Showing papers by "University of Massachusetts Amherst published in 2013"

Enhanced sensitivity of the LIGO gravitational wave detector by using squeezed states of light

Abstract: Nearly a century after Einstein first predicted the existence of gravitational waves, a global network of Earth-based gravitational wave observatories1, 2, 3, 4 is seeking to directly detect this faint radiation using precision laser interferometry. Photon shot noise, due to the quantum nature of light, imposes a fundamental limit on the attometre-level sensitivity of the kilometre-scale Michelson interferometers deployed for this task. Here, we inject squeezed states to improve the performance of one of the detectors of the Laser Interferometer Gravitational-Wave Observatory (LIGO) beyond the quantum noise limit, most notably in the frequency region down to 150 Hz, critically important for several astrophysical sources, with no deterioration of performance observed at any frequency. With the injection of squeezed states, this LIGO detector demonstrated the best broadband sensitivity to gravitational waves ever achieved, with important implications for observing the gravitational-wave Universe with unprecedented sensitivity.

Untangling the Genetic Basis of Fibrolytic Specialization by Lachnospiraceae and Ruminococcaceae in Diverse Gut Communities

Abstract: The Lachnospiraceae and Ruminococcaceae are two of the most abundant families from the order Clostridiales found in the mammalian gut environment, and have been associated with the maintenance of gut health While they are both diverse groups, they share a common role as active plant degraders By comparing the genomes of the Lachnospiraceae and Ruminococcaceae with the Clostridiaceae, a more commonly free-living group, we identify key carbohydrate-active enzymes, sugar transport mechanisms, and metabolic pathways that distinguish these two commensal groups as specialists for the degradation of complex plant material

The ATLAS3D project XV: benchmark for early-type galaxies scaling relations from 260 dynamical models: mass-to-light ratio, dark matter, fundamental plane and mass plane

Abstract: We study the volume-limited and nearly mass-selected (stellar mass M-stars greater than or similar to 6 x 10(9) M circle dot) ATLAS(3D) sample of 260 early-type galaxies (ETGs, ellipticals Es and lenticulars S0s). We construct detailed axisymmetric dynamical models (Jeans Anisotropic MGE), which allow for orbital anisotropy, include a dark matter halo and reproduce in detail both the galaxy images and the high-quality integral-field stellar kinematics out to about 1R(e), the projected half-light radius. We derive accurate total mass-to-light ratios (M/L)(e) and dark matter fractions f(DM), within a sphere of radius centred on the galaxies. We also measure the stellar (M/L)(stars) and derive a median dark matter fraction f(DM) = 13 per cent in our sample. We infer masses M-JAM equivalent to L x (M/L)(e) approximate to 2 x M-1/2, where M-1/2 is the total mass within a sphere enclosing half of the galaxy light. We find that the thin two-dimensional subset spanned by galaxies in the (M-JAM, sigma(e), R-e(maj)) coordinates system, which we call the Mass Plane (MP) has an observed rms scatter of 19 per cent, which implies an intrinsic one of 11 per cent. Here, is the major axis of an isophote enclosing half of the observed galaxy light, while Sigma(e) is measured within that isophote. The MP satisfies the scalar virial relation M-JAM proportional to sigma R-2(e)e(maj) within our tight errors. This show that the larger scatter in the Fundamental Plane (FP) (L, Sigma(e), R-e) is due to stellar population effects [including trends in the stellar initial mass function (IMF)]. It confirms that the FP deviation from the virial exponents is due to a genuine (M/L)(e) variation. However, the details of how both R-e and Sigma(e) are determined are critical in defining the precise deviation from the virial exponents. The main uncertainty in masses or M/L estimates using the scalar virial relation is in the measurement of R-e. This problem is already relevant for nearby galaxies and may cause significant biases in virial mass and size determinations at high redshift. Dynamical models can eliminate these problems. We revisit the (M/L)(e)-Sigma(e) relation, which describes most of the deviations between the MP and the FP. The best-fitting relation is (M/L)(e) sigma(0.72)(e) (r band). It provides an upper limit to any systematic increase of the IMF mass normalization with Sigma(e). The correlation is more shallow and has smaller scatter for slow rotating systems or for galaxies in Virgo. For the latter, when using the best distance estimates, we observe a scatter in (M/L)(e) of 11 per cent, and infer an intrinsic one of 8 per cent. We perform an accurate empirical study of the link between Sigma(e) and the galaxies circular velocity V-circ within 1R(e) (where stars dominate) and find the relation max (V-circ) approximate to 1.76 x Sigma(e), which has an observed scatter of 7 per cent. The accurate parameters described in this paper are used in the companion Paper XX (Cappellari et al.) of this series to explore the variation of global galaxy properties, including the IMF, on the projections of the MP.

