Showing papers by "University of Maryland, Baltimore County published in 2014"

A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students

Abstract: Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery and genomics. The course is situated within a broader scientific context aimed at understanding viral diversity, such that faculty and students are collaborators with established researchers in the field. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course has been widely implemented and has been taken by over 4,800 students at 73 institutions. We show here that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students’ interest in science, positively influences academic achievement, and enhances persistence in science, technology, engineering, and mathematics (STEM) disciplines. Broad application of this model by integrating other research areas with large numbers of early-career undergraduate students has the potential to be transformative in science education and research training. IMPORTANCE Engagement of undergraduate students in scientific research at early stages in their careers presents an opportunity to excite students about science, technology, engineering, and mathematics (STEM) disciplines and promote continued interests in these areas. Many excellent course-based undergraduate research experiences have been developed, but scaling these to a broader impact with larger numbers of students is challenging. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunting Advancing Genomics and Evolutionary Science (SEA-PHAGES) program takes advantage of the huge size and diversity of the bacteriophage population to engage students in discovery of new viruses, genome annotation, and comparative genomics, with strong impacts on bacteriophage research, increased persistence in STEM fields, and student self-identification with learning gains, motivation, attitude, and career aspirations.

Low-Threshold Stimulated Emission Using Colloidal Quantum Wells

Abstract: The use of colloidal semiconductor nanocrystals for optical amplification and lasing has been limited by the need for high input power densities. Here we show that colloidal nanoplatelets produce amplified spontaneous emission with thresholds as low as 6 μJ/cm2 and gain as high as 600 cm–1, both a significant improvement over colloidal nanocrystals; in addition, gain saturation occurs at pump fluences 2 orders of magnitude higher than the threshold. We attribute this exceptional performance to large optical cross-sections, slow Auger recombination rates, and narrow ensemble emission line widths.

The spectrum and morphology of the Fermi bubbles

Abstract: The Fermi bubbles are two large structures in the gamma-ray sky extending to 55 deg above and below the Galactic center. We analyze 50 months of Fermi Large Area Telescope data between 100 MeV and 500 GeV above 10 deg in Galactic latitude to derive the spectrum and morphology of the Fermi bubbles. We thoroughly explore the systematic uncertainties that arise when modeling the Galactic diffuse emission through two separate approaches. The gamma-ray spectrum is well described by either a log parabola or a power law with an exponential cutoff. We exclude a simple power law with more than 7 sigma significance. The power law with an exponential cutoff has an index of 1.90+/-0.2 and a cutoff energy of 110+/- 50 GeV. We find that the gamma-ray luminosity of the bubbles is 4.4(+)2.4(-0.9 ) 10(exp 37) erg s-1. We confirm a significant enhancement of gamma-ray emission in the south-eastern part of the bubbles, but we do not find significant evidence for a jet. No significant variation of the spectrum across the bubbles is detected. The width of the boundary of the bubbles is estimated to be 3.4(+)3.7(-)2.6 deg. Both inverse Compton (IC) models and hadronic models including IC emission from secondary leptons t the gamma-ray data well. In the IC scenario, the synchrotron emission from the same population of electrons can also explain the WMAP and Planck microwave haze with a magnetic field between 5 and 20 micro-G.

Fermi-LAT Observations of the Gamma-Ray Burst GRB 130427A

Abstract: The observations of the exceptionally bright gamma-ray burst (GRB) 130427A by the Large Area Telescope aboard the Fermi Gamma-ray Space Telescope provide constraints on the nature of these unique astrophysical sources. GRB 130427A had the largest fluence, highest-energy photon (95 GeV), longest gamma-ray duration (20 hours), and one of the largest isotropic energy releases ever observed from a GRB. Temporal and spectral analyses of GRB 130427A challenge the widely accepted model that the nonthermal high-energy emission in the afterglow phase of GRBs is synchrotron emission radiated by electrons accelerated at an external shock.

