Spatio-temporal patterns of beaked whale echolocation signals in the North Pacific.

At least ten species of beaked whales inhabit the North Pacific, but little is known about their abundance, ecology, and behavior, as they are elusive and difficult to distinguish visually at sea. Six of these species produce known species-specific frequency modulated (FM) echolocation pulses: Baird's, Blainville's, Cuvier's, Deraniyagala's, Longman's, and Stejneger's beaked whales. Additionally, one described FM pulse (BWC) from Cross Seamount, Hawai'i, and three unknown FM pulse types (BW40, BW43, BW70) have been identified from almost 11 cumulative years of autonomous recordings at 24 sites throughout the North Pacific. Most sites had a dominant FM pulse type with other types being either absent or limited. There was not a strong seasonal influence on the occurrence of these signals at any site, but longer time series may reveal smaller, consistent fluctuations. Only the species producing BWC signals, detected throughout the Pacific Islands region, consistently showed a diel cycle with nocturnal foraging. By comparing stranding and sighting information with acoustic findings, we hypothesize that BWC signals are produced by ginkgo-toothed beaked whales. BW43 signal encounters were restricted to Southern California and may be produced by Perrin's beaked whale, known only from Californian waters. BW70 signals were detected in the southern Gulf of California, which is prime habitat for Pygmy beaked whales. Hubb's beaked whale may have produced the BW40 signals encountered off central and southern California; however, these signals were also recorded off Pearl and Hermes Reef and Wake Atoll, which are well south of their known range

A predictive model for serous epithelial ovarian cancer chemo-response using clinical characteristics

One of the prognostic factors most highly associated with ovarian cancer survival is response to initial chemotherapy. Current prediction models of chemo-response built with comprehensive molecular datasets, like The Cancer Genome Atlas (TCGA), could be improved by including clinical and outcomes data designed to study response to treatment. The objective of this study was to create a prediction model of ovarian cancer chemo-response using clinical-pathological features, and to compare its performance with a similar TCGA clinical model

Genetic and seasonal determinants of vitamin D status in Confederated Salish and Kootenai Tribes (CSKT) participants

Background: Vitamin D is a hormone produced in the skin upon ultraviolet B (UVB) radiation. Vitamin D is a crucial regulator of calcium and phosphate levels for bone mineralization and other physiological roles. Vitamin D levels vary globally in human populations due to genetics, geography, and other demographic factors. It is estimated that 20-85 % of the variability in vitamin D levels is driven by genetic variation. To improve our understanding of contributors to vitamin D levels, we conducted a candidate-gene study in partnership with the Confederated Salish and Kootenai Tribes (CSKT). Methods: We recruited 472 CSKT study participants on the Flathead Reservation in Montana. Demographic factors included age, BMI, and gender (185 male and 287 female; ≥ 18 years old). Genomic DNA and plasma were isolated from whole blood. We sequenced 14 vitamin D regulatory candidate genes: CASR, CUBN, CYP2R1, CYP3A4,CYP24A1, CYP27B1, DHCR7, GC, RXRA, RXRB, RXRG, SULT2A1, UGT1A4, and VDR. We also measured plasma levels of vitamin D and vitamin D metabolites by liquid chromatography/mass-spectrometry (LC/MS), including the clinical marker of vitamin D status, 25-hydroxyvitamin D3 [25(OH)D3]. We tested demographic factors as well as common and rare genetic variants for statistical associations with vitamin D levels using bioinformatics software and R statistical programming language code. Results: We identified 7,370 total genetic variants with 8% (n = 585) of them being novel. We identified 60 genetic variants that may be of clinical significance (disease associated or predicted to influence medication response). Vitamin D levels were below sufficiency [25(OH)D3 + 25(OH)D2 levels \u3c 20 ng/mL] in 56 % of CSKT participants across the year. We observed seasonal vitamin D and metabolite level fluctuations in a seasonal, sinusoidal statistical model with peak concentrations in June – August and trough concentrations in December – February. In linear regression analysis, we found that age, BMI, season, and 5 variants in CUBN and CYP3A4 were significantly associated with 25(OH)D3 concentration (p-value\u3c 0.05). In logistic regression, we found that 4 variants in CUBN, CYP3A4, and UGT1A4 were associated with 25(OH)D sufficiency status [25(OH)D3 + 25(OH)D2 levels of 20 ng/mL] (p-value\u3c 0.05). Multivariate linear regression analysis revealed that genetic variation alone explained ~13% of the variability in 25(OH)D3 concentration in CSKT participants. Genetic variation and environmental factors together explained ~23 % of the variability in 25(OH)D3 concentration in CSKT participants. It is likely that genetic variation in additional genes and other environmental factors (e.g., dietary vitamin D intake) that were not included in this study explain the remaining variability in 25(OH)D3 concentration. Conclusion: This research addresses the need for increased inclusion of American Indian and Alaska Natives in precision medicine health research. We are the first to describe the contribution of season and genetics to vitamin D levels in an American Indian population. Our next steps will be to use these findings to perform mechanistic studies and develop interventional strategies for the CSKT people

The SUN protein UNC-84 is required only in force-bearing cells to maintain nuclear envelope architecture