The ATLAS3D project – XX. Mass–size and mass–σ distributions of early-type galaxies: bulge fraction drives kinematics, mass-to-light ratio, molecular gas fraction and stellar initial mass function

Abstract: In the companion Paper XV of this series, we derive accurate total mass-to-light ratios (M/L)(JAM) approximate to (M/L)(r = R-e) within a sphere of radius r = R-e centred on the galaxy, as well as stellar (M/L)(stars) (with the dark matter removed) for the volume-limited and nearly mass-selected (stellar mass M-star greater than or similar to 6 x 10(9) M-circle dot) ATLAS(3D) sample of 260 early-type galaxies (ETGs, ellipticals Es and lenticulars S0s). Here, we use those parameters to study the two orthogonal projections (M-JAM, sigma(e)) and (M-JAM, R-e(maj)) of the thin Mass Plane (MP) (M-JAM, sigma(e), R-e(maj)) which describes the distribution of the galaxy population, where M-JAM = L x (M/L)(JAM) approximate to M-star. The distribution of galaxy properties on both projections of the MP is characterized by: (i) the same zone of exclusion (ZOE), which can be transformed from one projection to the other using the scalar virial equation. The ZOE is roughly described by two power laws, joined by a break at a characteristic mass M-JAM approximate to 3 x 10(10) M-circle dot, which corresponds to the minimum R-e and maximum stellar density. This results in a break in the mean M-JAM-sigma(e) relation with trends M-JAM proportional to sigma(2.3)(e) and M-JAM proportional to sigma(4.7)(e) at small and large sigma(e), respectively; (ii) a characteristic mass M-JAM approximate to 2 x 10(11) M-circle dot which separates a population dominated by flat fast rotator with discs and spiral galaxies at lower masses, from one dominated by quite round slow rotators at larger masses; (iii) below that mass the distribution of ETGs' properties on the two projections of the MP tends to be constant along lines of roughly constant sigma(e), or equivalently along lines with R-e(maj) proportional to M-JAM, respectively (or even better parallel to the ZOE: R-maj(e) proportional to M-JAM(0.75)); (iv) it forms a continuous and parallel sequence with the distribution of spiral galaxies; (v) at even lower masses, the distribution of fast-rotator ETGs and late spirals naturally extends to that of dwarf ETGs (Sph) and dwarf irregulars (Im), respectively. We use dynamical models to analyse our kinematic maps. We show that Sigma(e) traces the bulge fraction, which appears to be the main driver for the observed trends in the dynamical (M/L)(JAM) and in indicators of the (M/L)(pop) of the stellar population like H beta and colour, as well as in the molecular gas fraction. A similar variation along contours of Sigma(e) is also observed for the mass normalization of the stellar initial mass function (IMF), which was recently shown to vary systematically within the ETGs' population. Our preferred relation has the form log(10)[(M/L)(stars)/(M/L)(Salp)] = a + b x log(10)(sigma(e)/130 km s(-1)) with a = -0.12 +/- 0.01 and b = 0.35 +/- 0.06. Unless there are major flaws in all stellar population models, this trend implies a transition of the mean IMF from Kroupa to Salpeter in the interval log(10)(sigma(e)/km s(-1)) approximate to 1.9-2.5 (or sigma e approximate to 90-290 km s-1), with a smooth variation in between, consistently with what was shown in Cappellari et al. The observed d205 (or sigma e istribution of galaxy properties on the MP provides a clean and novel view for a number of previously reported trends, which constitute special two-dimensional projections of the more general four-dimensional parameters trends on the MP. We interpret it as due to a combination of two main effects: (i) an increase of the bulge fraction, which increases Sigma(e), decreases R-e, and greatly enhance the likelihood for a galaxy to have its star formation quenched, and (ii) dry merging, increasing galaxy mass and R-e by moving galaxies along lines of roughly constant Sigma(e) (or steeper), while leaving the population nearly unchanged.