Does secure land tenure save forests? A meta-analysis of the relationship between land tenure and tropical deforestation

Abstract: Deforestation and degradation are tied to a complex array of socioeconomic and political factors. Many assume that among the most important of these are the particular bundles of rights regulating who can benefit from land (tenure form) and the overall assurance that those rights will be upheld (tenure security). This paper reviews literature that connects forest outcomes and land tenure to better understand broad interactions between tenure form, security and forest change. Papers from economic theory suggest tenure is embedded in a broader socioeconomic context, with the potential for either a positive or negative conservation impact on forested land. Empirically, we find 36 publications that link land cover change to tenure conditions while also controlling for other plausibly confounding variables. Publications often investigate more than one site and more than one form of tenure, so from these we derive 118 cases linking forest change with a specific tenure form in a particular location. From these cases, we find evidence that protected areas are associated with positive forest outcomes and that land tenure security is associated with less deforestation, regardless of the form of tenure. We conclude with a call for more robust identification of this relationship in future research, as well as set of recommendations for policymakers, particularly as forest carbon incentive programs such as REDD integrate further into national policies.

Female song is widespread and ancestral in songbirds.

Abstract: Bird song has historically been considered an almost exclusively male trait, an observation fundamental to the formulation of Darwin's theory of sexual selection. Like other male ornaments, song is used by male songbirds to attract females and compete with rivals. Thus, bird song has become a textbook example of the power of sexual selection to lead to extreme neurological and behavioural sex differences. Here we present an extensive survey and ancestral state reconstruction of female song across songbirds showing that female song is present in 71% of surveyed species including 32 families, and that females sang in the common ancestor of modern songbirds. Our results reverse classical assumptions about the evolution of song and sex differences in birds. The challenge now is to identify whether sexual selection alone or broader processes, such as social or natural selection, best explain the evolution of elaborate traits in both sexes.

Models of fluorescence and photosynthesis for interpreting measurements of solar-induced chlorophyll fluorescence.

Abstract: We have extended a conventional photosynthesis model to simulate field and laboratory measurements of chlorophyll fluorescence at the leaf scale. The fluorescence paramaterization is based on a close nonlinear relationship between the relative light saturation of photosynthesis and nonradiative energy dissipation in plants of different species. This relationship diverged only among examined data sets under stressed (strongly light saturated) conditions, possibly caused by differences in xanthophyll pigment concentrations. The relationship was quantified after analyzing data sets of pulse amplitude modulated measurements of chlorophyll fluorescence and gas exchange of leaves of different species exposed to different levels of light, CO2, temperature, nitrogen fertilization treatments, and drought. We used this relationship in a photosynthesis model. The coupled model enabled us to quantify the relationships between steady state chlorophyll fluorescence yield, electron transport rate, and photosynthesis in leaves under different environmental conditions.

Vegetation dynamics and rainfall sensitivity of the Amazon

Abstract: We show that the vegetation canopy of the Amazon rainforest is highly sensitive to changes in precipitation patterns and that reduction in rainfall since 2000 has diminished vegetation greenness across large parts of Amazonia. Large-scale directional declines in vegetation greenness may indicate decreases in carbon uptake and substantial changes in the energy balance of the Amazon. We use improved estimates of surface reflectance from satellite data to show a close link between reductions in annual precipitation, El Nino southern oscillation events, and photosynthetic activity across tropical and subtropical Amazonia. We report that, since the year 2000, precipitation has declined across 69% of the tropical evergreen forest (5.4 million km2) and across 80% of the subtropical grasslands (3.3 million km2). These reductions, which coincided with a decline in terrestrial water storage, account for about 55% of a satellite-observed widespread decline in the normalized difference vegetation index (NDVI). During El Nino events, NDVI was reduced about 16.6% across an area of up to 1.6 million km2 compared with average conditions. Several global circulation models suggest that a rise in equatorial sea surface temperature and related displacement of the intertropical convergence zone could lead to considerable drying of tropical forests in the 21st century. Our results provide evidence that persistent drying could degrade Amazonian forest canopies, which would have cascading effects on global carbon and climate dynamics.

