Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3

Abstract Background The antizyme family is a group of small proteins that play a role in cell growth and division by regulating the biosynthesis of polyamines (putrescine, spermidine, spermine). Antizymes regulate polyamine levels primarily through binding ornithine decarboxylase (ODC), an enzyme key to polyamine production, and targeting ODC for destruction by the 26S proteosome. Ornithine decarboxylase antizyme 3 (OAZ3) is a testis-specific antizyme paralog and the only antizyme expressed in the mid to late stages of spermatogenesis. Methods To see if mutations in the OAZ3 gene are responsible for some cases of male infertility, we sequenced and evaluated the genomic DNA of 192 infertile men, 48 men of known paternity, and 34 African aborigines from the Mbuti tribe in the Democratic Republic of the Congo. The coding sequence of OAZ3 was further screened for polymorphisms by SSCP analysis in the infertile group and an additional 250 general population controls. Identified polymorphisms in the OAZ3 gene were further subjected to a haplotype analysis using PHASE 2.02 and Arlequin 2.0 software programs. Results A total of 23 polymorphisms were identified in the promoter, exons or intronic regions of OAZ3. The majority of these fell within a region of less than two kilobases. Two of the polymorphisms, -239 A/G in the promoter and 4280 C/T, a missense polymorphism in exon 5, may show evidence of association with male infertility. Haplotype analysis identified 15 different haplotypes, which can be separated into two divergent clusters. Conclusion Mutations in the OAZ3 gene are not a common cause of male infertility. However, the presence of the two divergent haplotypes at high frequencies in all three of our subsamples (infertile, control, African) suggests that they have been maintained in the genome by balancing selection, which was supported by a test of Tajima's D statistic. Evidence for natural selection in this region implies that these haplotypes may be associated with a trait other than infertility. This trait may be related to another function of OAZ3 or a region in tight linkage disequilibrium to the gene.</p

Asymptotics of 10j symbols

The Riemannian 10j symbols are spin networks that assign an amplitude to each 4-simplex in the Barrett-Crane model of Riemannian quantum gravity. This amplitude is a function of the areas of the 10 faces of the 4-simplex, and Barrett and Williams have shown that one contribution to its asymptotics comes from the Regge action for all non-degenerate 4-simplices with the specified face areas. However, we show numerically that the dominant contribution comes from degenerate 4-simplices. As a consequence, one can compute the asymptotics of the Riemannian 10j symbols by evaluating a `degenerate spin network', where the rotation group SO(4) is replaced by the Euclidean group of isometries of R^3. We conjecture formulas for the asymptotics of a large class of Riemannian and Lorentzian spin networks in terms of these degenerate spin networks, and check these formulas in some special cases. Among other things, this conjecture implies that the Lorentzian 10j symbols are asymptotic to 1/16 times the Riemannian ones.Comment: 25 pages LaTeX with 8 encapsulated Postscript figures. v2 has various clarifications and better page breaks. v3 is the final version, to appear in Classical and Quantum Gravity, and has a few minor corrections and additional reference

Precision Primordial 4^4He Measurement with CMB Experiments

Big bang nucleosynthesis (BBN) and the cosmic microwave background (CMB) are two major pillars of cosmology. Standard BBN accurately predicts the primordial light element abundances ($^4$He, D, $^3$He and $^7$Li), depending on one parameter, the baryon density. Light element observations are used as a baryometers. The CMB anisotropies also contain information about the content of the universe which allows an important consistency check on the Big Bang model. In addition CMB observations now have sufficient accuracy to not only determine the total baryon density, but also resolve its principal constituents, H and $^4$He. We present a global analysis of all recent CMB data, with special emphasis on the concordance with BBN theory and light element observations. We find $\Omega_{B}h^{2}=0.025+0.0019-0.0026$ and $Y_{p}=0.250+0.010-0.014$ (fraction of baryon mass as $^4$He) using CMB data alone, in agreement with $^4$He abundance observations. With this concordance established we show that the inclusion of BBN theory priors significantly reduces the volume of parameter space. In this case, we find $\Omega_{B}h^2=0.0244+0.00137-0.00284$ and $Y_p = 0.2493+0.0006-0.001$. We also find that the inclusion of deuterium abundance observations reduces the $Y_p$ and $\Omega_{B}h^2$ ranges by a factor of $\sim$2. Further light element observations and CMB anisotropy experiments will refine this concordance and sharpen BBN and the CMB as tools for precision cosmology.Comment: 7 pages, 3 color figures made minor changes to bring inline with journal versio