Relation Extraction with Matrix Factorization and Universal Schemas

Abstract: © 2013 Association for Computational Linguistics. Traditional relation extraction predicts relations within some fixed and finite target schema. Machine learning approaches to this task require either manual annotation or, in the case of distant supervision, existing structured sources of the same schema. The need for existing datasets can be avoided by using a universal schema: the union of all involved schemas (surface form predicates as in OpenIE, and relations in the schemas of preexisting databases). This schema has an almost unlimited set of relations (due to surface forms), and supports integration with existing structured data (through the relation types of existing databases). To populate a database of such schema we present matrix factorization models that learn latent feature vectors for entity tuples and relations. We show that such latent models achieve substantially higher accuracy than a traditional classification approach. More importantly, by operating simultaneously on relations observed in text and in pre-existing structured DBs such as Freebase, we are able to reason about unstructured and structured data in mutually-supporting ways. By doing so our approach outperforms stateof- the-Art distant supervision.

Type I and II Endometrial Cancers: Have They Different Risk Factors?

Abstract: Purpose Endometrial cancers have long been divided into estrogen-dependent type I and the less common clinically aggressive estrogen-independent type II. Little is known about risk factors for type II tumors because most studies lack sufficient cases to study these much less common tumors separately. We examined whether so-called classical endometrial cancer risk factors also influence the risk of type II tumors. Patients and Methods Individual-level data from 10 cohort and 14 case-control studies from the Epidemiology of Endometrial Cancer Consortium were pooled. A total of 14,069 endometrial cancer cases and 35,312 controls were included. We classified endometrioid (n = 7,246), adenocarcinoma not otherwise specified (n = 4,830), and adenocarcinoma with squamous differentiation (n = 777) as type I tumors and serous (n = 508) and mixed cell (n = 346) as type II tumors. Results Parity, oral contraceptive use, cigarette smoking, age at menarche, and diabetes were associated with type I and type II tumors to...

Coastal flooding by tropical cyclones and sea-level rise

Abstract: The future impacts of climate change on landfalling tropical cyclones are unclear. Regardless of this uncertainty, flooding by tropical cyclones will increase as a result of accelerated sea-level rise. Under similar rates of rapid sea-level rise during the early Holocene epoch most low-lying sedimentary coastlines were generally much less resilient to storm impacts. Society must learn to live with a rapidly evolving shoreline that is increasingly prone to flooding from tropical cyclones. These impacts can be mitigated partly with adaptive strategies, which include careful stewardship of sediments and reductions in human-induced land subsidence.

Introduced annual grass increases regional fire activity across the arid western USA (1980–2009)

Abstract: Non-native, invasive grasses have been linked to altered grass-fire cycles worldwide. Although a few studies have quantified resulting changes in fire activity at local scales, and many have speculated about larger scales, regional alterations to fire regimes remain poorly documented. We assessed the influence of large-scale Bromus tectorum (hereafter cheatgrass) invasion on fire size, duration, spread rate, and interannual variability in comparison to other prominent land cover classes across the Great Basin, USA. We compared regional land cover maps to burned area measured using the Moderate Resolution Imaging Spectroradiometer (MODIS) for 2000–2009 and to fire extents recorded by the USGS registry of fires from 1980 to 2009. Cheatgrass dominates at least 6% of the central Great Basin (650 000 km 2 ). MODIS records show that 13% of these cheatgrass-dominated lands burned, resulting in a fire return interval of 78 years for any given location within cheatgrass. This proportion was more than double the amount burned across all other vegetation types (range: 0.5–6% burned). During the 1990s, this difference was even more extreme, with cheatgrass burning nearly four times more frequently than any native vegetation type (16% of cheatgrass burned compared to 1–5% of native vegetation). Cheatgrass was also disproportionately represented in the largest fires, comprising 24% of the land area of the 50 largest fires recorded by MODIS during the 2000s. Furthermore, multi-date fires that burned across multiple vegetation types were significantly more likely to have started in cheatgrass. Finally, cheatgrass fires showed a strong interannual response to wet years, a trend only weakly observed in native vegetation types. These results demonstrate that cheatgrass invasion has substantially altered the regional fire regime. Although this result has been suspected by managers for decades, this study is the first to document recent cheatgrass-driven fire regimes at a regional scale.

