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Sample records for sequence california evidence

  1. Detailed observations of California foreshock sequences: Implications for the earthquake initiation process

    Science.gov (United States)

    Dodge, D.A.; Beroza, G.C.; Ellsworth, W.L.

    1996-01-01

    We find that foreshocks provide clear evidence for an extended nucleation process before some earthquakes. In this study, we examine in detail the evolution of six California foreshock sequences, the 1986 Mount Lewis (ML, = 5.5), the 1986 Chalfant (ML = 6.4), the. 1986 Stone Canyon (ML = 4.7), the 1990 Upland (ML = 5.2), the 1992 Joshua Tree (MW= 6.1), and the 1992 Landers (MW = 7.3) sequence. Typically, uncertainties in hypocentral parameters are too large to establish the geometry of foreshock sequences and hence to understand their evolution. However, the similarity of location and focal mechanisms for the events in these sequences leads to similar foreshock waveforms that we cross correlate to obtain extremely accurate relative locations. We use these results to identify small-scale fault zone structures that could influence nucleation and to determine the stress evolution leading up to the mainshock. In general, these foreshock sequences are not compatible with a cascading failure nucleation model in which the foreshocks all occur on a single fault plane and trigger the mainshock by static stress transfer. Instead, the foreshocks seem to concentrate near structural discontinuities in the fault and may themselves be a product of an aseismic nucleation process. Fault zone heterogeneity may also be important in controlling the number of foreshocks, i.e., the stronger the heterogeneity, the greater the number of foreshocks. The size of the nucleation region, as measured by the extent of the foreshock sequence, appears to scale with mainshock moment in the same manner as determined independently by measurements of the seismic nucleation phase. We also find evidence for slip localization as predicted by some models of earthquake nucleation. Copyright 1996 by the American Geophysical Union.

  2. Diagnosis of Fatal Human Case of St. Louis Encephalitis Virus Infection by Metagenomic Sequencing, California, 2016.

    Science.gov (United States)

    Chiu, Charles Y; Coffey, Lark L; Murkey, Jamie; Symmes, Kelly; Sample, Hannah A; Wilson, Michael R; Naccache, Samia N; Arevalo, Shaun; Somasekar, Sneha; Federman, Scot; Stryke, Doug; Vespa, Paul; Schiller, Gary; Messenger, Sharon; Humphries, Romney; Miller, Steve; Klausner, Jeffrey D

    2017-10-01

    We used unbiased metagenomic next-generation sequencing to diagnose a fatal case of meningoencephalitis caused by St. Louis encephalitis virus in a patient from California in September 2016. This case is associated with the recent 2015-2016 reemergence of this virus in the southwestern United States.

  3. Sedimentation across the central California oxygen minimum zone: an alternative coastal upwelling sequence.

    Science.gov (United States)

    Vercoutere, T.L.; Mullins, H.T.; McDougall, K.; Thompson, J.B.

    1987-01-01

    Distribution, abundance, and diversity of terrigenous, authigenous, and biogenous material provide evidence of the effect of bottom currents and oxygen minimum zone (OMZ) on continental slope sedimentation offshore central California. Three major OMZ facies are identified, along the upper and lower edges of OMZ and one at its core.-from Authors

  4. Monogenetic origin of Ubehebe Crater maar volcano, Death Valley, California: Paleomagnetic and stratigraphic evidence

    Science.gov (United States)

    Champion, Duane E.; Cyr, Andy; Fierstein, Judy; Hildreth, Wes

    2018-04-01

    Paleomagnetic data for samples collected from outcrops of basaltic spatter at the Ubehebe Crater cluster, Death Valley National Park, California, record a single direction of remanent magnetization indicating that these materials were emplaced during a short duration, monogenetic eruption sequence 2100 years ago. This conclusion is supported by geochemical data encompassing a narrow range of oxide variation, by detailed stratigraphic studies of conformable phreatomagmatic tephra deposits showing no evidence of erosion between layers, by draping of sharp rimmed craters by later tephra falls, and by oxidation of later tephra layers by the remaining heat of earlier spatter. This model is also supported through a reinterpretation and recalculation of the published 10Be age results (Sasnett et al., 2012) from an innovative and bold exposure-age study on very young materials. Their conclusion of multiple and protracted eruptions at Ubehebe Crater cluster is here modified through the understanding that some of their quartz-bearing clasts inherited 10Be from previous exposure on the fan surface (too old), and that other clasts were only exposed at the surface by wind and/or water erosion centuries after their eruption (too young). Ubehebe Crater cluster is a well preserved example of young monogenetic maar type volcanism protected within a National Park, and it represents neither a protracted eruption sequence as previously thought, nor a continuing volcanic hazard near its location.

  5. Genome and Transcriptome Sequencing of the Ostreid herpesvirus 1 From Tomales Bay, California

    Science.gov (United States)

    Burge, C. A.; Langevin, S.; Closek, C. J.; Roberts, S. B.; Friedman, C. S.

    2016-02-01

    Mass mortalities of larval and seed bivalve molluscs attributed to the Ostreid herpesvirus 1 (OsHV-1) occur globally. OsHV-1 was fully sequenced and characterized as a member of the Family Malacoherpesviridae. Multiple strains of OsHV-1 exist and may vary in virulence, i.e. OsHV-1 µvar. For most global variants of OsHV-1, sequence data is limited to PCR-based sequencing of segments, including two recent genomes. In the United States, OsHV-1 is limited to detection in adjacent embayments in California, Tomales and Drakes bays. Limited DNA sequence data of OsHV-1 infecting oysters in Tomales Bay indicates the virus detected in Tomales Bay is similar but not identical to any one global variant of OsHV-1. In order to better understand both strain variation and virulence of OsHV-1 infecting oysters in Tomales Bay, we used genomic and transcriptomic sequencing. Meta-genomic sequencing (Illumina MiSeq) was conducted from infected oysters (n=4 per year) collected in 2003, 2007, and 2014, where full OsHV-1 genome sequences and low overall microbial diversity were achieved from highly infected oysters. Increased microbial diversity was detected in three of four samples sequenced from 2003, where qPCR based genome copy numbers of OsHV-1 were lower. Expression analysis (SOLiD RNA sequencing) of OsHV-1 genes expressed in oyster larvae at 24 hours post exposure revealed a nearly complete transcriptome, with several highly expressed genes, which are similar to recent transcriptomic analyses of other OsHV-1 variants. Taken together, our results indicate that genome and transcriptome sequencing may be powerful tools in understanding both strain variation and virulence of non-culturable marine viruses.

  6. Complete genomic sequences of two salmonella enterica subsp. enterica serogroup C2 (O:6,8) strains from central California

    Science.gov (United States)

    Salmonella enteric subsp. enterica strains RM11060, serotype 6,8:d:-, and RM11065, serotype 6,8:-:e,n,z15, were isolated from environmental sampling in Central California in 2009. We report the complete genome sequences and annotation of these two strains. These genomic sequences are distinct and wi...

  7. Conditional Probabilities of Large Earthquake Sequences in California from the Physics-based Rupture Simulator RSQSim

    Science.gov (United States)

    Gilchrist, J. J.; Jordan, T. H.; Shaw, B. E.; Milner, K. R.; Richards-Dinger, K. B.; Dieterich, J. H.

    2017-12-01

    Within the SCEC Collaboratory for Interseismic Simulation and Modeling (CISM), we are developing physics-based forecasting models for earthquake ruptures in California. We employ the 3D boundary element code RSQSim (Rate-State Earthquake Simulator of Dieterich & Richards-Dinger, 2010) to generate synthetic catalogs with tens of millions of events that span up to a million years each. This code models rupture nucleation by rate- and state-dependent friction and Coulomb stress transfer in complex, fully interacting fault systems. The Uniform California Earthquake Rupture Forecast Version 3 (UCERF3) fault and deformation models are used to specify the fault geometry and long-term slip rates. We have employed the Blue Waters supercomputer to generate long catalogs of simulated California seismicity from which we calculate the forecasting statistics for large events. We have performed probabilistic seismic hazard analysis with RSQSim catalogs that were calibrated with system-wide parameters and found a remarkably good agreement with UCERF3 (Milner et al., this meeting). We build on this analysis, comparing the conditional probabilities of sequences of large events from RSQSim and UCERF3. In making these comparisons, we consider the epistemic uncertainties associated with the RSQSim parameters (e.g., rate- and state-frictional parameters), as well as the effects of model-tuning (e.g., adjusting the RSQSim parameters to match UCERF3 recurrence rates). The comparisons illustrate how physics-based rupture simulators might assist forecasters in understanding the short-term hazards of large aftershocks and multi-event sequences associated with complex, multi-fault ruptures.

  8. RNA shotgun metagenomic sequencing of northern California (USA mosquitoes uncovers viruses, bacteria, and fungi

    Directory of Open Access Journals (Sweden)

    James Angus eChandler

    2015-03-01

    Full Text Available Mosquitoes, most often recognized for the microbial agents of disease they may carry, harbor diverse microbial communities that include viruses, bacteria, and fungi, collectively called the microbiota. The composition of the microbiota can directly and indirectly affect disease transmission through microbial interactions that could be revealed by its characterization in natural populations of mosquitoes. Furthermore, the use of shotgun metagenomic sequencing (SMS approaches could allow the discovery of unknown members of the microbiota. In this study, we use RNA SMS to characterize the microbiota of seven individual mosquitoes (species include Culex pipiens, Culiseta incidens, and Ochlerotatus sierrensis collected from a variety of habitats in California, USA. Sequencing was performed on the Illumina HiSeq platform and the resulting sequences were quality-checked and assembled into contigs using the A5 pipeline. Sequences related to single stranded RNA viruses of the Bunyaviridae and Rhabdoviridae were uncovered, along with an unclassified genus of double-stranded RNA viruses. Phylogenetic analysis finds that in all three cases, the closest relatives of the identified viral sequences are other mosquito-associated viruses, suggesting widespread host-group specificity among disparate viral taxa. Interestingly, we identified a Narnavirus of fungi, also reported elsewhere in mosquitoes, that potentially demonstrates a nested host-parasite association between virus, fungi, and mosquito. Sequences related to 8 bacterial families and 13 fungal families were found across the seven samples. Bacillus and Escherichia/Shigella were identified in all samples and Wolbachia was identified in all Cx. pipiens samples, while no single fungal genus was found in more than two samples. This study exemplifies the utility of RNA SMS in the characterization of the natural microbiota of mosquitoes and, in particular, the value of identifying all microbes associated with

  9. Combined evidence annotation of transposable elements in genome sequences.

    Directory of Open Access Journals (Sweden)

    Hadi Quesneville

    2005-07-01

    Full Text Available Transposable elements (TEs are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most efforts to annotate TEs in genome sequences rely on the results of a single computational program, RepeatMasker. In contrast, recent advances in gene annotation indicate that high-quality gene models can be produced from combining multiple independent sources of computational evidence. To elevate the quality of TE annotations to a level comparable to that of gene models, we have developed a combined evidence-model TE annotation pipeline, analogous to systems used for gene annotation, by integrating results from multiple homology-based and de novo TE identification methods. As proof of principle, we have annotated "TE models" in Drosophila melanogaster Release 4 genomic sequences using the combined computational evidence derived from RepeatMasker, BLASTER, TBLASTX, all-by-all BLASTN, RECON, TE-HMM and the previous Release 3.1 annotation. Our system is designed for use with the Apollo genome annotation tool, allowing automatic results to be curated manually to produce reliable annotations. The euchromatic TE fraction of D. melanogaster is now estimated at 5.3% (cf. 3.86% in Release 3.1, and we found a substantially higher number of TEs (n = 6,013 than previously identified (n = 1,572. Most of the new TEs derive from small fragments of a few hundred nucleotides long and highly abundant families not previously annotated (e.g., INE-1. We also estimated that 518 TE copies (8.6% are inserted into at least one other TE, forming a nest of elements. The pipeline allows rapid and thorough annotation of even the most complex TE models, including highly deleted and/or nested elements such as those often found in heterochromatic sequences. Our pipeline can be easily adapted to other genome sequences, such as those of the D. melanogaster heterochromatin or other

  10. Genome Sequences of Two Pseudomonas syringae pv. tomato Race 1 Strains, Isolated from Tomato Fields in California

    OpenAIRE

    Thapa, Shree P.; Coaker, Gitta

    2016-01-01

    Pseudomonas syringae pv. tomato race 1 strains have evolved to overcome genetic resistance in tomato. Here, we present the draft genome sequences of two race 1 P.?syringae pv. tomato strains, A9 and 407, isolated from diseased tomato plants in California.

  11. Whole genome sequencing of Mycobacterium bovis to obtain molecular fingerprints in human and cattle isolates from Baja California, Mexico.

    Science.gov (United States)

    Sandoval-Azuara, Sarai Estrella; Muñiz-Salazar, Raquel; Perea-Jacobo, Ricardo; Robbe-Austerman, Suelee; Perera-Ortiz, Alejandro; López-Valencia, Gilberto; Bravo, Doris M; Sanchez-Flores, Alejandro; Miranda-Guzmán, Daniela; Flores-López, Carlos Alberto; Zenteno-Cuevas, Roberto; Laniado-Laborín, Rafael; de la Cruz, Fabiola Lafarga; Stuber, Tod P

    2017-10-01

    To determine genetic diversity by comparing the whole genome sequences of cattle and human Mycobacterium bovis isolates from Baja California. A whole genome sequencing strategy was used to obtain the molecular fingerprints of 172 isolates of M. bovis obtained from Baja California, Mexico; 155 isolates were from cattle and 17 isolates were from humans. Spoligotypes were characterized in silico and single nucleotide polymorphism (SNP) differences between the isolates were evaluated. A total of 12 M. bovis spoligotype patterns were identified in cattle and humans. Two predominant spoligotypes patterns were seen in both cattle and humans: SB0145 and SB1040. The SB0145 spoligotype represented 59% of cattle isolates (n=91) and 65% of human isolates (n=11), while the SB1040 spoligotype represented 30% of cattle isolates (n=47) and 30% of human isolates (n=5). When evaluating SNP differences, the human isolates were intimately intertwined with the cattle isolates. All isolates from humans had spoligotype patterns that matched those observed in the cattle isolates, and all human isolates shared common ancestors with cattle in Baja California based on SNP analysis. This suggests that most human tuberculosis caused by M. bovis in Baja California is derived from M. bovis circulating in Baja California cattle. These results reinforce the importance of bovine tuberculosis surveillance and control in this region. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  12. The 2010 M w 7.2 El Mayor-Cucapah Earthquake Sequence, Baja California, Mexico and Southernmost California, USA: Active Seismotectonics along the Mexican Pacific Margin

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    Hauksson, Egill; Stock, Joann; Hutton, Kate; Yang, Wenzheng; Vidal-Villegas, J. Antonio; Kanamori, Hiroo

    2011-08-01

    The El Mayor-Cucapah earthquake sequence started with a few foreshocks in March 2010, and a second sequence of 15 foreshocks of M > 2 (up to M4.4) that occurred during the 24 h preceding the mainshock. The foreshocks occurred along a north-south trend near the mainshock epicenter. The M w 7.2 mainshock on April 4 exhibited complex faulting, possibly starting with a ~M6 normal faulting event, followed ~15 s later by the main event, which included simultaneous normal and right-lateral strike-slip faulting. The aftershock zone extends for 120 km from the south end of the Elsinore fault zone north of the US-Mexico border almost to the northern tip of the Gulf of California. The waveform-relocated aftershocks form two abutting clusters, each about 50 km long, as well as a 10 km north-south aftershock zone just north of the epicenter of the mainshock. Even though the Baja California data are included, the magnitude of completeness and the hypocentral errors increase gradually with distance south of the international border. The spatial distribution of large aftershocks is asymmetric with five M5+ aftershocks located to the south of the mainshock, and only one M5.7 aftershock, but numerous smaller aftershocks to the north. Further, the northwest aftershock cluster exhibits complex faulting on both northwest and northeast planes. Thus, the aftershocks also express a complex pattern of stress release along strike. The overall rate of decay of the aftershocks is similar to the rate of decay of a generic California aftershock sequence. In addition, some triggered seismicity was recorded along the Elsinore and San Jacinto faults to the north, but significant northward migration of aftershocks has not occurred. The synthesis of the El Mayor-Cucapah sequence reveals transtensional regional tectonics, including the westward growth of the Mexicali Valley and the transfer of Pacific-North America plate motion from the Gulf of California in the south into the southernmost San

  13. Analyses of Mitogenome Sequences Revealed that Asian Citrus Psyllids (Diaphorina citri) from California Were Related to Those from Florida.

    Science.gov (United States)

    Wu, Fengnian; Kumagai, Luci; Cen, Yijing; Chen, Jianchi; Wallis, Christopher M; Polek, MaryLou; Jiang, Hongyan; Zheng, Zheng; Liang, Guangwen; Deng, Xiaoling

    2017-08-31

    Asian citrus psyllid (ACP, Diaphorina citri Kuwayama) transmits "Candidatus Liberibacter asiaticus" (CLas), an unculturable alpha-proteobacterium associated with citrus Huanglongbing (HLB). CLas has recently been found in California. Understanding ACP population diversity is necessary for HLB regulatory practices aimed at reducing CLas spread. In this study, two circular ACP mitogenome sequences from California (mt-CApsy, ~15,027 bp) and Florida (mt-FLpsy, ~15,012 bp), USA, were acquired. Each mitogenome contained 13 protein coding genes, 2 ribosomal RNA and 22 transfer RNA genes, and a control region varying in sizes. The Californian mt-CApsy was identical to the Floridian mt-FLpsy, but different from the mitogenome (mt-GDpsy) of Guangdong, China, in 50 single nucleotide polymorphisms (SNPs). Further analyses were performed on sequences in cox1 and trnAsn regions with 100 ACPs, SNPs in nad1-nad4-nad5 locus through PCR with 252 ACP samples. All results showed the presence of a Chinese ACP cluster (CAC) and an American ACP cluster (AAC). We proposed that ACP in California was likely not introduced from China based on our current ACP collection but somewhere in America. However, more studies with ACP samples from around the world are needed. ACP mitogenome sequence analyses will facilitate ACP population research.

  14. Assessing Cat Flea Microbiomes in Northern and Southern California by 16S rRNA Next-Generation Sequencing.

    Science.gov (United States)

    Vasconcelos, Elton J R; Billeter, Sarah A; Jett, Lindsey A; Meinersmann, Richard J; Barr, Margaret C; Diniz, Pedro P V P; Oakley, Brian B

    2018-06-12

    Flea-borne diseases (FBDs) impact both human and animal health worldwide. Because adult fleas are obligately hematophagous and can harbor potential pathogens, fleas act as ectoparasites of vertebrates, as well as zoonotic disease vectors. Cat fleas (Ctenocephalides felis) are important vectors of two zoonotic bacterial genera listed as priority pathogens by the National Institute of Allergy and Infectious Diseases (NIAID-USA): Bartonella spp. and Rickettsia spp., causative agents of bartonelloses and rickettsioses, respectively. In this study, we introduce the first microbiome analysis of C. felis samples from California, determining the presence and abundance of relevant pathogenic genera by characterizing the cat flea microbiome through 16S rRNA next-generation sequencing (16S-NGS). Samples from both northern (NoCal) and southern (SoCal) California were assessed to expand current knowledge regarding FBDs in the state. We identified Rickettsia and Bartonella, as well as the endosymbiont Wolbachia, as the most abundant genera, followed by less abundant taxa. In comparison to our previous study screening Californian cat fleas for rickettsiae using PCR/digestion/sequencing of the ompB gene, the 16S-NGS approach applied herein showed a 95% level of agreement in detecting Rickettsia spp. There was no overall difference in microbiome diversity between NoCal and SoCal samples. Bacterial taxa identified by 16S-NGS in this study may help to improve epidemiological investigations, pathogen surveillance efforts, and clinical diagnostics of FBDs in California and elsewhere.

  15. Geochemical evidence for airborne dust additions to soils in Channel Islands National Park, California

    Science.gov (United States)

    Muhs, D.R.; Budahn, J.R.; Johnson, D.L.; Reheis, M.; Beann, J.; Skipp, G.; Fisher, E.; Jones, J.A.

    2008-01-01

    There is an increasing awareness that dust plays important roles in climate change, biogeochemical cycles, nutrient supply to ecosystems, and soil formation. In Channel Islands National Park, California, soils are clay-rich Vertisols or Alfisols and Mollisols with vertic properties. The soils are overlain by silt-rich mantles that contrast sharply with the underlying clay-rich horizons. Silt mantles contain minerals that are rare or absent in the volcanic rocks that dominate these islands. Immobile trace elements (Sc-Th-La and Ta-Nd-Cr) and rare-earth elements show that the basalt and andesite on the islands have a composition intermediate between upper-continental crust and oceanic crust. In contrast, the silt fractions and, to a lesser extent, clay fractions of the silt mantle have compositions closer to average upper-continental crust and very similar to Mojave Desert dust. Island shelves, exposed during the last glacial period, could have provided a source of eolian sediment for the silt mantles, but this is not supported by mineralogical data. We hypothesize that a more likely source for the silt-rich mantles is airborne dust from mainland California and Baja California, either from the Mojave Desert or from the continental shelf during glacial low stands of sea. Although average winds are from the northwest in coastal California, easterly winds occur numerous times of the year when "Santa Ana" conditions prevail, caused by a high-pressure cell centered over the Great Basin. The eolian silt mantles constitute an important medium of plant growth and provide evidence that abundant eolian silt and clay may be delivered to the eastern Pacific Ocean from inland desert sources. ?? 2007 Geological Society of America.

  16. In silico evidence for sequence-dependent nucleosome sliding

    Energy Technology Data Exchange (ETDEWEB)

    Lequieu, Joshua; Schwartz, David C.; de Pablo, Juan J.

    2017-10-18

    Nucleosomes represent the basic building block of chromatin and provide an important mechanism by which cellular processes are controlled. The locations of nucleosomes across the genome are not random but instead depend on both the underlying DNA sequence and the dynamic action of other proteins within the nucleus. These processes are central to cellular function, and the molecular details of the interplay between DNA sequence and nudeosome dynamics remain poorly understood. In this work, we investigate this interplay in detail by relying on a molecular model, which permits development of a comprehensive picture of the underlying free energy surfaces and the corresponding dynamics of nudeosome repositioning. The mechanism of nudeosome repositioning is shown to be strongly linked to DNA sequence and directly related to the binding energy of a given DNA sequence to the histone core. It is also demonstrated that chromatin remodelers can override DNA-sequence preferences by exerting torque, and the histone H4 tail is then identified as a key component by which DNA-sequence, histone modifications, and chromatin remodelers could in fact be coupled.

  17. Pleiades rapid rotators - evidence for an evolutionary sequence

    International Nuclear Information System (INIS)

    Butler, R.P.; Marcy, G.W.; Cohen, R.D.; Duncan, D.K.; California Univ., La Jolla; Space Telescope Science Institute, Baltimore, MD)

    1987-01-01

    Four rapidly rotating early-K dwarfs in the Pleiades are shown to contain an order of magnitude more Li than four slow rotators of the same spectral type, as would be expected if they were systematically younger. This supports the idea that late-type stars first arrive on the main sequence with V(rot) greater than about 100 km/s, that they spin down to V(rot) less than about 10 km/s in 10 to the 7th to 10 to the 8th yr, and that the Pleiades lower main sequence shows such an age spread. 14 references

  18. The Process of Adoption of Evidence-based Tobacco Use Prevention Programs in California Schools

    Science.gov (United States)

    Little, Melissa A.; Pokhrel, Pallav; Sussman, Steve; Rohrbach, Louise Ann

    2014-01-01

    Although there are a number of research-validated substance use prevention programs available for wide-scale dissemination, very little is known about the factors that influence adoption of evidence-based prevention programs in schools. We tested a model of the mechanisms of program adoption in schools that was guided by diffusion of innovations and social ecological theories. Cross-sectional data were collected from a sample of school district and county office of education tobacco use prevention education coordinators throughout California. Structural equation modeling was used to test the effects of community- and organizational variables on the adoption of prevention programs via school administrators’ beliefs and the organization’s receipt of funding for the program. Results supported the hypothesis that the process of adoption begins with forming beliefs about the program, leading to adoption through the receipt of funding. In addition, we found direct effects of various community- and organizational-level factors on beliefs, receipt of funding, and adoption. These results are likely to inform policies that affect school districts’ use of evidence-based substance use prevention programming, which should ultimately lead to reductions in negative health outcomes among adolescents. Specifically, this study identifies various factors that could be targeted for improvement to enhance evidence-based program adoption. To our knowledge, this is the first study to empirically elucidate the process of adoption of evidence-based tobacco prevention programs in schools. PMID:24398826

  19. Seismic Evidence for Conjugate Slip and Block Rotation Within the San Andreas Fault System, Southern California

    Science.gov (United States)

    Nicholson, Craig; Seeber, Leonardo; Williams, Patrick; Sykes, Lynn R.

    1986-08-01

    The pattern of seismicity in southern California indicates that much of the activity is presently occurring on secondary structures, several of which are oriented nearly orthogonal to the strikes of the major through-going faults. Slip along these secondary transverse features is predominantly left-lateral and is consistent with the reactivation of conjugate faults by the current regional stress field. Near the intersection of the San Jacinto and San Andreas faults, however, these active left-lateral faults appear to define a set of small crustal blocks, which in conjunction with both normal and reverse faulting earthquakes, suggests contemporary clockwise rotation as a result of regional right-lateral shear. Other left-lateral faults representing additional rotating block systems are identified in adjacent areas from geologic and seismologic data. Many of these structures predate the modern San Andreas system and may control the pattern of strain accumulation in southern California. Geodetic and paleomagnetic evidence confirm that block rotation by strike-slip faulting is nearly ubiquitous, particularly in areas where shear is distributed, and that it accommodates both short-term elastic and long-term nonelastic strain. A rotating block model accounts for a number of structural styles characteristic of strike-slip deformation in California, including: variable slip rates and alternating transtensional and transpressional features observed along strike of major wrench faults; domains of evenly-spaced antithetic faults that terminate against major fault boundaries; continued development of bends in faults with large lateral displacements; anomalous focal mechanisms; and differential uplift in areas otherwise expected to experience extension and subsidence. Since block rotation requires a detachment surface at depth to permit rotational movement, low-angle structures like detachments, of either local or regional extent, may be involved in the contemporary strike

  20. SNP discovery and High Resolution Melting Analysis from massive transcriptome sequencing in the California red abalone Haliotis rufescens.

    Science.gov (United States)

    Valenzuela-Muñoz, Valentina; Araya-Garay, José Miguel; Gallardo-Escárate, Cristian

    2013-06-01

    The California red abalone, Haliotis rufescens that belongs to the Haliotidae family, is the largest species of abalone in the world that has sustained the major fishery and aquaculture production in the USA and Mexico. This native mollusk has not been evaluated or assigned a conservation category even though in the last few decades it was heavily exploited until it disappeared in some areas along the California coast. In Chile, the red abalone was introduced in the 1970s from California wild abalone stocks for the purposes of aquaculture. Considering the number of years that the red abalone has been cultivated in Chile crucial genetic information is scarce and critical issues remain unresolved. This study reports and validates novel single nucleotide polymorphisms (SNP) markers for the red abalone H. rufescens using cDNA pyrosequencing. A total of 622 high quality SNPs were identified in 146 sequences with an estimated frequency of 1 SNP each 1000bp. Forty-five SNPs markers with functional information for gene ontology were selected. Of these, 8 were polymorphic among the individuals screened: Heat shock protein 70 (HSP70), vitellogenin (VTG), lysin, alginate lyase enzyme (AL), Glucose-regulated protein 94 (GRP94), fructose-bisphosphate aldolase (FBA), sulfatase 1A precursor (S1AP) and ornithine decarboxylase antizyme (ODC). Two additional sequences were also identified with polymorphisms but no similarities with known proteins were achieved. To validate the putative SNP markers, High Resolution Melting Analysis (HRMA) was conducted in a wild and hatchery-bred population. Additionally, SNP cross-amplifications were tested in two further native abalone species, Haliotis fulgens and Haliotis corrugata. This study provides novel candidate genes that could be used to evaluate loss of genetic diversity due to hatchery selection or inbreeding effects. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. Evidence, exaggeration, and error in historical accounts of chaparral wildfires in California.

    Science.gov (United States)

    Goforth, Brett R; Minnich, Richard A

    2007-04-01

    For more than half a century, ecologists and historians have been integrating the contemporary study of ecosystems with data gathered from historical sources to evaluate change over broad temporal and spatial scales. This approach is especially useful where ecosystems were altered before formal study as a result of natural resources management, land development, environmental pollution, and climate change. Yet, in many places, historical documents do not provide precise information, and pre-historical evidence is unavailable or has ambiguous interpretation. There are similar challenges in evaluating how the fire regime of chaparral in California has changed as a result of fire suppression management initiated at the beginning of the 20th century. Although the firestorm of October 2003 was the largest officially recorded in California (approximately 300,000 ha), historical accounts of pre-suppression wildfires have been cited as evidence that such a scale of burning was not unprecedented, suggesting the fire regime and patch mosaic in chaparral have not substantially changed. We find that the data do not support pre-suppression megafires, and that the impression of large historical wildfires is a result of imprecision and inaccuracy in the original reports, as well as a parlance that is beset with hyperbole. We underscore themes of importance for critically analyzing historical documents to evaluate ecological change. A putative 100 mile long by 10 mile wide (160 x 16 km) wildfire reported in 1889 was reconstructed to an area of chaparral approximately 40 times smaller by linking local accounts to property tax records, voter registration rolls, claimed insurance, and place names mapped with a geographical information system (GIS) which includes data from historical vegetation surveys. We also show that historical sources cited as evidence of other large chaparral wildfires are either demonstrably inaccurate or provide anecdotal information that is immaterial in the

  2. Microfaunal evidence of age and depositional environments of the Cerro Prieto section (Plio-Pleistocene), Baja California, Mexico

    Energy Technology Data Exchange (ETDEWEB)

    Ingle, J.C. Jr.

    1982-01-01

    Microfossils including benthic and planktic foraminifera, ostracodes, calcareous algae, fish skeletal material, and fragments of pelecypods were found in 14 core samples from depths of 185 to 1952 m in the Cerro Prieto geothermal field, providing evidence of both the age and depositional history of sediments comprising the 3000-m-thick Pliocene and Pleistocene section in this area. Ostracodes of brackish water and marine origin constitute the most common microfossils present in this sequence occurring in 8 samples; in situ littoral and neritic species of benthic foraminifera occur in 5 samples with planktic species present in 2 samples. Distributional patterns of ostracodes and foraminifera together with previously analyzed lithofacies (Lyons and van de Kamp, 1980) indicate that the Cerro Prieto section represents an intertonguing complex of alluvial, deltaic, estuarine, and shallow marine environments deposited along the front of the Colorado River delta as it prograded across the Salton Trough during Pliocene and Pleistocene time. Foraminiferal evidence indicates that a sand and shale unit commonly present at depths between 700 and 1100 m represents a significant mid-Pleistocene marine incursion in the Cerro Prieto area. Tentative correlation of the Cerro Prieto section with the well dated Palm Springs Formation of the Imperial Valley, California area suggests that the Pliocene/Pleistocene boundary occurs at a depth of approximately 2000 m in the area of well M-93. Reworked specimens of Cretaceous foraminifera and fragments of the Cretaceous pelecypod Inoceramus were found in five samples further substantiating the Colorado Plateau provenance of a significant portion of the Colorado River deltaic sediments in the Cerro Prieto area.

  3. Genome Sequencing of Museum Specimens Reveals Rapid Changes in the Genetic Composition of Honey Bees in California.

    Science.gov (United States)

    Cridland, Julie M; Ramirez, Santiago R; Dean, Cheryl A; Sciligo, Amber; Tsutsui, Neil D

    2018-02-01

    The western honey bee, Apis mellifera, is an enormously influential pollinator in both natural and managed ecosystems. In North America, this species has been introduced numerous times from a variety of different source populations in Europe and Africa. Since then, feral populations have expanded into many different environments across their broad introduced range. Here, we used whole genome sequencing of historical museum specimens and newly collected modern populations from California (USA) to analyze the impact of demography and selection on introduced populations during the past 105 years. We find that populations from both northern and southern California exhibit pronounced genetic changes, but have changed in different ways. In northern populations, honey bees underwent a substantial shift from western European to eastern European ancestry since the 1960s, whereas southern populations are dominated by the introgression of Africanized genomes during the past two decades. Additionally, we identify an isolated island population that has experienced comparatively little change over a large time span. Fine-scale comparison of different populations and time points also revealed SNPs that differ in frequency, highlighting a number of genes that may be important for recent adaptations in these introduced populations. © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  4. Correlates of virulence in a frog-killing fungal pathogen: evidence from a California amphibian decline.

    Science.gov (United States)

    Piovia-Scott, Jonah; Pope, Karen; Worth, S Joy; Rosenblum, Erica Bree; Poorten, Thomas; Refsnider, Jeanine; Rollins-Smith, Louise A; Reinert, Laura K; Wells, Heather L; Rejmanek, Dan; Lawler, Sharon; Foley, Janet

    2015-07-01

    The fungal pathogen Batrachochytrium dendrobatidis (Bd) has caused declines and extinctions in amphibians worldwide, and there is increasing evidence that some strains of this pathogen are more virulent than others. While a number of putative virulence factors have been identified, few studies link these factors to specific epizootic events. We documented a dramatic decline in juvenile frogs in a Bd-infected population of Cascades frogs (Rana cascadae) in the mountains of northern California and used a laboratory experiment to show that Bd isolated in the midst of this decline induced higher mortality than Bd isolated from a more stable population of the same species of frog. This highly virulent Bd isolate was more toxic to immune cells and attained higher density in liquid culture than comparable isolates. Genomic analyses revealed that this isolate is nested within the global panzootic lineage and exhibited unusual genomic patterns, including increased copy numbers of many chromosomal segments. This study integrates data from multiple sources to suggest specific phenotypic and genomic characteristics of the pathogen that may be linked to disease-related declines.

  5. Population diversity and evidence of introgression among the black oaks of California

    Science.gov (United States)

    Richard S. Dodd; Nasser Kashani; Zara Afzal-Rafii

    2002-01-01

    The black oaks of California include 4 tree species (California black oak, coast live oak, Shreve oak, interior live oak) that are known to hybridize. Complex patterns of population variation within each species are likely to result from these hybrid combinations and from subsequent introgressions. We have been studying population variation using biochemical and...

