Method and apparatus for eliminating luminol interference material

A method and apparatus for removing porphyrins from a fluid sample which are unrelated to the number of bacteria present in the sample and prior to combining the sample with luminol reagent to produce a light reaction is disclosed. The method involves a pre-incubation of the sample with a dilute concentration of hydrogen peroxide which inactivates the interfering soluble porphyrins. Further, by delaying taking a light measurement for a predetermined time period after combining the hydrogen peroxide-treated water sample with a luminol reagent, the luminescence produced by the reaction of the luminol reagent with ions present in the solution, being short lived, will have died out so that only porphyrins within the bacteria which have been released by rupturing the cells with the sodium hydroxide in the luminol reagent, will be measured. The measurement thus obtained can then be related to the concentration of live and dead bacteria in the fluid sample

Rapid, quantitative determination of bacteria in water

A bioluminescent assay for ATP in water borne bacteria is made by adding nitric acid to a water sample with concentrated bacteria to rupture the bacterial cells. The sample is diluted with sterile, deionized water, then mixed with a luciferase-luciferin mixture and the resulting light output of the bioluminescent reaction is measured and correlated with bacteria present. A standard and a blank also are presented so that the light output can be correlated to bacteria in the sample and system noise can be substracted from the readings. A chemiluminescent assay for iron porphyrins in water borne bacteria is made by adding luminol reagent to a water sample with concentrated bacteria and measuring the resulting light output of the chemiluminescent reaction

Asteroseismology and Spectropolarimetry of the Exoplanet Host Star λ Serpentis

The bright star lambda Ser hosts a hot Neptune with a minimum mass of 13.6 M & OPLUS; and a 15.5 day orbit. It also appears to be a solar analog, with a mean rotation period of 25.8 days and surface differential rotation very similar to the Sun. We aim to characterize the fundamental properties of this system and constrain the evolutionary pathway that led to its present configuration. We detect solar-like oscillations in time series photometry from the Transiting Exoplanet Survey Satellite, and we derive precise asteroseismic properties from detailed modeling. We obtain new spectropolarimetric data, and we use them to reconstruct the large-scale magnetic field morphology. We reanalyze the complete time series of chromospheric activity measurements from the Mount Wilson Observatory, and we present new X-ray and ultraviolet observations from the Chandra and Hubble space telescopes. Finally, we use the updated observational constraints to assess the rotational history of the star and estimate the wind braking torque. We conclude that the remaining uncertainty on the stellar age currently prevents an unambiguous interpretation of the properties of lambda Ser, and that the rate of angular momentum loss appears to be higher than for other stars with a similar Rossby number. Future asteroseismic observations may help to improve the precision of the stellar age

Dynamics and nucleation of dislocations in crystals

Hydrogen-poor superluminous supernovae (SLSNe-I) have been predominantly found in low-metallicity, star-forming dwarf galaxies. Here we identify Gaia17biu/SN 2017egm as an SLSN-I occurring in a "normal" spiral galaxy (NGC 3191) in terms of stellar mass (several times 10^10 M_sun) and metallicity (roughly Solar). At redshift z=0.031, Gaia17biu is also the lowest redshift SLSN-I to date, and the absence of a larger population of SLSNe-I in dwarf galaxies of similar redshift suggests that metallicity is likely less important to the production of SLSNe-I than previously believed. With the smallest distance and highest apparent brightness for an SLSN-I, we are able to study Gaia17biu in unprecedented detail. Its pre-peak near-ultraviolet to optical color is similar to that of Gaia16apd and among the bluest observed for an SLSN-I while its peak luminosity (M_g = -21 mag) is substantially lower than Gaia16apd. Thanks to the high signal-to-noise ratios of our spectra, we identify several new spectroscopic features that may help to probe the properties of these enigmatic explosions. We detect polarization at the ~0.5% level that is not strongly dependent on wavelength, suggesting a modest, global departure from spherical symmetry. In addition, we put the tightest upper limit yet on the radio luminosity of an SLSN-I with <5.4x10^26 erg/s/Hz (at 10 GHz), which is almost a factor of 40 better than previous upper limits and one of the few measured at an early stage in the evolution of an SLSN-I. This limit largely rules out an association of this SLSNe-I with known populations of gamma-ray burst (GRB) like central engines.Comment: Accepted for publication in ApJ. Ancillary ASCII tables added: TRL.txt -- blackbody temperature, radius and luminosity; uvw2uvm2uvw1uvu.txt -- UV photometry; BgVri.txt -- optical photometry; zJHK.txt -- NIR photometr

CARMENES input catalog of M dwarfs: VII. New rotation periods for the survey stars and their correlations with stellar activity