CANDELS multi-wavelength catalogs: source detection and photometry in the GOODS-South field

Abstract: We present a UV to mid-infrared multi-wavelength catalog in the CANDELS/GOODS-S field, combining the newly obtained CANDELS HST/WFC3 F105W, F125W, and F160W data with existing public data. The catalog is based on source detection in the WFC3 F160W band. The F160W mosaic includes the data from CANDELS deep and wide observations as well as previous ERS and HUDF09 programs. The mosaic reaches a 5? limiting depth (within an aperture of radius 0.''17) of 27.4, 28.2, and 29.7?AB for CANDELS wide, deep, and HUDF regions, respectively. The catalog contains 34,930 sources with the representative 50% completeness reaching 25.9, 26.6, and 28.1?AB in the F160W band for the three regions. In addition to WFC3 bands, the catalog also includes data from UV (U band from both CTIO/MOSAIC and VLT/VIMOS), optical (HST/ACS F435W, F606W, F775W, F814W, and F850LP), and infrared (HST/WFC3 F098M, VLT/ISAAC Ks, VLT/HAWK-I Ks, and Spitzer/IRAC 3.6, 4.5, 5.8, 8.0 ?m) observations. The catalog is validated via stellar colors, comparison with other published catalogs, zero-point offsets determined from the best-fit templates of the spectral energy distribution of spectroscopically observed objects, and the accuracy of photometric redshifts. The catalog is able to detect unreddened star-forming (passive) galaxies with stellar mass of 1010 M ? at a 50% completeness level to z ~ 3.4 (2.8), 4.6 (3.2), and 7.0 (4.2) in the three regions. As an example of application, the catalog is used to select both star-forming and passive galaxies at z ~ 2-4 via the Balmer break. It is also used to study the color-magnitude diagram of galaxies at 0 < z < 4.

A vast, thin plane of corotating dwarf galaxies orbiting the Andromeda galaxy

Abstract: Dwarf satellite galaxies are thought to be the remnants of the population of primordial structures that coalesced to form giant galaxies like the Milky Way. It has previously been suspected that dwarf galaxies may not be isotropically distributed around our Galaxy, because several are correlated with streams of H I emission, and may form coplanar groups. These suspicions are supported by recent analyses. It has been claimed that the apparently planar distribution of satellites is not predicted within standard cosmology, and cannot simply represent a memory of past coherent accretion. However, other studies dispute this conclusion. Here we report the existence of a planar subgroup of satellites in the Andromeda galaxy (M 31), comprising about half of the population. The structure is at least 400 kiloparsecs in diameter, but also extremely thin, with a perpendicular scatter of less than 14.1 kiloparsecs. Radial velocity measurements reveal that the satellites in this structure have the same sense of rotation about their host. This shows conclusively that substantial numbers of dwarf satellite galaxies share the same dynamical orbital properties and direction of angular momentum. Intriguingly, the plane we identify is approximately aligned with the pole of the Milky Way's disk and with the vector between the Milky Way and Andromeda.

The CO-to-H2 Conversion Factor and Dust-to-gas Ratio on Kiloparsec Scales in Nearby Galaxies

