Showing papers by "Louisiana State University published in 2009"
University of Michigan1, University of Massachusetts Amherst2, University of New Mexico3, University of British Columbia4, Texas A&M University5, University of Minnesota6, University of Warwick7, Dalhousie University8, Colorado School of Mines9, University of Ljubljana10, Graz University of Technology11, Louisiana State University12
TL;DR: M mothur is used as a case study to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments.
Abstract: mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.
17,350 citations
TL;DR: In this article, the authors present an assessment of 33 deltas chosen to represent the world's Deltas and find that in the past decade, 85% of them experienced severe flooding, resulting in the temporary submergence of 260,000 km2.
Abstract: Many of the world's deltas are densely populated and intensively farmed. An assessment of recent publications indicates that the majority of these deltas have been subject to intense flooding over the past decade, and that this threat will grow as global sea-level rises and as the deltas subside. Many of the world's largest deltas are densely populated and heavily farmed. Yet many of their inhabitants are becoming increasingly vulnerable to flooding and conversions of their land to open ocean. The vulnerability is a result of sediment compaction from the removal of oil, gas and water from the delta's underlying sediments, the trapping of sediment in reservoirs upstream and floodplain engineering in combination with rising global sea level. Here we present an assessment of 33 deltas chosen to represent the world's deltas. We find that in the past decade, 85% of the deltas experienced severe flooding, resulting in the temporary submergence of 260,000 km2. We conservatively estimate that the delta surface area vulnerable to flooding could increase by 50% under the current projected values for sea-level rise in the twenty-first century. This figure could increase if the capture of sediment upstream persists and continues to prevent the growth and buffering of the deltas.
1,825 citations
TL;DR: This Review focuses on non-long terminal repeat (LTR) retrotransposons, and discusses the many ways that they affect the human genome: from generating insertion mutations and genomic instability to altering gene expression and contributing to genetic innovation.
Abstract: Their ability to move within genomes gives transposable elements an intrinsic propensity to affect genome evolution. Non-long terminal repeat (LTR) retrotransposons — including LINE-1, Alu and SVA elements — have proliferated over the past 80 million years of primate evolution and now account for approximately one-third of the human genome. In this Review, we focus on this major class of elements and discuss the many ways that they affect the human genome: from generating insertion mutations and genomic instability to altering gene expression and contributing to genetic innovation. Increasingly detailed analyses of human and other primate genomes are revealing the scale and complexity of the past and current contributions of non-LTR retrotransposons to genomic change in the human lineage.
1,432 citations
University of Alberta1, ExxonMobil2, University of Houston3, Louisiana State University4, Queen's University5, University of Pretoria6, University of Nebraska–Lincoln7, University of Texas at Austin8, Dalhousie University9, New Mexico State University10, University of Texas at Arlington11, University of South Carolina12, University of Toronto13, Colorado School of Mines14, Chevron Corporation15, University of Saskatchewan16, University of Fribourg17, Durham University18, Royal Dutch Shell19
TL;DR: In this paper, a model-independent framework of genetic units and bounding surfaces for sequence stratigraphy has been proposed, based on the interplay of accommodation and sedimentation (i.e., forced regressive, lowstand and highstand normal regressive), which are bounded by sequence stratigraphic surfaces.
1,255 citations
TL;DR: Three post hoc strategies and the strategy of doing nothing within three sets of assumptions about CMV are evaluated, finding potential benefits and likely risks of using the different techniques.
Abstract: Many researchers who use same-source data face concerns about common method variance (CMV). Although post hoc statistical detection and correction techniques for CMV have been proposed, there is a lack of empirical evidence regarding their efficacy. Because of disagreement among scholars regarding the likelihood and nature of CMV in self-report data, the current study evaluates three post hoc strategies and the strategy of doing nothing within three sets of assumptions about CMV: that CMV does not exist, that CMV exists and has equal effects across constructs, and that CMV exists and has unequal effects across constructs. The implications of using each strategy within each of the three assumptions are examined empirically using 691,200 simulated data sets varying factors such as the amount of true variance and the amount and nature of CMV modeled. Based on analyses of these data, potential benefits and likely risks of using the different techniques are detailed.
1,197 citations
TL;DR: A rare example of luminescent MOFs, which exhibit interesting catalytic activities for the transesterification and Knoevenagel condensation, attributed to pyridyl and amide sites, are reported, highlighting the significance of such Lewis basic sites within porous MOFs for their functional properties.
