetic field. The signature of the solar axion is an increase in the rate of the X rays detected in a magnetic helioscope when the sun is within its acceptance. From the absence of such a signal we set a 95% confidence level limit on the axion coupling to two photons $g_{a\gamma\gamma}\equiv 1/M < 6.0\times 10^{-10}$ GeV$^{-1}$, provided the axion mass $m_a<0.03$ eV. The limit on the coupling is factor 4.5 more stringent than the recent experimental result. This is the first experiment whose sensitivity to $g_{a\gamma\gamma}$ is higher than the limit constrained by the solar age consideration.Comment: 11 pages, REVTeX, 4 eps figures included, submitted to PL

A Landmark Point Analysis with Cytotoxic Agents for Advanced NSCLC

IntroductionAs a result of recent publications, we hypothesized that period of 8 weeks after initiation of treatment is a useful landmark point for cytotoxic agents for advanced non-small cell lung cancer (NSCLC). To test this hypothesis, we conducted landmark analyses with clinical trials employing cytotoxic agents. Our goal was to assess the proper design of clinical trials with cytotoxic agents for NSCLC for maximizing patients’ benefit.MethodsWe conducted landmark analyses of a phase II study of pemetrexed in locally advanced or metastatic NSCLC and a phase III study of Four-Arm Cooperative Study for advanced NSCLC. A total of 806 patients who received chemotherapy (pemetrexed, cisplatin and irinotecan, paclitaxel and carboplatin, cisplatin and gemcitabine, cisplatin and vinorelbine) were included in this assessment.ResultsTumor-shrinkage rate at 8 weeks was significantly associated with longer survival in the study with pemetrexed (p = 0.043), whereas tumor-shrinkage rate at 4 weeks did not correlated with survival (p = 0.139). Similarly, using the Four-Arm Cooperative Study data, the optimal landmark point was 8 weeks (p = 0.002), not 4 weeks (p = 0.190).ConclusionThe landmark point for NSCLC was 8 weeks with all cytotoxic agents in our analysis when the therapy was given as a frontline or subsequent therapy. Our result suggests the concept of a disease-specific landmark point, which may lead to a change of phase II/III clinical study design to evaluate cytotoxic agents and clinical investigators, and their sponsors may consider an early look to assess the efficacy of cytotoxic agents for NSCLC

GESI: Gammachirp Envelope Similarity Index for Predicting Intelligibility of Simulated Hearing Loss Sounds

We propose an objective intelligibility measure (OIM), called the Gammachirp Envelope Similarity Index (GESI), which can predict the speech intelligibility (SI) of simulated hearing loss (HL) sounds for normal hearing (NH) listeners. GESI is an intrusive method that computes the SI metric using the gammachirp filterbank (GCFB), the modulation filterbank, and the extended cosine similarity measure. The unique features of GESI are that i) it reflects the hearing impaired (HI) listener's HL that appears in the audiogram and is caused by active and passive cochlear dysfunction, ii) it provides a single goodness metric, as in the widely used STOI and ESTOI, that can be used immediately to evaluate SE algorithms, and iii) it provides a simple control parameter to accept the level asymmetry of the reference and test sounds and to deal with individual listening conditions and environments. We evaluated GESI and the conventional OIMs, STOI, ESTOI, MBSTOI, and HASPI versions 1 and 2 by using four SI experiments on words of male and female speech sounds in both laboratory and remote environments. GESI was shown to outperform the other OIMs in the evaluations. GESI could be used to improve SE algorithms in assistive listening devices for individual HI listeners.Comment: This paper was submitted to JASA on March 14, 202