Noise Kernel and Stress Energy Bi-Tensor of Quantum Fields in Hot Flat Space and Gaussian Approximation in the Optical Schwarzschild Metric

Continuing our investigation of the regularization of the noise kernel in curved spacetimes [N. G. Phillips and B. L. Hu, Phys. Rev. D {\bf 63}, 104001 (2001)] we adopt the modified point separation scheme for the class of optical spacetimes using the Gaussian approximation for the Green functions a la Bekenstein-Parker-Page. In the first example we derive the regularized noise kernel for a thermal field in flat space. It is useful for black hole nucleation considerations. In the second example of an optical Schwarzschild spacetime we obtain a finite expression for the noise kernel at the horizon and recover the hot flat space result at infinity. Knowledge of the noise kernel is essential for studying issues related to black hole horizon fluctuations and Hawking radiation backreaction. We show that the Gaussian approximated Green function which works surprisingly well for the stress tensor at the Schwarzschild horizon produces significant error in the noise kernel there. We identify the failure as occurring at the fourth covariant derivative order.Comment: 21 pages, RevTeX

Cosmological parameters from SDSS and WMAP

We measure cosmological parameters using the three-dimensional power spectrum P(k) from over 200,000 galaxies in the Sloan Digital Sky Survey (SDSS) in combination with WMAP and other data. Our results are consistent with a ``vanilla'' flat adiabatic Lambda-CDM model without tilt (n=1), running tilt, tensor modes or massive neutrinos. Adding SDSS information more than halves the WMAP-only error bars on some parameters, tightening 1 sigma constraints on the Hubble parameter from h~0.74+0.18-0.07 to h~0.70+0.04-0.03, on the matter density from Omega_m~0.25+/-0.10 to Omega_m~0.30+/-0.04 (1 sigma) and on neutrino masses from <11 eV to <0.6 eV (95%). SDSS helps even more when dropping prior assumptions about curvature, neutrinos, tensor modes and the equation of state. Our results are in substantial agreement with the joint analysis of WMAP and the 2dF Galaxy Redshift Survey, which is an impressive consistency check with independent redshift survey data and analysis techniques. In this paper, we place particular emphasis on clarifying the physical origin of the constraints, i.e., what we do and do not know when using different data sets and prior assumptions. For instance, dropping the assumption that space is perfectly flat, the WMAP-only constraint on the measured age of the Universe tightens from t0~16.3+2.3-1.8 Gyr to t0~14.1+1.0-0.9 Gyr by adding SDSS and SN Ia data. Including tensors, running tilt, neutrino mass and equation of state in the list of free parameters, many constraints are still quite weak, but future cosmological measurements from SDSS and other sources should allow these to be substantially tightened.Comment: Minor revisions to match accepted PRD version. SDSS data and ppt figures available at http://www.hep.upenn.edu/~max/sdsspars.htm

Opportunistic experiments to constrain aerosol effective radiative forcing

Aerosol–cloud interactions (ACIs) are considered to be the most uncertain driver of present-day radiative forcing due to human activities. The nonlinearity of cloud-state changes to aerosol perturbations make it challenging to attribute causality in observed relationships of aerosol radiative forcing. Using correlations to infer causality can be challenging when meteorological variability also drives both aerosol and cloud changes independently. Natural and anthropogenic aerosol perturbations from well-defined sources provide “opportunistic experiments” (also known as natural experiments) to investigate ACI in cases where causality may be more confidently inferred. These perturbations cover a wide range of locations and spatiotemporal scales, including point sources such as volcanic eruptions or industrial sources, plumes from biomass burning or forest fires, and tracks from individual ships or shipping corridors. We review the different experimental conditions and conduct a synthesis of the available satellite datasets and field campaigns to place these opportunistic experiments on a common footing, facilitating new insights and a clearer understanding of key uncertainties in aerosol radiative forcing. Cloud albedo perturbations are strongly sensitive to background meteorological conditions. Strong liquid water path increases due to aerosol perturbations are largely ruled out by averaging across experiments. Opportunistic experiments have significantly improved process-level understanding of ACI, but it remains unclear how reliably the relationships found can be scaled to the global level, thus demonstrating a need for deeper investigation in order to improve assessments of aerosol radiative forcing and climate change