Abstract: The last two decades have witnessed significant progress in the design and synthesis of a new type of porous materials generally referred to as metal–organic frameworks (MOFs) and/or coordination polymers which can be readily selfassembled by the coordination of metal cations/clusters with organic linkers. Extensive efforts on such species have not only led to the creation of a huge number of MOFs of diverse topologies and aesthetic beauty, but also initiated a rational design strategy to construct porous materials with high surface areas, predictable structures, and tunable pore sizes to target some important applications, such as gas storage, separation, catalysis, magnetism, sensing, and imaging. Such progress within this field allows us to rationally design and synthesize porous MOFs with functional sites for specific host–guest recognition and thus to tune their functional properties. One of these extensively investigated methodologies is to immobilize unsaturated (open) Lewis acidic metal sites within porous MOFs for gas storage, catalysis, and sensing. Immobilization of Lewis basic sites within porous MOFs, however, has been more challenging, as such Lewis basic sites tend to bind other metal ions to form condensed structures. The very few examples of porous MOFs with Lewis basic sites include POST-1 with pyridyl sites, [Cd(4-btapa)2(NO3)2]·6 H2O·2DMF (4-btapa = 1,3,5-benzenetricarboxylic acid tris[N-(4-pyridyl)amide]) with amide sites and [Zn3(OH)3(2-stp)(bpy)1.5(H2O)]·EtOH·2H2O (2-stp = 2-sulfonylterephthalate; bpy = 4,4’bipyridine) with anionic sulfonate sites. Importantly, POST-1 and [Cd(4-btapa)2(NO3)2] exhibit interesting catalytic activities for the transesterification and Knoevenagel condensation, attributed to pyridyl and amide sites, respectively, highlighting the significance of such Lewis basic sites within porous MOFs for their functional properties. To make use of the preferential binding of lanthanide ions (Ln) to carboxylate oxygen atoms over pyridyl nitrogen atoms in Ln-pyridinecarboxylate complexes, 27] herein we report a rare example of luminescent MOFs, [Eu(pdc)1.5(dmf)]·(DMF)0.5(H2O)0.5 (1, pdc = pyridine-3,5-dicarboxylate), with Lewis basic pyridyl sites for the sensing of metal ions. Compound 1 was synthesized by the solvothermal reaction of [Eu(NO3)3]·(H2O)6 and H2pdc in DMF at 120 8C over night. It was formulated as [Eu(pdc)1.5(dmf)]·(DMF)0.5(H2O)0.5 by elemental microanalysis and single-crystal X-ray diffraction studies, and the phase purity of the bulk material was independently confirmed by powder X-ray diffraction (PXRD) and thermal gravimetric analysis (TGA) (see the Supporting Information, Figure S1-3). Complex 1 is isostructural with [Er(pdc)1.5(dmf)]·(solv)n and [Y(pdc)1.5(dmf)]·(solv)n, in which Eu atoms are bridged by pdc organic linkers to form a three-dimensional rodpacking structure. Each europium atom is coordinated by six oxygen atoms from the carboxylate groups of pdc, and capped by one distorted DMF molecule. One-dimensional hexagonal channels of about 6.3 8.5 along the a axis are filled by the capping DMF molecule, as well as free DMF and water molecules (Figure 1). TGA data indicated that 1 releases the free water and DMF, and terminal DMF molecules in the temperature range of 25–220 8C, to form a guest-free phase [Eu(pdc)1.5] (1 a) which is thermally stable up to 450 8C. The powder X-ray diffraction (PXRD) pattern of the guest-free phase 1a is almost identical with that of the as-synthesized 1, and matches well with that of the anhydrous [Er(pdc)1.5], indicating that the basic 3D framework is retained and the in situ-generated open Eu sites are occupied by carboxylate oxygen atoms, thus the 1D hexagonal channels are accessible to guest molecules. This shift of the carboxylate groups stabilizes the Eu sites and pores in 1a, so, even re-immersed in DMF, no solvent molecules are coordinated. Phase 1a exhibits type I isotherm characteristic N2 adsorption at 77 K with a Langmuir surface area of 537 m g (see the Supporting Information, Figure S4). The most significant structural feature is the presence of free Lewis basic pyridyl sites within the pores, highlighting the potential for their recognition of metal ions and thus for sensing functions. [*] Prof. Dr. B. Chen, L. Wang, Y. Xiao, Y. Cui, Prof. Dr. G. Qian Department of Materials Science & Engineering, State Key Laboratory of Silicon Materials, Zhejiang University Hangzhou 310027 (China) Fax: (+ 86)571-879-51234 E-mail: gdqian@zju.edu.cn
1,043 citations
TL;DR: Rabalais et al. as mentioned in this paper proposed that global climate changes will likely result in higher water temperatures, stronger stratification, and increased inflows of freshwater and nutrients to coastal waters in many areas of the globe.