Abstract: We present ~{}kiloparsec spatial resolution maps of the CO-to-H$_{2}$ conversion factor ({$α$}$_{CO}$) and dust-to-gas ratio (DGR) in 26 nearby, star-forming galaxies. We have simultaneously solved for {$α$}$_{CO}$ and the DGR by assuming that the DGR is approximately constant on kiloparsec scales. With this assumption, we can combine maps of dust mass surface density, CO-integrated intensity, and H I column density to solve for both {$α$}$_{CO}$ and the DGR with no assumptions about their value or dependence on metallicity or other parameters. Such a study has just become possible with the availability of high-resolution far-IR maps from the Herschel key program KINGFISH, $^{12}$CO J = (2-1) maps from the IRAM 30 m large program HERACLES, and H I 21 cm line maps from THINGS. We use a fixed ratio between the (2-1) and (1-0) lines to present our {$α$}$_{CO}$ results on the more typically used $^{12}$CO J = (1-0) scale and show using literature measurements that variations in the line ratio do not affect our results. In total, we derive 782 individual solutions for {$α$}$_{CO}$ and the DGR. On average, {$α$}$_{CO}$ = 3.1 M $_{☉}$ pc$^{–2}$ (K km s$^{–1}$)$^{–1}$ for our sample with a standard deviation of 0.3 dex. Within galaxies, we observe a generally flat profile of {$α$}$_{CO}$ as a function of galactocentric radius. However, most galaxies exhibit a lower {$α$}$_{CO}$ value in the central kiloparsec{mdash}a factor of ~{}2 below the galaxy mean, on average. In some cases, the central {$α$}$_{CO}$ value can be factors of 5-10 below the standard Milky Way (MW) value of {$α$}$_{CO, MW}$ = 4.4 M $_{☉}$ pc$^{–2}$ (K km s$^{–1}$)$^{–1}$. While for {$α$}$_{CO}$ we find only weak correlations with metallicity, the DGR is well-correlated with metallicity, with an approximately linear slope. Finally, we present several recommendations for choosing an appropriate {$α$}$_{CO}$ for studies of nearby galaxies.

Multi-stimuli responsive macromolecules and their assemblies

Abstract: In this review, we outline examples that illustrate the design criteria for achieving macromolecular assemblies that incorporate a combination of two or more chemical, physical or biological stimuli-responsive components. Progress in both fundamental investigation into the phase transformations of these polymers in response to multiple stimuli and their utilization in a variety of practical applications are highlighted. Using these examples, we aim to explain the origin of employed mechanisms of stimuli responsiveness which may serve as a guideline to inspire future design of multi-stimuli responsive materials.

Urban landscape sustainability and resilience: the promise and challenges of integrating ecology with urban planning and design

Abstract: The twenty-first century global population will be increasingly urban-focusing the sustainability challenge on cities and raising new challenges to address urban resilience capacity. Landscape ecologists are poised to contribute to this challenge in a transdisciplinary mode in which science and research are integrated with planning policies and design applications. Five strategies to build resilience capacity and transdisciplinary collaboration are proposed: biodiversity; urban ecological networks and connectivity; multifunctionality; redundancy and modularization, adaptive design. Key research questions for landscape ecologists, planners and designers are posed to advance the development of knowledge in an adaptive mode.

Improved luminosity determination in pp collisions at root s=7 TeV using the ATLAS detector at the LHC

Abstract: The luminosity calibration for the ATLAS detector at the LHC during pp collisions at root s = 7 TeV in 2010 and 2011 is presented. Evaluation of the luminosity scale is performed using several luminosity-sensitive detectors, and comparisons are made of the long-term stability and accuracy of this calibration applied to the pp collisions at root s = 7 TeV. A luminosity uncertainty of delta L/L = +/- 3.5 % is obtained for the 47 pb(-1) of data delivered to ATLAS in 2010, and an uncertainty of delta L/L = +/- 1.8 % is obtained for the 5.5 fb(-1) delivered in 2011.

ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function

Abstract: Many mutations disappear from the population because they impair protein function and/or stability. Thus, amino acid positions that are essential for proper function evolve more slowly than others, or in other words, the slow evolutionary rate of a position reflects its importance. Con- Surf (http://consurf.tau.ac.il), reviewed in this manuscript, exploits this to reveal key amino acid positions that are im- portant for maintaining the native conformation(s) of the protein and its function, be it binding, catalysis, transport, etc. Given the sequence or 3D structure of the query protein as input, a search for similar sequences is conducted and the sequences are aligned. The multiple sequence alignment is subsequently used to calculate the evolutionary rates of each amino acid site, using Bayesian or maximum-likelihood algorithms. Both algorithms take into account the evolution- ary relationships between the sequences, reflected in phylo- genetic trees, to alleviate problems due to uneven (biased) sampling in sequence space. This is particularly important when the number of sequences is low. The ConSurf-DB, a new release of which is presented here, provides precalcu- lated ConSurf conservation analysis of nearly all available structures in the Protein DataBank (PDB). The usefulness of ConSurf for the study of individual proteins and mutations, as well as a range of large-scale, genome-wide applications, is reviewed.