  6. Empirical evidence for multi-scaled controls on wildfire size distributions in California

    Science.gov (United States)

    Povak, N.; Hessburg, P. F., Sr.; Salter, R. B.

    2014-12-01

    Ecological theory asserts that regional wildfire size distributions are examples of self-organized critical (SOC) systems. Controls on SOC event-size distributions by virtue are purely endogenous to the system and include the (1) frequency and pattern of ignitions, (2) distribution and size of prior fires, and (3) lagged successional patterns after fires. However, recent work has shown that the largest wildfires often result from extreme climatic events, and that patterns of vegetation and topography may help constrain local fire spread, calling into question the SOC model's simplicity. Using an atlas of >12,000 California wildfires (1950-2012) and maximum likelihood estimation (MLE), we fit four different power-law models and broken-stick regressions to fire-size distributions across 16 Bailey's ecoregions. Comparisons among empirical fire size distributions across ecoregions indicated that most ecoregion's fire-size distributions were significantly different, suggesting that broad-scale top-down controls differed among ecoregions. One-parameter power-law models consistently fit a middle range of fire sizes (~100 to 10000 ha) across most ecoregions, but did not fit to larger and smaller fire sizes. We fit the same four power-law models to patch size distributions of aspect, slope, and curvature topographies and found that the power-law models fit to a similar middle range of topography patch sizes. These results suggested that empirical evidence may exist for topographic controls on fire sizes. To test this, we used neutral landscape modeling techniques to determine if observed fire edges corresponded with aspect breaks more often than expected by random. We found significant differences between the empirical and neutral models for some ecoregions, particularly within the middle range of fire sizes. Our results, combined with other recent work, suggest that controls on ecoregional fire size distributions are multi-scaled and likely are not purely SOC. California

  7. Developing evidence-based prescriptive ventilation rate standards for commercial buildings in California: a proposed framework

    Energy Technology Data Exchange (ETDEWEB)

    Mendell, Mark J.; Fisk, William J.

    2014-02-01

    Background - The goal of this project, with a focus on commercial buildings in California, was to develop a new framework for evidence-based minimum ventilation rate (MVR) standards that protect occupants in buildings while also considering energy use and cost. This was motivated by research findings suggesting that current prescriptive MVRs in commercial buildings do not provide occupants with fully safe and satisfactory indoor environments. Methods - The project began with a broad review in several areas ? the diverse strategies now used for standards or guidelines for MVRs or for environmental contaminant exposures, current knowledge about adverse human effects associated with VRs, and current knowledge about contaminants in commercial buildings, including their their presence, their adverse human effects, and their relationships with VRs. Based on a synthesis of the reviewed information, new principles and approaches are proposed for setting evidence-based VRs standards for commercial buildings, considering a range of human effects including health, performance, and acceptability of air. Results ? A review and evaluation is first presented of current approaches to setting prescriptive building ventilation standards and setting acceptable limits for human contaminant exposures in outdoor air and occupational settings. Recent research on approaches to setting acceptable levels of environmental exposures in evidence-based MVR standards is also described. From a synthesis and critique of these materials, a set of principles for setting MVRs is presented, along with an example approach based on these principles. The approach combines two sequential strategies. In a first step, an acceptable threshold is set for each adverse outcome that has a demonstrated relationship to VRs, as an increase from a (low) outcome level at a high reference ventilation rate (RVR, the VR needed to attain the best achievable levels of the adverse outcome); MVRs required to meet each

  8. Whole genome sequencing of Mycobacterium bovis to obtain molecular fingerprints in human and cattle isolates from Baja California, Mexico

    Directory of Open Access Journals (Sweden)

    Sarai Estrella Sandoval-Azuara

    2017-10-01

    Conclusions: All isolates from humans had spoligotype patterns that matched those observed in the cattle isolates, and all human isolates shared common ancestors with cattle in Baja California based on SNP analysis. This suggests that most human tuberculosis caused by M. bovis in Baja California is derived from M. bovis circulating in Baja California cattle. These results reinforce the importance of bovine tuberculosis surveillance and control in this region.

  9. Does Uninsurance Affect the Health Outcomes of the Insured? Evidence from Heart Attack Patients in California

    NARCIS (Netherlands)

    Meltem Daysal, N.

    2012-01-01

    Abstract: In this paper, I examine the impact of uninsured patients on the health of the insured, focusing on one health outcome - the in-hospital mortality rate of insured heart attack patients. I employ panel data models using patient discharge and hospital financial data from California

  10. Does uninsurance affect the health outcomes of the insured? Evidence from heart attack patients in California

    NARCIS (Netherlands)

    Meltem Daysal, N.

    2012-01-01

    In this paper, I examine the impact of uninsured patients on the in-hospital mortality rate of insured heart attack patients. I employ panel data models using patient discharge and hospital financial data from California (1999–2006). My results indicate that uninsured patients have an economically

  11. EVIDENCE FOR METAL ATTENUATION IN ACID MINE WATER BY SULFATE REDUCTION, PENN MINE, CALAVERAS COUNTY, CALIFORNIA

    Science.gov (United States)

    The Penn Mine in Calaveras County, California, produced Cu from massive sulfide ores from 1861 to 1953. Mine wastes were removed to a landfill during the late 1990s, improving surface-water quality, but deep mine workings were not remediated and contain metalliferous water with p...

  12. Etiology and evidence of systemic acidification in SOD-affected forests of California

    Science.gov (United States)

    Lee Klinger; Ralph Zingaro

    2006-01-01

    Pathologists investigating the widespread death of oak trees in the forest ecosystems of northern California concluded, in 2000, that the problem was due to a new plant disease, dubbed sudden oak death (SOD), which is caused by the fungal pathogen Phytophthora ramorum. Since then this one organism has been the focal point of notable efforts to...

  13. Discovery of three novel coccidian parasites infecting California sea lions (Zalophus californianus), with evidence of sexual replication and interspecies pathogenicity.

    Science.gov (United States)

    Colegrove, Kathleen M; Grigg, Michael E; Carlson-Bremer, Daphne; Miller, Robin H; Gulland, Frances M D; Ferguson, David J P; Rejmanek, Daniel; Barr, Bradd C; Nordhausen, Robert; Melli, Ann C; Conrad, Patricia A

    2011-10-01

    Enteric protozoal infection was identified in 5 stranded California sea lions (Zalophus californianus). Microscopically, the apical cytoplasm of distal jejunal enterocytes contained multiple stages of coccidian parasites, including schizonts with merozoites and spherical gametocytes, which were morphologically similar to coccidians. By histopathology, organisms appeared to be confined to the intestine and accompanied by only mild enteritis. Using electron microscopy, both sexual (microgametocytes, macrogamonts) and asexual (schizonts, merozoites) coccidian stages were identified in enterocytes within parasitophorous vacuoles, consistent with apicomplexan development in a definitive host. Serology was negative for tissue cyst-forming coccidians, and immunohistochemistry for Toxoplasma gondii was inconclusive and negative for Neospora caninum and Sarcocystis neurona. Analysis of ITS-1 gene sequences amplified from frozen or formalin-fixed paraffin-embedded intestinal sections identified DNA sequences with closest homology to Neospora sp. (80%); these novel sequences were referred to as belonging to coccidian parasites "A," "B," and "C." Subsequent molecular analyses completed on a neonatal harbor seal (Phoca vitulina) with protozoal lymphadenitis, hepatitis, myocarditis, and encephalitis showed that it was infected with a coccidian parasite bearing the "C" sequence type. Our results indicate that sea lions likely serve as definitive hosts for 3 newly described coccidian parasites, at least 1 of which is pathogenic in a marine mammal intermediate host species.

  14. DISCOVERY OF THREE NOVEL COCCIDIAN PARASITES INFECTING CALIFORNIA SEA LIONS (ZALOPHUS CALIFORNIANUS), WITH EVIDENCE OF SEXUAL REPLICATION AND INTERSPECIES PATHOGENICITY

    Science.gov (United States)

    Colegrove, Kathleen M.; Grigg, Michael E.; Carlson-Bremer, Daphne; Miller, Robin H.; Gulland, Frances M. D.; Ferguson, David J. P.; Rejmanek, Daniel; Barr, Bradd C.; Nordhausen, Robert; Melli, Ann C.; Conrad, Patricia A.

    2016-01-01

    Enteric protozoal infection was identified in 5 stranded California sea lions (Zalophus californianus). Microscopically, the apical cytoplasm of distal jejunal enterocytes contained multiple stages of coccidian parasites, including schizonts with merozoites and spherical gametocytes, which were morphologically similar to coccidians. By histopathology, organisms appeared to be confined to the intestine and accompanied by only mild enteritis. Using electron microscopy, both sexual (microgametocytes, macrogamonts) and asexual (schizonts, merozoites) coccidian stages were identified in enterocytes within parasitophorous vacuoles, consistent with apicomplexan development in a definitive host. Serology was negative for tissue cyst-forming coccidians, and immunohistochemistry for Toxoplasma gondii was inconclusive and negative for Neospora caninum and Sarcocystis neurona. Analysis of ITS-1 gene sequences amplified from frozen or formalin-fixed paraffin-embedded intestinal sections identified DNA sequences with closest homology to Neospora sp. (80%); these novel sequences were referred to as belonging to coccidian parasites ‘‘A,’’ ‘‘B,’’ and ‘‘C.’’ Subsequent molecular analyses completed on a neonatal harbor seal (Phoca vitulina) with protozoal lymphadenitis, hepatitis, myocarditis, and encephalitis showed that it was infected with a coccidian parasite bearing the ‘‘C’’ sequence type. Our results indicate that sea lions likely serve as definitive hosts for 3 newly described coccidian parasites, at least 1 of which is pathogenic in a marine mammal intermediate host species. PMID:21495828

  15. Drought Water Rationing Necessitates an Equitable and Multidimensional Approach: Evidence from California

    Science.gov (United States)

    Ponce de Leon Barido, D.; Fildier, B.; Cucchi, K.

    2016-12-01

    Since 2011 many areas across California have experienced their driest years on record, with conditions barely improving since then. Reservoirs and snowpack water content have recorded some of the lowest measurements ever, with users (individuals, towns and cities) using groundwater to buffer the potentially devastating effects of the drought. Among other strategies, rationing has been one of they key interventions that the state has adopted to better manage its water resources. April 1st 2015 marked the first day in California's history when mandatory water reductions were instated statewide. By executive order, Governor Brown directed the State Water Resources Control Board to impose a 25% reduction on California's 400 local water supply agencies, which serve 90% of California residents. Since then, local agencies have been responsible for allocating restrictions to reduce water consumption and monitor compliance. A variety of research organizations and media outlets have begun exploring the equity considerations of the drought, but their analyses are often one-dimensional (water consumption per capita). Here we explore the multi-dimensional dynamics of rationing and drought in California using Census and California Water Resources Board data for over 300 communities in the state. We use data mining, parallel coordinates, and a nearest neighbors clustering algorithm to explore relationships between rationing and community spatial distribution, weather, drought related climate variables, economic sector employment, race, localized income inequality, household size, and income. The data suggests that there are nine distinct rationing groups across the state, that rationing was performed without taking into account the localized effects of the drought (hard hit communities rationing as much as less affected communities), that severely drought affected low-income communities (using SPI and SPEI 3 year indices) were asked to ration as much (and sometimes more) than

  16. The value of powdery mildew resistance in grapes: Evidence from California

    Directory of Open Access Journals (Sweden)

    Kate Binzen Fuller

    2014-12-01

    Full Text Available Powdery mildew (PM is a fungal disease that damages many crops, including grapes. In California, wine, raisin, and table grapes contributed over $3.9 billion to the value of farm production in 2011. Grape varieties with resistance to powdery mildew are currently being developed, using either conventional or transgenic approaches, each of which has associated advantages and disadvantages. PM-resistant varieties of grapes could yield large economic benefits to California grape growers—potentially allowing cost savings as high as $48 million per year in the subset of the industry covered by our analysis (Crimson Seedless table grapes, all raisin grapes, and Central Coast Chardonnay wine grapes, but benefits range widely across the different grape production systems.

  17. Landsat satellite evidence of the decline of northern California bull kelp

    Science.gov (United States)

    Renshaw, A.; Houskeeper, H. F.; Kudela, R. M.

    2017-12-01

    Bull kelp (Nereocystis luetkeana), a species of canopy-forming brown macroalga dominant in the Pacific Northwest of North America, provides critical ecological services such as habitat for a diverse array of marine species, nutrient regulation, photosynthesis, and regional marine carbon cycling. Starting around 2014, annual aerial surveys of bull kelp forests along California's northern coastline conducted by the California Department of Fish and Wildlife (CDFW) have reported a sudden 93% reduction in bull kelp canopy area. Remote sensing using satellite imagery is a robust, highly accurate tool for detecting and quantifying the abundance of the canopy-forming giant kelp, Macrocystis pyrifera; however, it has not been successfully applied to measuring northern bull kelp forests. One of the main difficulties associated with bull kelp detection via satellite is the small surface area of bull kelp canopies. As a result, bull kelp beds often only constitute part of a satellite pixel, making it difficult to obtain a kelp reflectance signal significantly different than water's reflectance signal. As part of the NASA Student Airborne Research Program (SARP), we test a novel method for assessing bull kelp canopy using a multiple endmember spectral mixing analysis (MESMA) applied to Landsat 5 and Landsat 8 imagery from 2003-2016. Water and kelp spectral endmembers are selected along the northern California coastline from Havens Neck cape to Point Arena. MESMA results are ground truthed with the CDFW aerial multispectral imagery data. This project will present a satellite-based time series of bull kelp canopy area and evaluate canopy change in a northern California kelp ecosystem.

  18. The impact of advanced metering infrastructure on residential electricity consumption: Evidence from California

    OpenAIRE

    Paschmann, Martin Heinrich; Paulus, Simon

    2017-01-01

    One important pillar in the debate about energy-saving measures addresses energy conservation. In this paper, we focus on the deployment of advanced metering infrastructure to reduce the impact of limited information and bounded rationality of consumers. For California, we empirically analyze the influence of a statewide and policy-driven installation of advanced metering infrastructure. We apply synthetic control methods to derive a suitable control group. We then conduct a Difference-in-Dif...

  19. Airborne dust transport to the eastern Pacific Ocean off southern California: Evidence from San Clemente Island

    Science.gov (United States)

    Muhs, D.R.; Budahn, J.; Reheis, M.; Beann, J.; Skipp, G.; Fisher, E.

    2007-01-01

    Islands are natural dust traps, and San Clemente Island, California, is a good example. Soils on marine terraces cut into Miocene andesite on this island are clay-rich Vertisols or Alfisols with vertic properties. These soils are overlain by silt-rich mantles, 5-20 cm thick, that contrast sharply with the underlying clay-rich subsoils. The silt mantles have a mineralogy that is distinct from the island bedrock. Silt mantles are rich in quartz, which is rare in the island andesite. The clay fraction of the silt mantles is dominated by mica, also absent from local andesite, and contrasts with the subsoils, dominated by smectite. Ternary plots of immobile trace elements (Sc-Th-La and Ta-Nd-Cr) show that the island andesite has a composition intermediate between average upper continental crust and average oceanic crust. In contrast, the silt and, to a lesser extent, clay fractions of the silt mantles have compositions closer to average upper continental crust. The silt mantles have particle size distributions similar to loess and Mojave Desert dust, but are coarser than long-range-transported Asian dust. We infer from these observations that the silt mantles are derived from airborne dust from the North American mainland, probably river valleys in the coastal mountains of southern California and/or the Mojave Desert. Although average winds are from the northwest in coastal California, easterly winds occur numerous times of the year when "Santa Ana" conditions prevail, caused by a high-pressure cell centered over the Great Basin. Examination of satellite imagery shows that easterly Santa Ana winds carry abundant dust to the eastern Pacific Ocean and the California Channel Islands. Airborne dust from mainland North America may be an important component of the offshore sediment budget in the easternmost Pacific Ocean, a finding of potential biogeochemical and climatic significance.

  20. Evidence for a Complex Mosaic Genome Pattern in a Full-length Hepatitis C Virus Sequence

    Directory of Open Access Journals (Sweden)

    R.S. Ross

    2008-01-01

    Full Text Available The genome of the hepatitis C virus (HCV exhibits a high genetic variability. This remarkable heterogeneity is mainly attributed to the gradual accumulation of mutational changes, whereas the contribution of recombination events to the evolution of HCV remains controversial so far. While performing phylogenetic analyses including a large number of sequences deposited in the GenBank, we encountered a full-length HCV sequence (AY651061 that showed evidence for inter-subtype recombination and was, therefore, subjected to a detailed analysis of its molecular structure. The obtained results indicated that AY651061 does not represent a “simple” HCV 1c isolate, but a complex 1a/1c mosaic genome, showing five putative breakpoints in the core to NS3 regions. To our knowledge, this is the first report on a mosaic HCV full- length sequence with multiple breakpoints. The molecular structure of AY651061 is reminiscent of complex homologous recombinant variants occurring among other members of the flaviviridae family, e.g. GB virus C, dengue virus, and Japanese encephalitis virus. Our finding of a mosaic HCV sequence may have important implications for many fields of current HCV research which merit careful consideration.

  1. New evidence on the sequence of deglacial warming in the tropical Indian Ocean

    Digital Repository Service at National Institute of Oceanography (India)

    Naidu, P.D.; Govil, P.

    . Quat. Sci., vol.25(7); 2010; 1138-1143 A New Evidence on Sequence of Deglacial Warming in the Tropical Indian Ocean P. Divakar Naidu 1 , Pawan Govil 1,2 1 National Institute of Oceanography, Dona Paula 403 004, Goa, India 2 National Centre... relative timing of abrupt climate warming in the tropics versus the high latitudes should be known. Therefore, the present communication is aimed to address the start of deglaciation in the Indian Ocean based on sea surface temperature (SST) derived from...

  2. Serologic evidence for Borrelia hermsii infection in rodents on federally owned recreational areas in California.

    Science.gov (United States)

    Fritz, Curtis L; Payne, Jessica R; Schwan, Tom G

    2013-06-01

    Tick-borne relapsing fever (TBRF) is endemic in mountainous regions of the western United States. In California, the principal agent is the spirochete Borrelia hermsii, which is transmitted by the argasid tick Ornithodoros hermsi. Humans are at risk of TBRF when infected ticks leave an abandoned rodent nest in quest of a blood meal. Rodents are the primary vertebrate hosts for B. hermsii. Sciurid rodents were collected from 23 sites in California between August, 2006, and September, 2008, and tested for serum antibodies to B. hermsii by immunoblot using a whole-cell sonicate and a specific antigen, glycerophosphodiester phosphodiesterase (GlpQ). Antibodies were detected in 20% of rodents; seroprevalence was highest (36%) in chipmunks (Tamias spp). Seroprevalence in chipmunks was highest in the Sierra Nevada (41%) and Mono (43%) ecoregions and between 1900 and 2300 meters elevation (43%). The serological studies described here are effective in implicating the primary vertebrate hosts involved in the maintenance of the ticks and spirochetes in regions endemic for TBRF.

  3. Electricity-market price and nuclear power plant shutdown: Evidence from California

    International Nuclear Information System (INIS)

    Woo, C.K.; Ho, T.; Zarnikau, J.; Olson, A.; Jones, R.; Chait, M.; Horowitz, I.; Wang, J.

    2014-01-01

    Japan's Fukushima nuclear disaster, triggered by the March 11, 2011 earthquake, has led to calls for shutting down existing nuclear plants. To maintain resource adequacy for a grid's reliable operation, one option is to expand conventional generation, whose marginal unit is typically fueled by natural-gas. Two timely and relevant questions thus arise for a deregulated wholesale electricity market: (1) what is the likely price increase due to a nuclear plant shutdown? and (2) what can be done to mitigate the price increase? To answer these questions, we perform a regression analysis of a large sample of hourly real-time electricity-market price data from the California Independent System Operator (CAISO) for the 33-month sample period of April 2010–December 2012. Our analysis indicates that the 2013 shutdown of the state's San Onofre plant raised the CAISO real-time hourly market prices by $6/MWH to $9/MWH, and that the price increases could have been offset by a combination of demand reduction, increasing solar generation, and increasing wind generation. - Highlights: • Japan's disaster led to calls for shutting down existing nuclear plants. • We perform a regression analysis of California's real-time electricity-market prices. • We estimate that the San Onofre plant shutdown has raised the market prices by $6/MWH to $9/MWH. • The price increases could be offset by demand reduction and renewable generation increase

  4. Deep Sequencing Reveals the Complete Genome and Evidence for Transcriptional Activity of the First Virus-Like Sequences Identified in Aristotelia chilensis (Maqui Berry

    Directory of Open Access Journals (Sweden)

    Javier Villacreses

    2015-04-01

    Full Text Available Here, we report the genome sequence and evidence for transcriptional activity of a virus-like element in the native Chilean berry tree Aristotelia chilensis. We propose to name the endogenous sequence as Aristotelia chilensis Virus 1 (AcV1. High-throughput sequencing of the genome of this tree uncovered an endogenous viral element, with a size of 7122 bp, corresponding to the complete genome of AcV1. Its sequence contains three open reading frames (ORFs: ORFs 1 and 2 shares 66%–73% amino acid similarity with members of the Caulimoviridae virus family, especially the Petunia vein clearing virus (PVCV, Petuvirus genus. ORF1 encodes a movement protein (MP; ORF2 a Reverse Transcriptase (RT and a Ribonuclease H (RNase H domain; and ORF3 showed no amino acid sequence similarity with any other known virus proteins. Analogous to other known endogenous pararetrovirus sequences (EPRVs, AcV1 is integrated in the genome of Maqui Berry and showed low viral transcriptional activity, which was detected by deep sequencing technology (DNA and RNA-seq. Phylogenetic analysis of AcV1 and other pararetroviruses revealed a closer resemblance with Petuvirus. Overall, our data suggests that AcV1 could be a new member of Caulimoviridae family, genus Petuvirus, and the first evidence of this kind of virus in a fruit plant.

  5. Changes in state of stress on the southern san andreas fault resulting from the california earthquake sequence of april to june 1992.

    Science.gov (United States)

    Jaumé, S C; Sykes, L R

    1992-11-20

    The April to June 1992 Landers earthquake sequence in southern California modified the state of stress along nearby segments of the San Andreas fault, causing a 50-kilometer segment of the fault to move significantly closer to failure where it passes through a compressional bend near San Gorgonio Pass. The decrease in compressive normal stress may also have reduced fluid pressures along that fault segment. As pressures are reequilibrated by diffusion, that fault segment should move closer to failure with time. That fault segment and another to the southeast probably have not ruptured in a great earthquake in about 300 years.

  6. Late Pleistocene lithostratigraphy and sequences in the southwestern Mesopotamia (Argentina): Evidences of the last interglacial stage

    Science.gov (United States)

    Ernesto, Brunetto; Soledad, Ferrero Brenda; Ignacio, Noriega Jorge

    2015-03-01

    The aim of this paper is to show the stratigraphic record of the Late Pleistocene corresponding to the distal region of the Paraná River basin. It displays sedimentological, paleontological and geochronological evidences that characterise the last interglacial-glacial cycle. In particular, strong environmental records are shown for the Last Interglacial Stage (LIS). Salto Ander Egg Formation (SAEF) is defined as a new lithostratigraphic unit representative of the Late Pleistocene in southwestern Mesopotamia. This unit is formed of complex fluvial deposits, which contains a heterogeneous collection of sub-environments, of ages ranging from 120 to 60 ky BP. The clast-supported gravel facies containing sparse boulders indicate high flow during a humid climate. The large and middle-scale architectures of fluvial sedimentary bodies evidence the relationship between the sediment accommodation and the sea level oscillations. Three sub-sequences identified in the succession suggest a transgressive trend during the MIS5e, a highstand stage in MIS5c, and a minor transgressive cycle during MIS3. A Brazilian faunal association collected at the bottom of the sequence and sedimentological interpretations display wet and warm climatic conditions, typical of tropical or subtropical environments. Such environmental conditions are characteristic of the maximum of the last interglacial stage (MIS5e) and show a signal stronger than the signal of the current interglacial stage. All these data show a direct correlation between the increases of paleodischarges and the elevation of the sea level. The whole sequence is completed with transitional swampy deposits, accumulated probably during the MIS3/MIS2 transition, and the typical loess of the Tezanos Pinto Formation, mantled during the Last Maximum Glacial.

  7. Molecular and morphometric evidence for separate species of Uncinaria (Nematoda: Ancylostomatidae) in California sea lions and northern fur seals: hypothesis testing supplants verification.

    Science.gov (United States)

    Nadler, S A; Adams, B J; Lyons, E T; DeLong, R L; Melin, S R

    2000-10-01

    California sea lions (Zalophus californianus) and northern fur seals (Callorhinus ursinus) are each believed to host distinct hookworm species (Uncinaria spp.). However, a recent morphometric analysis suggested that a single species parasitizes multiple pinniped hosts, and that the observed differences are host-induced. To explore the systematics of these hookworms and test these competing hypotheses, we obtained nucleotide sequences of nuclear ribosomal DNA (D2/D3 28S, D18/D19 28S, and internal transcribed spacer [ITS] regions) from 20 individual hookworms parasitizing California sea lion and northern fur seal pups where their breeding grounds are sympatric. Five individuals from an allopatric population of California sea lions were also sampled for ITS-1 and D18/D19 28S sequences. The 28S D2/D3 sequences showed no diagnostic differences among hookworms sampled from individual sea lions and fur seals, whereas the 28S D18/D19 sequences had one derived (apomorphic) character demarcating hookworms from northern fur seals. ITS sequences were variable for 7 characters, with 4 derived (apomorphic) states in ITS-1 demarcating hookworms from California sea lions. Multivariate analysis of morphometric data also revealed significant differences between nematodes representing these 2 host-associated lineages. These results indicate that these hookworms represent 2 species that are not distributed indiscriminately between these host species, but instead exhibit host fidelity, evolving independently with each respective host species. This evolutionary approach to analyzing sequence data for species delimitation is contrasted with similarity-based methods that have been applied to numerous diagnostic studies of nematode parasites.

  8. Building a Culture of Evidence: A Case Study of a California Community College

    Science.gov (United States)

    Baker, Jill H.; Sax, Caren L.

    2012-01-01

    The purpose of this study was to better understand the practices associated with building a culture of evidence and to identify the factors influencing the success of such an endeavor. By definition, a culture of evidence is based upon practices employing data and research to inform decision making at all levels of the institution, with the…

  9. Use of DNA sequences to identify forensically important fly species and their distribution in the coastal region of Central California.

    Science.gov (United States)

    Nakano, Angie; Honda, Jeff

    2015-08-01

    Forensic entomology has gained prominence in recent years, as improvements in DNA technology and molecular methods have allowed insect and other arthropod evidence to become increasingly useful in criminal and civil investigations. However, comprehensive faunal inventories are still needed, including cataloging local DNA sequences for forensically significant Diptera. This multi-year fly-trapping study was built upon and expanded a previous survey of these flies in Santa Clara County, including the addition of genetic barcoding data from collected species of flies. Flies from the families Calliphoridae, Sarcophagidae, and Muscidae were trapped in meat-baited traps set in a variety of locations throughout the county. Flies were identified using morphological features and confirmed by molecular analysis. A total of 16 calliphorid species, 11 sarcophagid species, and four muscid species were collected and differentiated. This study found more species of flies than previous area surveys and established new county records for two calliphorid species: Cynomya cadaverina and Chrysomya rufifacies. Differences were found in fly fauna in different areas of the county, indicating the importance of microclimates in the distribution of these flies. Molecular analysis supported the use of DNA barcoding as an effective method of identifying cryptic fly species. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  10. High cancer mortality for US-born Latinos: evidence from California and Texas.

    Science.gov (United States)

    Pinheiro, Paulo S; Callahan, Karen E; Gomez, Scarlett Lin; Marcos-Gragera, Rafael; Cobb, Taylor R; Roca-Barcelo, Aina; Ramirez, Amelie G

    2017-07-11

    Latinos born in the US, 36 million, comprise 65% of all US Latinos. Yet their cancer experience is nearly always analyzed together with their foreign-born counterparts, 19 million, who constitute a steady influx of truly lower-risk populations from abroad. To highlight specific cancer vulnerabilities for US-born Latinos, we compare their cancer mortality to the majority non-Latino white (NLW) population, foreign-born Latinos, and non-Latino blacks. We analyzed 465,751 cancer deaths from 2008 to 2012 occurring among residents of California and Texas, the two most populous states, accounting for 47% of US Latinos. This cross-sectional analysis, based on granular data obtained from death certificates on cause of death, age, race, ethnicity and birthplace, makes use of normal standardization techniques and negative binomial regression models. While Latinos overall have lower all-cancers-combined mortality rates than NLWs, these numbers were largely driven by low rates among the foreign born while mortality rates for US-born Latinos approach those of NLWs. Among Texas males, rates were 210 per 100,000 for NLWs and 166 for Latinos combined, but 201 per 100,000 for US-born Latinos and 125 for foreign-born Latinos. Compared to NLWs, US-born Latino males in California had mortality rate ratios of 2.83 (95% CI: 2.52-3.18) for liver cancer, 1.44 (95% CI: 1.30-1.61) for kidney cancer, and 1.25 (95% CI: 1.17-1.34) for colorectal cancer (CRC). Texas results showed a similar site-specific pattern. Specific cancer patterns for US-born Latinos, who have relatively high cancer mortality, similar overall to NLWs, are masked by aggregation of all Latinos, US-born and foreign-born. While NLWs had high mortality for lung cancer, US-born Latinos had high mortality for liver, kidney and male colorectal cancers. HCV testing and reinforcement of the need for CRC screening should be a priority in this specific and understudied population. The unprecedented proximity of overall rates between

  11. Reaching High-Need Youth Populations With Evidence-Based Sexual Health Education in California.

    Science.gov (United States)

    Campa, Mary I; Leff, Sarah Z; Tufts, Margaret

    2018-02-01

    To explore the programmatic reach and experience of high-need adolescents who received sexual health education in 3 distinct implementation settings (targeted-prevention settings, traditional schools, and alternative schools) through a statewide sexual health education program. Data are from youth surveys collected between September 2013 and December 2014 in the California Personal Responsibility Education Program. A sample of high-need participants (n = 747) provided data to examine the impact of implementation setting on reach and program experience. Implementation in targeted-prevention settings was equal to or more effective at providing a positive program experience for high-need participants. More than 5 times as many high-need participants were served in targeted-prevention settings compared with traditional schools. Reaching the same number of high-need participants served in targeted-prevention settings over 15 months would take nearly 7 years of programming in traditional schools. To maximize the reach and experience of high-need youth populations receiving sexual health education, state and local agencies should consider the importance of implementation setting. Targeted resources and efforts should be directed toward high-need young people by expanding beyond traditional school settings.

  12. High quality maize centromere 10 sequence reveals evidence of frequent recombination events

    Directory of Open Access Journals (Sweden)

    Thomas Kai Wolfgruber

    2016-03-01

    Full Text Available The ancestral centromeres of maize contain long stretches of the tandemly arranged CentC repeat. The abundance of tandem DNA repeats and centromeric retrotransposons (CR have presented a significant challenge to completely assembling centromeres using traditional sequencing methods. Here we report a nearly complete assembly of the 1.85 Mb maize centromere 10 from inbred B73 using PacBio technology and BACs from the reference genome project. The error rates estimated from overlapping BAC sequences are 7 x 10-6 and 5 x 10-5 for mismatches and indels, respectively. The number of gaps in the region covered by the reassembly was reduced from 140 in the reference genome to three. Three expressed genes are located between 92 and 477 kb of the inferred ancestral CentC cluster, which lies within the region of highest centromeric repeat density. The improved assembly increased the count of full-length centromeric retrotransposons from 5 to 55 and revealed a 22.7 kb segmental duplication that occurred approximately 121,000 years ago. Our analysis provides evidence of frequent recombination events in the form of partial retrotransposons, deletions within retrotransposons, chimeric retrotransposons, segmental duplications including higher order CentC repeats, a deleted CentC monomer, centromere-proximal inversions, and insertion of mitochondrial sequences. Double-strand DNA break (DSB repair is the most plausible mechanism for these events and may be the major driver of centromere repeat evolution and diversity. This repair appears to be mediated by microhomology, suggesting that tandem repeats may have evolved to facilitate the repair of frequent DSBs in centromeres.

  13. When syntax meets action: Brain potential evidence of overlapping between language and motor sequencing.

    Science.gov (United States)

    Casado, Pilar; Martín-Loeches, Manuel; León, Inmaculada; Hernández-Gutiérrez, David; Espuny, Javier; Muñoz, Francisco; Jiménez-Ortega, Laura; Fondevila, Sabela; de Vega, Manuel

    2018-03-01

    This study aims to extend the embodied cognition approach to syntactic processing. The hypothesis is that the brain resources to plan and perform motor sequences are also involved in syntactic processing. To test this hypothesis, Event-Related brain Potentials (ERPs) were recorded while participants read sentences with embedded relative clauses, judging for their acceptability (half of the sentences contained a subject-verb morphosyntactic disagreement). The sentences, previously divided into three segments, were self-administered segment-by-segment in two different sequential manners: linear or non-linear. Linear self-administration consisted of successively pressing three buttons with three consecutive fingers in the right hand, while non-linear self-administration implied the substitution of the finger in the middle position by the right foot. Our aim was to test whether syntactic processing could be affected by the manner the sentences were self-administered. Main results revealed that the ERPs LAN component vanished whereas the P600 component increased in response to incorrect verbs, for non-linear relative to linear self-administration. The LAN and P600 components reflect early and late syntactic processing, respectively. Our results convey evidence that language syntactic processing and performing non-linguistic motor sequences may share resources in the human brain. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. The phylogeny of the social wasp subfamily Polistinae: evidence from microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters

    Directory of Open Access Journals (Sweden)

    Strassmann Joan E

    2004-03-01

    Full Text Available Abstract Background Social wasps in the subfamily Polistinae (Hymenoptera: Vespidae have been important in studies of the evolution of sociality, kin selection, and within colony conflicts of interest. These studies have generally been conducted within species, because a resolved phylogeny among species is lacking. We used nuclear DNA microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters to generate a phylogeny for the Polistinae (Hymenoptera using 69 species. Results Our phylogeny is largely concordant with previous phylogenies at higher levels, and is more resolved at the species level. Our results support the monophyly of the New World subgenera of Polistini, while the Old World subgenera are a paraphyletic group. All genera for which we had more than one exemplar were supported as monophyletic except Polybia which is not resolved, and may be paraphyletic. Conclusion The combination of DNA sequences from flanks of microsatellite repeats with mtCOI sequences and morphological characters proved to be useful characters establishing relationships among the different subgenera and species of the Polistini. This is the first detailed hypothesis for the species of this important group.