Abstract: Rabalais, N. N., Turner, R. E., Diaz, R. J., and Justic, D. 2009. Global change and eutrophication of coastal waters. - ICES Journal of Marine Science, 66: 1528-1537.The cumulative effects of global change, including climate change, increased population, and more intense industrialization and agribusiness, will likely continue and intensify the course of eutrophication in estuarine and coastal waters. As a result, the symptoms of eutrophication, such as noxious and harmful algal blooms, reduced water quality, loss of habitat and natural resources, and severity of hypoxia (oxygen depletion) and its extent in estuaries and coastal waters will increase. Global climate changes will likely result in higher water temperatures, stronger stratification, and increased inflows of freshwater and nutrients to coastal waters in many areas of the globe. Both past experience and model forecasts suggest that these changes will result in enhanced primary production, higher phytoplankton and macroalgal standing stocks, and more frequent or severe hypoxia. The negative consequences of increased nutrient loading and stratification may be partly, but only temporarily, compensated by stronger or more frequent tropical storm activity in low and mid-latitudes. In anticipation of the negative effects of global change, nutrient loadings to coastal waters need to be reduced now, so that further water quality degradation is prevented.
899 citations
TL;DR: This article showed that 10,000-13,500 km2 of the Mississippi Delta could be submerged by AD 2100 due to global sea-level rise, reduced sediment supply and subsidence.
Abstract: Global sea-level rise, reduced sediment supply and subsidence threaten the stability of the Mississippi Delta. Calculations of riverine sediment load and storage indicate that 10,000–13,500 km2 of the delta could be submerged by AD 2100.
861 citations
TL;DR: Sunitinib-based therapy has the potential to modulate antitumor immunity by reversing MDSC-mediated tumor-induced immunosuppression and is correlated with reversal of type 1 T-cell suppression.
Abstract: Purpose: Immune dysfunction reported in renal cell carcinoma (RCC) patients may contribute to tumor progression. Myeloid-derived suppressor cells (MDSC) represent one mechanism by which tumors induce T-cell suppression. Several factors pivotal to the accumulation of MDSC are targeted by the tyrosine kinase inhibitor, sunitinib. The effect of sunitinib on MDSC-mediated immunosuppression in RCC patients has been investigated. Experimental Design: Patient peripheral blood levels of MDSC and regulatory T-cell (Treg) and T-cell production of IFN-γ were evaluated before and after sunitinib treatment. Correlations between MDSC and Treg normalization as well as T-cell production of IFN-γ were examined. The in vitro effect of sunitinib on patient MDSC was evaluated. Results: Metastatic RCC patients had elevated levels of CD33 + HLA-DR − and CD15 + CD14 − MDSC, and these were partially overlapping populations. Treatment with sunitinib resulted in significant reduction in MDSC measured by several criteria. Sunitinib-mediated reduction in MDSC was correlated with reversal of type 1 T-cell suppression, an effect that could be reproduced by the depletion of MDSC in vitro . MDSC reduction in response to sunitinib correlated with a reversal of CD3 + CD4 + CD25 hi Foxp3 + Treg cell elevation. No correlation existed between a change in tumor burden and a change in MDSC, Treg, or T-cell production of IFN-γ. In vitro addition of sunitinib reduced MDSC viability and suppressive effect when used at ≥1.0 μg/mL. Sunitinib did not induce MDSC maturation in vitro . Conclusions: Sunitinib-based therapy has the potential to modulate antitumor immunity by reversing MDSC-mediated tumor-induced immunosuppression.
830 citations
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TL;DR: In this article, the authors examined whether audit quality is higher for industry audit specialists at the national and city-office levels using the framework developed in Ferguson et al. [2003] and Francis et al [2005].
Abstract: Our paper examines whether audit quality is higher for industry audit specialists at the national and city-office levels using the framework developed in Ferguson et al. [2003] and Francis et al. [2005]. We find that auditors who are both national and city-specific industry specialists have clients with the lowest abnormal accruals, suggesting that joint national and city-specific industry specialists have the highest audit quality. In addition, we find some evidence that abnormal accruals of firms audited by city-industry specialists alone (without also being national specific industry specialists) are lower than those audited by non-industry specialists. Using alternative measures of audit quality, we find that when the auditor is both a national and a city-specific industry specialist, its clients are less likely to meet or beat analysts’ earnings forecasts by one penny per share and more likely to be issued a going-concern audit opinion. Together these results provide consistent evidence that audit quality is higher when the auditor is both a national and city-specific industry specialist, suggesting that auditors’ national positive network synergies and the individual auditors’ deep industry knowledge at the office level are jointly important factors in delivering higher audit quality.