CANDELS: The progenitors of compact quiescent galaxies at z ~ 2

Abstract: We combine high-resolution Hubble Space Telescope/WFC3 images with multi-wavelength photometry to track the evolution of structure and activity of massive (M_*> 10^10 M_☉) galaxies at redshifts z = 1.4-3 in two fields of the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey. We detect compact, star-forming galaxies (cSFGs) whose number densities, masses, sizes, and star formation rates (SFRs) qualify them as likely progenitors of compact, quiescent, massive galaxies (cQGs) at z = 1.5-3. At z≲2, cSFGs present SFR = 100-200 M_☉ yr^–1, yet their specific star formation rates (sSFR ~ 10^–9 yr^–1) are typically half that of other massive SFGs at the same epoch, and host X-ray luminous active galactic nuclei (AGNs) 30 times (~30%) more frequently. These properties suggest that cSFGs are formed by gas-rich processes (mergers or disk-instabilities) that induce a compact starburst and feed an AGN, which, in turn, quench the star formation on dynamical timescales (few 10^8 yr). The cSFGs are continuously being formed at z = 2-3 and fade to cQGs down to z ~ 1.5. After this epoch, cSFGs are rare, thereby truncating the formation of new cQGs. Meanwhile, down to z = 1, existing cQGs continue to enlarge to match local QGs in size, while less-gas-rich mergers and other secular mechanisms shepherd (larger) SFGs as later arrivals to the red sequence. In summary, we propose two evolutionary tracks of QG formation: an early (z≲2), formation path of rapidly quenched cSFGs fading into cQGs that later enlarge within the quiescent phase, and a late-arrival (z≳2) path in which larger SFGs form extended QGs without passing through a compact state.

PUF Modeling Attacks on Simulated and Silicon Data

Abstract: We discuss numerical modeling attacks on several proposed strong physical unclonable functions (PUFs). Given a set of challenge-response pairs (CRPs) of a Strong PUF, the goal of our attacks is to construct a computer algorithm which behaves indistinguishably from the original PUF on almost all CRPs. If successful, this algorithm can subsequently impersonate the Strong PUF, and can be cloned and distributed arbitrarily. It breaks the security of any applications that rest on the Strong PUF's unpredictability and physical unclonability. Our method is less relevant for other PUF types such as Weak PUFs. The Strong PUFs that we could attack successfully include standard Arbiter PUFs of essentially arbitrary sizes, and XOR Arbiter PUFs, Lightweight Secure PUFs, and Feed-Forward Arbiter PUFs up to certain sizes and complexities. We also investigate the hardness of certain Ring Oscillator PUF architectures in typical Strong PUF applications. Our attacks are based upon various machine learning techniques, including a specially tailored variant of logistic regression and evolution strategies. Our results are mostly obtained on CRPs from numerical simulations that use established digital models of the respective PUFs. For a subset of the considered PUFs-namely standard Arbiter PUFs and XOR Arbiter PUFs-we also lead proofs of concept on silicon data from both FPGAs and ASICs. Over four million silicon CRPs are used in this process. The performance on silicon CRPs is very close to simulated CRPs, confirming a conjecture from earlier versions of this work. Our findings lead to new design requirements for secure electrical Strong PUFs, and will be useful to PUF designers and attackers alike.

The Atacama Cosmology Telescope: Cosmological Parameters from Three Seasons of Data

Abstract: We present constraints on cosmological and astrophysical parameters from high-resolution microwave background maps at 148 GHz and 218 GHz made by the Atacama Cosmology Telescope (ACT) in three seasons of observations from 2008 to 2010. A model of primary cosmological and secondary foreground parameters is fit to the map power spectra and lensing deflection power spectrum, including contributions from both the thermal Sunyaev-Zeldovich (tSZ) effect and the kinematic Sunyaev-Zeldovich (kSZ) effect, Poisson and correlated anisotropy from unresolved infrared sources, radio sources, and the correlation between the tSZ effect and infrared sources. The power l2Cl/2π of the thermal SZ power spectrum at 148 GHz is measured to be 3.4±1.4 μK2 at l = 3000, while the corresponding amplitude of the kinematic SZ power spectrum has a 95% confidence level upper limit of 8.6 μK2. Combining ACT power spectra with the WMAP 7-year temperature and polarization power spectra, we find excellent consistency with the LCDM model. We constrain the number of effective relativistic degrees of freedom in the early universe to be Neff = 2.79±0.56, in agreement with the canonical value of Neff = 3.046 for three massless neutrinos. We constrain the sum of the neutrino masses to be Σmν < 0.39 eV at 95% confidence when combining ACT and WMAP 7-year data with BAO and Hubble constant measurements. We constrain the amount of primordial helium to be Yp = 0.225±0.034, and measure no variation in the fine structure constant α since recombination, with α/α0 = 1.004±0.005. We also find no evidence for any running of the scalar spectral index, dns/dln k = −0.004±0.012.

Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities.

Abstract: The Amazon rainforest is the Earth’s largest reservoir of plant and animal diversity, and it has been subjected to especially high rates of land use change, primarily to cattle pasture. This conversion has had a strongly negative effect on biological diversity, reducing the number of plant and animal species and homogenizing communities. We report here that microbial biodiversity also responds strongly to conversion of the Amazon rainforest, but in a manner different from plants and animals. Local taxonomic and phylogenetic diversity of soil bacteria increases after conversion, but communities become more similar across space. This homogenization is driven by the loss of forest soil bacteria with restricted ranges (endemics) and results in a net loss of diversity. This study shows homogenization of microbial communities in response to human activities. Given that soil microbes represent the majority of biodiversity in terrestrial ecosystems and are intimately involved in ecosystem functions, we argue that microbial biodiversity loss should be taken into account when assessing the impact of land use change in tropical forests.

Robust Detection of Rare Species Using Environmental DNA: the Importance of Primer Specificity

Abstract: Environmental DNA (eDNA) is being rapidly adopted as a tool to detect rare animals. Quantitative PCR (qPCR) using probe-based chemistries may represent a particularly powerful tool because of the method’s sensitivity, specificity, and potential to quantify target DNA. However, there has been little work understanding the performance of these assays in the presence of closely related, sympatric taxa. If related species cause any cross-amplification or interference, false positives and negatives may be generated. These errors can be disastrous if false positives lead to overestimate the abundance of an endangered species or if false negatives prevent detection of an invasive species. In this study we test factors that influence the specificity and sensitivity of TaqMan MGB assays using co-occurring, closely related brook trout (Salvelinus fontinalis) and bull trout (S. confluentus) as a case study. We found qPCR to be substantially more sensitive than traditional PCR, with a high probability of detection at concentrations as low as 0.5 target copies/µl. We also found that number and placement of base pair mismatches between the Taqman MGB assay and non-target templates was important to target specificity, and that specificity was most influenced by base pair mismatches in the primers, rather than in the probe. We found that insufficient specificity can result in both false positive and false negative results, particularly in the presence of abundant related species. Our results highlight the utility of qPCR as a highly sensitive eDNA tool, and underscore the importance of careful assay design.

Observation of Associated Near-Side and Away-Side Long-Range Correlations in √sNN=5.02 TeV Proton-Lead Collisions with the ATLAS Detector

Abstract: Two-particle correlations in relative azimuthal angle (Delta phi) and pseudorapidity (Delta eta) are measured in root S-NN = 5.02 TeV p + Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1 mu b(-1) of data as a function of transverse momentum (p(T)) and the transverse energy (Sigma E-T(Pb)) summed over 3.1 < eta < 4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2 < vertical bar Delta eta vertical bar < 5) "near-side" (Delta phi similar to 0) correlation that grows rapidly with increasing Sigma E-T(Pb). A long-range "away-side" (Delta phi similar to pi) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small Sigma E-T(Pb), is found to match the near-side correlation in magnitude, shape (in Delta eta and Delta phi) and Sigma E-T(Pb) dependence. The resultant Delta phi correlation is approximately symmetric about pi/2, and is consistent with a dominant cos2 Delta phi modulation for all Sigma E-T(Pb) ranges and particle p(T).