Lenalidomide in combination with dexamethasone at first relapse in comparison with its use as later salvage therapy in relapsed or refractory multiple myeloma

This subset analysis of data from two phase III studies in patients with relapsed or refractory multiple myeloma (MM) evaluated the benefit of initiating lenalidomide plus dexamethasone at first relapse. Multivariate analysis showed that fewer prior therapies, along with β2-microglobulin (≤2.5 mg/L), predicted a better time to progression (TTP; study end-point) with lenalidomide plus dexamethasone treatment. Patients with one prior therapy showed a significant improvement in benefit after first relapse compared with those who received two or more therapies. Patients with one prior therapy had significantly prolonged median TTP (17.1 vs. 10.6 months; P=0.026) and progression-free survival (14.1 vs. 9.5 months, P=0.047) compared with patients treated in later lines. Overall response rates were higher (66.9% vs. 56.8%, P=0.06), and the complete response plus very good partial response rate was significantly higher in first relapse (39.8% vs. 27.7%, P=0.025). Importantly, overall survival was significantly prolonged for patients treated with lenalidomide plus dexamethasone with one prior therapy, compared with patients treated later in salvage (median of 42.0 vs. 35.8 months, P=0.041), with no differences in toxicity, dose reductions, or discontinuations despite longer treatment. Therefore, lenalidomide plus dexamethasone is both effective and tolerable for second-line MM therapy and the data suggest that the greatest benefit occurs with earlier use

Genetic Signatures of Exceptional Longevity in Humans

Like most complex phenotypes, exceptional longevity is thought to reflect a combined influence of environmental (e.g., lifestyle choices, where we live) and genetic factors. To explore the genetic contribution, we undertook a genome-wide association study of exceptional longevity in 801 centenarians (median age at death 104 years) and 914 genetically matched healthy controls. Using these data, we built a genetic model that includes 281 single nucleotide polymorphisms (SNPs) and discriminated between cases and controls of the discovery set with 89% sensitivity and specificity, and with 58% specificity and 60% sensitivity in an independent cohort of 341 controls and 253 genetically matched nonagenarians and centenarians (median age 100 years). Consistent with the hypothesis that the genetic contribution is largest with the oldest ages, the sensitivity of the model increased in the independent cohort with older and older ages (71% to classify subjects with an age at death>102 and 85% to classify subjects with an age at death>105). For further validation, we applied the model to an additional, unmatched 60 centenarians (median age 107 years) resulting in 78% sensitivity, and 2863 unmatched controls with 61% specificity. The 281 SNPs include the SNP rs2075650 in TOMM40/APOE that reached irrefutable genome wide significance (posterior probability of association = 1) and replicated in the independent cohort. Removal of this SNP from the model reduced the accuracy by only 1%. Further in-silico analysis suggests that 90% of centenarians can be grouped into clusters characterized by different “genetic signatures” of varying predictive values for exceptional longevity. The correlation between 3 signatures and 3 different life spans was replicated in the combined replication sets. The different signatures may help dissect this complex phenotype into sub-phenotypes of exceptional longevity

Multi-decadal changes in tundra environments and ecosystems: Synthesis of the International Polar Year-Back to the Future Project (IPY-BTF).

Understanding the responses of tundra systems to global change has global implications. Most tundra regions lack sustained environmental monitoring and one of the only ways to document multi-decadal change is to resample historic research sites. The International Polar Year (IPY) provided a unique opportunity for such research through the Back to the Future (BTF) project (IPY project #512). This article synthesizes the results from 13 papers within this Ambio Special Issue. Abiotic changes include glacial recession in the Altai Mountains, Russia; increased snow depth and hardness, permafrost warming, and increased growing season length in sub-arctic Sweden; drying of ponds in Greenland; increased nutrient availability in Alaskan tundra ponds, and warming at most locations studied. Biotic changes ranged from relatively minor plant community change at two sites in Greenland to moderate change in the Yukon, and to dramatic increases in shrub and tree density on Herschel Island, and in sub-arctic Sweden. The population of geese tripled at one site in northeast Greenland where biomass in non-grazed plots doubled. A model parameterized using results from a BTF study forecasts substantial declines in all snowbeds and increases in shrub tundra on Niwot Ridge, Colorado over the next century. In general, results support and provide improved capacities for validating experimental manipulation, remote sensing, and modeling studies