723 citations
Pennington Biomedical Research Center1, Thomas Jefferson University2, Cornell University3, University of Wisconsin-Madison4, University of Alabama at Birmingham5, Michigan State University6, Johns Hopkins University7, University of Auckland8, Louisiana State University9, University of Verona10, Wayne State University11, University of Louisville12, Baylor College of Medicine13
TL;DR: Evidence for microorganisms, epigenetics, increasing maternal age, greater fecundity among people with higher adiposity, assortative mating, sleep debt, endocrine disruptors, pharmaceutical iatrogenesis, reduction in variability of ambient temperatures, and intrauterine and intergenerational effects as contributing factors to the obesity epidemic are reviewed.
Abstract: The obesity epidemic is a global issue and shows no signs of abating, while the cause of this epidemic remains unclear. Marketing practices of energy-dense foods and institutionally-driven declines...
TL;DR: More studies are needed to examine the best tests of respiratory function in ALS, as well as the optimal time for starting PEG, the impact of PEG on quality of life and survival, and the effect of vitamins and supplements on ALS.
Abstract: Objective: To systematically review evidence bearing on the management of patients with amyotrophic lateral sclerosis (ALS). Methods: The authors analyzed studies from 1998 to 2007 to update the 1999 practice parameter. Topics covered in this section include slowing disease progression, nutrition, and respiratory management for patients with ALS. Results: The authors identified 8 Class I studies, 5 Class II studies, and 43 Class III studies in ALS. Important treatments are available for patients with ALS that are underutilized. Noninvasive ventilation (NIV), percutaneous endoscopic gastrostomy (PEG), and riluzole are particularly important and have the best evidence. More studies are needed to examine the best tests of respiratory function in ALS, as well as the optimal time for starting PEG, the impact of PEG on quality of life and survival, and the effect of vitamins and supplements on ALS. Recommendations: Riluzole should be offered to slow disease progression (Level A). PEG should be considered to stabilize weight and to prolong survival in patients with ALS (Level B). NIV should be considered to treat respiratory insufficiency in order to lengthen survival (Level B), and may be considered to slow the decline of forced vital capacity (Level C) and improve quality of life (Level C). Early initiation of NIV may increase compliance (Level C), and insufflation/exsufflation may be considered to help clear secretions (Level C). Neurology ® 2009;73:1218 –1226 GLOSSARY AAN American Academy of Neurology; ALS amyotrophic lateral sclerosis; FVC forced vital capacity; HFCWO high frequency chest wall oscillation; MIE mechanical insufflation/exsufflation; MIP maximal inspiratory pressure; NIV noninvasive ventilation; PCEF peak cough expiratory flow; Pdi transdiaphragmatic pressure; PEG percutaneous endoscopic gastrostomy; QOL quality of life; RIG radiologically inserted device; SNP sniff nasal pressure; TIV tracheostomy invasive ventilation.
TL;DR: The importance of miRNAs in regulating cellular differentiation and proliferation is not surprising, and their misregulation is linked to cancer.
Abstract: MicroRNAs (miRNAs) are small noncoding, double-stranded RNA molecules that can mediate the expression of target genes with complementary sequences. About 5,300 human genes have been implicated as targets for miRNAs, making them one of the most abundant classes of regulatory genes in humans. MiRNAs recognize their target mRNAs based on sequence complementarity and act on them to cause the inhibition of protein translation by degradation of mRNA. Besides contributing to development and normal function, microRNAs have functions in various human diseases. Given the importance of miRNAs in regulating cellular differentiation and proliferation, it is not surprising that their misregulation is linked to cancer. In cancer, miRNAs function as regulatory molecules, acting as oncogenes or tumor suppressors. Amplification or overexpression of miRNAs can down-regulate tumor suppressors or other genes involved in cell differentiation, thereby contributing to tumor formation by stimulating proliferation, angiogenesis, and invasion; i.e., they act as oncogenes. Similarly, miRNAs can down-regulate different proteins with oncogenic activity; i.e., they act as tumor suppressors. This review will highlight the recent discoveries regarding miRNAs and their importance in cancer.