The nuclear envelope (NE) consists of two evenly spaced bilayers, the inner and outer nuclear membranes. The Sad1p and UNC-84 (SUN) proteins and Klarsicht, ANC-1, and Syne homology (KASH) proteins that interact to form LINC (linker of nucleoskeleton and cytoskeleton) complexes connecting the nucleoskeleton to the cytoskeleton have been implicated in maintaining NE spacing. Surprisingly, the NE morphology of most Caenorhabditis elegans nuclei was normal in the absence of functional SUN proteins. Distortions of the perinuclear space observed in unc-84 mutant muscle nuclei resembled those previously observed in HeLa cells, suggesting that SUN proteins are required to maintain NE architecture in cells under high mechanical strain. The UNC-84 protein with large deletions in its luminal domain was able to form functional NE bridges but had no observable effect on NE architecture. Therefore, SUN-KASH bridges are only required to maintain NE spacing in cells subjected to increased mechanical forces. Furthermore, SUN proteins do not dictate the width of the NE

The Baryon Oscillation Spectroscopic Survey of SDSS-III

The Baryon Oscillation Spectroscopic Survey (BOSS) is designed to measure the scale of baryon acoustic oscillations (BAO) in the clustering of matter over a larger volume than the combined efforts of all previous spectroscopic surveys of large scale structure. BOSS uses 1.5 million luminous galaxies as faint as i=19.9 over 10,000 square degrees to measure BAO to redshifts z<0.7. Observations of neutral hydrogen in the Lyman alpha forest in more than 150,000 quasar spectra (g<22) will constrain BAO over the redshift range 2.15<z<3.5. Early results from BOSS include the first detection of the large-scale three-dimensional clustering of the Lyman alpha forest and a strong detection from the Data Release 9 data set of the BAO in the clustering of massive galaxies at an effective redshift z = 0.57. We project that BOSS will yield measurements of the angular diameter distance D_A to an accuracy of 1.0% at redshifts z=0.3 and z=0.57 and measurements of H(z) to 1.8% and 1.7% at the same redshifts. Forecasts for Lyman alpha forest constraints predict a measurement of an overall dilation factor that scales the highly degenerate D_A(z) and H^{-1}(z) parameters to an accuracy of 1.9% at z~2.5 when the survey is complete. Here, we provide an overview of the selection of spectroscopic targets, planning of observations, and analysis of data and data quality of BOSS.Comment: 49 pages, 16 figures, accepted by A

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: measurements of the growth of structure and expansion rate at z=0.57 from anisotropic clustering

We analyze the anisotropic clustering of massive galaxies from the Sloan Digital Sky Survey III Baryon Oscillation Spectroscopic Survey (BOSS) Data Release 9 (DR9) sample, which consists of 264,283 galaxies in the redshift range 0.43 < z < 0.7 spanning 3,275 square degrees. Both peculiar velocities and errors in the assumed redshift-distance relation ("Alcock-Paczynski effect") generate correlations between clustering amplitude and orientation with respect to the line-of-sight. Together with the sharp baryon acoustic oscillation (BAO) standard ruler, our measurements of the broadband shape of the monopole and quadrupole correlation functions simultaneously constrain the comoving angular diameter distance (2190 +/- 61 Mpc) to z=0.57, the Hubble expansion rate at z=0.57 (92.4 +/- 4.5 km/s/Mpc), and the growth rate of structure at that same redshift (d sigma8/d ln a = 0.43 +/- 0.069). Our analysis provides the best current direct determination of both DA and H in galaxy clustering data using this technique. If we further assume a LCDM expansion history, our growth constraint tightens to d sigma8/d ln a = 0.415 +/- 0.034. In combination with the cosmic microwave background, our measurements of DA, H, and growth all separately require dark energy at z > 0.57, and when combined imply \Omega_{\Lambda} = 0.74 +/- 0.016, independent of the Universe's evolution at z<0.57. In our companion paper (Samushia et al. prep), we explore further cosmological implications of these observations.Comment: 19 pages, 11 figures, submitted to MNRAS, comments welcom

Prognostic value of different anthropometric indices over different measurement intervals to predict mortality in 6-59-month-old children

Objective: To compare the prognostic value of mid-upper arm circumference (MUAC), weight-for-height z-score (WHZ) and weight-for-age z-score (WAZ) for predicting death over periods of one, three and six months follow-up in children. Design: Pooled analysis of 12 prospective studies examining survival after anthropometric assessment. Sensitivity and false-positive ratios to predict death within one, three and six months were compared for three individual anthropometric indices and their combinations. Setting: Community-based, prospective studies from 12 countries in Africa and Asia Participants: Children aged 6-59 months living in the study areas Results: For all anthropometric indices, the receiver operating characteristic curves were higher for shorter than for longer durations of follow-up. Sensitivity was higher for death with one month follow-up compared to six months by 49% (95% CI: 30-69%) for MUAC <115 mm (p<0.001), 48% (95%CI: 9.4-87%) for WHZ <-3 (p<0.01) and 28% (95%CI: 7.6-42%) for WAZ <-3 (p<0.005). This was accompanied by an increase in false-positives of only 3% or less. For all durations of follow-up, WAZ <-3 identified more children who died and were not identified by WHZ <-3 or by MUAC <115 mm, 120 mm or 125 mm but the use of WAZ <-3 led to an increased false-positive ratio up to 16.4% (95%CI: 12.0-20.9%) compared to 3.5% (0.4-6.5%) for MUAC <115 mm alone. Conclusions: Frequent anthropometric measurements significantly improve the identification of malnourished children with a high risk of death without markedly increasing false-positives. Combining two indices increases sensitivity but also increases false-positives among children meeting case definitions.publishedVersionPeer reviewe