Multi-decadal aerosol variations from 1980 to 2009: a perspective from observations and a global model

Abstract: . Aerosol variations and trends over different land and ocean regions from 1980 to 2009 are analyzed with the Goddard Chemistry Aerosol Radiation and Transport (GOCART) model and observations from multiple satellite sensors and available ground-based networks. Excluding time periods with large volcanic influence, aerosol optical depth (AOD) and surface concentration over polluted land regions generally vary with anthropogenic emissions, but the magnitude of this association can be dampened by the presence of natural aerosols, especially dust. Over the 30-year period in this study, the largest reduction in aerosol levels occurs over Europe, where AOD has decreased by 40–60% on average and surface sulfate concentrations have declined by a factor of up to 3–4. In contrast, East Asia and South Asia show AOD increases, but the relatively high level of dust aerosols in Asia reduces the correlation between AOD and pollutant emission trends. Over major dust source regions, model analysis indicates that the change of dust emissions over the Sahara and Sahel has been predominantly driven by the change of near-surface wind speed, but over Central Asia it has been largely influenced by the change of the surface wetness. The decreasing dust trend in the North African dust outflow region of the tropical North Atlantic and the receptor sites of Barbados and Miami is closely associated with an increase of the sea surface temperature in the North Atlantic. This temperature increase may drive the decrease of the wind velocity over North Africa, which reduces the dust emission, and the increase of precipitation over the tropical North Atlantic, which enhances dust removal during transport. Despite significant trends over some major continental source regions, the model-calculated global annual average AOD shows little change over land and ocean in the past three decades, because opposite trends in different land regions cancel each other out in the global average, and changes over large open oceans are negligible. This highlights the necessity for regional-scale assessment of aerosols and their climate impacts, as global-scale average values can obscure important regional changes.

Long interspersed element-1 protein expression is a hallmark of many human cancers

Abstract: Cancers comprise a heterogeneous group of human diseases. Unifying characteristics include unchecked abilities of tumor cells to proliferate and spread anatomically, and the presence of clonal advantageous genetic changes. However, universal and highly specific tumor markers are unknown. Herein, we report widespread long interspersed element-1 (LINE-1) repeat expression in human cancers. We show that nearly half of all human cancers are immunoreactive for a LINE-1–encoded protein. LINE-1 protein expression is a common feature of many types of high-grade malignant cancers, is rarely detected in early stages of tumorigenesis, and is absent from normal somatic tissues. Studies have shown that LINE-1 contributes to genetic changes in cancers, with somatic LINE-1 insertions seen in selected types of human cancers, particularly colon cancer. We sought to correlate this observation with expression of the LINE-1–encoded protein, open reading frame 1 protein, and found that LINE-1 open reading frame 1 protein is a surprisingly broad, yet highly tumor-specific, antigen.

Satellite observed widespread decline in Mongolian grasslands largely due to overgrazing

Abstract: The Mongolian Steppe is one of the largest remaining grassland ecosystems. Recent studies have reported widespread decline of vegetation across the steppe and about 70 percent of this ecosystem is now considered degraded. Among the scientific community there has been an active debate about whether the observed degradation is related to climate, or overgrazing, or both. Here, we employ a new atmospheric correction and cloud screening algorithm (MAIAC) to investigate trends in satellite observed vegetation phenology. We relate these trends to changes in climate and domestic animal populations. A series of harmonic functions is fitted to MODIS observed phenological curves to quantify seasonal and inter-annual changes in vegetation. Our results show a widespread decline (of about 12 percent on average) in MODIS observed NDVI across the country but particularly in the transition zone between grassland and the Gobi desert, where recent decline was as much as 40 percent below the 2002 mean NDVI. While we found considerable regional differences in the causes of landscape degradation, about 80 percent of the decline in NDVI could be attributed to increase in livestock. Changes in precipitation were able to explain about 30 percent of degradation across the country as a whole but up to 50 percent in areas with denser vegetation cover (p0.05). Temperature changes, while significant, played only a minor role (r20.10, p0.05). Our results suggest that the cumulative effect of overgrazing is a primary contributor to the degradation of the Mongolian steppe and is at least partially responsible for desertification reported in previous studies.