Abridged: We measured photometric and spectroscopic $P_{\rm rot}$ for a large sample of nearby bright M dwarfs with spectral types from M0 to M9, as part of our continual effort to fully characterize the Guaranteed Time Observation programme stars of the CARMENES survey. We determine $P_{\rm rot}$ for 129 stars. Combined with the literature, we tabulate $P_{\rm rot}$ for 261 stars, or 75% of our sample. We evaluate the plausibility of all periods available for this sample by comparing them with activity signatures and checking for consistency between multiple measurements. We find that 166 of these stars have independent evidence that confirmed their $P_{\rm rot}$. There are inconsistencies in 27 periods, which we classify as debated. A further 68 periods are identified as provisional detections that could benefit from independent verification. We provide an empirical relation for the $P_{\rm rot}$ uncertainty as a function of the $P_{\rm rot}$ value, based on the dispersion of the measurements. We show that published formal errors seem to be often underestimated for periods $\gtrsim 10$ d. We highlight the importance of independent verification on $P_{\rm rot}$ measurements, especially for inactive M dwarfs. We examine rotation-activity relations with emission in X-rays, H$\alpha$, Ca II H & K, and surface magnetic field strengths. We find overall agreement with previous works, as well as tentative differences in the partially versus fully convective subsamples. We show $P_{\rm rot}$ as a function of stellar mass, age, and galactic kinematics. With the notable exception of three transiting planet systems and TZ Ari, all known planet hosts in this sample have $P_{\rm rot} \gtrsim 15$ d. This indicates that important limitations need to be overcome before the radial velocity technique can be routinely used to detect and study planets around young and active stars.Comment: Accepted for publication in A&

A candidate super-Earth planet orbiting near the snow line of Barnard’s star

Barnard’s star is a red dwarf, and has the largest proper motion (apparent motion across the sky) of all known stars. At a distance of 1.8 parsecs, it is the closest single star to the Sun; only the three stars in the α Centauri system are closer. Barnard’s star is also among the least magnetically active red dwarfs known and has an estimated age older than the Solar System. Its properties make it a prime target for planetary searches; various techniques with different sensitivity limits have been used previously, including radial-velocity imaging, astrometry and direct imaging, but all ultimately led to negative or null results. Here we combine numerous measurements from high-precision radial-velocity instruments, revealing the presence of a low-amplitude periodic signal with a period of 233 days. Independent photometric and spectroscopic monitoring, as well as an analysis of instrumental systematic effects, suggest that this signal is best explained as arising from a planetary companion. The candidate planet around Barnard’s star is a cold super-Earth, with a minimum mass of 3.2 times that of Earth, orbiting near its snow line (the minimum distance from the star at which volatile compounds could condense). The combination of all radial-velocity datasets spanning 20 years of measurements additionally reveals a long-term modulation that could arise from a stellar magnetic-activity cycle or from a more distant planetary object. Because of its proximity to the Sun, the candidate planet has a maximum angular separation of 220 milliarcseconds from Barnard’s star, making it an excellent target for direct imaging and astrometric observations in the future. © 2018, Springer Nature Limited.The results are based on observations made with the CARMENES instrument at the 3.5-m telescope of the Centro Astronomico Hispano-Aleman de Calar Alto (CAHA, Almeria, Spain), funded by the German Max-Planck-Gesellschaft (MPG), the Spanish Consejo Superior de Investigaciones Cientificas (CSIC), the European Union and the CARMENES Consortium members; the 90-cm telescope at the Sierra Nevada Observatory (Granada, Spain) and the 40-cm robotic telescope at the SPACEOBS observatory (San Pedro de Atacama, Chile), both operated by the Instituto de Astrofisica de Andalucia (IAA); and the 80-cm Joan Oro Telescope (TJO) of the Montsec Astronomical Observatory (OAdM), owned by the Generalitat de Catalunya and operated by the Institute of Space Studies of Catalonia (IEEC). This research was supported by the following institutions, grants and fellowships: Spanish MINECO ESP2016-80435-C2-1-R, ESP2016-80435-C2-2-R, AYA2016-79425-C3-1-P, AYA2016-79245-C3-2-P, AYA2016-79425-C3-3-P, AYA2015-69350-C3-2-P, ESP2014-54362-P, AYA2014-56359-P, RYC-2013-14875; Generalitat de Catalunya/CERCA programme; Fondo Europeo de Desarrollo Regional (FEDER); German Science Foundation (DFG) Research Unit FOR2544, project JE 701/3-1; STFC Consolidated Grants ST/P000584/1, ST/P000592/1, ST/M001008/1; NSF AST-0307493; Queen Mary University of London Scholarship; Perren foundation grant; CONICYT-FONDECYT 1161218, 3180405; Swiss National Science Foundation (SNSF); Koshland Foundation and McDonald-Leapman grant; and NASA Hubble Fellowship grant HST-HF2-51399.001. J.T. is a Hubble Fellow

IL28B genetic variations are associated with high sustained virological response (SVR) of interferon-α plus ribavirin therapy in Taiwanese chronic HCV infection