  15. Decreased Odds of Injection Risk Behavior Associated With Direct Versus Indirect Use of Syringe Exchange: Evidence From Two California Cities.

    Science.gov (United States)

    Behrends, Czarina N; Li, Chin-Shang; Gibson, David R

    2017-07-29

    While there is substantial evidence that syringe exchange programs (SEPs) are effective in preventing HIV among people who inject drugs (PWID), nearly all the evidence comes from PWID who obtain syringes from an SEP directly. Much less is known about the benefits of secondary exchange to PWID who get syringes indirectly from friends or acquaintances who visit an SEP for them. We evaluated the effectiveness of direct versus indirect syringe exchange in reducing HIV-related high-risk injecting behavior among PWID in two separate studies conducted in Sacramento and San Jose, California, cities with quite different syringe exchange models. In both studies associations between direct and indirect syringe exchange and self-reported risk behavior were examined with multivariable logistic regression models. Study 1 assessed effects of a "satellite" home-delivery syringe exchange in Sacramento, while Study 2 evaluated a conventional fixed-site exchange in San Jose. Multivariable analyses revealed 95% and 69% reductions, respectively, in high-risk injection associated with direct use of the SEPs in Sacramento and San Jose, and a 46% reduction associated with indirect use of the SEP in Sacramento. Conclusions/Importance: The very large effect of direct SEP use in Sacramento was likely due in part to home delivery of sterile syringes. While more modest effects were associated with indirect use, such use nevertheless is valuable in reducing the risk of HIV transmission of PWID who are unable or unwilling to visit a syringe exchange.

  16. Correlates of virulence in a frog-killing fungal pathogen: evidence from a California amphibian decline

    Science.gov (United States)

    Jonah Piovia-Scott; Karen Pope; S. Joy Worth; Erica Bree Rosenblum; Dean Simon; Gordon Warburton; Louise A. Rollins-Smith; Laura K. Reinert; Heather L. Wells; Dan Rejmanek; Sharon Lawler; Janet Foley

    2015-01-01

    The fungal pathogen Batrachochytrium dendrobatidis (Bd) has caused declines and extinctions in amphibians worldwide, and there is increasing evidence that some strains of this pathogen are more virulent than others. While a number of putative virulence factors have been identified, few studies link these factors to specific epizootic events. We...

  17. Direct and indirect evidence for earthquakes; an example from the Lake Tahoe Basin, California-Nevada

    Science.gov (United States)

    Maloney, J. M.; Noble, P. J.; Driscoll, N. W.; Kent, G.; Schmauder, G. C.

    2012-12-01

    High-resolution seismic CHIRP data can image direct evidence of earthquakes (i.e., offset strata) beneath lakes and the ocean. Nevertheless, direct evidence often is not imaged due to conditions such as gas in the sediments, or steep basement topography. In these cases, indirect evidence for earthquakes (i.e., debris flows) may provide insight into the paleoseismic record. The four sub-basins of the tectonically active Lake Tahoe Basin provide an ideal opportunity to image direct evidence for earthquake deformation and compare it to indirect earthquake proxies. We present results from high-resolution seismic CHIRP surveys in Emerald Bay, Fallen Leaf Lake, and Cascade Lake to constrain the recurrence interval on the West Tahoe Dollar Point Fault (WTDPF), which was previously identified as potentially the most hazardous fault in the Lake Tahoe Basin. Recently collected CHIRP profiles beneath Fallen Leaf Lake image slide deposits that appear synchronous with slides in other sub-basins. The temporal correlation of slides between multiple basins suggests triggering by events on the WTDPF. If correct, we postulate a recurrence interval for the WTDPF of ~3-4 k.y., indicating that the WTDPF is near its seismic recurrence cycle. In addition, CHIRP data beneath Cascade Lake image strands of the WTDPF that offset the lakefloor as much as ~7 m. The Cascade Lake data combined with onshore LiDAR allowed us to map the geometry of the WTDPF continuously across the southern Lake Tahoe Basin and yielded an improved geohazard assessment.

  18. Microearthquake Study of the Salton Sea Geothermal Field, California: Evidence of Stress Triggering

    International Nuclear Information System (INIS)

    Holland, Austin A.

    2002-01-01

    A digital network of 24 seismograph stations was operated from September 15, 1987 to September 30, 1988, by Lawrence Livermore National Laboratory and Unocal as part of the Salton Sea Scientific Drilling Project to study seismicity related to tectonics and geothermal activity near the drilling site. More than 2001 microearthquakes were relocated in this study in order to image any pervasive structures that may exist within the Salton Sea geothermal field. First, detailed velocity models were obtained through standard 1-D inversion techniques. These velocity models were then used to relocate events using both single event methods and Double-Differencing, a joint hypocenter location method. An anisotropic velocity model was built from anisotropy estimates obtained from well logs within the study area. During the study period, the Superstition Hills sequence occurred with two moderate earthquakes of MS 6.2 and MS 6.6. These moderate earthquakes caused a rotation of the stress field as observed from the inversion of first motion data from microearthquakes at the Salton Sea geothermal field. Coulomb failure analysis also indicates that microearthquakes occurring after the Superstition Hills sequence are located within a region of stress increase suggesting stress triggering caused by the moderate earthquakes

  19. DNA sequence analyses reveal abundant diversity, endemism and evidence for Asian origin of the porcini mushrooms.

    Directory of Open Access Journals (Sweden)

    Bang Feng

    Full Text Available The wild gourmet mushroom Boletus edulis and its close allies are of significant ecological and economic importance. They are found throughout the Northern Hemisphere, but despite their ubiquity there are still many unresolved issues with regard to the taxonomy, systematics and biogeography of this group of mushrooms. Most phylogenetic studies of Boletus so far have characterized samples from North America and Europe and little information is available on samples from other areas, including the ecologically and geographically diverse regions of China. Here we analyzed DNA sequence variation in three gene markers from samples of these mushrooms from across China and compared our findings with those from other representative regions. Our results revealed fifteen novel phylogenetic species (about one-third of the known species and a newly identified lineage represented by Boletus sp. HKAS71346 from tropical Asia. The phylogenetic analyses support eastern Asia as the center of diversity for the porcini sensu stricto clade. Within this clade, B. edulis is the only known holarctic species. The majority of the other phylogenetic species are geographically restricted in their distributions. Furthermore, molecular dating and geological evidence suggest that this group of mushrooms originated during the Eocene in eastern Asia, followed by dispersal to and subsequent speciation in other parts of Asia, Europe, and the Americas from the middle Miocene through the early Pliocene. In contrast to the ancient dispersal of porcini in the strict sense in the Northern Hemisphere, the occurrence of B. reticulatus and B. edulis sensu lato in the Southern Hemisphere was probably due to recent human-mediated introductions.

  20. DNA Sequence Analyses Reveal Abundant Diversity, Endemism and Evidence for Asian Origin of the Porcini Mushrooms

    Science.gov (United States)

    Feng, Bang; Xu, Jianping; Wu, Gang; Zeng, Nian-Kai; Li, Yan-Chun; Tolgor, Bau; Kost, Gerhard W.; Yang, Zhu L.

    2012-01-01

    The wild gourmet mushroom Boletus edulis and its close allies are of significant ecological and economic importance. They are found throughout the Northern Hemisphere, but despite their ubiquity there are still many unresolved issues with regard to the taxonomy, systematics and biogeography of this group of mushrooms. Most phylogenetic studies of Boletus so far have characterized samples from North America and Europe and little information is available on samples from other areas, including the ecologically and geographically diverse regions of China. Here we analyzed DNA sequence variation in three gene markers from samples of these mushrooms from across China and compared our findings with those from other representative regions. Our results revealed fifteen novel phylogenetic species (about one-third of the known species) and a newly identified lineage represented by Boletus sp. HKAS71346 from tropical Asia. The phylogenetic analyses support eastern Asia as the center of diversity for the porcini sensu stricto clade. Within this clade, B. edulis is the only known holarctic species. The majority of the other phylogenetic species are geographically restricted in their distributions. Furthermore, molecular dating and geological evidence suggest that this group of mushrooms originated during the Eocene in eastern Asia, followed by dispersal to and subsequent speciation in other parts of Asia, Europe, and the Americas from the middle Miocene through the early Pliocene. In contrast to the ancient dispersal of porcini in the strict sense in the Northern Hemisphere, the occurrence of B. reticulatus and B. edulis sensu lato in the Southern Hemisphere was probably due to recent human-mediated introductions. PMID:22629418

  1. Seismic evidence of conjugate normal faulting: The 1994 Devil Canyon earthquake sequence near Challis, Idaho

    International Nuclear Information System (INIS)

    Jackson, S.M.

    1994-08-01

    In this study, the term ''conjugate'' refers to faults that occur in two intersecting sets and coordinated kinematically, with each set being distinctive in both orientation and sense of shear (Davis, 1984). Contemporaneous activity along the conjugate faults is defined as occurring within the time frame of the mainshock-aftershock sequence (three weeks for this sequence and generally less than one month in other observed cases). Detailed recordings of microearthquakes from a dense array of temporary analog seismic stations are analyzed. The focal mechanisms and hypocenter spatial and temporal characteristics are combined with geological information to assess the style, geometry, timing, kinematics, and mechanics of conjugate normal faulting. The characteristics of conjugate normal faulting observed in the Devil Canyon sequence are compared to other conjugate normal faulting sequences, and strike-slip and thrust conjugate sequences worldwide

  2. rbcL gene sequences provide evidence for the evolutionary lineages of leptosporangiate ferns.

    OpenAIRE

    Hasebe, M; Omori, T; Nakazawa, M; Sano, T; Kato, M; Iwatsuki, K

    1994-01-01

    Pteriodophytes have a longer evolutionary history than any other vascular land plant and, therefore, have endured greater loss of phylogenetically informative information. This factor has resulted in substantial disagreements in evaluating characters and, thus, controversy in establishing a stable classification. To compare competing classifications, we obtained DNA sequences of a chloroplast gene. The sequence of 1206 nt of the large subunit of the ribulose-bisphosphate carboxylase gene (rbc...

  3. Comparative analysis of the complete genome sequence of the California MSW strain of myxoma virus reveals potential host adaptations.

    Science.gov (United States)

    Kerr, Peter J; Rogers, Matthew B; Fitch, Adam; Depasse, Jay V; Cattadori, Isabella M; Hudson, Peter J; Tscharke, David C; Holmes, Edward C; Ghedin, Elodie

    2013-11-01

    Myxomatosis is a rapidly lethal disease of European rabbits that is caused by myxoma virus (MYXV). The introduction of a South American strain of MYXV into the European rabbit population of Australia is the classic case of host-pathogen coevolution following cross-species transmission. The most virulent strains of MYXV for European rabbits are the Californian viruses, found in the Pacific states of the United States and the Baja Peninsula, Mexico. The natural host of Californian MYXV is the brush rabbit, Sylvilagus bachmani. We determined the complete sequence of the MSW strain of Californian MYXV and performed a comparative analysis with other MYXV genomes. The MSW genome is larger than that of the South American Lausanne (type) strain of MYXV due to an expansion of the terminal inverted repeats (TIRs) of the genome, with duplication of the M156R, M154L, M153R, M152R, and M151R genes and part of the M150R gene from the right-hand (RH) end of the genome at the left-hand (LH) TIR. Despite the extreme virulence of MSW, no novel genes were identified; five genes were disrupted by multiple indels or mutations to the ATG start codon, including two genes, M008.1L/R and M152R, with major virulence functions in European rabbits, and a sixth gene, M000.5L/R, was absent. The loss of these gene functions suggests that S. bachmani is a relatively recent host for MYXV and that duplication of virulence genes in the TIRs, gene loss, or sequence variation in other genes can compensate for the loss of M008.1L/R and M152R in infections of European rabbits.

  4. ACCELERATED EVOLUTION OF LAND SNAILS MANDARINA IN THE OCEANIC BONIN ISLANDS: EVIDENCE FROM MITOCHONDRIAL DNA SEQUENCES.

    Science.gov (United States)

    Chiba, Satoshi

    1999-04-01

    An endemic land snail genus Mandarina of the oceanic Bonin (Ogasawara) Islands shows exceptionally rapid evolution not only of morphological and ecological traits, but of DNA sequence. A phylogenetic relationship based on mitochondrial DNA (mtDNA) sequences suggests that morphological differences equivalent to the differences between families were produced between Mandarina and its ancestor during the Pleistocene. The inferred phylogeny shows that species with similar morphologies and life habitats appeared repeatedly and independently in different lineages and islands at different times. Sequential adaptive radiations occurred in different islands of the Bonin Islands and species occupying arboreal, semiarboreal, and terrestrial habitat arose independently in each island. Because of a close relationship between shell morphology and life habitat, independent evolution of the same life habitat in different islands created species possesing the same shell morphology in different islands and lineages. This rapid evolution produced some incongruences between phylogenetic relationship and species taxonomy. Levels of sequence divergence of mtDNA among the species of Mandarina is extremely high. The maximum level of sequence divergence at 16S and 12S ribosomal RNA sequence within Mandarina are 18.7% and 17.7%, respectively, and this suggests that evolution of mtDNA of Mandarina is extremely rapid, more than 20 times faster than the standard rate in other animals. The present examination reveals that evolution of morphological and ecological traits occurs at extremely high rates in the time of adaptive radiation, especially in fragmented environments. © 1999 The Society for the Study of Evolution.

  5. Benign and Deleterious Cystic Fibrosis Transmembrane Conductance Regulator Mutations Identified by Sequencing in Positive Cystic Fibrosis Newborn Screen Children from California.

    Science.gov (United States)

    Salinas, Danieli B; Sosnay, Patrick R; Azen, Colleen; Young, Suzanne; Raraigh, Karen S; Keens, Thomas G; Kharrazi, Martin

    2016-01-01

    Of the 2007 Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) mutations, 202 have been assigned disease liability. California's racially diverse population, along with CFTR sequencing as part of newborn screening model, provides the opportunity to examine the phenotypes of children with uncategorized mutations to help inform disease liability and penetrance. We conducted a retrospective cohort study based on children screened from 2007 to 2011 and followed for two to six years. Newborns that screened positive were divided into three genotype groups: those with two CF-causing mutations (CF-C); those with one mutation of varying clinic consequence (VCC); and those with one mutation of unknown disease liability (Unknown). Sweat chloride tests, pancreatic sufficiency status, and Pseudomonas aeruginosa colonization were compared. Children with two CF-causing mutations had a classical CF phenotype, while 5% of VCC (4/78) and 11% of Unknown (27/244) met diagnostic criteria of CF. Children carrying Unknown mutations 2215insG with D836Y, and T1036N had early and classical CF phenotype, while others carrying 1525-42G>A, L320V, L967S, R170H, and 296+28A>G had a benign clinical presentation, suggesting that these are non-CF causing. While most infants with VCC and Unknown CFTR mutations do not meet diagnostic criteria for CF, a small proportion do. These findings highlight the range of genotypes and phenotypes in the first few years of life following CF newborn screening when CFTR sequencing is performed.

  6. Benign and Deleterious Cystic Fibrosis Transmembrane Conductance Regulator Mutations Identified by Sequencing in Positive Cystic Fibrosis Newborn Screen Children from California.

    Directory of Open Access Journals (Sweden)

    Danieli B Salinas

    Full Text Available Of the 2007 Cystic Fibrosis Transmembrane Conductance Regulator (CFTR mutations, 202 have been assigned disease liability. California's racially diverse population, along with CFTR sequencing as part of newborn screening model, provides the opportunity to examine the phenotypes of children with uncategorized mutations to help inform disease liability and penetrance.We conducted a retrospective cohort study based on children screened from 2007 to 2011 and followed for two to six years. Newborns that screened positive were divided into three genotype groups: those with two CF-causing mutations (CF-C; those with one mutation of varying clinic consequence (VCC; and those with one mutation of unknown disease liability (Unknown. Sweat chloride tests, pancreatic sufficiency status, and Pseudomonas aeruginosa colonization were compared.Children with two CF-causing mutations had a classical CF phenotype, while 5% of VCC (4/78 and 11% of Unknown (27/244 met diagnostic criteria of CF. Children carrying Unknown mutations 2215insG with D836Y, and T1036N had early and classical CF phenotype, while others carrying 1525-42G>A, L320V, L967S, R170H, and 296+28A>G had a benign clinical presentation, suggesting that these are non-CF causing.While most infants with VCC and Unknown CFTR mutations do not meet diagnostic criteria for CF, a small proportion do. These findings highlight the range of genotypes and phenotypes in the first few years of life following CF newborn screening when CFTR sequencing is performed.

  7. Procedural learning in Tourette syndrome, ADHD, and comorbid Tourette-ADHD: Evidence from a probabilistic sequence learning task.

    Science.gov (United States)

    Takács, Ádám; Shilon, Yuval; Janacsek, Karolina; Kóbor, Andrea; Tremblay, Antoine; Németh, Dezső; Ullman, Michael T

    2017-10-01

    Procedural memory, which is rooted in the basal ganglia, plays an important role in the implicit learning of motor and cognitive skills. Few studies have examined procedural learning in either Tourette syndrome (TS) or Attention Deficit Hyperactivity Disorder (ADHD), despite basal ganglia abnormalities in both of these neurodevelopmental disorders. We aimed to assess procedural learning in children with TS (n=13), ADHD (n=22), and comorbid TS-ADHD (n=20), as well as in typically developing children (n=21). Procedural learning was measured with a well-studied implicit probabilistic sequence learning task, the alternating serial reaction time task. All four groups showed evidence of sequence learning, and moreover did not differ from each other in sequence learning. This result, from the first study to examine procedural memory across TS, ADHD and comorbid TS-ADHD, is consistent with previous findings of intact procedural learning of sequences in both TS and ADHD. In contrast, some studies have found impaired procedural learning of non-sequential probabilistic categories in TS. This suggests that sequence learning may be spared in TS and ADHD, while at least some other forms of learning in procedural memory are impaired, at least in TS. Our findings indicate that disorders associated with basal ganglia abnormalities do not necessarily show procedural learning deficits, and provide a possible path for more effective diagnostic tools, and educational and training programs. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Influenza virus sequence feature variant type analysis: evidence of a role for NS1 in influenza virus host range restriction.

    Science.gov (United States)

    Noronha, Jyothi M; Liu, Mengya; Squires, R Burke; Pickett, Brett E; Hale, Benjamin G; Air, Gillian M; Galloway, Summer E; Takimoto, Toru; Schmolke, Mirco; Hunt, Victoria; Klem, Edward; García-Sastre, Adolfo; McGee, Monnie; Scheuermann, Richard H

    2012-05-01

    Genetic drift of influenza virus genomic sequences occurs through the combined effects of sequence alterations introduced by a low-fidelity polymerase and the varying selective pressures experienced as the virus migrates through different host environments. While traditional phylogenetic analysis is useful in tracking the evolutionary heritage of these viruses, the specific genetic determinants that dictate important phenotypic characteristics are often difficult to discern within the complex genetic background arising through evolution. Here we describe a novel influenza virus sequence feature variant type (Flu-SFVT) approach, made available through the public Influenza Research Database resource (www.fludb.org), in which variant types (VTs) identified in defined influenza virus protein sequence features (SFs) are used for genotype-phenotype association studies. Since SFs have been defined for all influenza virus proteins based on known structural, functional, and immune epitope recognition properties, the Flu-SFVT approach allows the rapid identification of the molecular genetic determinants of important influenza virus characteristics and their connection to underlying biological functions. We demonstrate the use of the SFVT approach to obtain statistical evidence for effects of NS1 protein sequence variations in dictating influenza virus host range restriction.

  9. DISCOVERY OF THREE NOVEL COCCIDIAN PARASITES INFECTING CALIFORNIA SEA LIONS (ZALOPHUS CALIFORNIANUS), WITH EVIDENCE OF SEXUAL REPLICATION AND INTERSPECIES PATHOGENICITY

    OpenAIRE

    Colegrove, Kathleen M.; Grigg, Michael E.; Carlson-Bremer, Daphne; Miller, Robin H.; Gulland, Frances M. D.; Ferguson, David J. P.; Rejmanek, Daniel; Barr, Bradd C.; Nordhausen, Robert; Melli, Ann C.; Conrad, Patricia A.

    2011-01-01

    Enteric protozoal infection was identified in 5 stranded California sea lions (Zalophus californianus). Microscopically, the apical cytoplasm of distal jejunal enterocytes contained multiple stages of coccidian parasites, including schizonts with merozoites and spherical gametocytes, which were morphologically similar to coccidians. By histopathology, organisms appeared to be confined to the intestine and accompanied by only mild enteritis. Using electron microscopy, both sexual (microgametoc...

  10. Romanian crustal earthquake sequences: evidence for space and time clustering in correlation with seismic source properties

    International Nuclear Information System (INIS)

    Popescu, E.; Popa, M.; Radulian, M.

    2002-01-01

    The study of seismic sequences is important from both scientific point of view, and its socio-economical impact on human society. In this paper we analyze the crustal earthquake sequences in correlation with the seismogenic zones delimited on the Romanian territory using geological and tectonic information available. We consider on one hand the sequences typical for the Carpathians foreland region (Ramnicu Sarat, Vrancioaia and Sinaia seismic zones), which are associated with the Vrancea subduction process and, on the other hand the sequences typical for the contact between the Pannonian Basin and Carpathians orogen (Banat seismic zone). To analyze the seismicity and source properties, we applied the fractal statistics and relative methods such as spectral ratio and deconvolution with the empirical Green's functions. On the basis of the retrieved source parameters for small and moderate size events the scaling relations for the characteristic properties of the seismic source are estimated. The scaling and earthquake clustering properties are correlated with the geological and rheological properties of the studied seismic areas. (authors)

  11. Sequencing the real time of the elderly: Evidence from South Africa

    Directory of Open Access Journals (Sweden)

    Erofili Grapsa

    2016-09-01

    Full Text Available Background: Understanding how the elderly in developing countries spend their time has received little attention. Moreover, the potential of time use data to discern variation in activity patterns has not been fully realized by methods which use a mean added time approach. Objective: To uncover patterns of time use among the elderly (60 years and older in South Africa by applying an innovative methodology that incorporates the timing, duration, and frequency of activities in the analysis. Methods: We use sequence analysis, which treats the daily series of activities of each individual as a sequence, and cluster analysis, to group these sequences into common clusters of time use behaviour. We then estimate multinomial logit regressions to identify the characteristics of the elderly which predict cluster membership. Results: We find that the time use behaviour of the elderly in South Africa can be divided into five distinct clusters, according to the relative importance in their day of personal care, household maintenance, work, mass media, and social or cultural activities. In comparison to men, women are overrepresented in the cluster where household work dominates, while they are underrepresented in the cluster of the elderly who engage in production work. A range of other individual and household characteristics are also important in predicting cluster membership. Contribution: Sequence and cluster analysis permit a nuanced examination of the differences and commonalities in time use patterns among the elderly in South Africa. There is considerable potential to extend these methods to other studies of time use behaviour.

  12. Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida.

    Science.gov (United States)

    Vincent, Antony T; Trudel, Mélanie V; Freschi, Luca; Nagar, Vandan; Gagné-Thivierge, Cynthia; Levesque, Roger C; Charette, Steve J

    2016-01-12

    Aeromonads make up a group of Gram-negative bacteria that includes human and fish pathogens. The Aeromonas salmonicida species has the peculiarity of including five known subspecies. However, few studies of the genomes of A. salmonicida subspecies have been reported to date. We sequenced the genomes of additional A. salmonicida isolates, including three from India, using next-generation sequencing in order to gain a better understanding of the genomic and phylogenetic links between A. salmonicida subspecies. Their relative phylogenetic positions were confirmed by a core genome phylogeny based on 1645 gene sequences. The Indian isolates, which formed a sub-group together with A. salmonicida subsp. pectinolytica, were able to grow at either at 18 °C and 37 °C, unlike the A. salmonicida psychrophilic isolates that did not grow at 37 °C. Amino acid frequencies, GC content, tRNA composition, loss and gain of genes during evolution, pseudogenes as well as genes under positive selection and the mobilome were studied to explain this intraspecies dichotomy. Insertion sequences appeared to be an important driving force that locked the psychrophilic strains into their particular lifestyle in order to conserve their genomic integrity. This observation, based on comparative genomics, is in agreement with previous results showing that insertion sequence mobility induced by heat in A. salmonicida subspecies causes genomic plasticity, resulting in a deleterious effect on the virulence of the bacterium. We provide a proof-of-concept that selfish DNAs play a major role in the evolution of bacterial species by modeling genomes.

  13. Possible evidence for metal accretion onto the surfaces of metal-poor main-sequence stars

    Energy Technology Data Exchange (ETDEWEB)

    Hattori, Kohei; Yoshii, Yuzuru [Institute of Astronomy, School of Science, University of Tokyo, 2-21-1 Osawa, Mitaka, Tokyo 181-0015 (Japan); Beers, Timothy C. [National Optical Astronomy Observatories, Tucson, AZ 85719 (United States); Carollo, Daniela [Department of Physics and Astronomy, Macquarie University, Sydney, 2109 NSW (Australia); Lee, Young Sun, E-mail: khattori@ioa.s.u-tokyo.ac.jp [Department of Astronomy, New Mexico State University, Las Cruces, NM 88003 (United States)

    2014-04-01

    The entire evolution of the Milky Way, including its mass-assembly and star-formation history, is imprinted onto the chemo-dynamical distribution function of its member stars, f(x, v, [X/H]), in the multi-dimensional phase space spanned by position, velocity, and elemental abundance ratios. In particular, the chemo-dynamical distribution functions for low-mass stars (e.g., G- or K-type dwarfs) are precious tracers of the earliest stages of the Milky Way's formation, since their main-sequence lifetimes approach or exceed the age of the universe. A basic tenet of essentially all previous analyses is that the stellar metallicity, usually parameterized as [Fe/H], is conserved over time for main-sequence stars (at least those that have not been polluted due to mass transfer from binary companions). If this holds true, any correlations between metallicity and kinematics for long-lived main-sequence stars of different masses, effective temperatures, or spectral types must strictly be the same, since they reflect the same mass-assembly and star-formation histories. By analyzing a sample of nearby metal-poor halo and thick-disk stars on the main sequence, taken from Data Release 8 of the Sloan Digital Sky Survey, we find that the median metallicity of G-type dwarfs is systematically higher (by about 0.2 dex) than that of K-type dwarfs having the same median rotational velocity about the Galactic center. If it can be confirmed, this finding may invalidate the long-accepted assumption that the atmospheric metallicities of long-lived stars are conserved over time.

  14. The search for geologic evidence of distant-source tsunamis using new field data in California: Chapter C in The SAFRR (Science Application for Risk Reduction) Tsunami Scenario

    Science.gov (United States)

    Wilson, Rick; Hemphill-Haley, Eileen; Jaffe, Bruce; Richmond, Bruce; Peters, Robert; Graehl, Nick; Kelsey, Harvey; Leeper, Robert; Watt, Steve; McGann, Mary; Hoirup, Don F.; Chagué-Goff, Catherine; Goff, James; Caldwell, Dylan; Loofbourrow, Casey

    2014-01-01

    A statewide assessment for geological evidence of tsunamis, primarily from distant-source events, found tsunami deposits at several locations, though evidence was absent at most locations evaluated. Several historical distant-source tsunamis, including the 1946 Aleutian, 1960 Chile, and 1964 Alaska events, caused inundation along portions of the northern and central California coast. Recent numerical tsunami modeling results identify the eastern Aleutian Islands subduction zone as the “worstcase” distant-source region, with the potential for causing tsunami runups of 7–10 m in northern and central California and 3–4 m in southern California. These model results, along with a review of historical topographic maps and past geotechnical evaluations, guided site selection for tsunami deposit surveys. A reconnaissance of 20 coastal marshlands was performed through site visits and coring of shallow surface sediments to determine if evidence for past tsunamis existed. Although conclusive evidence of tsunami deposits was not found at most of the sites evaluated, geologic evidence consistent with tsunami inundation was found at two locations: Three marshes in the Crescent City area and Pillar Point marsh near Half Moon Bay. Potential tsunami deposits were also evaluated at the Carpinteria Salt Marsh Reserve in Santa Barbara County. In Crescent City, deposits were ascribed to tsunamis on the basis of stratigraphic architecture, particle size, and microfossil content, and they were further assigned to the 1964 Alaska and 1700 Cascadia tsunamis on the basis of dating by cesium-137 and radiocarbon methods, respectively. The 1946 tsunami sand deposit was clearly identified throughout Pillar Point marsh, and one to two other similar but highly discontinuous sand layers were present within 0.5 m of the surface. A tsunami-origin interpretation for sand layers at Carpinteria is merely consistent with graded bedding and unsupported by diatom or foraminiferal assemblages

  15. Molecular evidence of the protozoan parasite Marteilia refringens in Crassostrea gigas and Crassostrea corteziensis from the Gulf of California

    Directory of Open Access Journals (Sweden)

    José Manuel Grijalva-Chon

    2015-09-01

    Full Text Available The search for exotic pathogens related to the outbreaks and in surveillance samplings of the Mexican oyster farms, is a recent activity achieved by academic institutions and state committees for Aquatic Animal Health, with remarkable results. In samples of Crassostrea gigas collected through December 2009, January 2010 and November 2010, and of C. corteziensis in September 2011, the protozoan Marteilia refringens was detected for the first time in the Gulf of California. The carrier oysters were from cultures without abnormal mortality rates, whereby, the use of histology, in situ hybridization and transmission electron microscopy studies are necessary to determine if M. refringens has become established in the Gulf of California oyster cultures. Detection of M. refringens is of great concern to the global oyster farming industry.

  16. Segmenting wine markets with diverse price functions: Evidence from California red and white wines sold in British Columbia

    Directory of Open Access Journals (Sweden)

    Richard Carew

    2017-06-01

    Full Text Available Previous hedonic price studies on wine market segments, exploring diverse price functions, are constrained by pre-determined price breakpoints, the total number of segments, or both. Using British Columbia Liquor Distribution Branch (BCLDB retail price data of California red and white wines, this study adopts an endogenous approach to explore the total number of market segments and identify breakpoints in price dispersion simultaneously. Results show that red and white California wines are grouped into two (breaking at Can$14 per bottle and three (breaking at Can$16 and $30 per bottle price segments, respectively. Also, implicit prices of wine attributes such as grape variety and geographic origin differ for red and white wines across market segments.

  17. The Role of Neighborhood Characteristics in the Adoption and Frequency of Working at Home: Empirical Evidence from Northern California

    OpenAIRE

    Tang, Wei; Mokhtarian, Patricia; Handy, Susan

    2008-01-01

    Working at home is widely viewed as a useful travel-reduction strategy, and partly for that reason, considerable research related to telecommuting and home-based work has been conducted in the last two decades. The contribution of this study is to examine the effect of residential neighborhood built environment (BE) factors on working at home. Using data from a survey of eight neighborhoods in Northern California, we develop a multinomial logit (MNL) model of work-at-home (WAH) frequency. Pot...

  18. Stable isotope and DNA evidence for ritual sequences in Inca child sacrifice

    DEFF Research Database (Denmark)

    Wilson, Andrew S; Taylor, Timothy; Ceruti, Maria Constanza

    2007-01-01

    Four recently discovered frozen child mummies from two of the highest peaks in the south central Andes now yield tantalizing evidence of the preparatory stages leading to Inca ritual killing as represented by the unique capacocha rite. Our interdisciplinary study examined hair from the mummies to...

  19. California Bioregions

    Data.gov (United States)

    California Natural Resource Agency — California regions developed by the Inter-agency Natural Areas Coordinating Committee (INACC) were digitized from a 1:1,200,000 California Department of Fish and...

  20. rbcL gene sequences provide evidence for the evolutionary lineages of leptosporangiate ferns.

    Science.gov (United States)

    Hasebe, M; Omori, T; Nakazawa, M; Sano, T; Kato, M; Iwatsuki, K

    1994-06-07

    Pteriodophytes have a longer evolutionary history than any other vascular land plant and, therefore, have endured greater loss of phylogenetically informative information. This factor has resulted in substantial disagreements in evaluating characters and, thus, controversy in establishing a stable classification. To compare competing classifications, we obtained DNA sequences of a chloroplast gene. The sequence of 1206 nt of the large subunit of the ribulose-bisphosphate carboxylase gene (rbcL) was determined from 58 species, representing almost all families of leptosporangiate ferns. Phlogenetic trees were inferred by the neighbor-joining and the parsimony methods. The two methods produced almost identical phylogenetic trees that provided insights concerning major general evolutionary trends in the leptosporangiate ferns. Interesting findings were as follows: (i) two morphologically distinct heterosporous water ferns, Marsilea and Salvinia, are sister genera; (ii) the tree ferns (Cyatheaceae, Dicksoniaceae, and Metaxyaceae) are monophyletic; and (iii) polypodioids are distantly related to the gleichenioids in spite of the similarity of their exindusiate soral morphology and are close to the higher indusiate ferns. In addition, the affinities of several "problematic genera" were assessed.

  1. Stars of type MS with evidence of white dwarf companions. [IUE, Main Sequence (MS)

    Science.gov (United States)

    Peery, Benjamin F., Jr.

    1986-01-01

    A search for white dwarf companions of MS-type stars was conducted, using IUE. The overendowments of these stars in typical S-process nuclides suggest that they, like the Ba II stars, may owe their peculiar compositions to earlier mass transfer. Short-wavelength IUE spectra show striking emission line variability in HD35155, HD61913, and 4 Ori; HD35155 and 4 Ori show evidence of white dwarf companions.