Nannochloropsis Genomes Reveal Evolution of Microalgal Oleaginous Traits

Abstract: Oleaginous microalgae are promising feedstock for biofuels, yet the genetic diversity, origin and evolution of oleaginous traits remain largely unknown. Here we present a detailed phylogenomic analysis of five oleaginous Nannochloropsis species (a total of six strains) and one time-series transcriptome dataset for triacylglycerol (TAG) synthesis on one representative strain. Despite small genome sizes, high coding potential and relative paucity of mobile elements, the genomes feature small cores of ca. 2,700 protein-coding genes and a large pan-genome of >38,000 genes. The six genomes share key oleaginous traits, such as the enrichment of selected lipid biosynthesis genes and certain glycoside hydrolase genes that potentially shift carbon flux from chrysolaminaran to TAG synthesis. The eleven type II diacylglycerol acyltransferase genes (DGAT-2) in every strain, each expressed during TAG synthesis, likely originated from three ancient genomes, including the secondary endosymbiosis host and the engulfed green and red algae. Horizontal gene transfers were inferred in most lipid synthesis nodes with expanded gene doses and many glycoside hydrolase genes. Thus multiple genome pooling and horizontal genetic exchange, together with selective inheritance of lipid synthesis genes and species-specific gene loss, have led to the enormous genetic apparatus for oleaginousness and the wide genomic divergence among present-day Nannochloropsis. These findings have important implications in the screening and genetic engineering of microalgae for biofuels.

Evaluation of the New Version of the Laser-Optical Disdrometer, OTT Parsivel2

Abstract: A comparative study of raindrop size distribution measurements has been conducted at NASA's Goddard Space Flight Center where the focus was to evaluate the performance of the upgraded laser-optical OTT Particle Size Velocity (Parsivel2; P2) disdrometer The experimental setup included a collocated pair of tipping-bucket rain gauges, OTT Parsivel (P1) and P2 disdrometers, and Joss-Waldvogel (JW) disdrometers Excellent agreement between the two collocated rain gauges enabled their use as a relative reference for event rain totals A comparison of event total showed that the P2 had a 6%absolute bias with respect to the reference gauges, considerably lower than the P1 and JW disdrometers Good agreement was also evident between the JW and P2 in hourly raindrop spectra for drop diameters between 05 and 4 mm The P2 drop concentrations mostly increased toward small sizes, and the peak concentrations were mostly observed in the first three measurable size bins The P1, on the other hand, underestimated small drops and overestimated the large drops, particularly in heavy rain rates From the analysis performed, it appears that the P2 is an improvement over the P1 model for both drop size and rainfall measurements P2 mean fall velocities follow accepted terminal fall speed relationships at drop sizes less than 1 mm As a caveat, the P2 had approximately 1ms21 slower mean fall speed with respect to the terminal fall speed near 1 mm, and the difference between the mean measured and terminal fall speeds reduced with increasing drop size This caveat was recognized as a software bug by the manufacturer and is currently being investigated

Scientific Impact of MODIS C5 Calibration Degradation and C6+ Improvements

Abstract: . The Collection 6 (C6) MODIS (Moderate Resolution Imaging Spectroradiometer) land and atmosphere data sets are scheduled for release in 2014. C6 contains significant revisions of the calibration approach to account for sensor aging. This analysis documents the presence of systematic temporal trends in the visible and near-infrared (500 m) bands of the Collection 5 (C5) MODIS Terra and, to lesser extent, in MODIS Aqua geophysical data sets. Sensor degradation is largest in the blue band (B3) of the MODIS sensor on Terra and decreases with wavelength. Calibration degradation causes negative global trends in multiple MODIS C5 products including the dark target algorithm's aerosol optical depth over land and Angstrom exponent over the ocean, global liquid water and ice cloud optical thickness, as well as surface reflectance and vegetation indices, including the normalized difference vegetation index (NDVI) and enhanced vegetation index (EVI). As the C5 production will be maintained for another year in parallel with C6, one objective of this paper is to raise awareness of the calibration-related trends for the broad MODIS user community. The new C6 calibration approach removes major calibrations trends in the Level 1B (L1B) data. This paper also introduces an enhanced C6+ calibration of the MODIS data set which includes an additional polarization correction (PC) to compensate for the increased polarization sensitivity of MODIS Terra since about 2007, as well as detrending and Terra–Aqua cross-calibration over quasi-stable desert calibration sites. The PC algorithm, developed by the MODIS ocean biology processing group (OBPG), removes residual scan angle, mirror side and seasonal biases from aerosol and surface reflectance (SR) records along with spectral distortions of SR. Using the multiangle implementation of atmospheric correction (MAIAC) algorithm over deserts, we have also developed a detrending and cross-calibration method which removes residual decadal trends on the order of several tenths of 1% of the top-of-atmosphere (TOA) reflectance in the visible and near-infrared MODIS bands B1–B4, and provides a good consistency between the two MODIS sensors. MAIAC analysis over the southern USA shows that the C6+ approach removed an additional negative decadal trend of Terra ΔNDVI ~ 0.01 as compared to Aqua data. This change is particularly important for analysis of vegetation dynamics and trends in the tropics, e.g., Amazon rainforest, where the morning orbit of Terra provides considerably more cloud-free observations compared to the afternoon Aqua measurements.