Genome-wide association studies identify four ER negative-specific breast cancer risk loci

Abstract: Estrogen receptor (ER)-negative tumors represent 20-30% of all breast cancers, with a higher proportion occurring in younger women and women of African ancestry. The etiology and clinical behavior of ER-negative tumors are different from those of tumors expressing ER (ER positive), including differences in genetic predisposition. To identify susceptibility loci specific to ER-negative disease, we combined in a meta-analysis 3 genome-wide association studies of 4,193 ER-negative breast cancer cases and 35,194 controls with a series of 40 follow-up studies (6,514 cases and 41,455 controls), genotyped using a custom Illumina array, iCOGS, developed by the Collaborative Oncological Gene-environment Study (COGS). SNPs at four loci, 1q32.1 (MDM4, P = 2.1 × 10(-12) and LGR6, P = 1.4 × 10(-8)), 2p24.1 (P = 4.6 × 10(-8)) and 16q12.2 (FTO, P = 4.0 × 10(-8)), were associated with ER-negative but not ER-positive breast cancer (P > 0.05). These findings provide further evidence for distinct etiological pathways associated with invasive ER-positive and ER-negative breast cancers.

Mn-doped monolayer MoS 2 : An atomically thin dilute magnetic semiconductor

Abstract: We investigate the electronic and magnetic properties of Mn-doped monolayer MoS${}_{2}$ using a combination of first-principles density functional theory (DFT) calculations and Monte Carlo simulations. Mn dopants that are substitutionally inserted at Mo sites are shown to couple ferromagnetically via a double-exchange mechanism. This interaction is relatively short ranged, making percolation a key factor in controlling long-range magnetic order. The DFT results are parameterized using an empirical model to facilitate Monte Carlo studies of concentration- and temperature-dependent ordering in these systems, through which we obtain Curie temperatures in excess of room temperature for Mn doping in the range of 10--15$%$. Our studies demonstrate the potential for engineering a new class of atomically thin dilute magnetic semiconductors based on Mn-doped MoS${}_{2}$ monolayers.

Designing electrospun nanofiber mats to promote wound healing – a review

Abstract: Current strategies to treat chronic wounds offer limited relief to the 7.75 million patients who suffer from burns or chronic skin ulcers. Thus, as long as chronic wounds remain a global healthcare problem, the development of alternate treatments remain desperately needed. This review explores the recent strategies employed to tailor electrospun nanofiber mats towards accelerating the wound healing process. Porous nanofiber mats readily produced by the electrospinning process offer a promising solution to the management of wounds. The matrix chemistry, surface functionality, and mat degradation rate all can be fine-tuned to govern the interactions that occur at the materials-biology interface. In this review, first we briefly discuss the wound healing process and then highlight recent advances in drug release, biologics encapsulation, and antibacterial activity that have been demonstrated via electrospinning. While this versatile biomaterial has shown much progress, commercializing nanofiber mats that fully address the needs of an individual patient remains an ambitious challenge.

A 40-million-year history of atmospheric CO2

Abstract: The alkenonepCO2 methodology has been used to reconstruct the partial pressure of ancient atmospheric carbon dioxide (pCO2) for the past 45 million years of Earth's history (Middle Eocene to Pleist...

The COS-Halos Survey: Rationale, Design, and a Census of Circumgalactic Neutral Hydrogen

Abstract: We present the design and methods of the COS-Halos survey, a systematic investigation of the gaseous halos of 44 z = 0.15-0.35 galaxies using background QSOs observed with the Cosmic Origins Spectrograph aboard the Hubble Space Telescope. This survey has yielded 39 spectra of z $_{em}$ ~{}= 0.5 QSOs with S/N ~{}10-15 per resolution element. The QSO sightlines pass within 150 physical kpc of the galaxies, which span early and late types over stellar mass log M $_{*}$/M $_{☉}$ = 9.5-11.5. We find that the circumgalactic medium exhibits strong H I, averaging ~{}= 1 a in Ly{$α$} equivalent width out to 150 kpc, with 100% covering fraction for star-forming galaxies and 75% covering for passive galaxies. We find good agreement in column densities between this survey and previous studies over similar range of impact parameter. There is weak evidence for a difference between early- and late-type galaxies in the strength and distribution of H I. Kinematics indicate that the detected material is bound to the host galaxy, such that {gt}~{} 90% of the detected column density is confined within {plusmn}200 km s$^{–1}$ of the galaxies. This material generally exists well below the halo virial temperatures at T {lt}~{} 10$^{5}$ K. We evaluate a number of possible origin scenarios for the detected material, and in the end favor a simple model in which the bulk of the detected H I arises in a bound, cool, low-density photoionized diffuse medium that is generic to all L* galaxies and may harbor a total gaseous mass comparable to galactic stellar masses. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. These observations are associated with program GO11598.