  2. Stable isotope and DNA evidence for ritual sequences in Inca child sacrifice

    Science.gov (United States)

    Wilson, Andrew S.; Taylor, Timothy; Ceruti, Maria Constanza; Chavez, Jose Antonio; Reinhard, Johan; Grimes, Vaughan; Meier-Augenstein, Wolfram; Cartmell, Larry; Stern, Ben; Richards, Michael P.; Worobey, Michael; Barnes, Ian; Gilbert, M. Thomas P.

    2007-01-01

    Four recently discovered frozen child mummies from two of the highest peaks in the south central Andes now yield tantalizing evidence of the preparatory stages leading to Inca ritual killing as represented by the unique capacocha rite. Our interdisciplinary study examined hair from the mummies to obtain detailed genetic and diachronic isotopic information. This approach has allowed us to reconstruct aspects of individual identity and diet, make inferences concerning social background, and gain insight on the hitherto unknown processes by which victims were selected, elevated in social status, prepared for a high-altitude pilgrimage, and killed. Such direct information amplifies, yet also partly contrasts with, Spanish historical accounts. PMID:17923675

  3. Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation.

    Science.gov (United States)

    Yoo, Jejoong; Kim, Hajin; Aksimentiev, Aleksei; Ha, Taekjip

    2016-03-22

    Although proteins mediate highly ordered DNA organization in vivo, theoretical studies suggest that homologous DNA duplexes can preferentially associate with one another even in the absence of proteins. Here we combine molecular dynamics simulations with single-molecule fluorescence resonance energy transfer experiments to examine the interactions between duplex DNA in the presence of spermine, a biological polycation. We find that AT-rich DNA duplexes associate more strongly than GC-rich duplexes, regardless of the sequence homology. Methyl groups of thymine acts as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA-DNA attraction. Indeed, methylation of cytosines makes attraction between GC-rich DNA as strong as that between AT-rich DNA. Recent genome-wide chromosome organization studies showed that remote contact frequencies are higher for AT-rich and methylated DNA, suggesting that direct DNA-DNA interactions that we report here may play a role in the chromosome organization and gene regulation.

  4. Delimiting species of Protaphorura (Collembola: Onychiuridae): integrative evidence based on morphology, DNA sequences and geography.

    Science.gov (United States)

    Sun, Xin; Zhang, Feng; Ding, Yinhuan; Davies, Thomas W; Li, Yu; Wu, Donghui

    2017-08-15

    Species delimitation remains a significant challenge when the diagnostic morphological characters are limited. Integrative taxonomy was applied to the genus Protaphorura (Collembola: Onychiuridae), which is one of most difficult soil animals to distinguish taxonomically. Three delimitation approaches (morphology, molecular markers and geography) were applied providing rigorous species validation criteria with an acceptably low error rate. Multiple molecular approaches, including distance- and evolutionary model-based methods, were used to determine species boundaries based on 144 standard barcode sequences. Twenty-two molecular putative species were consistently recovered across molecular and geographical analyses. Geographic criteria were was proved to be an efficient delimitation method for onychiurids. Further morphological examination, based on the combination of the number of pseudocelli, parapseudocelli and ventral mesothoracic chaetae, confirmed 18 taxa of 22 molecular units, with six of them described as new species. These characters were found to be of high taxonomical value. This study highlights the potential benefits of integrative taxonomy, particularly simultaneous use of molecular/geographical tools, as a powerful way of ascertaining the true diversity of the Onychiuridae. Our study also highlights that discovering new morphological characters remains central to achieving a full understanding of collembolan taxonomy.

  5. The Effects of Urbanization and Flood Control on Sediment Discharge of a Southern California River, Evidence of a Dilution Effect

    Science.gov (United States)

    Warrick, J. A.; Orzech, K. M.; Rubin, D. M.

    2004-12-01

    The southern California landscape has undergone dramatic urbanization and population growth during the past 60 years and currently supports almost 20 million inhabitants. During this time, rivers of the region have been altered with damming, channel straightening and hardening, and water transfer engineering. These changes have drastically altered water and sediment discharge from most of the region's drainage basins. Here we focus on changes in sediment discharge from the largest watershed of southern California, the Santa Ana River. Order-of-magnitude drops in the suspended sediment rating curves (the relationship between suspended sediment concentration and instantaneous river discharge) are observed between 1967 and 2001, long after the construction of a major flood control dam in 1941. These sediment concentration decreases do not, however, represent alteration of the total sediment flux from the basin (a common interpretation of sediment rating curves), but rather a dilution of suspended sediment by increases (approx. 4x) in stormwater discharge associated with urbanization. Increases in peak and total stormwater discharge are consistent with runoff patterns from urbanizing landscapes, supporting our hypothesis that the diluting water originated from stormwater runoff generated in urban areas both up- and downstream of dams. Our dilution hypothesis is further supported with water and sediment budgets, dilution calculations, and suspended and bed grain size information.

  6. Evidences of Paleoearthquakes in Palaeolithic settlements within fluvial sequences of the Tagus Basin (Madrid, Central Spain).

    Science.gov (United States)

    Silva, Pablo G.; Rodríguez Pascua, M. A.; Pérez López, R.; Giner Robles, J. L.; Roquero, E.; Tapias, F.; López Recio, M.; Rus, I.; Morin, J.

    2010-05-01

    Multiple evidences of soft-sediment to brittle deformation within the Pleistocene fluvial terraces of the Tagus, Jarama, Tajuña and Manzanares river valleys have been described since the middle 20th Century. Cryoturbation, hydroplastic deformations due to underlying karstic collapses or halokinesis on the substratum of neogene gypsums, and seismic shaking have been proposed to interpret these structures. These deformations are typically concentrated in the +18-20 m terrace levels, and closely linked to well-known Palaeolithic sites, in some cases overlaying and/or affecting true prehistoric settlements (i.e. Arganda, Arriaga and Tafesa sites) within the Jarama and Manzanares valleys. The affected settlements typically display acheulian lithic industry linked to the scavenging of large Pleistocene mammals (i.e. Elephas antiquus). Commonly, deformational structures are concentrated in relatively thin horizons (10-50 cm thick) bracketed by undeformed fluvial sands and gravels. The soft-sediment deformations usually consist on medium to fine sized sands injected and protruded in overlaying flood-plain clayey silts, showing a wide variety of convolutes, injections, sand-dikes, dish and pillar structures, mud volcanoes, faults and folds, some times it is possible to undertake their 3D geometrical analysis due to the exceptional conservation of the structures (Tafesa). Recent geo-archaeological prospecting on the for the Palaeolithic Site of Arriaga (South Madrid City) conducted during the year 2009, let to find out an exceptional horizon of deformation of about 1.20 m thick. It consisted on highly disturbed and pervasively liquefacted sands, which hardly can be attributed to no-seismic processes. The acheulian lithic industry of the Madrid Region have been classically attributed the Late Middle Pleistocene (Comunidad de Madrid, AUDEMA S.A. (Proyecto Arriaga-2009). This is a contribution of GQM-AEQUA.

  7. Hedysarum L. (Fabaceae: Hedysareae) Is Not Monophyletic - Evidence from Phylogenetic Analyses Based on Five Nuclear and Five Plastid Sequences.

    Science.gov (United States)

    Liu, Pei-Liang; Wen, Jun; Duan, Lei; Arslan, Emine; Ertuğrul, Kuddisi; Chang, Zhao-Yang

    2017-01-01

    The legume family (Fabaceae) exhibits a high level of species diversity and evolutionary success worldwide. Previous phylogenetic studies of the genus Hedysarum L. (Fabaceae: Hedysareae) showed that the nuclear and the plastid topologies might be incongruent, and the systematic position of the Hedysarum sect. Stracheya clade was uncertain. In this study, phylogenetic relationships of Hedysarum were investigated based on the nuclear ITS, ETS, PGDH, SQD1, TRPT and the plastid psbA-trnH, trnC-petN, trnL-trnF, trnS-trnG, petN-psbM sequences. Both nuclear and plastid data support two major lineages in Hedysarum: the Hedysarum s.s. clade and the Sartoria clade. In the nuclear tree, Hedysarum is biphyletic with the Hedysarum s.s. clade sister to the Corethrodendron + Eversmannia + Greuteria + Onobrychis clade (the CEGO clade), whereas the Sartoria clade is sister to the genus Taverniera DC. In the plastid tree, Hedysarum is monophyletic and sister to Taverniera. The incongruent position of the Hedysarum s.s. clade between the nuclear and plastid trees may be best explained by a chloroplast capture hypothesis via introgression. The Hedysarum sect. Stracheya clade is resolved as sister to the H. sect. Hedysarum clade in both nuclear and plastid trees, and our analyses support merging Stracheya into Hedysarum. Based on our new evidence from multiple sequences, Hedysarum is not monophyletic, and its generic delimitation needs to be reconsidered.

  8. Hedysarum L. (Fabaceae: Hedysareae) Is Not Monophyletic – Evidence from Phylogenetic Analyses Based on Five Nuclear and Five Plastid Sequences

    Science.gov (United States)

    Liu, Pei-Liang; Wen, Jun; Duan, Lei; Arslan, Emine; Ertuğrul, Kuddisi; Chang, Zhao-Yang

    2017-01-01

    The legume family (Fabaceae) exhibits a high level of species diversity and evolutionary success worldwide. Previous phylogenetic studies of the genus Hedysarum L. (Fabaceae: Hedysareae) showed that the nuclear and the plastid topologies might be incongruent, and the systematic position of the Hedysarum sect. Stracheya clade was uncertain. In this study, phylogenetic relationships of Hedysarum were investigated based on the nuclear ITS, ETS, PGDH, SQD1, TRPT and the plastid psbA-trnH, trnC-petN, trnL-trnF, trnS-trnG, petN-psbM sequences. Both nuclear and plastid data support two major lineages in Hedysarum: the Hedysarum s.s. clade and the Sartoria clade. In the nuclear tree, Hedysarum is biphyletic with the Hedysarum s.s. clade sister to the Corethrodendron + Eversmannia + Greuteria + Onobrychis clade (the CEGO clade), whereas the Sartoria clade is sister to the genus Taverniera DC. In the plastid tree, Hedysarum is monophyletic and sister to Taverniera. The incongruent position of the Hedysarum s.s. clade between the nuclear and plastid trees may be best explained by a chloroplast capture hypothesis via introgression. The Hedysarum sect. Stracheya clade is resolved as sister to the H. sect. Hedysarum clade in both nuclear and plastid trees, and our analyses support merging Stracheya into Hedysarum. Based on our new evidence from multiple sequences, Hedysarum is not monophyletic, and its generic delimitation needs to be reconsidered. PMID:28122062

  9. Pollen-based evidence of extreme drought during the last Glacial (32.6-9.0 ka) in coastal southern California

    Science.gov (United States)

    Heusser, Linda E.; Kirby, Matthew E.; Nichols, Jonathan E.

    2015-10-01

    High resolution pollen analyses of sediment core LEDC10-1 from Lake Elsinore yield the first well-dated, terrestrial record of sub-centennial-scale ecologic change in coastal southern California between ˜32 and 9 ka. In the Lake Elsinore watershed, the initial, mesic montane conifer forests dominated by Pinus, and Cupressaceae with trace amounts of Abies and Picea were replaced by a sequence of multiple, extended severe mega-droughts between ˜27.5 and ˜25.5 ka, in which halophytic and xerophytic herbs and shrubs occupied an ephemeral lake. This prolonged and extended dry interval, which corresponds with warm waters offshore, imply strengthening of the North Pacific High and persistent below-average winter precipitation. The subsequent, contrasting monotonic occurrence of montane conifers reflects little variation in cold, mesic climate until ˜15 ka. Postglacial development of Quercus woodland and chaparral mark the return to more xeric, warmer conditions at this time. A brief reversal at ˜13.1-˜12.1 ka, as reflected by an expansion of Pinus, is correlative with the Younger Dryas and interrupts development of warm, postglacial climate. Subsequent gradual expansion of xeric vegetation post - Younger Dryas denotes the establishment of a winter hydroclimate regime in coastal southern California that is more similar to modern conditions. Pollen-based reconstructions of temperature and precipitation at Lake Elsinore are generally correlative with pollen-based paleoclimatic reconstructions and foraminifera-based sea surface temperatures from Santa Barbara Basin in marine core ODP 893. The conspicuous absence of the ˜27.5-˜25.5 ka glacial "mega-drought" in the Santa Barbara Basin pollen record highlights the sensitivity of Lake Elsinore to hydroclimate change, and thus, the importance of this new record that indicates that mega-drought can occur during the full glacial when climatic boundary conditions and forcings differed substantially from the present.

  10. Pedogenic calcite as evidence for an early Holocene dry period in the San Francisco Bay area, California

    Science.gov (United States)

    Borchardt, G.; Lienkaemper, J.J.

    1999-01-01

    Rainfall at the site of Union City, California, during early Holocene time appears to have been about half that of today, 470 mm/yr. We base this conclusion on detailed descriptions and particle-size analyses of 12 soil profiles and 1:20 scale logs of the fluvial stratigraphy in two 100-m-long, 5-m-deep excavations dug perpendicular to the axis of an alluvial fan along the Hayward fault. Subsidence and right-lateral movement along the fault allowed an offset stream to produce a nearly continuous alluvial record documented by 35 14C ages on detrital charcoal. Bk (calcitic) horizons in paleosols developed in the fan suggest that a relatively dry climatic period occurred from 10 to 7 ka (calendar-corrected ages). The pedogenic calcite exists primarily as vertically oriented filaments and fine, cavernous nodules formed at ped intersections. Soils and paleosols formed before 10 ka or since 7 ka did not have Bk horizons. Bk horizons that were buried suddenly at 7 ka were overlain by leached zones averaging 41 ?? 3 cm thick - about half the current depth of leaching.

  11. Marine subsidies of island communities in the Gulf of California: evidence from stable carbon and nitrogen isotopes

    International Nuclear Information System (INIS)

    Anderson, W.B.; Polis, G.A.

    1998-01-01

    Coastal sites support larger (2 to > 100 x) populations of many consumers than inland sites on islands in the Gulf of California. Previous data suggested that subsidies of energy and nutrients from the ocean allowed large coastal populations. Stable carbon and nitrogen isotopes are frequently used to analyse diet composition of organisms: they are particularly useful to distinguish between diet sources with distinct isotopic signatures, such as marine and terrestrial diets. We analyzed the 13 C and 15 N concentrations of coastal versus inland spiders and scorpions to test the hypothesis that coastal individuals exhibited more strongly marine-based diets than inland individuals. Coastal spiders and scorpions were significantly more enriched in 13 C and 15 N than inland spiders and scorpions, suggesting that the coastal individuals consumed more marine-based foods than their inland counterparts. These patterns existed in both drought years and wet El Nino years. However, the marine influence was stronger in drought years when terrestrial productivity was nearly non-existent, than in wet years when terrestrial productivity increased by an order of magnitude. (au)

  12. Genetic and experimental evidence for a mixed-age, mixed-origin bank of kelp microscopic stages in southern California.

    Science.gov (United States)

    Carney, Laura T; Bohonak, Andrew J; Edwards, Matthew S; Alberto, Filipe

    2013-09-01

    Laboratory studies have demonstrated that the microscopic stages of kelps can rapidly resume development from a delayed state. Like terrestrial seeds or aquatic resting eggs, banks of delayed kelp stages may supplement population recovery after periods of stress, playing an important role for kelp populations that experience adult sporophyte absences due to seasonal or interannual disturbances. We found that removing the microscopic stages from natural rock substratum could prevent the appearance of juvenile kelp sporophytes for three months and the establishment of a diverse kelp assemblage for over four months within a southern California kelp forest. Juveniles were observed within one month in plots where microscopic stages were left intact, which may confer an advantage for the resulting sporophytes as they attain larger sizes before later recruiting neighbors. Microsatellite diversity was high (expected heterozygosity HE approximately 0.9) for juveniles and adults within our sites. Using a microsatellite-based parentage analysis for the dominant kelp, Macrocystis pyrifera, we estimated that a portion of the new M. pyrifera sporophyte recruits had originated from their parents at least seven months after their parents had disappeared. Similar delay durations have been demonstrated in recent laboratory studies. Additionally, our results suggest that zoospore dispersal distances > 50 m may be supported by including additional microsatellite loci in the analysis. We propose a mixed-age and, potentially, a mixed-origin bank of M. pyrifera gametophytes promotes maximal genetic diversity in recovering populations and reduces population genetic subdivision and self-fertilization rates for intact populations by promoting the survival of zoospores dispersed > 10 m and during inhospitable environmental conditions.

  13. Prevention of Filipino Youth Behavioral Health Disparities: Identifying Barriers and Facilitators to Participating in "Incredible Years," an Evidence-Based Parenting Intervention, Los Angeles, California, 2012.

    Science.gov (United States)

    Flores, Nicole; Supan, Jocelyn; Kreutzer, Cary B; Samson, Allan; Coffey, Dean M; Javier, Joyce R

    2015-10-22

    Evidence-based interventions for training parents are proven to prevent onset and escalation of childhood mental health problems. However, participation in such programs is low, especially among hard-to-reach, underserved populations such as Filipino Americans. Filipinos, the largest Asian subgroup in California, have significant behavioral health disparities compared with non-Hispanic whites and other Asian subgroups. The purpose of this study was to learn about Filipinos' barriers and facilitators to participating in "Incredible Years" (IY), a parenting program. We conducted 4 focus groups in Los Angeles, California, in 2012; the groups consisted of 20 Filipino parents of children aged 6 to 12 years who recently completed the IY parenting program, which was offered as a prevention workshop. Three reviewers, including two co-authors (A.S., J.J.) and a research assistant used content analysis to independently code the interview transcripts and extract subthemes. Grounded theory analytic methods were used to analyze interview transcripts. Parents' perceived benefits of participation in IY were learning more effective parenting techniques, networking with other parents, improved spousal relationships, and improvements in their children's behavior. Parents' most common motivating factor for enrollment in IY was to improve their parenting skills and their relationships with their children. The most common barriers to participation were being uncomfortable sharing problems with others and the fear of being stigmatized by others judging their parenting skills. Participants said that parent testimonials would be the most effective way to promote IY. Many recommended outreach at schools, pediatricians' offices, and churches. Increasing Filipino American parent enrollment in IY in culturally relevant ways will reduce the incidence of mental health disorders among children in this growing population.

  14. Career-Technical Education and Labor Market Outcomes: Evidence from California Community Colleges. A CAPSEE Working Paper

    Science.gov (United States)

    Stevens, Ann; Kurlaender, Michal; Grosz, Michel

    2015-01-01

    This paper estimates the earnings returns to vocational, or career-technical, education programs in the nation's largest community college system. While career-technical education (CTE) programs have often been mentioned as an attractive alternative to four-year colleges for some students, very little systematic evidence exists on the returns to…

  15. Evident?

    DEFF Research Database (Denmark)

    Plant, Peter

    2012-01-01

    Quality assurance and evidence in career guidance in Europe are often seen as self-evident approaches, but particular interests lie behind......Quality assurance and evidence in career guidance in Europe are often seen as self-evident approaches, but particular interests lie behind...

  16. Amphibian populations in the terrestrial environment: Is there evidence of declines of terrestrial forest amphibians in northwestern California?

    Science.gov (United States)

    Hartwell H. Welsh Jr.; Gary M. Fellers; Amy J. Lind

    2007-01-01

    Amphibian declines have been documented worldwide; however the vast majority are species associated with aquatic habitats. Information on the status and trends of terrestrial amphibians is almost entirely lacking. Here we use data collected across a 12-yr period (sampling from 1984–86 and from 1993–95) to address the question of whether evidence exists for declines...

  17. A multigenerational family study of oral and hand motor sequencing ability provides evidence for a familial speech sound disorder subtype

    Science.gov (United States)

    Peter, Beate; Raskind, Wendy H.

    2011-01-01

    Purpose To evaluate phenotypic expressions of speech sound disorder (SSD) in multigenerational families with evidence of familial forms of SSD. Method Members of five multigenerational families (N = 36) produced rapid sequences of monosyllables and disyllables and tapped computer keys with repetitive and alternating movements. Results Measures of repetitive and alternating motor speed were correlated within and between the two motor systems. Repetitive and alternating motor speeds increased in children and decreased in adults as a function of age. In two families with children who had severe speech deficits consistent with disrupted praxis, slowed alternating, but not repetitive, oral movements characterized most of the affected children and adults with a history of SSD, and slowed alternating hand movements were seen in some of the biologically related participants as well. Conclusion Results are consistent with a familial motor-based SSD subtype with incomplete penetrance, motivating new clinical questions about motor-based intervention not only in the oral but also the limb system. PMID:21909176

  18. Complete plastid genome sequence of Primula sinensis (Primulaceae: structure comparison, sequence variation and evidence for accD transfer to nucleus

    Directory of Open Access Journals (Sweden)

    Tong-Jian Liu

    2016-06-01

    Full Text Available Species-rich genus Primula L. is a typical plant group with which to understand genetic variance between species in different levels of relationships. Chloroplast genome sequences are used to be the information resource for quantifying this difference and reconstructing evolutionary history. In this study, we reported the complete chloroplast genome sequence of Primula sinensis and compared it with other related species. This genome of chloroplast showed a typical circular quadripartite structure with 150,859 bp in sequence length consisting of 37.2% GC base. Two inverted repeated regions (25,535 bp were separated by a large single-copy region (82,064 bp and a small single-copy region (17,725 bp. The genome consists of 112 genes, including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Among them, seven coding genes, seven tRNA genes and four rRNA genes have two copies due to their locations in the IR regions. The accD and infA genes lacking intact open reading frames (ORF were identified as pseudogenes. SSR and sequence variation analyses were also performed on the plastome of Primula sinensis, comparing with another available plastome of P. poissonii. The four most variable regions, rpl36–rps8, rps16–trnQ, trnH–psbA and ndhC–trnV, were identified. Phylogenetic relationship estimates using three sub-datasets extracted from a matrix of 57 protein-coding gene sequences showed the identical result that was consistent with previous studies. A transcript found from P. sinensis transcriptome showed a high similarity to plastid accD functional region and was identified as a putative plastid transit peptide at the N-terminal region. The result strongly suggested that plastid accD has been functionally transferred to the nucleus in P. sinensis.

  19. Photomosaics and event evidence from the Frazier Mountain paleoseismic site, trench 1, cuts 1–4, San Andreas Fault Zone, southern California (2007–2009)

    Science.gov (United States)

    Scharer, Katherine M.; Fumal, Tom E.; Weldon, Ray J.; Streig, Ashley R.

    2014-01-01

    The Frazier Mountain paleoseismic site is located at the northwest end of the Mojave section of the San Andreas Fault, in a small, closed depression at the base of Frazier Mountain near Tejon Pass, California (lat 34.8122° N., long 118.9034° W.). The site was known to contain a good record of earthquakes due to previous excavations by Lindvall and others (2002). This report provides data resulting from four nested excavations, or cuts, along trench 1 (T1) in 2007 and 2009 at the Frazier Mountain site. The four cuts were excavated progressively deeper and wider in an orientation perpendicular to the San Andreas Fault, exposing distal fan and marsh sediments deposited since ca. A.D. 1200. The results of the trenching show that earthquakes that ruptured the site have repeatedly produced a small depression or sag on the surface, which is subsequently infilled with sand and silt deposits. This report provides high-resolution photomosaics and logs for the T1 cuts, a detailed stratigraphic column for the deposits, and a table summarizing all of the evidence for ground rupturing paleoearthquakes logged in the trenches.

  20. Early Pliocene Hiatus in Sand Output by the Colorado River: Evidence From Marine Deposits in the Salton Trough, Southern California

    Science.gov (United States)

    Dorsey, R. J.; Bykerk-Kauffman, A.

    2015-12-01

    Early Pliocene deposits in the western Salton Trough preserve a high-fidelity record of sediment dispersal into the marine realm during initiation and early evolution of the Colorado River (CR). Grain-size fractionation, sediment routing, and transport dynamics of the early CR delta are recorded in sediments of the Fish Creek - Vallecito basin, which was located ~100 km south of Yuma along the transform plate boundary at 5 Ma. Early Pliocene delivery of CR sand to the basin took place in two distinct pulses: (1) deposition of sandy turbidites (Wind Caves Mbr of the Latrania Fm) in a restricted submarine canyon at Split Mt Gorge between ~5.3 and 5.1 Ma; and (2) progradation of a thick, widespread, coarsening-up deltaic sequence of marine mudstone, sandstone, and coquinas (Deguynos Fm) between ~4.8 and 4.2 Ma. Estimated flux of CR sediment during Wind Caves deposition was weak (~3-5 Mt/yr) compared to the long-term average (172±64 Mt/yr). The two pulses of CR sand input are separated by the Coyote Clay (CC, ~5.1-4.8 Ma), a regionally correlable, greenish-yellow-weathering marine claystone unit at the base of the Deguynos Fm. CC gradationally overlies Wind Caves turbidites in the area of the paleocanyon. In contrast, in the Coyote Mts 15-23 km to the south and SE, CC rests on coarse-grained locally-derived late Miocene sedimentary rocks, Alverson volcanics, and metamorphic basement rock along a regional unconformity. Identical claystone facies occur in the NW Indio Hills (restores to Yuma at the mouth of the CR at 5 Ma), and Sierra Cucapa in Mexico (~200 km south of Yuma at 5 Ma). Marine localities outside of the Wind Caves paleocanyon experienced slow to negligible sedimentation along a rugged rocky shoreline until abrupt arrival of CR-derived clay. CC accumulated in a sand-starved, pro-delta marine setting (Winker, 1987) over an inferred N-S distance of ~200 km. We therefore reject an alternate hypothesis that CC accumulated on the muddy slope of the prograding CR

  1. Experimental and geochemical evidence for derivation of the El Capitan Granite, California, by partial melting of hydrous gabbroic lower crust

    Science.gov (United States)

    Ratajeski, K.; Sisson, T.W.; Glazner, A.F.

    2005-01-01

    Partial melting of mafic intrusions recently emplaced into the lower crust can produce voluminous silicic magmas with isotopic ratios similar to their mafic sources. Low-temperature (825 and 850??C) partial melts synthesized at 700 MPa in biotite-hornblende gabbros from the central Sierra Nevada batholith (Sisson et al. in Contrib Mineral Petrol 148:635-661, 2005) have major-element and modeled trace-element (REE, Rb, Ba, Sr, Th, U) compositions matching those of the Cretaceous El Capitan Granite, a prominent granite and silicic granodiorite pluton in the central part of the Sierra Nevada batholith (Yosemite, CA, USA) locally mingled with coeval, isotopically similar quartz diorite through gabbro intrusions (Ratajeski et al. in Geol Soc Am Bull 113:1486-1502, 2001). These results are evidence that the El Capitan Granite, and perhaps similar intrusions in the Sierra Nevada batholith with lithospheric-mantle-like isotopic values, were extracted from LILE-enriched, hydrous (hornblende-bearing) gabbroic rocks in the Sierran lower crust. Granitic partial melts derived by this process may also be silicic end members for mixing events leading to large-volume intermediate composition Sierran plutons such as the Cretaceous Lamarck Granodiorite. Voluminous gabbroic residues of partial melting may be lost to the mantle by their conversion to garnet-pyroxene assemblages during batholithic magmatic crustal thickening. ?? Springer-Verlag 2005.

  2. No Evidence of XMRV or MuLV Sequences in Prostate Cancer, Diffuse Large B-Cell Lymphoma, or the UK Blood Donor Population

    Directory of Open Access Journals (Sweden)

    Mark James Robinson

    2011-01-01

    Full Text Available Xenotropic murine leukaemia virus-related virus (XMRV is a recently described retrovirus which has been claimed to infect humans and cause associated pathology. Initially identified in the US in patients with prostate cancer and subsequently in patients with chronic fatigue syndrome, doubt now exists that XMRV is a human pathogen. We studied the prevalence of genetic sequences of XMRV and related MuLV sequences in human prostate cancer, from B cell lymphoma patients and from UK blood donors. Nucleic acid was extracted from fresh prostate tissue biopsies, formalin-fixed paraffin-embedded (FFPE prostate tissue and FFPE B-cell lymphoma. The presence of XMRV-specific LTR or MuLV generic gag-like sequences was investigated by nested PCR. To control for mouse DNA contamination, a PCR that detected intracisternal A-type particle (IAP sequences was included. In addition, DNA and RNA were extracted from whole blood taken from UK blood donors and screened for XMRV sequences by real-time PCR. XMRV or MuLV-like sequences were not amplified from tissue samples. Occasionally MuLV gag and XMRV-LTR sequences were amplified from Indian prostate cancer samples, but were always detected in conjunction with contaminating murine genomic DNA. We found no evidence of XMRV or MuLV infection in the UK blood donors.

  3. Latest Quaternary paleoseismology and evidence of distributed dextral shear along the Mohawk Valley fault zone, northern Walker Lane, California

    Science.gov (United States)

    Gold, Ryan D.; Briggs, Richard; Personius, Stephen; Crone, Anthony J.; Mahan, Shannon; Angster, Stephen

    2014-01-01

    The dextral-slip Mohawk Valley fault zone (MVFZ) strikes northwestward along the eastern margin of the Sierra Nevada in the northern Walker Lane. Geodetic block modeling indicates that the MVFZ may accommodate ~3 mm/yr of regional dextral strain, implying that it is the highest slip-rate strike-slip fault in the region; however, only limited geologic data are available to constrain the system’s slip rate and earthquake history. We mapped the MVFZ using airborne lidar data and field observations and identified a site near Sulphur Creek for paleoseismic investigation. At this site, oblique dextral-normal faulting on the steep valley margin has created a closed depression that floods annually during spring snowmelt to form an ephemeral pond. We excavated three fault-perpendicular trenches at the site and exposed pond sediment that interfingers with multiple colluvial packages eroded from the scarp that bounds the eastern side of the pond. We documented evidence for four surface-rupturing earthquakes on this strand of the MVFZ. OxCal modeling of radiocarbon and luminescence ages indicates that these earthquakes occurred at 14.0 ka, 12.8 ka, 5.7 ka, and 1.9 ka. The mean ~4 kyr recurrence interval is inconsistent with slip rates of ~3 mm/yr; these rates imply surface ruptures of more than 10 m per event, which is geologically implausible for the subdued geomorphic expression and 60 km length of the MVFZ. We propose that unidentified structures not yet incorporated into geodetic models may accommodate significant dextral shear across the northern Walker Lane, highlighting the role of distributed deformation in this region.

  4. Environmental assessment for the proposed construction and operation of a Genome Sequencing Facility in Building 64 at Lawrence Berkeley Laboratory, Berkeley, California

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-04-01

    This document is an Environmental Assessment (EA) for a proposed project to modify 14,900 square feet of an existing building (Building 64) at Lawrence Berkeley Laboratory (LBL) to operate as a Genome Sequencing Facility. This EA addresses the potential environmental impacts from the proposed modifications to Building 64 and operation of the Genome Sequencing Facility. The proposed action is to modify Building 64 to provide space and equipment allowing LBL to demonstrate that the Directed DNA Sequencing Strategy can be scaled up from the current level of 750,000 base pairs per year to a facility that produces over 6,000,000 base pairs per year, while still retaining its efficiency.

  5. Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory

    Science.gov (United States)

    Crisan, Anamaria; McKee, Geoffrey; Munzner, Tamara

    2018-01-01

    Background Microbial genome sequencing is now being routinely used in many clinical and public health laboratories. Understanding how to report complex genomic test results to stakeholders who may have varying familiarity with genomics—including clinicians, laboratorians, epidemiologists, and researchers—is critical to the successful and sustainable implementation of this new technology; however, there are no evidence-based guidelines for designing such a report in the pathogen genomics domain. Here, we describe an iterative, human-centered approach to creating a report template for communicating tuberculosis (TB) genomic test results. Methods We used Design Study Methodology—a human centered approach drawn from the information visualization domain—to redesign an existing clinical report. We used expert consults and an online questionnaire to discover various stakeholders’ needs around the types of data and tasks related to TB that they encounter in their daily workflow. We also evaluated their perceptions of and familiarity with genomic data, as well as its utility at various clinical decision points. These data shaped the design of multiple prototype reports that were compared against the existing report through a second online survey, with the resulting qualitative and quantitative data informing the final, redesigned, report. Results We recruited 78 participants, 65 of whom were clinicians, nurses, laboratorians, researchers, and epidemiologists involved in TB diagnosis, treatment, and/or surveillance. Our first survey indicated that participants were largely enthusiastic about genomic data, with the majority agreeing on its utility for certain TB diagnosis and treatment tasks and many reporting some confidence in their ability to interpret this type of data (between 58.8% and 94.1%, depending on the specific data type). When we compared our four prototype reports against the existing design, we found that for the majority (86.7%) of design

  6. Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory

    Directory of Open Access Journals (Sweden)

    Anamaria Crisan

    2018-01-01

    Full Text Available Background Microbial genome sequencing is now being routinely used in many clinical and public health laboratories. Understanding how to report complex genomic test results to stakeholders who may have varying familiarity with genomics—including clinicians, laboratorians, epidemiologists, and researchers—is critical to the successful and sustainable implementation of this new technology; however, there are no evidence-based guidelines for designing such a report in the pathogen genomics domain. Here, we describe an iterative, human-centered approach to creating a report template for communicating tuberculosis (TB genomic test results. Methods We used Design Study Methodology—a human centered approach drawn from the information visualization domain—to redesign an existing clinical report. We used expert consults and an online questionnaire to discover various stakeholders’ needs around the types of data and tasks related to TB that they encounter in their daily workflow. We also evaluated their perceptions of and familiarity with genomic data, as well as its utility at various clinical decision points. These data shaped the design of multiple prototype reports that were compared against the existing report through a second online survey, with the resulting qualitative and quantitative data informing the final, redesigned, report. Results We recruited 78 participants, 65 of whom were clinicians, nurses, laboratorians, researchers, and epidemiologists involved in TB diagnosis, treatment, and/or surveillance. Our first survey indicated that participants were largely enthusiastic about genomic data, with the majority agreeing on its utility for certain TB diagnosis and treatment tasks and many reporting some confidence in their ability to interpret this type of data (between 58.8% and 94.1%, depending on the specific data type. When we compared our four prototype reports against the existing design, we found that for the majority (86.7% of

  7. Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory.