Chronic hepatitis C virus (HCV) infection patients exhibit different sustained virological responses (SVRs) following the treatment with pegylated interferon-α (IFN-α) and ribavirin. Genome-wide association studies consistently linked SVR of IFN-α-based therapy to the IL28B single-nucleotide polymorphisms (SNPs) on chromosome 19q.13 in various populations. This study was undertaken to investigate the association of IL28B SNPs with SVR in a cohort of Taiwanese chronic HCV patients. Ten SNPs of IL28B were genotyped in 728 chronic HCV patients and 960 healthy controls. Genotype distributions, allele frequencies and haplotypes were tested for SVR and susceptibility in Taiwanese chronic HCV patients. Non-genotype 1 infection (adjusted P=3.3 × 10−12, odds ratio (OR) 0.179; 95% confidence interval (CI): 0.110–0.290) and low HCV viral load (<400 000 IU ml–1) (adjusted P=3.5 × 10−9, OR 0.299; 95% CI: 0.200–0.446) were two major factors identified for high SVR. Notably, eight IL28B SNPs including previously described disease-associated SNPs (Trend test P=0.005) were significantly associated with SVR. Our data indicate that IL28B polymorphisms are the essential contributing factors for high SVR in Taiwanese chronic HCV patients. Combination of virus genotyping and host genetic data may be used to select the optimal treatment regimes in IFN-based therapy

Sequence and Structure Signatures of Cancer Mutation Hotspots in Protein Kinases

Protein kinases are the most common protein domains implicated in cancer, where somatically acquired mutations are known to be functionally linked to a variety of cancers. Resequencing studies of protein kinase coding regions have emphasized the importance of sequence and structure determinants of cancer-causing kinase mutations in understanding of the mutation-dependent activation process. We have developed an integrated bioinformatics resource, which consolidated and mapped all currently available information on genetic modifications in protein kinase genes with sequence, structure and functional data. The integration of diverse data types provided a convenient framework for kinome-wide study of sequence-based and structure-based signatures of cancer mutations. The database-driven analysis has revealed a differential enrichment of SNPs categories in functional regions of the kinase domain, demonstrating that a significant number of cancer mutations could fall at structurally equivalent positions (mutational hotspots) within the catalytic core. We have also found that structurally conserved mutational hotspots can be shared by multiple kinase genes and are often enriched by cancer driver mutations with high oncogenic activity. Structural modeling and energetic analysis of the mutational hotspots have suggested a common molecular mechanism of kinase activation by cancer mutations, and have allowed to reconcile the experimental data. According to a proposed mechanism, structural effect of kinase mutations with a high oncogenic potential may manifest in a significant destabilization of the autoinhibited kinase form, which is likely to drive tumorigenesis at some level. Structure-based functional annotation and prediction of cancer mutation effects in protein kinases can facilitate an understanding of the mutation-dependent activation process and inform experimental studies exploring molecular pathology of tumorigenesis

Identification of a BRCA2-Specific modifier locus at 6p24 related to breast cancer risk

Common genetic variants contribute to the observed variation in breast cancer risk for BRCA2 mutation carriers; those known to date have all been found through population-based genome-wide association studies (GWAS). To comprehensively identify breast cancer risk modifying loci for BRCA2 mutation carriers, we conducted a deep replication of an ongoing GWAS discovery study. Using the ranked P-values of the breast cancer associations with the imputed genotype of 1.4 M SNPs, 19,029 SNPs were selected and designed for inclusion on a custom Illumina array that included a total of 211,155 SNPs as part of a multi-consortial project. DNA samples from 3,881 breast cancer affected and 4,330 unaffected BRCA2 mutation carriers from 47 studies belonging to the Consortium of Investigators of Modifiers of BRCA1/2 were genotyped and available for analysis. We replicated previously reported breast cancer susceptibility alleles in these BRCA2 mutation carriers and for several regions (including FGFR2, MAP3K1, CDKN2A/B, and PTHLH) identified SNPs that have stronger evidence of association than those previously published. We also identified a novel susceptibility allele at 6p24 that was inversely associated with risk in BRCA2 mutation carriers (rs9348512; per allele HR = 0.85, 95% CI 0.80-0.90, P = 3.9×10−8). This SNP was not associated with breast cancer risk either in the general population or in BRCA1 mutation carriers. The locus lies within a region containing TFAP2A, which encodes a transcriptional activation protein that interacts with several tumor suppressor genes. This report identifies the first breast cancer risk locus specific to a BRCA2 mutation background. This comprehensive update of novel and previously reported breast cancer susceptibility loci contributes to the establishment of a panel of SNPs that modify breast cancer risk in BRCA2 mutation carriers. This panel may have clinical utility for women with BRCA2 mutations weighing options for medical prevention of breast cancer