Victoria University of Wellington1, GNS Science2, Northern Illinois University3, University of Nebraska–Lincoln4, University of Otago5, University of Siena6, Ohio State University7, National Institute of Geophysics and Volcanology8, University of Massachusetts Amherst9, Harvard University10, Pennsylvania State University11, New Mexico Institute of Mining and Technology12, Appalachian State University13, Johns Hopkins University14, University of Milano-Bicocca15, Colorado School of Mines16, Denver Federal Center17, University of Wisconsin–Oshkosh18, University of Parma19, Iowa State University20, Stanford University21, University of Alberta22, Louisiana State University23, Albion College24, Lamont–Doherty Earth Observatory25
TL;DR: A marine glacial record from the upper 600 m of the AND-1B sediment core recovered from beneath the northwest part of the Ross ice shelf is presented and well-dated, ∼40-kyr cyclic variations in ice-sheet extent linked to cycles in insolation influenced by changes in the Earth’s axial tilt (obliquity) during the Pliocene are demonstrated.
Abstract: Thirty years after oxygen isotope records from microfossils deposited in ocean sediments confirmed the hypothesis that variations in the Earth's orbital geometry control the ice ages, fundamental questions remain over the response of the Antarctic ice sheets to orbital cycles. Furthermore, an understanding of the behaviour of the marine-based West Antarctic ice sheet (WAIS) during the 'warmer-than-present' early-Pliocene epoch ( approximately 5-3 Myr ago) is needed to better constrain the possible range of ice-sheet behaviour in the context of future global warming. Here we present a marine glacial record from the upper 600 m of the AND-1B sediment core recovered from beneath the northwest part of the Ross ice shelf by the ANDRILL programme and demonstrate well-dated, approximately 40-kyr cyclic variations in ice-sheet extent linked to cycles in insolation influenced by changes in the Earth's axial tilt (obliquity) during the Pliocene. Our data provide direct evidence for orbitally induced oscillations in the WAIS, which periodically collapsed, resulting in a switch from grounded ice, or ice shelves, to open waters in the Ross embayment when planetary temperatures were up to approximately 3 degrees C warmer than today and atmospheric CO(2) concentration was as high as approximately 400 p.p.m.v. (refs 5, 6). The evidence is consistent with a new ice-sheet/ice-shelf model that simulates fluctuations in Antarctic ice volume of up to +7 m in equivalent sea level associated with the loss of the WAIS and up to +3 m in equivalent sea level from the East Antarctic ice sheet, in response to ocean-induced melting paced by obliquity. During interglacial times, diatomaceous sediments indicate high surface-water productivity, minimal summer sea ice and air temperatures above freezing, suggesting an additional influence of surface melt under conditions of elevated CO(2).
TL;DR: Improved protocols to generate highly concentrated lentiviral vector pseudotypes involving different envelope glycoproteins are described, which result in high-titer vector preparations that show reduced toxicity compared with lentIViral vectors produced using standard protocols involving ultracentrifugation-based methods.
Abstract: Over the past decade, lentiviral vectors have emerged as powerful tools for transgene delivery. The use of lentiviral vectors has become commonplace and applications in the fields of neuroscience, hematology, developmental biology, stem cell biology and transgenesis are rapidly emerging. Also, lentiviral vectors are at present being explored in the context of human clinical trials. Here we describe improved protocols to generate highly concentrated lentiviral vector pseudotypes involving different envelope glycoproteins. In this protocol, vector stocks are prepared by transient transfection using standard cell culture media or serum-free media. Such stocks are then concentrated by ultracentrifugation and/or ion exchange chromatography, or by precipitation using polyethylene glycol 6000, resulting in vector titers of up to 10(10) transducing units per milliliter and above. We also provide reliable real-time PCR protocols to titrate lentiviral vectors based on proviral DNA copies present in genomic DNA extracted from transduced cells or on vector RNA. These production/concentration methods result in high-titer vector preparations that show reduced toxicity compared with lentiviral vectors produced using standard protocols involving ultracentrifugation-based methods. The vector production and titration protocol described here can be completed within 8 d.
Oregon State University1, Yale University2, Duke University3, Clark University4, University of Tennessee5, Kaiserslautern University of Technology6, Centraalbureau voor Schimmelcultures7, University of Copenhagen8, University of Tabriz9, Harvard University10, University of Pretoria11, ATCC12, Louisiana State University13, University of Texas at Austin14, Aberystwyth University15, United States Department of Agriculture16, Field Museum of Natural History17, Pennsylvania State University18, University of California, Berkeley19, University of North Carolina at Chapel Hill20, Stellenbosch University21, Free University of Berlin22, Washington State University23, Brandon University24, Landcare Research25, University of Helsinki26, University of Giessen27, University of Nottingham28, Swedish Museum of Natural History29, Royal Botanic Garden Edinburgh30
TL;DR: A 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi, and a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions support a terrestrial, saprobic ecology as ancestral are presented.
Abstract: We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.