    Science.gov (United States)

    Crisan, Anamaria; McKee, Geoffrey; Munzner, Tamara; Gardy, Jennifer L

    2018-01-01

    Microbial genome sequencing is now being routinely used in many clinical and public health laboratories. Understanding how to report complex genomic test results to stakeholders who may have varying familiarity with genomics-including clinicians, laboratorians, epidemiologists, and researchers-is critical to the successful and sustainable implementation of this new technology; however, there are no evidence-based guidelines for designing such a report in the pathogen genomics domain. Here, we describe an iterative, human-centered approach to creating a report template for communicating tuberculosis (TB) genomic test results. We used Design Study Methodology-a human centered approach drawn from the information visualization domain-to redesign an existing clinical report. We used expert consults and an online questionnaire to discover various stakeholders' needs around the types of data and tasks related to TB that they encounter in their daily workflow. We also evaluated their perceptions of and familiarity with genomic data, as well as its utility at various clinical decision points. These data shaped the design of multiple prototype reports that were compared against the existing report through a second online survey, with the resulting qualitative and quantitative data informing the final, redesigned, report. We recruited 78 participants, 65 of whom were clinicians, nurses, laboratorians, researchers, and epidemiologists involved in TB diagnosis, treatment, and/or surveillance. Our first survey indicated that participants were largely enthusiastic about genomic data, with the majority agreeing on its utility for certain TB diagnosis and treatment tasks and many reporting some confidence in their ability to interpret this type of data (between 58.8% and 94.1%, depending on the specific data type). When we compared our four prototype reports against the existing design, we found that for the majority (86.7%) of design comparisons, participants preferred the

  8. Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein.

    Science.gov (United States)

    Schroeter, Elena R; DeHart, Caroline J; Cleland, Timothy P; Zheng, Wenxia; Thomas, Paul M; Kelleher, Neil L; Bern, Marshall; Schweitzer, Mary H

    2017-02-03

    Sequence data from biomolecules such as DNA and proteins, which provide critical information for evolutionary studies, have been assumed to be forever outside the reach of dinosaur paleontology. Proteins, which are predicted to have greater longevity than DNA, have been recovered from two nonavian dinosaurs, but these results remain controversial. For proteomic data derived from extinct Mesozoic organisms to reach their greatest potential for investigating questions of phylogeny and paleobiology, it must be shown that peptide sequences can be reliably and reproducibly obtained from fossils and that fragmentary sequences for ancient proteins can be increasingly expanded. To test the hypothesis that peptides can be repeatedly detected and validated from fossil tissues many millions of years old, we applied updated extraction methodology, high-resolution mass spectrometry, and bioinformatics analyses on a Brachylophosaurus canadensis specimen (MOR 2598) from which collagen I peptides were recovered in 2009. We recovered eight peptide sequences of collagen I: two identical to peptides recovered in 2009 and six new peptides. Phylogenetic analyses place the recovered sequences within basal archosauria. When only the new sequences are considered, B. canadensis is grouped more closely to crocodylians, but when all sequences (current and those reported in 2009) are analyzed, B. canadensis is placed more closely to basal birds. The data robustly support the hypothesis of an endogenous origin for these peptides, confirm the idea that peptides can survive in specimens tens of millions of years old, and bolster the validity of the 2009 study. Furthermore, the new data expand the coverage of B. canadensis collagen I (a 33.6% increase in collagen I alpha 1 and 116.7% in alpha 2). Finally, this study demonstrates the importance of reexamining previously studied specimens with updated methods and instrumentation, as we obtained roughly the same amount of sequence data as the

  9. Draft genome sequences of Escherichia coli O113:H21 strains recovered from a major produce-production region in California

    Science.gov (United States)

    Shiga toxin-producing Escherichia coli is a foodborne and waterborne pathogen and is responsible for outbreaks of human gastroenteritis. This report documents the draft genome sequences of seven O113:H21 strains recovered from livestock, wildlife, and soil samples collected in a major agricultural r...

  10. Geomorphic and geologic evidence for slip along the San Bernardino strand of the San Andreas Fault System through the San Gorgonio Pass structural knot, southern California

    Science.gov (United States)

    Kendrick, K. J.; Matti, J. C.

    2017-12-01

    The San Gorgonio Pass (SGP) region of southern California represents an extraordinarily complex section of the San Andreas Fault (SAF) zone, often referred to as a structural knot. Complexity is expressed both structurally and geomorphically, and arises because multiple strands of the SAF have evolved here in Quaternary time. Our integration of geologic and geomorphic analyses led to recognition of multiple fault-bounded blocks characterized by crystalline rocks that have similar physical properties. Hence, any morphometric differences in hypsometric analysis, slope, slope distribution, texture, and stream-power measurements and discontinuities reflect landscape response to tectonic processes rather than differences in lithology. We propose that the differing morphometry of the two blocks on either side of the San Bernardino strand (SBS) of the SAF, the high-standing Kitching Peak block to the east and the lower, more subdued Pisgah Peak block to the west, strongly suggests that the blocks experienced different uplift histories. This difference in uplift histories, in turn suggests that dextral slip occurred over a long time interval on the SBS—despite long-lived controversy raised by the fact that, at the surface, a throughgoing trace of the SBS is not present at this location. A different tectonic history between the two blocks is consistent with the gravity data which indicate that low-density rocks underthrusting the Kitching Peak block are absent below the Pisgah Peak block (Langenheim et al., 2015). Throughgoing slip on the SBS implied by geomorphic differences between the two blocks is also consistent with displaced geologic and geomorphic features. We find compelling evidence for discrete offsets of between 0.6 and 6 km of dextral slip on the SBS, including offset of fluvial and landslide deposits, and beheaded drainages. Although we lack numerical age control for the offset features, the degree of soil development associated with displaced landforms

  11. On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence

    Directory of Open Access Journals (Sweden)

    Theobald Douglas L

    2011-11-01

    Full Text Available Abstract Background The universal common ancestry (UCA of all known life is a fundamental component of modern evolutionary theory, supported by a wide range of qualitative molecular evidence. Nevertheless, recently both the status and nature of UCA has been questioned. In earlier work I presented a formal, quantitative test of UCA in which model selection criteria overwhelmingly choose common ancestry over independent ancestry, based on a dataset of universally conserved proteins. These model-based tests are founded in likelihoodist and Bayesian probability theory, in opposition to classical frequentist null hypothesis tests such as Karlin-Altschul E-values for sequence similarity. In a recent comment, Koonin and Wolf (K&W claim that the model preference for UCA is "a trivial consequence of significant sequence similarity". They support this claim with a computational simulation, derived from universally conserved proteins, which produces similar sequences lacking phylogenetic structure. The model selection tests prefer common ancestry for this artificial data set. Results For the real universal protein sequences, hierarchical phylogenetic structure (induced by genealogical history is the overriding reason for why the tests choose UCA; sequence similarity is a relatively minor factor. First, for cases of conflicting phylogenetic structure, the tests choose independent ancestry even with highly similar sequences. Second, certain models, like star trees and K&W's profile model (corresponding to their simulation, readily explain sequence similarity yet lack phylogenetic structure. However, these are extremely poor models for the real proteins, even worse than independent ancestry models, though they explain K&W's artificial data well. Finally, K&W's simulation is an implementation of a well-known phylogenetic model, and it produces sequences that mimic homologous proteins. Therefore the model selection tests work appropriately with the artificial

  12. Translating working memory into action: behavioral and neural evidence for using motor representations in encoding visuo-spatial sequences.

    Science.gov (United States)

    Langner, Robert; Sternkopf, Melanie A; Kellermann, Tanja S; Grefkes, Christian; Kurth, Florian; Schneider, Frank; Zilles, Karl; Eickhoff, Simon B

    2014-07-01

    The neurobiological organization of action-oriented working memory is not well understood. To elucidate the neural correlates of translating visuo-spatial stimulus sequences into delayed (memory-guided) sequential actions, we measured brain activity using functional magnetic resonance imaging while participants encoded sequences of four to seven dots appearing on fingers of a left or right schematic hand. After variable delays, sequences were to be reproduced with the corresponding fingers. Recall became less accurate with longer sequences and was initiated faster after long delays. Across both hands, encoding and recall activated bilateral prefrontal, premotor, superior and inferior parietal regions as well as the basal ganglia, whereas hand-specific activity was found (albeit to a lesser degree during encoding) in contralateral premotor, sensorimotor, and superior parietal cortex. Activation differences after long versus short delays were restricted to motor-related regions, indicating that rehearsal during long delays might have facilitated the conversion of the memorandum into concrete motor programs at recall. Furthermore, basal ganglia activity during encoding selectively predicted correct recall. Taken together, the results suggest that to-be-reproduced visuo-spatial sequences are encoded as prospective action representations (motor intentions), possibly in addition to retrospective sensory codes. Overall, our study supports and extends multi-component models of working memory, highlighting the notion that sensory input can be coded in multiple ways depending on what the memorandum is to be used for. Copyright © 2013 Wiley Periodicals, Inc.

  13. Molecular phylogeny of grey mullets (Teleostei: Mugilidae) in Greece: evidence from sequence analysis of mtDNA segments.

    Science.gov (United States)

    Papasotiropoulos, Vasilis; Klossa-Kilia, Elena; Alahiotis, Stamatis N; Kilias, George

    2007-08-01

    Mitochondrial DNA sequence analysis has been used to explore genetic differentiation and phylogenetic relationships among five species of the Mugilidae family, Mugil cephalus, Chelon labrosus, Liza aurata, Liza ramada, and Liza saliens. DNA was isolated from samples originating from the Messolongi Lagoon in Greece. Three mtDNA segments (12s rRNA, 16s rRNA, and CO I) were PCR amplified and sequenced. Sequencing analysis revealed that the greatest genetic differentiation was observed between M. cephalus and all the other species studied, while C. labrosus and L. aurata were the closest taxa. Dendrograms obtained by the neighbor-joining method and Bayesian inference analysis exhibited the same topology. According to this topology, M. cephalus is the most distinct species and the remaining taxa are clustered together, with C. labrosus and L. aurata forming a single group. The latter result brings into question the monophyletic origin of the genus Liza.

  14. No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution

    DEFF Research Database (Denmark)

    Workman, Christopher; Krogh, Anders Stærmose

    1999-01-01

    This work investigates whether mRNA has a lower estimated folding free energy than random sequences. The free energy estimates are calculated by the mfold program for prediction of RNA secondary structures. For a set of 46 mRNAs it is shown that the predicted free energy is not significantly diff...

  15. Evolution of R5 and X4 human immunodeficiency virus type 1 gag sequences in vivo: evidence for recombination

    International Nuclear Information System (INIS)

    Rij, Ronald P. van; Worobey, Michael; Visser, Janny A.; Schuitemaker, Hanneke

    2003-01-01

    Human immunodeficiency virus type 1 (HIV-1) infection is in general established by CCR5-utilizing (R5) virus variants, which persist throughout the course of infection. R5 HIV-1 variants evolve into CXCR4-utilizing (X4) HIV-1 variants in approximately half of the infected individuals. We have previously observed an ongoing genetic evolution with a continuous divergence of envelope gp120 sequences of coexisting R5 and X4 virus variants over time. Here, we studied evolution of gag p17 sequences in two patients who developed X4 variants in the course of infection. In contrast to the envelope gp120 sequences, gag p17 sequences of R5 and X4 virus populations intermingled in phylogenetic trees and did not diverge from each other over time. Statistical evaluation using the Shimodaira-Hasegawa test indicated that the different genomic regions evolved along different topologies, supporting the hypothesis of recombination. Therefore, our data imply that recombination between R5 and X4 HIV-1 variants occurs in vivo

  16. MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization

    Directory of Open Access Journals (Sweden)

    Kuczmarski Thomas A

    2006-10-01

    Full Text Available Abstract Background MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. Description MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. Conclusion MannDB comprises a large number of genomes and comprehensive protein

  17. Evidence of Alternative Cystatin C Signal Sequence Cleavage Which Is Influenced by the A25T Polymorphism.

    Directory of Open Access Journals (Sweden)

    Annie Nguyen

    Full Text Available Cystatin C (Cys C is a small, potent, cysteine protease inhibitor. An Ala25Thr (A25T polymorphism in Cys C has been associated with both macular degeneration and late-onset Alzheimer's disease. Previously, studies have suggested that this polymorphism may compromise the secretion of Cys C. Interestingly, we found that untagged A25T, A25T tagged C-terminally with FLAG, or A25T FLAG followed by green fluorescent protein (GFP, were all secreted as efficiently from immortalized human cells as their wild-type (WT counterparts (e.g., 112%, 100%, and 88% of WT levels from HEK-293T cells, respectively. Supporting these observations, WT and A25T Cys C variants also showed similar intracellular steady state levels. Furthermore, A25T Cys C did not activate the unfolded protein response and followed the same canonical endoplasmic reticulum (ER-Golgi trafficking pathway as WT Cys C. WT Cys C has been shown to undergo signal sequence cleavage between residues Gly26 and Ser27. While the A25T polymorphism did not affect Cys C secretion, we hypothesized that it may alter where the Cys C signal sequence is preferentially cleaved. Under normal conditions, WT and A25T Cys C have the same signal sequence cleavage site after Gly26 (referred to as 'site 2' cleavage. However, in particular circumstances when the residues around site 2 are modified (such as by the presence of an N-terminal FLAG tag immediately after Gly26, or by a Gly26Lys (G26K mutation, A25T has a significantly higher likelihood than WT Cys C of alternative signal sequence cleavage after Ala20 ('site 1' or even earlier in the Cys C sequence. Overall, our results indicate that the A25T polymorphism does not cause a significant reduction in Cys C secretion, but instead predisposes the protein to be cleaved at an alternative signal sequence cleavage site if site 2 is hindered. Additional N-terminal amino acids resulting from alternative signal sequence cleavage may, in turn, affect the protease

  18. Impact of participation in the California Healthcare-Associated Infection Prevention Initiative on adoption and implementation of evidence-based practices for patient safety and health care-associated infection rates in a cohort of acute care general hospitals.

    Science.gov (United States)

    Halpin, Helen Ann; McMenamin, Sara B; Simon, Lisa Payne; Jacobsen, Diane; Vanneman, Megan; Shortell, Stephen; Milstein, Arnold

    2013-04-01

    In 2008, hospitals were selected to participate in the California Healthcare-Associated Infection Prevention Initiative (CHAIPI). This research evaluates the impact of CHAIPI on hospital adoption and implementation of evidence-based patient safety practices and reduction of health care-associated infection (HAI) rates. Statewide computer-assisted telephone surveys of California's general acute care hospitals were conducted in 2008 and 2010 (response rates, 80% and 76%, respectively). Difference-in-difference analyses were used to compare changes in process and HAI rate outcomes in CHAIPI hospitals (n = 34) and non-CHAIPI hospitals (n = 149) that responded to both waves of the survey. Compared with non-CHAIPI hospitals, CHAIPI hospitals demonstrated greater improvements between 2008 and 2010 in adoption (P = .021) and implementation (P = .012) of written evidence-based practices for overall patient safety and prevention of HAIs and in assessing their compliance (P = .033) with these practices. However, there were no significant differences in the changes in HAI rates between CHAIPI and non-CHAIPI hospitals over this time period. Participation in the CHAIPI collaborative was associated with significant improvements in evidence-based patient safety practices in hospitals. However, determining how evidence-based practices translate into changes in HAI rates may take more time. Our results suggest that all hospitals be offered the opportunity to participate in an active learning collaborative to improve patient safety. Copyright © 2013 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Mosby, Inc. All rights reserved.

  19. Seismic reflection-based evidence of a transfer zone between the Wagner and Consag basins: implications for defining the structural geometry of the northern Gulf of California

    Science.gov (United States)

    González-Escobar, Mario; Suárez-Vidal, Francisco; Hernández-Pérez, José Antonio; Martín-Barajas, Arturo

    2010-12-01

    This study examines the structural characteristics of the northern Gulf of California by processing and interpreting ca. 415 km of two-dimensional multi-channel seismic reflection lines (data property of Petróleos Mexicanos PEMEX) collected in the vicinity of the border between the Wagner and Consag basins. The two basins appear to be a link between the Delfín Superior Basin to the south, and the Cerro Prieto Basin to the north in the Mexicali-Imperial Valley along the Pacific-North America plate boundary. The seismic data are consistent with existing knowledge of four main structures (master faults) in the region, i.e., the Percebo, Santa María, Consag Sur, and Wagner Sur faults. The Wagner and Consag basins are delimited to the east by the Wagner Sur Fault, and to the west by the Consag Sur Fault. The Percebo Fault borders the western margin of the modern Wagner Basin depocenter, and is oriented N10°W, dipping (on average) ˜40° to the northeast. The trace of the Santa María Fault located in the Wagner Basin strikes N19°W, dipping ˜40° to the west. The Consag Sur Fault is oriented N14°W, and dips ˜42° to the east over a distance of 21 km. To the east of the study area, the Wagner Sur Fault almost parallels the Consag Sur Fault over a distance of ˜86 km, and is oriented N10°W with an average dip of 59° to the east. Moreover, the data provide new evidence that the Wagner Fault is discontinuous between the two basins, and that its structure is more complex than previously reported. A structural high separates the northern Consag Basin from the southern Wagner Basin, comprising several secondary faults oriented NE oblique to the main faults of N-S direction. These could represent a zone of accommodation, or transfer zone, where extension could be transferred from the Wagner to the Consag Basin, or vice versa. This area shows no acoustic basement and/or intrusive body, which is consistent with existing gravimetric and magnetic data for the region.

  20. Stratigraphy and paleogeographic significance of a Late Pennsylvanian to Early Permian channeled slope sequence in the Darwin Basin, southern Darwin Hills, east-central California

    Science.gov (United States)

    Stevens, Calvin H.; Stone, Paul; Magginetti, Robert T.; Ritter, Scott M.

    2015-01-01

    The complex stratigraphy of late Paleozoic rocks in the southern Darwin Hills consists of regionally extensive Mississippian and Early to Middle Pennsylvanian rocks overlain by latest Pennsylvanian to Early Permian rocks, herein called the Darwin Hills sequence. Deposition of this latter sequence marked the beginning of the Darwin Basin. In Mississippian time, a carbonate platform prograded westward over slightly older slope deposits. In the Late Mississippian this platform was exposed to erosion and siliciclastic sediments were deposited. In Early to Middle Pennsylvanian time the area subsided, forming a west-facing ramp that was subjected to deformation and erosion in Middle or early Late Pennsylvanian time. Later this area was tilted westward and deep-water sediments were deposited on this slope. In latest Pennsylvanian to earliest Permian time, a major channel was cut through the older Pennsylvanian rocks and into the Upper Mississippian strata. This channel was gradually filled with increasingly finer grained, deep-water sediment as the area evolved into a basin floor by Early Permian (Sakmarian) time. Expansion of the Darwin Basin in Artinskian time led to a second phase of deposition represented by strata of the regionally extensive Darwin Canyon Formation. The geology in this small area thus documents tectonic events occurring during the early development of the Darwin Basin.

  1. Synergy temporal sequences and topography in the spinal cord: evidence for a traveling wave in frog locomotion.

    Science.gov (United States)

    Saltiel, Philippe; d'Avella, Andrea; Wyler-Duda, Kuno; Bizzi, Emilio

    2016-11-01

    Locomotion is produced by a central pattern generator. Its spinal cord organization is generally considered to be distributed, with more rhythmogenic rostral lumbar segments. While this produces a rostrocaudally traveling wave in undulating species, this is not thought to occur in limbed vertebrates, with the exception of the interneuronal traveling wave demonstrated in fictive cat scratching (Cuellar et al. J Neurosci 29:798-810, 2009). Here, we reexamine this hypothesis in the frog, using the seven muscle synergies A to G previously identified with intraspinal NMDA (Saltiel et al. J Neurophysiol 85:605-619, 2001). We find that locomotion consists of a sequence of synergy activations (A-B-G-A-F-E-G). The same sequence is observed when focal NMDA iontophoresis in the spinal cord elicits a caudal extension-lateral force-flexion cycle (flexion onset without the C synergy). Examining the early NMDA-evoked motor output at 110 sites reveals a rostrocaudal topographic organization of synergy encoding by the lumbar cord. Each synergy is preferentially activated from distinct regions, which may be multiple, and partially overlap between different synergies. Comparing the sequence of synergy activation in locomotion with their spinal cord topography suggests that the locomotor output is achieved by a rostrocaudally traveling wave of activation in the swing-stance cycle. A two-layer circuitry model, based on this topography and a traveling wave reproduces this output and explores its possible modifications under different afferent inputs. Our results and simulations suggest that a rostrocaudally traveling wave of excitation takes advantage of the topography of interneuronal regions encoding synergies, to activate them in the proper sequence for locomotion.

  2. Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein

    OpenAIRE

    Schroeter, Elena R.; DeHart, Caroline J.; Cleland, Timothy P.; Zheng, Wenxia; Thomas, Paul M.; Kelleher, Neil L.; Bern, Marshall; Schweitzer, Mary H.

    2017-01-01

    Sequence data from biomolecules such as DNA and proteins, which provide critical information for evolutionary studies, have been assumed to be forever outside the reach of dinosaur paleontology. Proteins, which are predicted to have greater longevity than DNA, have been recovered from two nonavian dinosaurs, but these results remain controversial. For proteomic data derived from extinct Mesozoic organisms to reach their greatest potential for investigating questions of phylogeny and paleobiol...

  3. Tertiary montane origin of the Central Asian flora, evidence inferred from cpDNA sequences of Atraphaxis (Polygonaceae)

    Science.gov (United States)

    Ming-Li Zhang; Stewart C. Sanderson; Yan-Xia Sun; Byalt V. Vyacheslav; Xiao-Li Hao

    2014-01-01

    Atraphaxis has approximately 25 species and a distribution center in Central Asia. It has been previously used to hypothesize an origin from montane forest. We sampled 18 species covering three sections within the genus and sequenced five cpDNA spacers, atpB-rbcL, psbK-psbI, psbAtrnH, rbcL, and trnL-trnF. BEAST was used to reconstruct phylogenetic relationship and time...

  4. District Allocation of Human Resources Utilizing the Evidence Based Model: A Study of One High Achieving School District in Southern California

    Science.gov (United States)

    Lane, Amber Marie

    2013-01-01

    This study applies the Gap Analysis Framework to understand the gaps that exist in human resource allocation of one Southern California school district. Once identified, gaps are closed with the reallocation of human resources, according to the Evidenced Based Model, requiring the re-purposing of core classroom teachers, specialists, special…

  5. Evidence for divergence in cuticular hydrocarbon sex pheromone between California and Mississippi (United States of America) populations of bark beetle parasitoid Roptrocerus xylophagorum (Hymenoptera: Pteromalidae).

    Science.gov (United States)

    Brian Sullivan; Nadir Erbilgin

    2014-01-01

    Roptrocerus xylophagorum (Ratzeburg) (Hymenoptera: Pteromalidae) is a common Holarctic parasitoid of the larvae and pupae of bark beetles (Coleoptera: Curculionidae: Scotytinae). In no-choice laboratory bioassays, we found that male wasps derived either from northern California or southwestern Mississippi, United States of America more frequently displayed sexual...

  6. A paleomagnetic investigation of vertical-axis rotations in coastal Sonora, Mexico: Evidence for distributed transtensional deformation during the Proto-Gulf shift from a subduction-dominated to transform-dominated plate boundary in the Gulf of California

    Science.gov (United States)

    Herman, Scott William

    The history of late Miocene (Proto-Gulf) deformation on the Sonoran margin of the Gulf of California is key to understanding how Baja California was captured by the Pacific plate and how strain was partitioned during the Proto-Gulf period (12.5-6 Ma). The Sierra el Aguaje and Sierra Tinajas del Carmen are located in southwestern coastal Sonora, Mexico, and represent the eastern rifted margin of the central Gulf of California. The ranges are composed of volcanic units and their corresponding volcaniclastic units which are the result of persistent magmatic activity between 20 and 8.8 Ma, including three packages of basalt and andesite that make excellent paleomagnetic recorders. Based on cross cutting relations and geochronologic data for pre-, syn-, and post-tectonic volcanic units, most of the faulting and tilting in the Sierra El Aguaje is bracketed between 11.9 and 9.0 Ma, thus falling entirely within Proto-Gulf time. A paleomagnetic investigation into possible vertical axis rotations in the Sierra el Aguaje has uncovered evidence of clockwise rotations between ~13º and ~105º with possible translations. These results are consistent with existing field relations, which suggest the presence of large (>45°) vertical axis rotations in this region. This evidence includes: a) abrupt changes in the strike of tilted strata in different parts of the range, including large domains characterized by E-W strikes b) ubiquitous NE-SW striking faults with left lateral-normal oblique slip, that terminate against major NW-trending right lateral faults, and c) obliquity between the general strike of tilted strata and the strike of faults. These rotations occurred after 12 Ma and largely prior to 9 Ma, thus falling into the Proto-Gulf period. Such large-scale rotations lend credence to the theory that the area inboard of Baja California was experiencing transtension during the Proto-Gulf period, rather than the pure extension that would be the result of strain partitioning

  7. Complete Genome Sequence of Yersinis pestis Strains Antiqua and Nepa1516: Evidence of Gene Reduction in an Emerging Pathogen

    Energy Technology Data Exchange (ETDEWEB)

    Chain, Patrick S [ORNL; Hu, Ping [Lawrence Berkeley National Laboratory (LBNL); Malfatti, Stephanie [Lawrence Livermore National Laboratory (LLNL); Radnedge, Lyndsay [Lawrence Livermore National Laboratory (LLNL); Larimer, Frank W [ORNL; Vergez, Lisa [Lawrence Livermore National Laboratory (LLNL); Worsham, Patricia [U.S. Army Medical Research Institute of Infectious Diseases; Chu, May C [Centers for Disease Control and Prevention; Anderson, Gary L [Lawrence Berkeley National Laboratory (LBNL)

    2006-01-01

    Yersinia pestis, the causative agent of bubonic and pneumonic plagues, has undergone detailed study at the molecular level. To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the ''classical'' antiqua biovar, strains Antiqua and Nepal516. The genomes of Antiqua and Nepal516 are 4.7 Mb and 4.5 Mb and encode 4,138 and 3,956 open reading frames, respectively. Though both strains belong to one of the three classical biovars, they represent separate lineages defined by recent phylogenetic studies. We compare all five currently sequenced Y. pestis genomes and the corresponding features in Yersinia pseudotuberculosis. There are strain-specific rearrangements, insertions, deletions, single nucleotide polymorphisms, and a unique distribution of insertion sequences. We found 453 single nucleotide polymorphisms in protein-coding regions, which were used to assess the evolutionary relationships of these Y. pestis strains. Gene reduction analysis revealed that the gene deletion processes are under selective pressure, and many of the inactivations are probably related to the organism's interaction with its host environment. The results presented here clearly demonstrate the differences between the two biovar antiqua lineages and support the notion that grouping Y. pestis strains based strictly on the classical definition of biovars (predicated upon two biochemical assays) does not accurately reflect the phylogenetic relationships within this species. A comparison of four virulent Y. pestis strains with the human-avirulent strain 91001 provides further insight into the genetic basis of virulence to humans.

  8. The Complete Genome Sequence of Herpesvirus Papio 2 (Cercopithecine Herpesvirus 16) Shows Evidence of Recombination Events among Various Progenitor Herpesviruses†

    Science.gov (United States)

    Tyler, Shaun D.; Severini, Alberto

    2006-01-01

    We have sequenced the entire genome of herpesvirus papio 2 (HVP-2; Cercopithecine herpesvirus 16) strain X313, a baboon herpesvirus with close homology to other primate alphaherpesviruses, such as SA8, monkey B virus, and herpes simplex virus (HSV) type 1 and type 2. The genome of HVP-2 is 156,487 bp in length, with an overall GC content of 76.5%. The genome organization is identical to that of the other members of the genus Simplexvirus, with a long and a short unique region, each bordered by inverted repeats which end with an “a” sequence. All of the open reading frames detected in this genome were homologous and colinear with those of SA8 and B virus. The HSV gene RL1 (γ134.5; neurovirulence factor) is not present in HVP-2, as is the case for SA8 and B virus. The HVP-2 genome is 85% homologous to its closest relative, SA8. However, segment-by-segment bootstrap analysis of the genome revealed at least two regions that display closer homology to the corresponding sequences of B virus. The first region comprises the UL41 to UL44 genes, and the second region is located within the UL36 gene. We hypothesize that this localized and defined shift in homology is due to recombination events between an SA8-like progenitor of HVP-2 and a herpesvirus species more closely related to the B virus. Since some of the genes involved in these putative recombination events are determinants of virulence, a comparative analysis of their function may provide insight into the pathogenic mechanism of simplexviruses. PMID:16414998

  9. The complete genome sequence of herpesvirus papio 2 (Cercopithecine herpesvirus 16) shows evidence of recombination events among various progenitor herpesviruses.

    Science.gov (United States)

    Tyler, Shaun D; Severini, Alberto

    2006-02-01

    We have sequenced the entire genome of herpesvirus papio 2 (HVP-2; Cercopithecine herpesvirus 16) strain X313, a baboon herpesvirus with close homology to other primate alphaherpesviruses, such as SA8, monkey B virus, and herpes simplex virus (HSV) type 1 and type 2. The genome of HVP-2 is 156,487 bp in length, with an overall GC content of 76.5%. The genome organization is identical to that of the other members of the genus Simplexvirus, with a long and a short unique region, each bordered by inverted repeats which end with an "a" sequence. All of the open reading frames detected in this genome were homologous and colinear with those of SA8 and B virus. The HSV gene RL1 (gamma(1)34.5; neurovirulence factor) is not present in HVP-2, as is the case for SA8 and B virus. The HVP-2 genome is 85% homologous to its closest relative, SA8. However, segment-by-segment bootstrap analysis of the genome revealed at least two regions that display closer homology to the corresponding sequences of B virus. The first region comprises the UL41 to UL44 genes, and the second region is located within the UL36 gene. We hypothesize that this localized and defined shift in homology is due to recombination events between an SA8-like progenitor of HVP-2 and a herpesvirus species more closely related to the B virus. Since some of the genes involved in these putative recombination events are determinants of virulence, a comparative analysis of their function may provide insight into the pathogenic mechanism of simplexviruses.

  10. Selectivity by host plants affects the distribution of arbuscular mycorrhizal fungi: evidence from ITS rDNA sequence metadata

    Directory of Open Access Journals (Sweden)

    Yang Haishui

    2012-04-01

    Full Text Available Abstract Background Arbuscular mycorrhizal fungi (AMF can form obligate symbioses with the vast majority of land plants, and AMF distribution patterns have received increasing attention from researchers. At the local scale, the distribution of AMF is well documented. Studies at large scales, however, are limited because intensive sampling is difficult. Here, we used ITS rDNA sequence metadata obtained from public databases to study the distribution of AMF at continental and global scales. We also used these sequence metadata to investigate whether host plant is the main factor that affects the distribution of AMF at large scales. Results We defined 305 ITS virtual taxa (ITS-VTs among all sequences of the Glomeromycota by using a comprehensive maximum likelihood phylogenetic analysis. Each host taxonomic order averaged about 53% specific ITS-VTs, and approximately 60% of the ITS-VTs were host specific. Those ITS-VTs with wide host range showed wide geographic distribution. Most ITS-VTs occurred in only one type of host functional group. The distributions of most ITS-VTs were limited across ecosystem, across continent, across biogeographical realm, and across climatic zone. Non-metric multidimensional scaling analysis (NMDS showed that AMF community composition differed among functional groups of hosts, and among ecosystem, continent, biogeographical realm, and climatic zone. The Mantel test showed that AMF community composition was significantly correlated with plant community composition among ecosystem, among continent, among biogeographical realm, and among climatic zone. The structural equation modeling (SEM showed that the effects of ecosystem, continent, biogeographical realm, and climatic zone were mainly indirect on AMF distribution, but plant had strongly direct effects on AMF. Conclusion The distribution of AMF as indicated by ITS rDNA sequences showed a pattern of high endemism at large scales. This pattern indicates high specificity

  11. Selectivity by host plants affects the distribution of arbuscular mycorrhizal fungi: evidence from ITS rDNA sequence metadata.

    Science.gov (United States)

    Yang, Haishui; Zang, Yanyan; Yuan, Yongge; Tang, Jianjun; Chen, Xin

    2012-04-12

    Arbuscular mycorrhizal fungi (AMF) can form obligate symbioses with the vast majority of land plants, and AMF distribution patterns have received increasing attention from researchers. At the local scale, the distribution of AMF is well documented. Studies at large scales, however, are limited because intensive sampling is difficult. Here, we used ITS rDNA sequence metadata obtained from public databases to study the distribution of AMF at continental and global scales. We also used these sequence metadata to investigate whether host plant is the main factor that affects the distribution of AMF at large scales. We defined 305 ITS virtual taxa (ITS-VTs) among all sequences of the Glomeromycota by using a comprehensive maximum likelihood phylogenetic analysis. Each host taxonomic order averaged about 53% specific ITS-VTs, and approximately 60% of the ITS-VTs were host specific. Those ITS-VTs with wide host range showed wide geographic distribution. Most ITS-VTs occurred in only one type of host functional group. The distributions of most ITS-VTs were limited across ecosystem, across continent, across biogeographical realm, and across climatic zone. Non-metric multidimensional scaling analysis (NMDS) showed that AMF community composition differed among functional groups of hosts, and among ecosystem, continent, biogeographical realm, and climatic zone. The Mantel test showed that AMF community composition was significantly correlated with plant community composition among ecosystem, among continent, among biogeographical realm, and among climatic zone. The structural equation modeling (SEM) showed that the effects of ecosystem, continent, biogeographical realm, and climatic zone were mainly indirect on AMF distribution, but plant had strongly direct effects on AMF. The distribution of AMF as indicated by ITS rDNA sequences showed a pattern of high endemism at large scales. This pattern indicates high specificity of AMF for host at different scales (plant taxonomic

  12. Phylogenetic analyses of the polyprotein coding sequences of serotype O foot-and-mouth disease viruses in East Africa: evidence for interserotypic recombination

    DEFF Research Database (Denmark)

    Balinda, Sheila; Siegismund, Hans; Muwanika, Vincent

    2010-01-01

    from both serotypes A and O. Conclusions Sequences of the VP1 coding region from recent serotype O FMDVs from Kenya and Uganda are all representatives of a specific East African lineage (topotype EA-2), a probable indication that hardly any FMD introductions of this serotype have occurred from outside...... the region in the recent past. Furthermore, evidence for interserotypic recombination, within the non-structural protein coding regions, between FMDVs of serotypes A and O has been obtained. In addition to characterization using the VP1 coding region, analyses involving the non-structural protein coding...