Overview and State-of-the-Art of Uncertainty Visualization

Abstract: The goal of visualization is to effectively and accurately communicate data. Visualization research has often overlooked the errors and uncertainty which accompany the scientific process and describe key characteristics used to fully understand the data. The lack of these representations can be attributed, in part, to the inherent difficulty in defining, characterizing, and controlling this uncertainty, and in part, to the difficulty in including additional visual metaphors in a well designed, potent display. However, the exclusion of this information cripples the use of visualization as a decision making tool due to the fact that the display is no longer a true representation of the data. This systematic omission of uncertainty commands fundamental research within the visualization community to address, integrate, and expect uncertainty information. In this chapter, we outline sources and models of uncertainty, give an overview of the state-of-the-art, provide general guidelines, outline small exemplary applications, and finally, discuss open problems in uncertainty visualization.

Diversity in Independent Component and Vector Analyses: Identifiability, algorithms, and applications in medical imaging

Abstract: Starting with a simple generative model and the assumption of statistical independence of the underlying components, independent component analysis (ICA) decomposes a given set of observations by making use of the diversity in the data, typically in terms of statistical properties of the signal. Most of the ICA algorithms introduced to date have considered one of the two types of diversity: non-Gaussianity?i.e., higher-order statistics (HOS)?or, sample dependence. A recent generalization of ICA, independent vector analysis (IVA), generalizes ICA to multiple data sets and adds the use of one more diversity, dependence across multiple data sets for achieving an independent decomposition, jointly across multiple data sets. Finally, both ICA and IVA, when implemented in the complex domain, enjoy the addition of yet another type of diversity, noncircularity of the sources?underlying components. Mutual information rate provides a unifying framework such that all these statistical properties?types of diversity?can be jointly taken into account for achieving the independent decomposition. Most of the ICA methods developed to date can be cast as special cases under this umbrella, as well as the more recently developed IVA methods. In addition, this formulation allows us to make use of maximum likelihood theory to study large sample properties of the estimator, derive the Cram?r?Rao lower bound (CRLB) and determine the conditions for the identifiability of the ICA and IVA models. In this overview article, we first present ICA, and then its generalization to multiple data sets, IVA, both using mutual information rate, present conditions for the identifiability of the given linear mixing model and derive the performance bounds. We address how various methods fall under this umbrella and give examples of performance for a few sample algorithms compared with the performance bound. We then discuss the importance of approaching the performance bound depending on the goal, and use medical image analysis as the motivating example.

Functional and molecular features of the Id4+ germline stem cell population in mouse testes

Abstract: The maintenance of cycling cell lineages relies on undifferentiated subpopulations consisting of stem and progenitor pools. Features that delineate these cell types are undefined for many lineages, including spermatogenesis, which is supported by an undifferentiated spermatogonial population. Here, we generated a transgenic mouse line in which spermatogonial stem cells are marked by expression of an inhibitor of differentiation 4 (Id4)-green fluorescent protein (Gfp) transgene. We found that Id4-Gfp(+) cells exist primarily as a subset of the type A(single) pool, and their frequency is greatest in neonatal development and then decreases in proportion during establishment of the spermatogenic lineage, eventually comprising ∼ 2% of the undifferentiated spermatogonial population in adulthood. RNA sequencing analysis revealed that expression of 11 and 25 genes is unique for the Id4-Gfp(+)/stem cell and Id4-Gfp(-)/progenitor fractions, respectively. Collectively, these findings provide the first definitive evidence that stem cells exist as a rare subset of the A(single) pool and reveal transcriptome features distinguishing stem cell and progenitor states within the mammalian male germline.