TL;DR: A review of the recent theoretical and experimental advances in this exciting new field of quantum optical metrology, focusing on examples that exploit a particular two-mode entangled photon state is given in this article.
Abstract: Quantum states of light, such as squeezed states or entangled states, can be used to make measurements (metrology), produce images, and sense objects with a precision that far exceeds what is possible classically, and also exceeds what was once thought to be possible quantum mechanically. The primary idea is to exploit quantum effects to beat the shot-noise limit in metrology and the Rayleigh diffraction limit in imaging and sensing. Quantum optical metrology has received a boost in recent years with an influx of ideas from the rapidly evolving field of optical quantum information processing. Both areas of research exploit the creation and manipulation of quantum-entangled states of light. We will review some of the recent theoretical and experimental advances in this exciting new field of quantum optical metrology, focusing on examples that exploit a particular two-mode entangled photon state -- the High-N00N state.
University of California, Santa Cruz1, National Institutes of Health2, Broad Institute3, University of Los Andes4, University of Guelph5, University of Nottingham6, University of California, Berkeley7, Pennsylvania State University8, Royal Ontario Museum9, Texas A&M University10, Louisiana State University11, Agency for Science, Technology and Research12, University of Kansas13, University of Montana14, American Museum of Natural History15, Oregon State University16, Villanova University17, University of Porto18, Smithsonian Institution19, Oswaldo Cruz Foundation20, Okinawa Institute of Science and Technology21, University of Sheffield22, Harvard University23, Swedish Museum of Natural History24, University of Copenhagen25, Novosibirsk State University26, Australian National University27, Max Planck Society28, Field Museum of Natural History29, Commonwealth Scientific and Industrial Research Organisation30, Science Applications International Corporation31, Stanford University32, University of Illinois at Urbana–Champaign33, George Washington University34, Global Viral35, University of Bedfordshire36, Federal University of Rio de Janeiro37, University of California, Davis38, University of California, Riverside39, Museum Victoria40, University College Dublin41, Monterey Bay Aquarium Research Institute42, Washington University in St. Louis43, University of California, Los Angeles44, Kunming Institute of Zoology45
TL;DR: A precipitous drop in costs and increase in sequencing efficiency is anticipated, with concomitant development of improved annotation technology, and it is proposed to create a collection of tissue and DNA specimens for 10,000 vertebrate species specifically designated for whole-genome sequencing in the very near future.
Abstract: American Genetic Association, Gordon and Betty Moore Foundation, NHGRI Intramural Sequencing Center, and UCSC Alumni Association to cost of the Genome 10K workshop; Howard Hughes Medical Institute to D. H.; Gordon and Betty Moore Foundation to S. C. S.; A
TL;DR: Results support attention-based models of anxiety and suggest that attention training is a promising alternative or complementary intervention for social anxiety in patients with a primary diagnosis of generalized SAD.
Abstract: Attentional bias toward negative social cues is thought to serve an etiological and/or maintaining role in social anxiety disorder (SAD). The current study tested whether training patients to disengage from negative social cues may ameliorate social anxiety in patients (N = 36) with a primary diagnosis of generalized SAD. Patients were randomly assigned to either an attention training condition (n = 18), in which patients completed a modified dot-probe task designed to facilitate attentional disengagement from disgusted faces, or a control dot-probe task condition (n = 18). As predicted, patients in the attention training condition exhibited significantly greater reductions in social anxiety and trait anxiety, compared with patients in the control condition. At termination, 72% of patients in the active treatment condition, relative to 11% of patients in the control condition, no longer met Diagnostic and Statistical Manual of Mental Disorders (4th ed.) criteria for SAD. At 4-month follow-up, patients in the attention training condition continued to maintain their clinical improvement, and diagnostic differences across conditions were also maintained. Results support attention-based models of anxiety and suggest that attention training is a promising alternative or complementary intervention.
TL;DR: The concepts of keratins and of keratinized or cornified epithelia need clarification and revision concerning the structure and function of kerATins and keratin filaments in various epithelium of different species, as well as of Keratin genes and their modifications in view of recent research.