  13. Stress diffusion along the san andreas fault at parkfield, california.

    Science.gov (United States)

    Malin, P E; Alvarez, M G

    1992-05-15

    Beginning in January 1990, the epicenters of microearthquakes associated with a 12-month increase in seismicity near Parkfield, California, moved northwest to southeast along the San Andreas fault. During this sequence of events, the locally variable rate of cumulative seismic moment increased. This increase implies a local increase in fault slip. These data suggest that a southeastwardly diffusing stress front propagated along the San Andreas fault at a speed of 30 to 50 kilometers per year. Evidently, this front did not load the Parkfield asperities fast enough to produce a moderate earthquake; however, a future front might do so.

  14. Dynamics of delayed triggering in multi-segmented foreshock sequence: Evidence from the 2016 Kumamoto, Japan, earthquake

    Science.gov (United States)

    Arai, H.; Ando, R.; Aoki, Y.

    2017-12-01

    The 2016 Kumamoto earthquake sequence hit the SW Japan, from April 14th to 16th and its sequence includes two M6-class foreshocks and the main shock (Mw 7.0). Importantly, the detailed surface displacement caused solely by the two foreshocks could be captured by a SAR observation isolated from the mainshock deformation. The foreshocks ruptured the previously mapped Hinagu fault and their hypocentral locations and the aftershock distribution indicates the involvement of two different subparallel faults. Therefore we assumed that the 1st and the 2nd foreshocks respectively ruptured each of the subparallel faults (faults A and B). One of the interesting points of this earthquake is that the two major foreshocks had a temporal gap of 2.5 hours even though the fault A and B are quite close by each other. This suggests that the stress perturbation due to the 1st foreshock is not large enough to trigger the 2nd one right away but that it's large enough to bring about the following earthquake after a delay time.We aim to reproduce the foreshock sequence such as rupture jumping over the subparallel faults by using dynamic rupture simulations. We employed a spatiotemporal-boundary integral equation method accelerated by the Fast Domain Partitioning Method (Ando, 2016, GJI) since this method allows us to construct a complex fault geometry in 3D media. Our model has two faults and a free ground surface. We conducted rupture simulation with various sets of parameters to identify the optimal condition describing the observation.Our simulation results are roughly categorized into 3 cases with regard to the criticality for the rupture jumping. The case 1 (supercritical case) shows the fault A and B ruptured consecutively without any temporal gap. In the case 2 (nearly critical), the rupture on the fault B started with a temporal gap after the fault A finished rupturing, which is what we expected as a reproduction. In the case 3 (subcritical), only the fault A ruptured and its

  15. Succession of earthquakes in the Ebro Delta. A sequence to research pupils’ ideas and the prac tice of using evidence

    Directory of Open Access Journals (Sweden)

    Blanca Puig Mauriz

    2015-01-01

    Full Text Available A “socially live” issue related to Geology is dealt with: the controversy surrounding the succession of earthquakes in the Ebro Delta (Spain. This article examines both students’ ideas about earthquakes and the practice of using evidence in the context of choosing a causal explanation of Delta’s earthquakes. The study is part of the researches on reasoning about socioscientific issues in Geology. Three groups are involved: one belonging to CSE 4th grade (students aged from 16 to 17 and two to baccalaureate 1st grade (aged from 17 to 18. The results indicate that most of students understand an earthquake as a common phenomenon, and relate it exclusively to the tectonics plates. Regarding the controversy of Ebro Delta most choose as the cause of earthquakes the combination of natural causes and human activity, and focus on building an explanation, rather than justify their choice based on evidence.

  16. Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing.

    Science.gov (United States)

    Jeong, Hyeonsoo; Song, Ki-Duk; Seo, Minseok; Caetano-Anollés, Kelsey; Kim, Jaemin; Kwak, Woori; Oh, Jae-Don; Kim, EuiSoo; Jeong, Dong Kee; Cho, Seoae; Kim, Heebal; Lee, Hak-Kyo

    2015-08-20

    Natural and artificial selection following domestication has led to the existence of more than a hundred pig breeds, as well as incredible variation in phenotypic traits. Berkshire pigs are regarded as having superior meat quality compared to other breeds. As the meat production industry seeks selective breeding approaches to improve profitable traits such as meat quality, information about genetic determinants of these traits is in high demand. However, most of the studies have been performed using trained sensory panel analysis without investigating the underlying genetic factors. Here we investigate the relationship between genomic composition and this phenotypic trait by scanning for signatures of positive selection in whole-genome sequencing data. We generated genomes of 10 Berkshire pigs at a total of 100.6 coverage depth, using the Illumina Hiseq2000 platform. Along with the genomes of 11 Landrace and 13 Yorkshire pigs, we identified genomic variants of 18.9 million SNVs and 3.4 million Indels in the mapped regions. We identified several associated genes related to lipid metabolism, intramuscular fatty acid deposition, and muscle fiber type which attribute to pork quality (TG, FABP1, AKIRIN2, GLP2R, TGFBR3, JPH3, ICAM2, and ERN1) by applying between population statistical tests (XP-EHH and XP-CLR). A statistical enrichment test was also conducted to detect breed specific genetic variation. In addition, de novo short sequence read assembly strategy identified several candidate genes (SLC25A14, IGF1, PI4KA, CACNA1A) as also contributing to lipid metabolism. Results revealed several candidate genes involved in Berkshire meat quality; most of these genes are involved in lipid metabolism and intramuscular fat deposition. These results can provide a basis for future research on the genomic characteristics of Berkshire pigs.

  17. Evidence for Human Fronto-Central Gamma Activity during Long-Term Memory Encoding of Word Sequences

    Science.gov (United States)

    Meeuwissen, Esther Berendina; Takashima, Atsuko; Fernández, Guillén; Jensen, Ole

    2011-01-01

    Although human gamma activity (30–80 Hz) associated with visual processing is often reported, it is not clear to what extend gamma activity can be reliably detected non-invasively from frontal areas during complex cognitive tasks such as long term memory (LTM) formation. We conducted a memory experiment composed of 35 blocks each having three parts: LTM encoding, working memory (WM) maintenance and LTM retrieval. In the LTM encoding and WM maintenance parts, participants had to respectively encode or maintain the order of three sequentially presented words. During LTM retrieval subjects had to reproduce these sequences. Using magnetoencephalography (MEG) we identified significant differences in the gamma and beta activity. Robust gamma activity (55–65 Hz) in left BA6 (supplementary motor area (SMA)/pre-SMA) was stronger during LTM rehearsal than during WM maintenance. The gamma activity was sustained throughout the 3.4 s rehearsal period during which a fixation cross was presented. Importantly, the difference in gamma band activity correlated with memory performance over subjects. Further we observed a weak gamma power difference in left BA6 during the first half of the LTM rehearsal interval larger for successfully than unsuccessfully reproduced word triplets. In the beta band, we found a power decrease in left anterior regions during LTM rehearsal compared to WM maintenance. Also this suppression of beta power correlated with memory performance over subjects. Our findings show that an extended network of brain areas, characterized by oscillatory activity in different frequency bands, supports the encoding of word sequences in LTM. Gamma band activity in BA6 possibly reflects memory processes associated with language and timing, and suppression of beta activity at left frontal sensors is likely to reflect the release of inhibition directly associated with the engagement of language functions. PMID:21738641

  18. Evidence for human fronto-central gamma activity during long-term memory encoding of word sequences.

    Directory of Open Access Journals (Sweden)

    Esther Berendina Meeuwissen

    Full Text Available Although human gamma activity (30-80 Hz associated with visual processing is often reported, it is not clear to what extend gamma activity can be reliably detected non-invasively from frontal areas during complex cognitive tasks such as long term memory (LTM formation. We conducted a memory experiment composed of 35 blocks each having three parts: LTM encoding, working memory (WM maintenance and LTM retrieval. In the LTM encoding and WM maintenance parts, participants had to respectively encode or maintain the order of three sequentially presented words. During LTM retrieval subjects had to reproduce these sequences. Using magnetoencephalography (MEG we identified significant differences in the gamma and beta activity. Robust gamma activity (55-65 Hz in left BA6 (supplementary motor area (SMA/pre-SMA was stronger during LTM rehearsal than during WM maintenance. The gamma activity was sustained throughout the 3.4 s rehearsal period during which a fixation cross was presented. Importantly, the difference in gamma band activity correlated with memory performance over subjects. Further we observed a weak gamma power difference in left BA6 during the first half of the LTM rehearsal interval larger for successfully than unsuccessfully reproduced word triplets. In the beta band, we found a power decrease in left anterior regions during LTM rehearsal compared to WM maintenance. Also this suppression of beta power correlated with memory performance over subjects. Our findings show that an extended network of brain areas, characterized by oscillatory activity in different frequency bands, supports the encoding of word sequences in LTM. Gamma band activity in BA6 possibly reflects memory processes associated with language and timing, and suppression of beta activity at left frontal sensors is likely to reflect the release of inhibition directly associated with the engagement of language functions.

  19. California mild CTV strains that break resistance in Trifoliate Orange

    Science.gov (United States)

    This is the final report of a project to characterize California isolates of Citrus tristeza virus (CTV) that replicate in Poncirus trifoliata (trifoliate orange). Next Generation Sequencing (NGS) of viral small interfering RNAs (siRNAs) and assembly of full-length sequences of mild California CTV i...

  20. Constraints on the rheology of the lower crust in a strike-slip plate boundary: evidence from the San Quintín xenoliths, Baja California, Mexico

    Science.gov (United States)

    van der Werf, Thomas; Chatzaras, Vasileios; Marcel Kriegsman, Leo; Kronenberg, Andreas; Tikoff, Basil; Drury, Martyn R.

    2017-12-01

    The rheology of lower crust and its transient behavior in active strike-slip plate boundaries remain poorly understood. To address this issue, we analyzed a suite of granulite and lherzolite xenoliths from the upper Pleistocene-Holocene San Quintín volcanic field of northern Baja California, Mexico. The San Quintín volcanic field is located 20 km east of the Baja California shear zone, which accommodates the relative movement between the Pacific plate and Baja California microplate. The development of a strong foliation in both the mafic granulites and lherzolites, suggests that a lithospheric-scale shear zone exists beneath the San Quintín volcanic field. Combining microstructural observations, geothermometry, and phase equilibria modeling, we estimated that crystal-plastic deformation took place at temperatures of 750-890 °C and pressures of 400-560 MPa, corresponding to 15-22 km depth. A hot crustal geotherm of 40 ° C km-1 is required to explain the estimated deformation conditions. Infrared spectroscopy shows that plagioclase in the mafic granulites is relatively dry. Microstructures are interpreted to show that deformation in both the uppermost lower crust and upper mantle was accommodated by a combination of dislocation creep and grain-size-sensitive creep. Recrystallized grain size paleopiezometry yields low differential stresses of 12-33 and 17 MPa for plagioclase and olivine, respectively. The lower range of stresses (12-17 MPa) in the mafic granulite and lherzolite xenoliths is interpreted to be associated with transient deformation under decreasing stress conditions, following an event of stress increase. Using flow laws for dry plagioclase, we estimated a low viscosity of 1.1-1.3×1020 Pa ṡ s for the high temperature conditions (890 °C) in the lower crust. Significantly lower viscosities in the range of 1016-1019 Pa ṡ s, were estimated using flow laws for wet plagioclase. The shallow upper mantle has a low viscosity of 5.7×1019 Pa ṡ s

  1. Sequence variation of functional HTLV-II tax alleles among isolates from an endemic population: lack of evidence for oncogenic determinant in tax.

    Science.gov (United States)

    Hjelle, B; Chaney, R

    1992-02-01

    Human T-cell leukemia-lymphoma virus type II (HTLV-II) has been isolated from patients with hairy cell leukemia (HCL). We previously described a population with longstanding endemic HTLV-II infection, and showed that there is no increased risk for HCL in the affected groups. We thus have direct evidence that the endemic form(s) of HTLV-II cause HCL infrequently, if at all. By comparison, there is reason to suspect that the viruses isolated from patients with HCL had an etiologic role in the disease in those patients. One way to reconcile these conflicting observations is to consider that isolates of HTLV-II might differ in oncogenic potential. To determine whether the structure of the putative oncogenic determinant of HTLV-II, tax2, might differ in the new isolates compared to the tax of the prototype HCL isolate, MO, four new functional tax cDNAs were cloned from new isolates. Sequence analysis showed only minor (0.9-2.0%) amino acid variation compared to the published sequence of MO tax2. Some codons were consistently different from published sequences of the MO virus, but in most cases, such variations were also found in each of two tax2 clones we isolated from the MO T-cell line. These variations rendered the new clones more similar to the tax1 of the pathogenic virus HTLV-I. Thus we find no evidence that pathologic determinants of HTLV-II can be assigned to the tax gene.

  2. Less frequently mutated genes in colorectal cancer: evidences from next-generation sequencing of 653 routine cases.

    Science.gov (United States)

    Malapelle, Umberto; Pisapia, Pasquale; Sgariglia, Roberta; Vigliar, Elena; Biglietto, Maria; Carlomagno, Chiara; Giuffrè, Giuseppe; Bellevicine, Claudio; Troncone, Giancarlo

    2016-09-01

    The incidence of RAS/RAF/PI3KA and TP53 gene mutations in colorectal cancer (CRC) is well established. Less information, however, is available on other components of the CRC genomic landscape, which are potential CRC prognostic/predictive markers. Following a previous validation study, ion-semiconductor next-generation sequencing (NGS) was employed to process 653 routine CRC samples by a multiplex PCR targeting 91 hotspot regions in 22 CRC significant genes. A total of 796 somatic mutations in 499 (76.4%) tumours were detected. Besides RAS/RAF/PI3KA and TP53, other 12 genes showed at least one mutation including FBXW7 (6%), PTEN (2.8%), SMAD4 (2.1%), EGFR (1.2%), CTNNB1 (1.1%), AKT1 (0.9%), STK11 (0.8%), ERBB2 (0.6%), ERBB4 (0.6%), ALK (0.2%), MAP2K1 (0.2%) and NOTCH1 (0.2%). In a routine diagnostic setting, NGS had the potential to generate robust and comprehensive genetic information also including less frequently mutated genes potentially relevant for prognostic assessments or for actionable treatments. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  3. Complete Genome Sequence of Yersinia pestis Strains Antiqua andNepal516: Evidence of Gene Reduction in an Emerging Pathogen

    Energy Technology Data Exchange (ETDEWEB)

    Chain, Patrick S.G.; Hu, Ping; Malfatti, Stephanie A.; Radnedge,Lyndsay; Larimer, Frank; Vergez, Lisa M.; Worsham, Patricia; Chu, May C.; Andersen, Gary L.

    2006-01-16

    Yersinia pestis, the causative agent of bubonic andpneumonicplague, has undergone detailed study at the molecular level. Tofurther investigate the genomic diversity among this group and to helpcharacterize lineages of the plague organism that have no sequencedmembers, we present here the genomes of two isolates of the "classical"Antiqua biovar, strains Antiqua and Nepal516. The genomes of Antiqua andNepal516 are 4.7 Mb and 4.5 Mb and encode 4,138 and 3,956 open readingframes respectively. Though both strains belong to one of the threeclassical biovars, they represent separate lineages defined by recentphylogenetic studies. We compare all five currently sequenced Y. pestisgenomes and the corresponding features in Y. pseudotuberculosis. Thereare strain-specific rearrangements, insertions, deletions, singlenucleotide polymorphisms and a unique distribution of insertionsequences. We found 453 single nucleotide polymorphisms in protein codingregions, which were used to assess evolutionary relationships of these Y.pestis strains. Gene reduction analysis revealed that the gene deletionprocesses are under selective pressure and many of the inactivations areprobably related to the organism s interaction with its host environment.The results presented here clearly demonstrate the differences betweenthe two Antiqua lineages and support the notion that grouping Y. pestisstrains based strictly on the classical definition of biovars (predicatedupon two biochemical assays) does not accurately reflect the phylogeneticrelationships within this species. Comparison of four virulent Y. pestisstrains with the human-avirulent strain 91001 provides further insightinto the genetic basis of virulence to humans.

  4. Evidence of cyclic climatic changes recorded in clay mineral assemblages from a continental Paleocene-Eocene sequence, northwestern Argentina

    Science.gov (United States)

    Do Campo, Margarita; Bauluz, Blanca; del Papa, Cecilia; White, Timothy; Yuste, Alfonso; Mayayo, Maria Jose

    2018-06-01

    The continental Paleocene-Eocene sequence investigated in this study belongs to the Salta Group, deposited in an intracontinental rift, the Salta Basin (NW Argentina), that evolved from the lower Cretaceous to the middle Paleogene, and is subdivided into the Pirgua, the Balbuena and the Santa Barbara Subgroups. The Maíz Gordo Formation (200 m thick) is the middle unit of the Santa Bárbara Subgroup, deposited during late post-rift sedimentation. We studied the mineralogy of fine-grained horizons of this formation by X-ray diffraction and Scanning Electron Microscopy (SEM) in order to examine the connection between vertical changes in clay mineralogy in alluvial sediments and paleosols, and global paleoclimatic changes registered during the Paleogene. Paleosols vary from calcic vertisols in the lowermost levels, to inseptisols and gleysols in intermediate positions, to gleyed oxisols in the upper section, indicating increased chemical weathering through time. Clay mineral relative abundances vary with a general increase in kaolinite content from bottom to top. However, at one site there are significant variations in kaolinite/muscovite (Kln/Ms) that define five cycles of kaolinite abundance and Kln/Ms. that indicate cyclic patterns of paleoprecipitation and paleotemperature. These are interpreted as several short-lived hyperthermals during the Paleocene-early Eocene in the Southern Hemisphere, which correlate with well-established episodes of warmth documented from the Northern Hemisphere.

  5. Exome Sequencing Provides Evidence of Polygenic Adaptation to a Fat-Rich Animal Diet in Indigenous Siberian Populations.

    Science.gov (United States)

    Hsieh, PingHsun; Hallmark, Brian; Watkins, Joseph; Karafet, Tatiana M; Osipova, Ludmila P; Gutenkunst, Ryan N; Hammer, Michael F

    2017-11-01

    Siberia is one of the coldest environments on Earth and has great seasonal temperature variation. Long-term settlement in northern Siberia undoubtedly required biological adaptation to severe cold stress, dramatic variation in photoperiod, and limited food resources. In addition, recent archeological studies show that humans first occupied Siberia at least 45,000 years ago; yet our understanding of the demographic history of modern indigenous Siberians remains incomplete. In this study, we use whole-exome sequencing data from the Nganasans and Yakuts to infer the evolutionary history of these two indigenous Siberian populations. Recognizing the complexity of the adaptive process, we designed a model-based test to systematically search for signatures of polygenic selection. Our approach accounts for stochasticity in the demographic process and the hitchhiking effect of classic selective sweeps, as well as potential biases resulting from recombination rate and mutation rate heterogeneity. Our demographic inference shows that the Nganasans and Yakuts diverged ∼12,000-13,000 years ago from East-Asian ancestors in a process involving continuous gene flow. Our polygenic selection scan identifies seven candidate gene sets with Siberian-specific signals. Three of these gene sets are related to diet, especially to fat metabolism, consistent with the hypothesis of adaptation to a fat-rich animal diet. Additional testing rejects the effect of hitchhiking and favors a model in which selection yields small allele frequency changes at multiple unlinked genes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Strand bias in complementary single-nucleotide polymorphisms of transcribed human sequences: evidence for functional effects of synonymous polymorphisms

    Directory of Open Access Journals (Sweden)

    Majewski Jacek

    2006-08-01

    Full Text Available Abstract Background Complementary single-nucleotide polymorphisms (SNPs may not be distributed equally between two DNA strands if the strands are functionally distinct, such as in transcribed genes. In introns, an excess of A↔G over the complementary C↔T substitutions had previously been found and attributed to transcription-coupled repair (TCR, demonstrating the valuable functional clues that can be obtained by studying such asymmetry. Here we studied asymmetry of human synonymous SNPs (sSNPs in the fourfold degenerate (FFD sites as compared to intronic SNPs (iSNPs. Results The identities of the ancestral bases and the direction of mutations were inferred from human-chimpanzee genomic alignment. After correction for background nucleotide composition, excess of A→G over the complementary T→C polymorphisms, which was observed previously and can be explained by TCR, was confirmed in FFD SNPs and iSNPs. However, when SNPs were separately examined according to whether they mapped to a CpG dinucleotide or not, an excess of C→T over G→A polymorphisms was found in non-CpG site FFD SNPs but was absent from iSNPs and CpG site FFD SNPs. Conclusion The genome-wide discrepancy of human FFD SNPs provides novel evidence for widespread selective pressure due to functional effects of sSNPs. The similar asymmetry pattern of FFD SNPs and iSNPs that map to a CpG can be explained by transcription-coupled mechanisms, including TCR and transcription-coupled mutation. Because of the hypermutability of CpG sites, more CpG site FFD SNPs are relatively younger and have confronted less selection effect than non-CpG FFD SNPs, which can explain the asymmetric discrepancy of CpG site FFD SNPs vs. non-CpG site FFD SNPs.

  8. Genome Sequence Analysis of New Isolates of the Winona Strain of Plum pox virus and the First Definitive Evidence of Intrastrain Recombination Events.

    Science.gov (United States)

    James, Delano; Sanderson, Dan; Varga, Aniko; Sheveleva, Anna; Chirkov, Sergei

    2016-04-01

    Plum pox virus (PPV) is genetically diverse with nine different strains identified. Mutations, indel events, and interstrain recombination events are known to contribute to the genetic diversity of PPV. This is the first report of intrastrain recombination events that contribute to PPV's genetic diversity. Fourteen isolates of the PPV strain Winona (W) were analyzed including nine new strain W isolates sequenced completely in this study. Isolates of other strains of PPV with more than one isolate with the complete genome sequence available in GenBank were included also in this study for comparison and analysis. Five intrastrain recombination events were detected among the PPV W isolates, one among PPV C strain isolates, and one among PPV M strain isolates. Four (29%) of the PPV W isolates analyzed are recombinants; one of which (P2-1) is a mosaic, with three recombination events identified. A new interstrain recombinant event was identified between a strain M isolate and a strain Rec isolate, a known recombinant. In silico recombination studies and pairwise distance analyses of PPV strain D isolates indicate that a threshold of genetic diversity exists for the detectability of recombination events, in the range of approximately 0.78×10(-2) to 1.33×10(-2) mean pairwise distance. RDP4 analyses indicate that in the case of PPV Rec isolates there may be a recombinant breakpoint distinct from the obvious transition point of strain sequences. Evidence was obtained that indicates that the frequency of PPV recombination is underestimated, which may be true for other RNA viruses where low genetic diversity exists.

  9. Sequencing and characterisation of rearrangements in three S. pastorianus strains reveals the presence of chimeric genes and gives evidence of breakpoint reuse.

    Directory of Open Access Journals (Sweden)

    Sarah K Hewitt

    Full Text Available Gross chromosomal rearrangements have the potential to be evolutionarily advantageous to an adapting organism. The generation of a hybrid species increases opportunity for recombination by bringing together two homologous genomes. We sought to define the location of genomic rearrangements in three strains of Saccharomyces pastorianus, a natural lager-brewing yeast hybrid of Saccharomyces cerevisiae and Saccharomyces eubayanus, using whole genome shotgun sequencing. Each strain of S. pastorianus has lost species-specific portions of its genome and has undergone extensive recombination, producing chimeric chromosomes. We predicted 30 breakpoints that we confirmed at the single nucleotide level by designing species-specific primers that flank each breakpoint, and then sequencing the PCR product. These rearrangements are the result of recombination between areas of homology between the two subgenomes, rather than repetitive elements such as transposons or tRNAs. Interestingly, 28/30 S. cerevisiae-S. eubayanus recombination breakpoints are located within genic regions, generating chimeric genes. Furthermore we show evidence for the reuse of two breakpoints, located in HSP82 and KEM1, in strains of proposed independent origin.

  10. California Political Districts

    Data.gov (United States)

    California Natural Resource Agency — This is a series of district layers pertaining to California'spolitical districts, that are derived from the California State Senateand State Assembly information....

  11. Structural and Tectonic Map Along the Pacific-North America Plate Boundary in Northern Gulf of California, Sonora Desert and Valle de Mexicali, Mexico, from Seismic Reflection Evidence

    Science.gov (United States)

    Gonzalez-Escobar, M.; Suarez-Vidal, F.; Mendoza-Borunda, R.; Martin Barajas, A.; Pacheco-Romero, M.; Arregui-Estrada, S.; Gallardo-Mata, C.; Sanchez-Garcia, C.; Chanes-Martinez, J.

    2012-12-01

    Between 1978 and 1983, Petróleos Mexicanos (PEMEX) carried on an intense exploration program in the northern Gulf of California, the Sonora Desert and the southern part of the Mexicali Valley. This program was supported by a seismic reflection field operation. The collected seismic data was 2D, with travel time of 6 s recording, in 48 channels, and the source energy was: dynamite, vibroseis and air guns. Since 2007 to present time, the existing seismic data has been re-processing and ire-interpreting as part of a collaboration project between the PEMEX's Subdirección de Exploración (PEMEX) and CICESE. The study area is located along a large portion of the Pacific-North America plate boundary in the northern Gulf of California and the Southern part of the Salton Trough tectonic province (Mexicali Valley). We present the result of the processes reflection seismic lines. Many of the previous reported known faults were identify along with the first time described located within the study region. We identified regions with different degree of tectonic activity. In structural map it can see the location of many of these known active faults and their associated seismic activity, as well as other structures with no associated seismicity. Where some faults are mist placed they were deleted or relocated based on new information. We included historical seismicity for the region. We present six reflection lines that cross the aftershocks zone of the El Mayor-Cucapah earthquake of April 4, 2010 (Mw7.2). The epicenter of this earthquake and most of the aftershocks are located in a region where pervious to this earthquake no major earthquakes are been reported. A major result of this study is to demonstrate that there are many buried faults that increase the seismic hazard.

  12. Beaver Evidence - Historical Range of Beaver in the State of California, with an emphasis on areas within the range of coho salmon and steelhead trout

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This project examines historical, archaeological, and geological evidence to re-evaluate the existing management paradigm that beaver are non-native to most of...

  13. Chromium carcinogenicity: California strategies.

    Science.gov (United States)

    Alexeeff, G V; Satin, K; Painter, P; Zeise, L; Popejoy, C; Murchison, G

    1989-10-01

    Hexavalent chromium was identified by California as a toxic air contaminant (TAC) in January 1986. The California Department of Health Services (CDHS) concurred with the findings of the International Agency for Research on Cancer that there is sufficient evidence to demonstrate the carcinogenicity of chromium in both animals and humans. CDHS did not find any compelling evidence demonstrating the existence of a threshold with respect to chromium carcinogenesis. Experimental data was judged inadequate to assess potential human reproductive risks from ambient exposures. Other health effects were not expected to occur at ambient levels. The theoretically increased lifetime carcinogenic risk from a continuous lifetime exposure to hexavalent chromium fell within the range 12-146 cancer cases per nanogram hexavalent chromium per cubic meter of air per million people exposed, depending on the potency estimate used. The primary sources found to contribute significantly to the risk of exposure were chrome platers, chromic acid anodizing facilities and cooling towers utilizing hexavalent chromium as a corrosion inhibitor. Evaluation of genotoxicity data, animal studies and epidemiological studies indicates that further consideration should be given to the potential carcinogenicity of hexavalent chromium via the oral route.

  14. Pleistocene Brawley and Ocotillo Formations: Evidence for initial strike-slip deformation along the San Felipe and San Jacinto fault zonez, Southern California

    Science.gov (United States)

    Kirby, S.M.; Janecke, S.U.; Dorsey, R.J.; Housen, B.A.; Langenheim, V.E.; McDougall, K.A.; Steeley, A.N.

    2007-01-01

    We examine the Pleistocene tectonic reorganization of the Pacific-North American plate boundary in the Salton Trough of southern California with an integrated approach that includes basin analysis, magnetostratigraphy, and geologic mapping of upper Pliocene to Pleistocene sedimentary rocks in the San Felipe Hills. These deposits preserve the earliest sedimentary record of movement on the San Felipe and San Jacinto fault zones that replaced and deactivated the late Cenozoic West Salton detachment fault. Sandstone and mudstone of the Brawley Formation accumulated between ???1.1 and ???0.6-0.5 Ma in a delta on the margin of an arid Pleistocene lake, which received sediment from alluvial fans of the Ocotillo Formation to the west-southwest. Our analysis indicates that the Ocotillo and Brawley formations prograded abruptly to the east-northeast across a former mud-dominated perennial lake (Borrego Formation) at ???1.1 Ma in response to initiation of the dextral-oblique San Felipe fault zone. The ???25-km-long San Felipe anticline initiated at about the same time and produced an intrabasinal basement-cored high within the San Felipe-Borrego basin that is recorded by progressive unconformities on its north and south limbs. A disconformity at the base of the Brawley Formation in the eastern San Felipe Hills probably records initiation and early blind slip at the southeast tip of the Clark strand of the San Jacinto fault zone. Our data are consistent with abrupt and nearly synchronous inception of the San Jacinto and San Felipe fault zones southwest of the southern San Andreas fault in the early Pleistocene during a pronounced southwestward broadening of the San Andreas fault zone. The current contractional geometry of the San Jacinto fault zone developed after ???0.5-0.6 Ma during a second, less significant change in structural style. ?? 2007 by The University of Chicago. All rights reserved.

  15. Structural and metamorphic evolution of the Orocopia Schist and related rocks, southern California: Evidence for late movement on the Orocopia fault

    Science.gov (United States)

    Jacobson, Carl E.; Dawson, M. Robert

    1995-08-01

    The Pelona, Orocopia, and Rand Schists (POR schists) of southern California and southwesternmost Arizona are late Mesozoic or early Tertiary subduction complexes that underlie Precambrian to Mesozoic continental basement along the low-angle Vincent-Chocolate Mountains (VCM) fault system. The VCM faults are often considered to be remnants of the original subduction zone, but recent work indicates that many have undergone substantial postsubduction reactivation. In the Orocopia Mountains, for example, the Orocopia Schist exhibits an exceptionally complex structural and metamorphic history due to multiple periods of movement along the Orocopia fault. Structures in the schist include isoclinal folds with axial-planar schistosity, open-to-tight folds that fold schistosity, penetrative stretching lineations, and crenulation lineations, all of which show a nearly 360° range in trend. Folds and lineations that trend approximately NE-SW occur throughout the schist and are thought to be part of an early phase of deformation related to subduction. Folds of this orientation show no consistent vergence. Folds and lineations that trend approximately NW-SE are concentrated near the Orocopia fault and are interpreted to have formed during exhumation of the schist. The NW-SE trending folds, and shear indicators in late-stage mylonite at the top of the schist, consistently verge NE. The exhumation event culminated in emplacement of the schist against brittlely deformed upper plate. Exhumation of the Orocopia Schist was accompanied by retrograde replacement of garnet, biotite, epidote, and calcic amphibole by chlorite, calcite, and sericite. Matrix amphibole has a lower Na/Al ratio than amphibole inclusions in albite, consistent with a late-stage decrease in pressure. As NE vergence in the Orocopia Mountains is associated with exhumation of the schist, the NE movement along other segments of the VCM fault may also be late and therefore have no bearing on the facing direction of the

  16. Prevention of Filipino Youth Behavioral Health Disparities: Identifying Barriers and Facilitators to Participating in “Incredible Years,” an Evidence-Based Parenting Intervention, Los Angeles, California, 2012

    Science.gov (United States)

    Flores, Nicole; Supan, Jocelyn; Kreutzer, Cary B.; Samson, Allan; Coffey, Dean M.

    2015-01-01

    Introduction Evidence-based interventions for training parents are proven to prevent onset and escalation of childhood mental health problems. However, participation in such programs is low, especially among hard-to-reach, underserved populations such as Filipino Americans. Filipinos, the largest Asian subgroup in California, have significant behavioral health disparities compared with non-Hispanic whites and other Asian subgroups. The purpose of this study was to learn about Filipinos’ barriers and facilitators to participating in “Incredible Years” (IY), a parenting program. Methods We conducted 4 focus groups in Los Angeles, California, in 2012; the groups consisted of 20 Filipino parents of children aged 6 to 12 years who recently completed the IY parenting program, which was offered as a prevention workshop. Three reviewers, including two co-authors (A.S., J.J.) and a research assistant used content analysis to independently code the interview transcripts and extract subthemes. Grounded theory analytic methods were used to analyze interview transcripts. Results Parents’ perceived benefits of participation in IY were learning more effective parenting techniques, networking with other parents, improved spousal relationships, and improvements in their children's behavior. Parents’ most common motivating factor for enrollment in IY was to improve their parenting skills and their relationships with their children. The most common barriers to participation were being uncomfortable sharing problems with others and the fear of being stigmatized by others judging their parenting skills. Participants said that parent testimonials would be the most effective way to promote IY. Many recommended outreach at schools, pediatricians’ offices, and churches. Conclusion Increasing Filipino American parent enrollment in IY in culturally relevant ways will reduce the incidence of mental health disorders among children in this growing population. PMID:26491813

  17. Stable isotope evidence for an atmospheric origin of desert nitrate deposits in northern Chile and southern California, U.S.A.

    Science.gov (United States)

    Böhlke, J.K.; Ericksen, G.E.; Revesz, K.

    1997-01-01

    Natural surficial accumulations of nitrate-rich salts in the Atacama Desert, northern Chile, and in the Death Valley region of the Mojave Desert, southern California, are well known, but despite many geologic and geochemical studies, the origins of the nitrates have remained controversial. N and O isotopes in nitrate, and S isotopes in coexisting soluble sulfate, were measured to determine if some proposed N sources could be supported or rejected, and to determine if the isotopic signature of these natural deposits could be used to distinguish them from various types of anthropogenic nitrate contamination that might be found in desert groundwaters. High-grade caliche-type nitrate deposits from both localities have ??15N values that range from -5 to +5???, but are mostly near 0???. Values of ??15N near 0??? are consistent with either bulk atmospheric N deposition or microbial N fixation as major sources of the N in the deposits. ??18O values of those desert nitrates with ??15N near 0??? range from about +31 to + 50??? (V-SMOW), significantly higher than that of atmospheric O2 (+ 23.5???). Such high values of ??18O are considered unlikely to result entirely from nitrification of reduced N, but rather resemble those of modern atmospheric nitrate in precipitation from some other localities. Assuming that limited modern atmospheric isotope data are applicable to the deposits, and allowing for nitrification of co-deposited ammonium, it is estimated that the fraction of the nitrate in the deposits that could be accounted for isotopically by atmospheric N deposition may be at least 20% and possibly as much as 100%. ??34S values are less diagnostic but could also be consistent with atmospheric components in some of the soluble sulfates associated with the deposits. The stable isotope data support the hypothesis that some high-grade caliche-type nitrate-rich salt deposits in some of the Earth's hyperarid deserts represent long-term accumulations of atmospheric deposition

  18. Fault zone architecture, San Jacinto fault zone, southern California: evidence for focused fluid flow and heat transfer in the shallow crust

    Science.gov (United States)

    Morton, N.; Girty, G. H.; Rockwell, T. K.

    2011-12-01

    We report results of a new study of the San Jacinto fault zone architecture in Horse Canyon, SW of Anza, California, where stream incision has exposed a near-continuous outcrop of the fault zone at ~0.4 km depth. The fault zone at this location consists of a fault core, transition zone, damage zone, and lithologically similar wall rocks. We collected and analyzed samples for their bulk and grain density, geochemical data, clay mineralogy, and textural and modal mineralogy. Progressive deformation within the fault zone is characterized by mode I cracking, subsequent shearing of already fractured rock, and cataclastic flow. Grain comminution advances towards the strongly indurated cataclasite fault core. Damage progression towards the core is accompanied by a decrease in bulk and grain density, and an increase in porosity and dilational volumetric strain. Palygorskite and mixed-layer illite/smectite clay minerals are present in the damage and transition zones and are the result of hydrolysis reactions. The estimated percentage of illite in illite/smectite increases towards the fault core where the illite/smectite to illite conversion is complete, suggesting elevated temperatures that may have reached 150°C. Chemical alteration and elemental mass changes are observed throughout the fault zone and are most pronounced in the fault core. We conclude that the observed chemical and mineralogical changes can only be produced by the interaction of fractured wall rocks and chemically active fluids that are mobilized through the fault zone by thermo-pressurization during and after seismic events. Based on the high element mobility and absence of illite/smectite in the fault core, we expect that greatest water/rock ratios occur within the fault core. These results indicate that hot pore fluids circulate upwards through the fractured fault core and into the surrounding damage zone. Though difficult to constrain, the site studied during this investigation may represent the top

  19. Photomosaics and event evidence from the Frazier Mountain paleoseismic site, trench 1, cuts 5–24, San Andreas Fault Zone, southern California (2010–2012)

    Science.gov (United States)

    Scharer, Katherine M.; Fumal, Tom E.; Weldon, Ray J.; Streig, Ashley R.

    2015-08-24

    The Frazier Mountain paleoseismic site is located within the northern Big Bend of the southern San Andreas Fault (lat 34.8122° N., lon 118.9034° W.), in a small structural basin formed by the fault (fig. 1). The site has been the focus of over a decade of paleoseismic study due to high stratigraphic resolution and abundant dateable material. Trench 1 (T1) was initially excavated as a 50-m long, fault-perpendicular trench crossing the northern half of the basin (Lindvall and others, 2002; Scharer and others, 2014a). Owing to the importance of a high-resolution trench site at this location on a 200-km length of the fault with no other long paleoseismic records, later work progressively lengthened and deepened T1 in a series of excavations, or cuts, that enlarged the original excavation. Scharer and others (2014a) provide the photomosaics and event evidence for the first four cuts, which largely show the upper section of the site, represented by alluvial deposits that date from about A.D. 1500 to present. Scharer and others (2014b) discuss the earthquake evidence and dating at the site within the context of prehistoric rupture lengths and magnitudes on the southern San Andreas Fault. Here we present the photomosaics and event evidence for a series of cuts from the lower section, covering sediments that were deposited from about A.D. 500 to 1500 (fig. 2).

  20. Phylogenetic analyses of the polyprotein coding sequences of serotype O foot-and-mouth disease viruses in East Africa: evidence for interserotypic recombination

    Directory of Open Access Journals (Sweden)

    Balinda Sheila N

    2010-08-01

    Full Text Available Abstract Background Foot-and-mouth disease (FMD is endemic in East Africa with the majority of the reported outbreaks attributed to serotype O virus. In this study, phylogenetic analyses of the polyprotein coding region of serotype O FMD viruses from Kenya and Uganda has been undertaken to infer evolutionary relationships and processes responsible for the generation and maintenance of diversity within this serotype. FMD virus RNA was obtained from six samples following virus isolation in cell culture and in one case by direct extraction from an oropharyngeal sample. Following RT-PCR, the single long open reading frame, encoding the polyprotein, was sequenced. Results Phylogenetic comparisons of the VP1 coding region showed that the recent East African viruses belong to one lineage within the EA-2 topotype while an older Kenyan strain, K/52/1992 is a representative of the topotype EA-1. Evolutionary relationships between the coding regions for the leader protease (L, the capsid region and almost the entire coding region are monophyletic except for the K/52/1992 which is distinct. Furthermore, phylogenetic relationships for the P2 and P3 regions suggest that the K/52/1992 is a probable recombinant between serotypes A and O. A bootscan analysis of K/52/1992 with East African FMD serotype A viruses (A21/KEN/1964 and A23/KEN/1965 and serotype O viral isolate (K/117/1999 revealed that the P2 region is probably derived from a serotype A strain while the P3 region appears to be a mosaic derived from both serotypes A and O. Conclusions Sequences of the VP1 coding region from recent serotype O FMDVs from Kenya and Uganda are all representatives of a specific East African lineage (topotype EA-2, a probable indication that hardly any FMD introductions of this serotype have occurred from outside the region in the recent past. Furthermore, evidence for interserotypic recombination, within the non-structural protein coding regions, between FMDVs of serotypes A

  1. Converging evidence that sequence variations in the novel candidate gene MAP2K7 (MKK7) are functionally associated with schizophrenia.

    Science.gov (United States)

    Winchester, Catherine L; Ohzeki, Hiromitsu; Vouyiouklis, Demetrius A; Thompson, Rhiannon; Penninger, Josef M; Yamagami, Keiji; Norrie, John D; Hunter, Robert; Pratt, Judith A; Morris, Brian J

    2012-11-15

    Schizophrenia is a debilitating psychiatric disease with a strong genetic contribution, potentially linked to altered glutamatergic function in brain regions such as the prefrontal cortex (PFC). Here, we report converging evidence to support a functional candidate gene for schizophrenia. In post-mortem PFC from patients with schizophrenia, we detected decreased expression of MKK7/MAP2K7-a kinase activated by glutamatergic activity. While mice lacking one copy of the Map2k7 gene were overtly normal in a variety of behavioural tests, these mice showed a schizophrenia-like cognitive phenotype of impaired working memory. Additional support for MAP2K7 as a candidate gene came from a genetic association study. A substantial effect size (odds ratios: ~1.9) was observed for a common variant in a cohort of case and control samples collected in the Glasgow area and also in a replication cohort of samples of Northern European descent (most significant P-value: 3 × 10(-4)). While some caution is warranted until these association data are further replicated, these results are the first to implicate the candidate gene MAP2K7 in genetic risk for schizophrenia. Complete sequencing of all MAP2K7 exons did not reveal any non-synonymous mutations. However, the MAP2K7 haplotype appeared to have functional effects, in that it influenced the level of expression of MAP2K7 mRNA in human PFC. Taken together, the results imply that reduced function of the MAP2K7-c-Jun N-terminal kinase (JNK) signalling cascade may underlie some of the neurochemical changes and core symptoms in schizophrenia.

  2. Complete genome sequences of two avian infectious bronchitis viruses isolated in Egypt: Evidence for genetic drift and genetic recombination in the circulating viruses.

    Science.gov (United States)

    Abozeid, Hassanein H; Paldurai, Anandan; Khattar, Sunil K; Afifi, Manal A; El-Kady, Magdy F; El-Deeb, Ayman H; Samal, Siba K

    2017-09-01

    Avian infectious bronchitis virus (IBV) is highly prevalent in chicken populations and is responsible for severe economic losses to poultry industry worldwide. In this study, we report the complete genome sequences of two IBV field strains, CU/1/2014 and CU/4/2014, isolated from vaccinated chickens in Egypt in 2014. The genome lengths of the strains CU/1/2014 and CU/4/2014 were 27,615 and 27,637 nucleotides, respectively. Both strains have a common genome organization in the order of 5'-UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-UTR-poly(A) tail-3'. Interestingly, strain CU/1/2014 showed a novel 15-nt deletion in the 4b-4c gene junction region. Phylogenetic analysis of the full S1 genes showed that the strains CU/1/2014 and CU/4/2014 belonged to IBV genotypes GI-1 lineage and GI-23 lineage, respectively. The genome of strain CU/1/2014 is closely related to vaccine strain H120 but showed genome-wide point mutations that lead to 27, 14, 11, 1, 1, 2, 2, and 2 amino acid differences between the two strains in 1a, 1b, S, 3a, M, 4b, 4c, and N proteins, respectively, suggesting that strain CU/1/2014 is probably a revertant of the vaccine strain H120 and evolved by accumulation of point mutations. Recombination analysis of strain CU/4/2014 showed evidence for recombination from at least three different IBV strains, namely, the Italian strain 90254/2005 (QX-like strain), 4/91, and H120. These results indicate the continuing evolution of IBV field strains by genetic drift and by genetic recombination leading to outbreaks in the vaccinated chicken populations in Egypt. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Molecular phylogeny of ateline new world monkeys (Platyrrhini, atelinae) based on gamma-globin gene sequences: evidence that brachyteles is the sister group of lagothrix.

    Science.gov (United States)

    Meireles, C M; Czelusniak, J; Schneider, M P; Muniz, J A; Brigido, M C; Ferreira, H S; Goodman, M

    1999-06-01

    Nucleotide sequences, each spanning approximately 7 kb of the contiguous gamma1 and gamma2 globin genomic loci, were determined for seven species representing all extant genera (Ateles, Lagothrix, Brachyteles, and Alouatta) of the New World monkey subfamily Atelinae. After aligning these seven ateline sequences with outgroup sequences from several other primate (non-ateline) genera, they were analyzed by maximum parsimony, maximum likelihood, and neighbor-joining algorithms. All three analyzes estimated the same phylogenetic relationships: [Alouatta [Ateles (Brachyteles, Lagothrix)

  4. Lead and strontium isotopic evidence for crustal interaction and compositional zonation in the source regions of Pleistocene basaltic and rhyolitic magmas of the Coso volcanic field, California

    Science.gov (United States)

    Bacon, C.R.; Kurasawa, H.; Delevaux, M.H.; Kistler, R.W.; Doe, B.R.

    1984-01-01

    The isotopic compositions of Pb and Sr in Pleistocene basalt, high-silica rhyolite, and andesitic inclusions in rhyolite of the Coso volcanic field indicate that these rocks were derived from different levels of compositionally zoned magmatic systems. The 2 earliest rhyolites probably were tapped from short-lived silicic reservoirs, in contrast to the other 36 rhyolite domes and lava flows which the isotopic data suggest may have been leaked from the top of a single, long-lived magmatic system. Most Coso basalts show isotopic, geochemical, and mineralogic evidence of interaction with crustal rocks, but one analyzed flow has isotopic ratios that may represent mantle values (87Sr/86Sr=0.7036,206Pb/204Pb=19.05,207Pb/204Pb=15.62,208Pb/204Pb= 38.63). The (initial) isotopic composition of typical rhyolite (87Sr/86Sr=0.7053,206Pb/204Pb=19.29,207Pb/204Pb= 15.68,208Pb/204Pb=39.00) is representative of the middle or upper crust. Andesitic inclusions in the rhyolites are evidently samples of hybrid magmas from the silicic/mafic interface in vertically zoned magma reservoirs. Silicic end-member compositions inferred for these mixed magmas, however, are not those of erupted rhyolite but reflect the zonation within the silicic part of the magma reservoir. The compositional contrast at the interface between mafic and silicic parts of these systems apparently was greater for the earlier, smaller reservoirs. ?? 1984 Springer-Verlag.

  5. Inferring species trees from gene trees in a radiation of California trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus.

    Directory of Open Access Journals (Sweden)

    Jordan D Satler

    Full Text Available The California Floristic Province is a biodiversity hotspot, reflecting a complex geologic history, strong selective gradients, and a heterogeneous landscape. These factors have led to high endemic diversity across many lifeforms within this region, including the richest diversity of mygalomorph spiders (tarantulas, trapdoor spiders, and kin in North America. The trapdoor spider genus Aliatypus encompasses twelve described species, eleven of which are endemic to California. Several Aliatypus species show disjunct distributional patterns in California (some are found on both sides of the vast Central Valley, and the genus as a whole occupies an impressive variety of habitats.We collected specimens from 89 populations representing all described species. DNA sequence data were collected from seven gene regions, including two newly developed for spider systematics. Bayesian inference (in individual gene tree and species tree approaches recovered a general "3 clade" structure for the genus (A. gulosus, californicus group, erebus group, with three other phylogenetically isolated species differing slightly in position across different phylogenetic analyses. Because of extremely high intraspecific divergences in mitochondrial COI sequences, the relatively slowly evolving 28S rRNA gene was found to be more useful than mitochondrial data for identification of morphologically indistinguishable immatures. For multiple species spanning the Central Valley, explicit hypothesis testing suggests a lack of monophyly for regional populations (e.g., western Coast Range populations. Phylogenetic evidence clearly shows that syntopy is restricted to distant phylogenetic relatives, consistent with ecological niche conservatism.This study provides fundamental insight into a radiation of trapdoor spiders found in the biodiversity hotspot of California. Species relationships are clarified and undescribed lineages are discovered, with more geographic sampling likely to

  6. The California Valley grassland

    Science.gov (United States)

    Keeley, J.E.; Schoenherr, Allan A.

    1990-01-01

    Grasslands are distributed throughout California from Oregon to Baja California Norte and from the coast to the desert (Brown 1982) (Figure 1). This review will focus on the dominant formation in cismontane California, a community referred to as Valley Grassland (Munz 1959). Today, Valley Grassland is dominated by non-native annual grasses in genera such as Avena (wild oat), Bromus (brome grass), and Hordeum (barley), and is often referred to as the California annual grassland. On localized sites, native perennial bunchgrasses such as Stipa pultra (purple needle grass) may dominate and such sites are interpreted to be remnants of the pristine valley grassland. In northwestern California a floristically distinct formation of the Valley Grassland, known as Coast Prairie (Munz 1959) or Northern Coastal Grassland (Holland and Keil 1989) is recognized. The dominant grasses include many native perennial bunchgrasses in genera such as Agrostis, Calamagrostis, Danthonia, Deschampsia, Festuca, Koeleria and Poa (Heady et al. 1977). Non-native annuals do not dominate, but on some sites non-native perennials like Anthoxanthum odoratum may colonize the native grassland (Foin and Hektner 1986). Elevationally, California's grasslands extend from sea level to at leas 1500 m. The upper boundary is vague because montane grassland formations are commonly referred to as meadows; a community which Munz (1959) does not recognize. Holland and Keil (1989) describe the montane meadow as an azonal community; that is, a community restricted not so much to a particular climatic zone but rather controlled by substrate characteristics. They consider poor soil-drainage an over-riding factor in the development of montane meadows and, in contrast to grasslands, meadows often remain green through the summer drought. Floristically, meadows are composed of graminoids; Cyperaceae, Juncaceae, and rhizomatous grasses such as Agropyron (wheat grass). Some bunchgrasses, such as Muhlenbergia rigens, are

  7. California Condor Critical Habitat

    Data.gov (United States)

    California Natural Resource Agency — These Data identify (in general) the areas where critical habitat for the California Condor occur. Critical habitat for the species consists of the following 10...

  8. Teale California shoreline

    Data.gov (United States)

    California Natural Resource Agency — California Spatial Information System (CaSIL) is a project designed to improve access to geo-spatial and geo-spatial related data information throughout the state of...

  9. California Workforce: California Faces a Skills Gap

    Science.gov (United States)

    Public Policy Institute of California, 2011

    2011-01-01

    California's education system is not keeping up with the changing demands of the state's economy--soon, California will face a shortage of skilled workers. Projections to 2025 suggest that the economy will continue to need more and more highly educated workers, but that the state will not be able to meet that demand. If current trends persist,…

  10. Sacramento Metropolitan Area, California

    Science.gov (United States)

    1992-02-01

    addition, several Federal candidate species, the California Hibiscus , California tiger salamander, Sacramento Anthicid Beetle, Sacramento Valley tiger...Board, California Waste Management Board, and Department of Health Services contribute to this list. The Yolo County Health Services Agency maintains and...operation and maintenance of the completed recreational facility. Recreation development is limited to project lands unless health and safety

  11. Origin of the Y genome in Elymus and its relationship to other genomes in Triticeae based on evidence from elongation factor G (EF-G) gene sequences.

    Science.gov (United States)

    Sun, Genlou; Komatsuda, Takao

    2010-08-01

    It is well known that Elymus arose through hybridization between representatives of different genera. Cytogenetic analyses show that all its members include the St genome in combination with one or more of four other genomes, the H, Y, P, and W genomes. The origins of the H, P, and W genomes are known, but not for the Y genome. We analyzed the single copy nuclear gene coding for elongation factor G (EF-G) from 28 accessions of polyploid Elymus species and 45 accessions of diploid Triticeae species in order to investigate origin of the Y genome and its relationship to other genomes in the tribe Triticeae. Sequence comparisons among the St, H, Y, P, W, and E genomes detected genome-specific polymorphisms at 66 nucleotide positions. The St and Y genomes are relatively dissimilar. The phylogeny of the Y genome sequences was investigated for the first time. They were most similar to the W genome sequences. The Y genome sequences were placed in two different groups. These two groups were included in an unresolved clade that included the W and E sequences as well as sequences from many annual species. The H genomes sequences were in a clade with the F, P, and Ns genome sequences as sister groups. These two clades were more closely related to each other and to the L and Xp genomes than they were to the St genome sequences. These data support the hypothesis that the Y genome evolved in a diploid species and has a different origin from the St genome. Copyright 2010 Elsevier Inc. All rights reserved.

  12. XMM-NEWTON MONITORING OF THE CLOSE PRE-MAIN-SEQUENCE BINARY AK SCO. EVIDENCE OF TIDE-DRIVEN FILLING OF THE INNER GAP IN THE CIRCUMBINARY DISK

    Energy Technology Data Exchange (ETDEWEB)

    Gomez de Castro, Ana Ines [S. D. Astronomia y Geodesia and Instituto de Matematica Interdisciplinar, Fac. de CC Matematicas, Universidad Complutense, E-28040 Madrid (Spain); Lopez-Santiago, Javier [Departamento de Astrofisica, Fac de CC Fisicas, Universidad Complutense, E-28040 Madrid (Spain); Talavera, Antonio [European Space Astronomy Center, Villanueva de la Canada, E-28691, Madrid (Spain); Sytov, A. Yu.; Bisikalo, D. [Institute of Astronomy of the Russian Academy of Sciences, Pyatnitskaya St. 48, 109017 Moscow (Russian Federation)

    2013-03-20

    AK Sco stands out among pre-main-sequence binaries because of its prominent ultraviolet excess, the high eccentricity of its orbit, and the strong tides driven by it. AK Sco consists of two F5-type stars that get as close as 11 R{sub *} at periastron passage. The presence of a dense (n{sub e} {approx} 10{sup 11} cm{sup -3}) extended envelope has been unveiled recently. In this article, we report the results from an XMM-Newton-based monitoring of the system. We show that at periastron, X-ray and UV fluxes are enhanced by a factor of {approx}3 with respect to the apastron values. The X-ray radiation is produced in an optically thin plasma with T {approx} 6.4 Multiplication-Sign 10{sup 6} K and it is found that the N{sub H} column density rises from 0.35 Multiplication-Sign 10{sup 21} cm{sup -2} at periastron to 1.11 Multiplication-Sign 10{sup 21} cm{sup -2} at apastron, in good agreement with previous polarimetric observations. The UV emission detected in the Optical Monitor band seems to be caused by the reprocessing of the high-energy magnetospheric radiation on the circumstellar material. Further evidence of the strong magnetospheric disturbances is provided by the detection of line broadening of 278.7 km s{sup -1} in the N V line with Hubble Space Telescope/Space Telescope Imaging Spectrograph. Numerical simulations of the mass flow from the circumbinary disk to the components have been carried out. They provide a consistent scenario with which to interpret AK Sco observations. We show that the eccentric orbit acts like a gravitational piston. At apastron, matter is dragged efficiently from the inner disk border, filling the inner gap and producing accretion streams that end as ring-like structures around each component of the system. At periastron, the ring-like structures come into contact, leading to angular momentum loss, and thus producing an accretion outburst.

  13. Large Sequence Polymorphisms of the Euro-American lineage of Mycobacterium tuberculosis: a phylogenetic reconstruction and evidence for convergent evolution in the DR locus.

    Science.gov (United States)

    Rindi, Laura; Lari, Nicoletta; Garzelli, Carlo

    2012-10-01

    The Euro-American lineage of the Mycobacterium tuberculosis complex consists of 10 sublineages, each defined by a deletion of a large genomic region (RD, region of difference); by spoligotyping, that probes the polymorphism of the Direct Repeat (DR) locus, the Euro-American strains are classified into 5 lineages (T, Haarlem, LAM, S and X) and 34 sublineages, but the relationships between the RD-defined sublineages and the spoligotype groupings are largely unclear. By testing a global sample of 158 Euro-American strains, mutually exclusive deletions of RD115, RD122, RD174, RD182, RD183, RD193, RD219, RD726 or RD761 were found in 122 strains; deletion of RD724, typical of strains from Central Africa, was not found. The RD-defined sublineages, tested for katG463/gyrA95 polymorphism, belonged to Principal Genotypic Group (PGG) 2, with the exception of RD219 sublineage belonging to PGG3; the 36 strains with no deletion were of either PGG2 or 3. Based on these polymorphisms, a phylogenetic reconstruction of the Euro-American lineage, that integrates the previously reported phylogeny, is proposed. Although certain deletions were found to be associated to certain spoligotype lineages (i.e., deletion RD115 to T and LAM, RD174 to LAM, RD182 to Haarlem, RD219 to T), our analysis indicates a general lack of concordance between RD-defined sublineages and spoligotype groupings. Moreover, of the 42 spoligotypes detected among the study strains, sixteen were shared by strains belonging to different RD sublineages. IS6110-RFLP analysis of strains sharing spoligotypes confirmed a poor genetic relatedness between strains of different RD sublineages. These findings provide evidence for the occurrence of a high degree of homoplasy in the DR locus leading to convergent evolution to identical spoligotypes. The incongruence between Large Sequence Polymorphism and spoligotype polymorphism argues against the use of spoligotyping for establishing phylogenetic relationships within the Euro

  14. Peptide and nucleotide sequences of rat CD4 (W3/25) antigen: evidence for derivation from a structure with four immunoglobulin-related domains

    International Nuclear Information System (INIS)

    Clark, S.J.; Jefferies, W.A.; Barclay, A.N.; Gagnon, J.; Williams, A.F.

    1987-01-01

    The rat W3/25 antigen was the first marker antigen of helper T lymphocytes to be identified. Subsequently, the human OKT4 antigen (now called CD4) was described, and cell distribution and functional data suggested that W3/25 and OKT4 antigens were homologous. This is now confirmed by the matching of peptide sequences from W3/25 antigen with sequence predicted from rat cDNA clones detected by cross-hybridization with a cDNA probe for human CD4. Analysis of the two sequences suggests an evolutionary origin from a structure with four immunoglobulin-related domains, although only domain 1 at the NH 2 terminus meets the standard criteria for an immunoglobulin-related sequence. CD4 domains 2 and 4 contain disulfide bonds but seem like truncated immunoglobulin domains, whereas domain 3 may have a pattern of β-strands like an immunoglobulin variable domain, but without the disulfide bond

  15. Complementary DNA and derived amino acid sequence of the α subunit of human complement protein C8: evidence for the existence of a separate α subunit messenger RNA

    International Nuclear Information System (INIS)

    Rao, A.G.; Howard, O.M.Z.; Ng, S.C.; Whitehead, A.S.; Colten, H.R.; Sodetz, J.M.

    1987-01-01

    The entire amino acid sequence of the α subunit (M/sub r/ 64,000) of the eight component of complement (C8) was determined by characterizing cDNA clones isolated from a human liver cDNA library. Two clones with overlapping inserts of net length 2.44 kilobases (kb) were isolated and found to contain the entire α coding region [1659 base pairs (bp)]. The 5' end consists of an untranslated region and a leader sequence of 30 amino acids. This sequence contains an apparent initiation Met, signal peptide, and propeptide which ends with an arginine-rich sequence that is characteristic of proteolytic processing sites found in the pro form of protein precursors. The 3' untranslated region contains two polyadenylation signals and a poly(A)sequence. RNA blot analysis of total cellular RNA from the human hepatoma cell line HepG2 revealed a message size of ∼2.5 kb. Features of the 5' and 3' sequences and the message size suggest that a separate mRNA codes for α and argues against the occurrence of a single-chain precursor form of the disulfide-linked α-λ subunit found in mature C8. Analysis of the derived amino acid sequence revealed several membrane surface seeking domains and a possible transmembrane domain. Analysis of the carbohydrate composition indicates 1 or 2 asparagine-linked but no O-linked oligosaccharide chains, a result consistent with predictions from the amino acid sequence. Most significantly, it exhibits a striking overall homology to human C9, with values of 24% on the basis of identity and 46% when conserved substitutions are allowed. As described in an accompanying report this homology also extends to the β subunit of C8

  16. The complete genome sequence of a south Indian isolate of Rice tungro spherical virus reveals evidence of genetic recombination between distinct isolates.

    Science.gov (United States)

    Sailaja, B; Anjum, Najreen; Patil, Yogesh K; Agarwal, Surekha; Malathi, P; Krishnaveni, D; Balachandran, S M; Viraktamath, B C; Mangrauthia, Satendra K

    2013-12-01

    In this study, complete genome of a south Indian isolate of Rice tungro spherical virus (RTSV) from Andhra Pradesh (AP) was sequenced, and the predicted amino acid sequence was analysed. The RTSV RNA genome consists of 12,171 nt without the poly(A) tail, encoding a putative typical polyprotein of 3,470 amino acids. Furthermore, cleavage sites and sequence motifs of the polyprotein were predicted. Multiple alignment with other RTSV isolates showed a nucleotide sequence identity of 95% to east Indian isolates and 90% to Philippines isolates. A phylogenetic tree based on complete genome sequence showed that Indian isolates clustered together, while Vt6 and PhilA isolates of Philippines formed two separate clusters. Twelve recombination events were detected in RNA genome of RTSV using the Recombination Detection Program version 3. Recombination analysis suggested significant role of 5' end and central region of genome in virus evolution. Further, AP and Odisha isolates appeared as important RTSV isolates involved in diversification of this virus in India through recombination phenomenon. The new addition of complete genome of first south Indian isolate provided an opportunity to establish the molecular evolution of RTSV through recombination analysis and phylogenetic relationship.

  17. Analyses of Twelve New Whole Genome Sequences of Cassava Brown Streak Viruses and Ugandan Cassava Brown Streak Viruses from East Africa: Diversity, Supercomputing and Evidence for Further Speciation

    Science.gov (United States)

    Ndunguru, Joseph; Sseruwagi, Peter; Tairo, Fred; Stomeo, Francesca; Maina, Solomon; Djinkeng, Appolinaire; Kehoe, Monica; Boykin, Laura M.

    2015-01-01

    Cassava brown streak disease is caused by two devastating viruses, Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) which are frequently found infecting cassava, one of sub-Saharan Africa’s most important staple food crops. Each year these viruses cause losses of up to $100 million USD and can leave entire families without their primary food source, for an entire year. Twelve new whole genomes, including seven of CBSV and five of UCBSV were uncovered in this research, doubling the genomic sequences available in the public domain for these viruses. These new sequences disprove the assumption that the viruses are limited by agro-ecological zones, show that current diagnostic primers are insufficient to provide confident diagnosis of these viruses and give rise to the possibility that there may be as many as four distinct species of virus. Utilizing NGS sequencing technologies and proper phylogenetic practices will rapidly increase the solution to sustainable cassava production. PMID:26439260

  18. Analyses of Twelve New Whole Genome Sequences of Cassava Brown Streak Viruses and Ugandan Cassava Brown Streak Viruses from East Africa: Diversity, Supercomputing and Evidence for Further Speciation.

    Directory of Open Access Journals (Sweden)

    Joseph Ndunguru

    Full Text Available Cassava brown streak disease is caused by two devastating viruses, Cassava brown streak virus (CBSV and Ugandan cassava brown streak virus (UCBSV which are frequently found infecting cassava, one of sub-Saharan Africa's most important staple food crops. Each year these viruses cause losses of up to $100 million USD and can leave entire families without their primary food source, for an entire year. Twelve new whole genomes, including seven of CBSV and five of UCBSV were uncovered in this research, doubling the genomic sequences available in the public domain for these viruses. These new sequences disprove the assumption that the viruses are limited by agro-ecological zones, show that current diagnostic primers are insufficient to provide confident diagnosis of these viruses and give rise to the possibility that there may be as many as four distinct species of virus. Utilizing NGS sequencing technologies and proper phylogenetic practices will rapidly increase the solution to sustainable cassava production.

  19. Does Deccan Volcanic Sequence contain more reversals than the three-Chron N-R-N flow magnetostratigraphy?- A paleomagnetic evidence from the dyke-swarm near Mumbai

    Science.gov (United States)

    Basavaiah, N.; Satyanarayana, KVV; Deenadayalan, K.; Prasad, JN

    2018-02-01

    .5 respectively, indicating a latitudinal drift of ˜4.4° of the sampled location between the acquisition of two magnetizations. Six lava flows sampled from the basement of the host Deccan flow sequence nearby sampled dykes yielded reverse polarity ChRM mean at Dm = 128°, Im = 47° (k = 156, α95 = 5.4°) with corresponding pole positions at 21° S, 121° E (A95 = 5.3°). This pole falls near the GII poles, indicating a probable contemporaneous time of emplacement. In the absence of radiometric dates, no magnetochron can be assigned for GII magnetization. However, on the basis of published analyses of several paleomagnetic and geochronological data of the flows and dykes within DVP and Deccan related dykes from the neighbouring areas, it seems plausible that GII -R magnetization belongs to either Chron 30R or 31R and GII -N magnetization pertains to 31 N. Conclusive evidence in support of the presence of these reversals in the DVP, however, has to wait for new geochronological data from the undated dykes investigated in this study, and fresh updating of the stratigraphy of the lowermost flow sequence in the sampled area which also remains undated. This study, however, does indicate the possible presence of two more reversals revealed by GII magnetization on the older side beyond well-established three-Chron magnetostratigraphy.

  20. Primary motor and premotor cortex in implicit sequence learning--evidence for competition between implicit and explicit human motor memory systems.

    Science.gov (United States)

    Kantak, Shailesh S; Mummidisetty, Chaithanya K; Stinear, James W

    2012-09-01

    Implicit and explicit memory systems for motor skills compete with each other during and after motor practice. Primary motor cortex (M1) is known to be engaged during implicit motor learning, while dorsal premotor cortex (PMd) is critical for explicit learning. To elucidate the neural substrates underlying the interaction between implicit and explicit memory systems, adults underwent a randomized crossover experiment of anodal transcranial direct current stimulation (AtDCS) applied over M1, PMd or sham stimulation during implicit motor sequence (serial reaction time task, SRTT) practice. We hypothesized that M1-AtDCS during practice will enhance online performance and offline learning of the implicit motor sequence. In contrast, we also hypothesized that PMd-AtDCS will attenuate performance and retention of the implicit motor sequence. Implicit sequence performance was assessed at baseline, at the end of acquisition (EoA), and 24 h after practice (retention test, RET). M1-AtDCS during practice significantly improved practice performance and supported offline stabilization compared with Sham tDCS. Performance change from EoA to RET revealed that PMd-AtDCS during practice attenuated offline stabilization compared with M1-AtDCS and sham stimulation. The results support the role of M1 in implementing online performance gains and offline stabilization for implicit motor sequence learning. In contrast, enhancing the activity within explicit motor memory network nodes such as the PMd during practice may be detrimental to offline stabilization of the learned implicit motor sequence. These results support the notion of competition between implicit and explicit motor memory systems and identify underlying neural substrates that are engaged in this competition. © 2012 The Authors. European Journal of Neuroscience © 2012 Federation of European Neuroscience Societies and Blackwell Publishing Ltd.

  1. SEQUENCE OF THE STRUCTURAL GENE FOR GRANULE-BOUND STARCH SYNTHASE OF POTATO (SOLANUM-TUBEROSUM L) AND EVIDENCE FOR A SINGLE POINT DELETION IN THE AMF ALLELE

    NARCIS (Netherlands)

    van der Leij, Feike R.; VISSER, RGF; Ponstein, Anne S.; Jacobsen, Evert; Feenstra, Willem

    The genomic sequence of the potato gene for starch granule-bound starch synthase (GBSS; "waxy protein") has been determined for the wild-type allele of a monoploid genotype from which an amylose-free (amf) mutant was derived, and for the mutant part of the amf allele. Comparison of the wild-type

  2. Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences

    Directory of Open Access Journals (Sweden)

    Hongying Ma

    2018-06-01

    Full Text Available Objectives There are large populations of indigenous horse (Equus caballus in China and some other parts of East Asia. However, their matrilineal genetic diversity and origin remained poorly understood. Using a combination of mitochondrial DNA (mtDNA and hypervariable region (HVR-1 sequences, we aim to investigate the origin of matrilineal inheritance in these domestic horses. Methods To investigate patterns of matrilineal inheritance in domestic horses, we conducted a phylogenetic study using 31 de novo mtDNA genomes together with 317 others from the GenBank. In terms of the updated phylogeny, a total of 5,180 horse mitochondrial HVR-1 sequences were analyzed. Results Eightteen haplogroups (Aw-Rw were uncovered from the analysis of the whole mitochondrial genomes. Most of which have a divergence time before the earliest domestication of wild horses (about 5,800 years ago and during the Upper Paleolithic (35–10 KYA. The distribution of some haplogroups shows geographic patterns. The Lw haplogroup contained a significantly higher proportion of European horses than the horses from other regions, while haplogroups Jw, Rw, and some maternal lineages of Cw, have a higher frequency in the horses from East Asia. The 5,180 sequences of horse mitochondrial HVR-1 form nine major haplogroups (A-I. We revealed a corresponding relationship between the haplotypes of HVR-1 and those of whole mitochondrial DNA sequences. The data of the HVR-1 sequences also suggests that Jw, Rw, and some haplotypes of Cw may have originated in East Asia while Lw probably formed in Europe. Conclusions Our study supports the hypothesis of the multiple origins of the maternal lineage of domestic horses and some maternal lineages of domestic horses may have originated from East Asia.