Abstract: Historically, the term ‘keratin’ stood for all of the proteins extracted from skin modifications, such as horns, claws and hooves. Subsequently, it was realized that this keratin is actually a mixture of keratins, keratin filament-associated proteins and other proteins, such as enzymes. Keratins were then defined as certain filament-forming proteins with specific physicochemical properties and extracted from the cornified layer of the epidermis, whereas those filament-forming proteins that were extracted from the living layers of the epidermis were grouped as ‘prekeratins’ or ‘cytokeratins’. Currently, the term ‘keratin’ covers all intermediate filament-forming proteins with specific physicochemical properties and produced in any vertebrate epithelia. Similarly, the nomenclature of epithelia as cornified, keratinized or non-keratinized is based historically on the notion that only the epidermis of skin modifications such as horns, claws and hooves is cornified, that the non-modified epidermis is a keratinized stratified epithelium, and that all other stratified and non-stratified epithelia are non-keratinized epithelia. At this point in time, the concepts of keratins and of keratinized or cornified epithelia need clarification and revision concerning the structure and function of keratin and keratin filaments in various epithelia of different species, as well as of keratin genes and their modifications, in view of recent research, such as the sequencing of keratin proteins and their genes, cell culture, transfection of epithelial cells, immunohistochemistry and immunoblotting. Recently, new functions of keratins and keratin filaments in cell signaling and intracellular vesicle transport have been discovered. It is currently understood that all stratified epithelia are keratinized and that some of these keratinized stratified epithelia cornify by forming a Stratum corneum. The processes of keratinization and cornification in skin modifications are different especially with respect to the keratins that are produced. Future research in keratins will provide a better understanding of the processes of keratinization and cornification of stratified epithelia, including those of skin modifications, of the adaptability of epithelia in general, of skin diseases, and of the changes in structure and function of epithelia in the course of evolution. This review focuses on keratins and keratin filaments in mammalian tissue but keratins in the tissues of some other vertebrates are also considered.
TL;DR: In this article, the authors systematically review evidence bearing on the management of patients with amyotrophic lateral sclerosis (ALS), including breaking the news, multidisciplinary clinics, symptom management, cognitive and behavioral impairment, communication, and palliative care for patients with ALS.
Abstract: Objective: To systematically review evidence bearing on the management of patients with amyotrophic lateral sclerosis (ALS). Methods: The authors analyzed studies from 1998 to 2007 to update the 1999 practice parameter. Topics covered in this section include breaking the news, multidisciplinary clinics, symptom management, cognitive and behavioral impairment, communication, and palliative care for patients with ALS. Results: The authors identified 2 Class I studies, 8 Class II studies, and 30 Class III studies in ALS, but many important areas have been little studied. More high-quality, controlled studies of symptomatic therapies and palliative care are needed to guide management and assess outcomes in patients with ALS. Recommendations: Multidisciplinary clinic referral should be considered for managing patients with ALS to optimize health care delivery and prolong survival (Level B) and may be considered to enhance quality of life (Level C). For the treatment of refractory sialorrhea, botulinum toxin B should be considered (Level B) and low-dose radiation therapy to the salivary glands may be considered (Level C). For treatment of pseudobulbar affect, dextromethorphan and quinidine should be considered if approved by the US Food and Drug Administration (Level B). For patients who develop fatigue while taking riluzole, withholding the drug may be considered (Level C). Because many patients with ALS demonstrate cognitive impairment, which in some cases meets criteria for dementia, screening for cognitive and behavioral impairment should be considered in patients with ALS (Level B). Other management strategies all lack strong evidence.
United States Department of Agriculture1, Agriculture and Agri-Food Canada2, Louisiana State University3, University of Warwick4, National Center for Agricultural Utilization Research5, Obihiro University of Agriculture and Veterinary Medicine6, International Centre of Insect Physiology and Ecology7, National Agrarian University (Nicaragua)8, University of Tennessee9, Rothamsted Research10, University of Paraíba Valley11
TL;DR: The recently discovered roles played by many entomopathogenic fungi are reviewed and new research strategies focused on alternate uses for these fungi are proposed.
TL;DR: UNLABELLED STEM is a software package written in the C language to obtain maximum likelihood (ML) estimates for phylogenetic species trees given a sample of gene trees under the coalescent model.
Abstract: STEM is a software package written in the C language to obtain maximum likelihood (ML) estimates for phylogenetic species trees given a sample of gene trees under the coalescent model. It includes options to compute the ML species tree, search the space of all species trees for the k trees of highest likelihood and compute ML branch lengths for a user-input species tree. Availability: The STEM package, including source code, is freely available at http://www.stat.osu.edu/∼lkubatko/software/STEM/. Contact: lkubatko@stat.osu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
TL;DR: It is demonstrated that the miR‐27 gene family is downregulated during adipogenic differentiation, and represents a new class of adipogenic inhibitors and may play a role in the pathological development of obesity.
Abstract: MicroRNAs (miRNAs) are involved in a plethora of important biological processes, from embryonic development to homeostasis in adult tissues. Recently, miRNAs have emerged as a class of epigenetic regulators of metabolism and energy homeostasis. We have investigated the role of miRNAs in the regulation of adipogenic differentiation. In this article, we demonstrate that the miR-27 gene family is downregulated during adipogenic differentiation. Overexpression of miR-27 specifically inhibited adipocyte formation, without affecting myogenic differentiation. We also found that expression of miR-27 resulted in blockade of expression of PPARγ and C/EBPα, the two master regulators of adipogenesis. Importantly, expression of miR-27 was increased in fat tissue of obese mice and was regulated by hypoxia, an important extracellular stress associated with obesity. Our data strongly suggest that miR-27 represents a new class of adipogenic inhibitors and may play a role in the pathological development of obesity.
TL;DR: The routine application and presentation of rigorous skill assessment metrics will also serve the broader interests of the modeling community, ultimately resulting in improved forecasting abilities as well as helping us recognize the authors' limitations.
TL;DR: The results suggest that unless specifically stabilized, certain brain-enriched miRNAs represent a rapidly executed signaling system employing highly transient effectors of CNS gene expression, and that in AD temporal lobe neocortex specific brain mi RNAs are significantly up-regulated in abundance and strongly correlate with the presence of AD-type neuropatholgical change.
TL;DR: A better understanding of effective population sizes is needed and studies that infer parentage or kinship and coalescent analyses employing more markers are both likely to spur progress, with analyses based on linkage disequilibrium potentially bridging results from studies and reconciling patterns that vary at ecological and evolutionary timescales.
Abstract: Successful dispersal between populations leaves a genetic wake that can reveal historical and contemporary patterns of connectivity. Genetic studies of differentiation in the sea suggest the role of larval dispersal is often tempered by adult ecology, that changes in differentiation with geographic distance are limited by disequilibrium between drift and migration, and that phylogeographic breaks reflect shared barriers to movement in the present more than common historical divisions. Recurring complications include the presence of cryptic species, selection on markers, and a failure to account for differences in heterozygosity among markers and species. A better understanding of effective population sizes is needed. Studies that infer parentage or kinship and coalescent analyses employing more markers are both likely to spur progress, with analyses based on linkage disequilibrium potentially bridging results from these studies and reconciling patterns that vary at ecological and evolutionary timescales.
TL;DR: In this paper, the authors reported limits on the amplitude of the stochastic gravitational-wave background using the data from a two-year science run of the Laser Interferometer Gravitational-wave Observatory (LIGO).
Abstract: A stochastic background of gravitational waves is expected to arise from a superposition of a large number of unresolved gravitational-wave sources of astrophysical and cosmological origin. It should carry unique signatures from the earliest epochs in the evolution of the Universe, inaccessible to standard astrophysical observations. Direct measurements of the amplitude of this background are therefore of fundamental importance for understanding the evolution of the Universe when it was younger than one minute. Here we report limits on the amplitude of the stochastic gravitational-wave background using the data from a two-year science run of the Laser Interferometer Gravitational-wave Observatory (LIGO). Our result constrains the energy density of the stochastic gravitational-wave background normalized by the critical energy density of the Universe, in the frequency band around 100 Hz, to be <6.9 times 10-6 at 95% confidence. The data rule out models of early Universe evolution with relatively large equation-of-state parameter, as well as cosmic (super)string models with relatively small string tension that are favoured in some string theory models. This search for the stochastic background improves on the indirect limits from Big Bang nucleosynthesis and cosmic microwave background at 100 Hz.
TL;DR: In this article, the Johnson-Kron-Cousins photometric system was extended to include 202 stars around the sky, and centered at the celestial equator, and the entire list of standard stars in this paper encompasses the magnitude range 8.90 < V < 16.30 and the color index range −0.35 < (B − V) < +2.30.
Abstract: New broadband UBVRI photoelectric observations on the Johnson-Kron-Cousins photometric system have been made of 202 stars around the sky, and centered at the celestial equator. These stars constitute both an update of and additions to a previously published list of equatorial photometric standard stars. The list is capable of providing, for both celestial hemispheres, an internally consistent homogeneous broadband standard photometric system around the sky. When these new measurements are included with those previously published by Landolt (1992), the entire list of standard stars in this paper encompasses the magnitude range 8.90 < V < 16.30, and the color index range –0.35 < (B – V) < +2.30.
TL;DR: It is argued that heuristics are consequential in explaining variations in learning and this work seeks to provide a more complete model of entrepreneurial learning that allows for examination of the influence of judgments on learning and to expose conditions that can benefit or limit effective action in an entrepreneurial setting.
Abstract: We extend existing theories of entrepreneurial learning and highlight the effects of heuristics under two different learning contexts: experiential learning and vicarious learning. Specifically, we...