  3. Analysis of S-RNase alleles of almond (Prunus dulcis): characterization of new sequences, resolution of synonyms and evidence of intragenic recombination.

    Science.gov (United States)

    Ortega, Encarnación; Bosković, Radovan I; Sargent, Daniel J; Tobutt, Kenneth R

    2006-11-01

    Cross-compatibility relationships in almond are controlled by a gametophytically expressed incompatibility system partly mediated by stylar RNases, of which 29 have been reported. To resolve possible synonyms and to provide data for phylogenetic analysis, 21 almond S-RNase alleles were cloned and sequenced from SP (signal peptide region) or C1 (first conserved region) to C5, except for the S29 allele, which could be cloned only from SP to C1. Nineteen sequences (S4, S6, S11-S22, S25-S29)) were potentially new whereas S10 and S24 had previously been published but with different labels. The sequences for S16 and S17 were identical to that for S1, published previously; likewise, S15 was identical to S5. In addition, S4 and S20 were identical, as were S13 and S19. A revised version of the standard table of almond incompatibility genotypes is presented. Several alleles had AT or GA tandem repeats in their introns. Sequences of the 23 distinct newly cloned or already published alleles were aligned. Sliding windows analysis of Ka/Ks identified regions where positive selection may operate; in contrast to the Maloideae, most of the region from the beginning of C3 to the beginning of RC4 appeared not to be under positive selection. Phylogenetic analysis indicated four pairs of alleles had "bootstrap" support > 80%: S5/S10, S4/S8, S11/S24, and S3/S6. Various motifs up to 19 residues long occurred in at least two alleles, and their distributions were consistent with intragenic recombination, as were separate phylogenetic analyses of the 5' and 3' sections. Sequence comparison of phylogenetically related alleles indicated the significance of the region between RC4 and C5 in defining specificity.

  4. Sequence analysis of the PIP5K locus in Eimeria maxima provides further evidence for eimerian genome plasticity and segmental organization.

    Science.gov (United States)

    Song, B K; Pan, M Z; Lau, Y L; Wan, K L

    2014-07-29

    Commercial flocks infected by Eimeria species parasites, including Eimeria maxima, have an increased risk of developing clinical or subclinical coccidiosis; an intestinal enteritis associated with increased mortality rates in poultry. Currently, infection control is largely based on chemotherapy or live vaccines; however, drug resistance is common and vaccines are relatively expensive. The development of new cost-effective intervention measures will benefit from unraveling the complex genetic mechanisms that underlie host-parasite interactions, including the identification and characterization of genes encoding proteins such as phosphatidylinositol 4-phosphate 5-kinase (PIP5K). We previously identified a PIP5K coding sequence within the E. maxima genome. In this study, we analyzed two bacterial artificial chromosome clones presenting a ~145-kb E. maxima (Weybridge strain) genomic region spanning the PIP5K gene locus. Sequence analysis revealed that ~95% of the simple sequence repeats detected were located within regions comparable to the previously described feature-rich segments of the Eimeria tenella genome. Comparative sequence analysis with the orthologous E. maxima (Houghton strain) region revealed a moderate level of conserved synteny. Unique segmental organizations and telomere-like repeats were also observed in both genomes. A number of incomplete transposable elements were detected and further scrutiny of these elements in both orthologous segments revealed interesting nesting events, which may play a role in facilitating genome plasticity in E. maxima. The current analysis provides more detailed information about the genome organization of E. maxima and may help to reveal genotypic differences that are important for expression of traits related to pathogenicity and virulence.

  5. Paralogues of nuclear ribosomal genes conceal phylogenetic signals within the invasive Asian fish tapeworm lineage: evidence from next generation sequencing data

    Czech Academy of Sciences Publication Activity Database

    Brabec, Jan; Kuchta, Roman; Scholz, Tomáš; Littlewood, D. T. J.

    2016-01-01

    Roč. 46, č. 9 (2016), s. 555-562 ISSN 0020-7519 R&D Projects: GA MŠk(CZ) EE2.3.30.0032; GA ČR GA15-14198S Grant - others:GA MŠk(CZ) LM2010005 Institutional support: RVO:60077344 Keywords : Schyzocotyle acheilognathi * Asian fish tapeworm * Bothriocephalus acheilognathi * invasive parasite * mitochondrial genome * ribosomal RNA * illumina sequencing * phylogeny Subject RIV: EG - Zoology Impact factor: 3.730, year: 2016

  6. High-throughput sequencing of natively paired antibody chains provides evidence for original antigenic sin shaping the antibody response to influenza vaccination.

    Science.gov (United States)

    Tan, Yann-Chong; Blum, Lisa K; Kongpachith, Sarah; Ju, Chia-Hsin; Cai, Xiaoyong; Lindstrom, Tamsin M; Sokolove, Jeremy; Robinson, William H

    2014-03-01

    We developed a DNA barcoding method to enable high-throughput sequencing of the cognate heavy- and light-chain pairs of the antibodies expressed by individual B cells. We used this approach to elucidate the plasmablast antibody response to influenza vaccination. We show that >75% of the rationally selected plasmablast antibodies bind and neutralize influenza, and that antibodies from clonal families, defined by sharing both heavy-chain VJ and light-chain VJ sequence usage, do so most effectively. Vaccine-induced heavy-chain VJ regions contained on average >20 nucleotide mutations as compared to their predicted germline gene sequences, and some vaccine-induced antibodies exhibited higher binding affinities for hemagglutinins derived from prior years' seasonal influenza as compared to their affinities for the immunization strains. Our results show that influenza vaccination induces the recall of memory B cells that express antibodies that previously underwent affinity maturation against prior years' seasonal influenza, suggesting that 'original antigenic sin' shapes the antibody response to influenza vaccination. Published by Elsevier Inc.

  7. AGUA TIBIA PRIMITIVE AREA, CALIFORNIA.

    Science.gov (United States)

    Irwin, William P.; Thurber, Horace K.

    1984-01-01

    The Agua Tibia Primitive Area in southwestern California is underlain by igneous and metamorphic rocks that are siilar to those widely exposed throughout much of the Peninsular Ranges. To detect the presence of any concealed mineral deposits, samples of stream sediments were collected along the various creeks that head in the mountain. As an additional aid in evaluating the mineral potential, an aeromagnetic survey was made and interpreted. A search for records of past or existing mining claims within the primitive area was made but none was found. Evidence of deposits of metallic or nonmetallic minerals was not seen during the study.

  8. Spain: Europe's California.

    Science.gov (United States)

    Wilvert, Calvin

    1994-01-01

    Contends that, as Spain integrates into the European Economic Community, it is considered to be Europe's California. Asserts that making regional comparisons between California and Spain can be an effective teaching method. Provides comparisons in such areas as agriculture and tourism. (CFR)

  9. Evidence for Sequence Scrambling and Divergent H/D Exchange Reactions of Doubly-Charged Isobaric b-Type Fragment Ions

    Science.gov (United States)

    Zekavat, Behrooz; Miladi, Mahsan; Al-Fdeilat, Abdullah H.; Somogyi, Arpad; Solouki, Touradj

    2014-02-01

    To date, only a limited number of reports are available on structural variants of multiply-charged b-fragment ions. We report on observed bimodal gas-phase hydrogen/deuterium exchange (HDX) reaction kinetics and patterns for substance P b10 2+ that point to presence of isomeric structures. We also compare HDX reactions, post-ion mobility/collision-induced dissociation (post-IM/CID), and sustained off-resonance irradiation-collision induced dissociation (SORI-CID) of substance P b10 2+ and a cyclic peptide with an identical amino acid (AA) sequence order to substance P b10. The observed HDX patterns and reaction kinetics and SORI-CID pattern for the doubly charged head-to-tail cyclized peptide were different from either of the presumed isomers of substance P b10 2+, suggesting that b10 2+ may not exist exclusively as a head-to-tail cyclized structure. Ultra-high mass measurement accuracy was used to assign identities of the observed SORI-CID fragment ions of substance P b10 2+; over 30 % of the observed SORI-CID fragment ions from substance P b10 2+ had rearranged (scrambled) AA sequences. Moreover, post-IM/CID experiments revealed the presence of two conformer types for substance P b10 2+, whereas only one conformer type was observed for the head-to-tail cyclized peptide. We also show that AA sequence scrambling from CID of doubly-charged b-fragment ions is not unique to substance P b10 2+.

  10. Evidence for sequence scrambling and divergent H/D exchange reactions of doubly-charged isobaric b-type fragment ions.

    Science.gov (United States)

    Zekavat, Behrooz; Miladi, Mahsan; Al-Fdeilat, Abdullah H; Somogyi, Arpad; Solouki, Touradj

    2014-02-01

    To date, only a limited number of reports are available on structural variants of multiply-charged b-fragment ions. We report on observed bimodal gas-phase hydrogen/deuterium exchange (HDX) reaction kinetics and patterns for substance P b10(2+) that point to presence of isomeric structures. We also compare HDX reactions, post-ion mobility/collision-induced dissociation (post-IM/CID), and sustained off-resonance irradiation-collision induced dissociation (SORI-CID) of substance P b10(2+) and a cyclic peptide with an identical amino acid (AA) sequence order to substance P b10. The observed HDX patterns and reaction kinetics and SORI-CID pattern for the doubly charged head-to-tail cyclized peptide were different from either of the presumed isomers of substance P b10(2+), suggesting that b10(2+) may not exist exclusively as a head-to-tail cyclized structure. Ultra-high mass measurement accuracy was used to assign identities of the observed SORI-CID fragment ions of substance P b10(2+); over 30% of the observed SORI-CID fragment ions from substance P b10(2+) had rearranged (scrambled) AA sequences. Moreover, post-IM/CID experiments revealed the presence of two conformer types for substance P b10(2+), whereas only one conformer type was observed for the head-to-tail cyclized peptide. We also show that AA sequence scrambling from CID of doubly-charged b-fragment ions is not unique to substance P b10(2+).

  11. The complete genomic sequence of lytic bacteriophage gh-1 infecting Pseudomonas putida--evidence for close relationship to the T7 group

    International Nuclear Information System (INIS)

    Kovalyova, Irina V.; Kropinski, Andrew M.

    2003-01-01

    The genome of the lytic Pseudomonas putida bacteriophage gh-1 is linear double-stranded DNA containing 37,359 bp with 216-bp direct terminal repeats. Like other members of the T7 group, the gh-1 genome contains regions of high homology to T7 interspersed with nonhomologous regions that contain small open reading frames of unknown function. The genome shares 31 genes in common with other members of the T7 group, including RNA polymerase, and an additional 12 unique putative genes. A major difference between gh-1 and other members of this group is the absence of any open reading frames between the left direct terminal repeat and gene 1. Sequence analysis of the gh-1 genome also revealed the presence of 10 putative phage promoters with a consensus sequence similar to the promoters of T3 and phiYeO3-12 (consensus: TAAAAACCCTCACTRTGGCHSCM). P. putida mutants resistant to gh-1 were demonstrated to have an altered lipopolysaccharide structure, indicating that members of this group use lipopolysaccharide as their cellular receptor

  12. Species tree phylogeny and character evolution in the genus Centipeda (Asteraceae): evidence from DNA sequences from coding and non-coding loci from the plastid and nuclear genomes.

    Science.gov (United States)

    Nylinder, Stephan; Cronholm, Bodil; de Lange, Peter J; Walsh, Neville; Anderberg, Arne A

    2013-08-01

    A species tree phylogeny of the Australian/New Zealand genus Centipeda (Asteraceae) is estimated based on nucleotide sequence data. We analysed sequences of nuclear ribosomal DNA (ETS, ITS) and three plasmid loci (ndhF, psbA-trnH, and trnL-F) using the multi-species coalescent module in BEAST. A total of 129 individuals from all 10 recognised species of Centipeda were sampled throughout the species distribution ranges, including two subspecies. We conclude that the inferred species tree topology largely conform previous assumptions on species relationships. Centipeda racemosa (Snuffweed) is the sister to remaining species, which is also the only consistently perennial representative in the genus. Centipeda pleiocephala (Tall Sneezeweed) and C. nidiformis (Cotton Sneezeweed) constitute a species pair, as does C. borealis and C. minima (Spreading Sneezeweed), all sharing the symplesiomorphic characters of spherical capitulum and convex receptacle with C. racemosa. Another species group comprising C. thespidioides (Desert Sneezeweed), C. cunninghamii (Old man weed, or Common sneeze-weed), C. crateriformis is well-supported but then include the morphologically aberrant C. aotearoana, all sharing the character of having capitula that mature more slowly relative the subtending shoot. Centipeda elatinoides takes on a weakly supported intermediate position between the two mentioned groups, and is difficult to relate to any of the former groups based on morphological characters. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. California Institute for Water Resources - California Institute for Water

    Science.gov (United States)

    Resources Skip to Content Menu California Institute for Water Resources Share Print Site Map Resources Publications Keep in Touch QUICK LINKS Our Blog: The Confluence Drought & Water Information University of California California Institute for Water Resources California Institute for Water Resources

  14. A probable prehistoric case of meningococcal disease from San Francisco Bay: Next generation sequencing of Neisseria meningitidis from dental calculus and osteological evidence.

    Science.gov (United States)

    Eerkens, Jelmer W; Nichols, Ruth V; Murray, Gemma G R; Perez, Katherine; Murga, Engel; Kaijankoski, Phil; Rosenthal, Jeffrey S; Engbring, Laurel; Shapiro, Beth

    2018-05-25

    Next Generation Sequencing (NGS) of ancient dental calculus samples from a prehistoric site in San Francisco Bay, CA-SCL-919, reveals a wide range of potentially pathogenic bacteria. One older adult woman, in particular, had high levels of Neisseria meningitidis and low levels of Haemophilus influenzae, species that were not observed in the calculus from three other individuals. Combined with the presence of incipient endocranial lesions and pronounced meningeal grooves, we interpret this as an ancient case of meningococcal disease. This disease afflicts millions around the globe today, but little is known about its (pre)history. With additional sampling, we suggest NGS of calculus offers an exciting new window into the evolutionary history of these bacterial species and their interactions with humans. Copyright © 2018 Elsevier Inc. All rights reserved.

  15. Deep sequencing of atrial fibrillation patients with mitral valve regurgitation shows no evidence of mosaicism but reveals novel rare germline variants

    DEFF Research Database (Denmark)

    Gregers, Emilie; Ahlberg, Gustav; Christensen, Thea

    2017-01-01

    the HaloPlex Target Enrichment System. MuTect software was used for identification of somatic point variants. We functionally characterized selected variants using electrophysiologic techniques. RESULTS: No somatic variants were identified in the cardiac tissue. Thirty-three patients (75%) had a rare...... patient population undergoing surgery for mitral valve regurgitation (MVR) to determine whether these patients are genetically predisposed to AF. METHODS: DNA was extracted from blood and left atrial tissue from 44 AF patients with MVR. Using next-generation sequencing, we investigated 110 genes using...... germline variation in ≥1 candidate genes. Fourteen variants were novel. Fifteen variants were predicted damaging or likely damaging in ≥6 in silico predictions. We identified rare variants in genes never directly associated with AF: KCNE4, SCN4B, NEURL1, and CAND2. Interestingly, 7 patients (16%) had...

  16. Complete genome sequence of two tomato-infecting begomoviruses in Venezuela: evidence of a putative novel species and a novel recombinant strain.

    Science.gov (United States)

    Romay, Gustavo; Chirinos, Dorys T; Geraud-Pouey, Francis; Gillis, Annika; Mahillon, Jacques; Bragard, Claude

    2018-02-01

    At least six begomovirus species have been reported infecting tomato in Venezuela. In this study the complete genomes of two tomato-infecting begomovirus isolates (referred to as Trujillo-427 and Zulia-1084) were cloned and sequenced. Both isolates showed the typical genome organization of New World bipartite begomoviruses, with DNA-A genomic components displaying 88.8% and 90.3% similarity with established begomoviruses, for isolates Trujillo-427 and Zulia-1084, respectively. In accordance to the guidelines for begomovirus species demarcation, the Trujillo-427 isolate represents a putative new species and the name "Tomato wrinkled mosaic virus" is proposed. Meanwhile, Zulia-1084 represents a putative new strain classifiable within species Tomato chlorotic leaf distortion virus, for which a recombinant origin is suggested.

  17. Evidence for a novel coding sequence overlapping the 5'-terminal ~90 codons of the Gill-associated and Yellow head okavirus envelope glycoprotein gene

    Directory of Open Access Journals (Sweden)

    Atkins John F

    2009-12-01

    Full Text Available Abstract The genus Okavirus (order Nidovirales includes a number of viruses that infect crustaceans, causing major losses in the shrimp industry. These viruses have a linear positive-sense ssRNA genome of ~26-27 kb, encoding a large replicase polyprotein that is expressed from the genomic RNA, and several additional proteins that are expressed from a nested set of 3'-coterminal subgenomic RNAs. In this brief report, we describe the bioinformatic discovery of a new, apparently coding, ORF that overlaps the 5' end of the envelope glycoprotein encoding sequence, ORF3, in the +2 reading frame. The new ORF has a strong coding signature and, in fact, is more conserved at the amino acid level than the overlapping region of ORF3. We propose that translation of the new ORF initiates at a conserved AUG codon separated by just 2 nt from the ORF3 AUG initiation codon, resulting in a novel 86 amino acid protein.

  18. A 100-year average recurrence interval for the san andreas fault at wrightwood, california.

    Science.gov (United States)

    Fumal, T E; Schwartz, D P; Pezzopane, S K; Weldon, R J

    1993-01-08

    Evidence for five large earthquakes during the past five centuries along the San Andreas fault zone 70 kilometers northeast of Los Angeles, California, indicates that the average recurrence interval and the temporal variability are significantly smaller than previously thought. Rapid sedimentation during the past 5000 years in a 150-meter-wide structural depression has produced a greater than 21-meter-thick sequence of debris flow and stream deposits interbedded with more than 50 datable peat layers. Fault scarps, colluvial wedges, fissure infills, upward termination of ruptures, and tilted and folded deposits above listric faults provide evidence for large earthquakes that occurred in A.D. 1857, 1812, and about 1700, 1610, and 1470.

  19. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  20. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  1. Paleoclimatic and paleolatitude settings of accumulation of radiolarian siliceous-volcanogenic sequences in the middle Mesozoic Pacific: Evidence from allochthons of East Asia

    Science.gov (United States)

    Vishnevskaya, V. S.; Filatova, N. I.

    2017-09-01

    Jurassic-Cretaceous siliceous-volcanogenic rocks from nappes of tectonostratigraphic sequences of the East Asia Middle Cretaceous Okhotsk-Koryak orogenic belt are represented by a wide range of geodynamic sedimentation settings: oceanic (near-spreading zones, seamounts, and deep-water basins), marginal seas, and island arcs. The taxonomic compositions of radiolarian communities are used as paleolatitude indicators in the Northern Pacific. In addition, a tendency toward climate change in the Mesozoic is revealed based on these communities: from the warm Triassic to the cold Jurassic with intense warming from the Late Jurassic to the Early Cretaceous. Cretaceous warming led to heating of ocean waters even at moderately high latitudes and to the development of Tethyan radiolarians there. These data are confirmed by a global Cretaceous temperature peak coinciding with a high-activity pulse of the planetary mantle superplume system, which created thermal anomalies and the greenhouse effect. In addition, the Pacific superplume attributed to this system caused accelerated movement of oceanic plates, which resulted in a compression setting on the periphery of the Pacific and the formation of the Okhotsk-Koryak orogenic belt on its northwestern framing in the Middle Cretaceous, where Mesozoic rocks of different geodynamic and latitudinal-climate settings were juxtaposed into allochthonous units.

  2. New evidence for the role of calpain 10 in autosomal recessive intellectual disability: identification of two novel nonsense variants by exome sequencing in Iranian families.

    Science.gov (United States)

    Oladnabi, Morteza; Musante, Luciana; Larti, Farzaneh; Hu, Hao; Abedini, Seyedeh Sedigheh; Wienker, Thomas; Ropers, Hans Hilger; Kahrizi, Kimia; Najmabadi, Hossein

    2015-03-01

    Knowledge of the genes responsible for intellectual disability, particularly autosomal recessive forms, is rapidly expanding. Increasing numbers of the gene show great heterogeneity and supports the hypothesis that human genome may contain over 2000 causative genes with a critical role in brain development. Since 2004, we have applied genome-wide SNP genotyping and next-generation sequencing in large consanguineous Iranian families with intellectual disability, to identify the genes harboring disease-causing mutations. The current study paved the way for identification of responsible genes in two unrelated Iranian families. We found two novel nonsense mutations, p.C77* and p.Q115*, in the calpain catalytic domain of CAPN10, which is a cysteine protease known to be involved in pathogenesis of noninsulin-dependent diabetes mellitus. Another different mutation in this gene (p.S138_R139ins5) has previously been reported in an Iranian family. All of these patients have common clinical features in spite of specific brain structural abnormalities on MRI. Different mutations in CAPN10 have already been found in three independent Iranian families. These results have strongly supported the possible role of CAPN10 in human brain development. Altogether, we proposed CAPN10 as a promising candidate gene for intellectual disability, which should be considered in diagnostic gene panels.

  3. Grateloupia ramosa Wang & Luan sp. nov. (Halymeniaceae, Rhodophyta), a new species from China based on morphological evidence and comparative rbcL sequences

    Science.gov (United States)

    Cao, Cuicui; Liu, Miao; Guo, Shaoru; Zhao, Dan; Luan, Rixiao; Wang, Hongwei

    2016-03-01

    Grateloupia ramosa Wang & Luan sp. nov. (Halymeniaceae, Rhodophyta) is newly described from Hainan Province, southern China. The organism has the following morphological features: (1) purplish red, cartilaginous and lubricous thalli 5-10 cm in height; (2) compressed percurrent axes bearing abundant branches with opposite arrangement; (3) claw-like apices on top, constricted to 2-4 cm at the base; (4) cortex consisting of 3-6 layers of elliptical or anomalous cells and a medulla covered by compact medullary filaments; (5) reproductive structures distributed throughout the thallus, especially centralized at the bottom of the end portion of the branches; and (6) 4-celled Carpogonial branches and 3-celled auxiliary-cell branches, both of the Grateloupia-type. The morphological diff erences were supported by molecular phylogenetics based on ribulose-1, 5-bisphosphate carboxylase/oxygenase ( rbcL) gene sequence analysis. There was only a 1 bp divergence between specimens collected from Wenchang and Lingshui of Hainan province. The new species was embedded in the large Grateloupia clade of the Halymeniaceae. The pairwise distances between G. ramosa and other species within Grateloupia ranged from 26 to 105 bp, within pairwise distances of 13-111 bp between species of the large genus Grateloupia in Halymeniaceae. Thus, we propose this new species as G. ramosa Wang & Luan sp. nov.

  4. Formation mechanisms and sequence response of authigenic grain-coating chlorite: evidence from the Upper Triassic Xujiahe Formation in the southern Sichuan Basin, China

    Directory of Open Access Journals (Sweden)

    Yu Yu

    2016-11-01

    Full Text Available Abstract Authigenic grain-coating chlorite is widely distributed in the clastic rocks of many sedimentary basins around the world. These iron minerals were mainly derived from flocculent precipitates formed when rivers flow into the ocean, especially in deltaic environments with high hydrodynamic conditions. At the same time, sandstone sequences with grain-coating chlorites also tend to have relatively high glauconite and pyrite content. EPMA composition analysis shows that glauconites with “high Al and low Fe” content indicate slightly to semi-saline marine environments with weak alkaline and weakly reducing conditions. By analyzing the chlorite-containing sandstone bodies of the southern Sichuan Xujiahe Formation, this study found that chlorite was mainly distributed in sedimentary microfacies, including underwater distributary channels, distributary channels, shallow lake sandstone dams, and mouth bars. Chlorite had a tendency to form in the upper parts of sandstone bodies with signs of increased base level, representing the influence of marine (lacustrine transgression. This is believed to be influenced by megamonsoons in the Middle and Upper Yangtze Region during the Late Triassic Epoch. During periods of abundant precipitation, river discharges increased and more Fe particulates flowed into the ocean (lake. In the meantime, increases or decreases in lake level were only affected by precipitation for short periods of time. The sedimentary environment shifted from weakly oxidizing to weak alkaline, weakly reducing conditions as sea level increased, and Fe-rich minerals as authigenic chlorite and glauconite began to form and deposit.

  5. Morphologic and molecular study of hemoparasites in wild corvids and evidence of sequence identity with Plasmodium DNA detected in captive black-footed penguins (Spheniscus demersus).

    Science.gov (United States)

    Leclerc, Antoine; Chavatte, Jean-Marc; Landau, Irène; Snounou, Georges; Petit, Thierry

    2014-09-01

    A morphologic and molecular epidemiologic investigation was conducted on a captive African black-footed penguin (Spheniscus demersus) colony with a history of Plasmodium infections at La Palmyre Zoo (France). Each penguin received 12.5 mg of pyrimethamine twice a week as a prophylaxis every year from April to November. Although Plasmodium parasites were not detected in blood smears and tissues collected from the penguins, various blood parasites were recorded in blood smears from wild Eurasian magpies (Pica pica) and carrion crows (Corvus corone) sampled at the same time in the study area. These parasites consisted of several Plasmodium spp. (P. lenoblei, P. dorsti, P bioccai, P. relictum, P. dherteae, P. beaucournui, P. maior, P. tranieri, and P. snounoui), Parahaemoproteus spp., Trypanosoma spp., and Leucocytozoon spp. On the other hand, nested polymerase chain reaction enabled detection of Plasmodium DNA in 28/44 (64%) penguins, 15/25 (60%) magpies, and 4/9 (44%) crows. Sequencing and phylogenetic analyses indicated that the parasite DNA amplified from the penguins, magpies, and crows were similar. Magpies and crows could therefore act as a reservoir for penguin Plasmodium infections, which may be more prevalent than previously thought. Morphologic characterization of the Plasmodium spp. detected in the penguins, as well as further biological and epidemiologic studies, are needed to fully understand the transmission of Plasmodium parasites to captive penguins.

  6. University of Southern California

    Data.gov (United States)

    Federal Laboratory Consortium — The focus of the University of Southern California (USC) Children''s Environmental Health Center is to develop a better understanding of how host susceptibility and...

  7. Coastal California Digital Imagery

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This digital ortho-imagery dataset is a survey of coastal California. The project area consists of approximately 3774 square miles. The project design of the digital...

  8. California Harpoon Fishery

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains vessel logbook and landings data from harpoon vessels that fish within 200 miles of the California coast, from 1974 to present. The harpoon...

  9. Kelp distribution off California

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set delineates kelp beds (Nereocystis leutkeana and Macrocystis spp.) along the Pacific Coast of California. Multiple years of kelp mapping data for the...

  10. California Ocean Uses Atlas

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset is a result of the California Ocean Uses Atlas Project: a collaboration between NOAA's National Marine Protected Areas Center and Marine Conservation...

  11. California Watershed Hydrologic Units

    Data.gov (United States)

    California Natural Resource Agency — This dataset is intended to be used as a tool for water-resource management and planning activities, particularly for site-specific and localized studies requiring a...

  12. The origin of the 5S ribosomal RNA molecule could have been caused by a single inverse duplication: strong evidence from its sequences.

    Science.gov (United States)

    Branciamore, Sergio; Di Giulio, Massimo

    2012-04-01

    The secondary structure of the 5S ribosomal RNA (5S rRNA) molecule shows a high degree of symmetry. In order to explain the origin of this symmetry, it has been conjectured that one half of the 5S rRNA molecule was its precursor and that an indirect duplication of this precursor created the other half and thus the current symmetry of the molecule. Here, we have subjected to an empirical test both the indirect duplication model, analysing a total of 684 5S rRNA sequences for complementarity between the two halves of the 5S rRNA, and the direct duplication model analysing in this case the similarity between the two halves of this molecule. In intra- and inter-molecule and intra- and inter-domain comparisons, we find a high statistical support to the hypothesis of a complementarity relationship between the two halves of the 5S rRNA molecule, denying vice versa the hypothesis of similarity between these halves. Therefore, these observations corroborate the indirect duplication model at the expense of the direct duplication model, as reason of the origin of the 5S rRNA molecule. More generally, we discuss and favour the hypothesis that all RNAs and proteins, which present symmetry, did so through gene duplication and not by gradualistic accumulation of few monomers or segments of molecule into a gradualistic growth process. This would be the consequence of the very high propensity that nucleic acids have to be subjected to duplications.

  13. The population genetics of Quechuas, the largest native South American group: autosomal sequences, SNPs, and microsatellites evidence high level of diversity.

    Science.gov (United States)

    Scliar, Marilia O; Soares-Souza, Giordano B; Chevitarese, Juliana; Lemos, Livia; Magalhães, Wagner C S; Fagundes, Nelson J; Bonatto, Sandro L; Yeager, Meredith; Chanock, Stephen J; Tarazona-Santos, Eduardo

    2012-03-01

    Elucidating the pattern of genetic diversity for non-European populations is necessary to make the benefits of human genetics research available to individuals from these groups. In the era of large human genomic initiatives, Native American populations have been neglected, in particular, the Quechua, the largest South Amerindian group settled along the Andes. We characterized the genetic diversity of a Quechua population in a global setting, using autosomal noncoding sequences (nine unlinked loci for a total of 16 kb), 351 unlinked SNPs and 678 microsatellites and tested predictions of the model of the evolution of Native Americans proposed by (Tarazona-Santos et al.: Am J Hum Genet 68 (2001) 1485-1496). European admixture is Quechua or Melanesian populations, which is concordant with the African origin of modern humans and the fact that South America was the last part of the world to be peopled. The diversity in the Quechua population is comparable with that of Eurasian populations, and the allele frequency spectrum based on resequencing data does not reflect a reduction in the proportion of rare alleles. Thus, the Quechua population is a large reservoir of common and rare genetic variants of South Amerindians. These results are consistent with and complement our evolutionary model of South Amerindians (Tarazona-Santos et al.: Am J Hum Genet 68 (2001) 1485-1496), proposed based on Y-chromosome data, which predicts high genomic diversity due to the high level of gene flow between Andean populations and their long-term effective population size. Copyright © 2012 Wiley Periodicals, Inc.

  14. Constraints on the rheology of the lower crust in a strike-slip plate boundary: evidence from the San Quintín xenoliths, Baja California, Mexico

    Directory of Open Access Journals (Sweden)

    T. van der Werf

    2017-12-01

    Full Text Available The rheology of lower crust and its transient behavior in active strike-slip plate boundaries remain poorly understood. To address this issue, we analyzed a suite of granulite and lherzolite xenoliths from the upper Pleistocene–Holocene San Quintín volcanic field of northern Baja California, Mexico. The San Quintín volcanic field is located 20 km east of the Baja California shear zone, which accommodates the relative movement between the Pacific plate and Baja California microplate. The development of a strong foliation in both the mafic granulites and lherzolites, suggests that a lithospheric-scale shear zone exists beneath the San Quintín volcanic field. Combining microstructural observations, geothermometry, and phase equilibria modeling, we estimated that crystal-plastic deformation took place at temperatures of 750–890 °C and pressures of 400–560 MPa, corresponding to 15–22 km depth. A hot crustal geotherm of 40 ° C km−1 is required to explain the estimated deformation conditions. Infrared spectroscopy shows that plagioclase in the mafic granulites is relatively dry. Microstructures are interpreted to show that deformation in both the uppermost lower crust and upper mantle was accommodated by a combination of dislocation creep and grain-size-sensitive creep. Recrystallized grain size paleopiezometry yields low differential stresses of 12–33 and 17 MPa for plagioclase and olivine, respectively. The lower range of stresses (12–17 MPa in the mafic granulite and lherzolite xenoliths is interpreted to be associated with transient deformation under decreasing stress conditions, following an event of stress increase. Using flow laws for dry plagioclase, we estimated a low viscosity of 1.1–1.3×1020 Pa ⋅ s for the high temperature conditions (890 °C in the lower crust. Significantly lower viscosities in the range of 1016–1019 Pa ⋅ s, were estimated using flow laws for wet plagioclase. The

  15. Evaluating Options for Improving California's Drought Resilience

    Science.gov (United States)

    Ray, P. A.; Schwarz, A.; Wi, S.; Correa, M.; Brown, C.

    2015-12-01

    Through a unique collaborative arrangement, the University of Massachusetts (UMass) and the California Department of Water Resources (DWR) have together performed a baseline climate change analysis of the California state (State Water Project) and federal (Central Valley Project) water systems. The first step in the baseline analysis was development of an improved basinwide hydrologic model covering a large area of California including all major tributaries to the state and federal water systems. The CalLite modeling system used by DWR for planning purposes allowed simulation of the system of reservoirs, rivers, control points, and deliveries which are then used to create performance metrics that quantify a wide range of system characteristics including water deliveries, water quality, and environmental/ecological factors. A baseline climate stress test was conducted to identify current vulnerabilities to climate change through the linking of the modeling chain with Decision Scaling concepts through the UMass bottom-up climate stress-testing algorithm. This procedure allowed the first comprehensive climate stress analysis of the California state and federal water systems not constrained by observed historical variability and wet-dry year sequences. A forward-looking drought vulnerability and adaptation assessment of the water systems based on this workflow is ongoing and preliminary results will be presented. Presentation of results will include discussion of the collaborative arrangement between DWR and UMass, which is instrumental to both the success of the research and the education of policy makers.

  16. Phylogenetic relationships of Acheilognathidae (Cypriniformes: Cyprinoidea) as revealed from evidence of both nuclear and mitochondrial gene sequence variation: evidence for necessary taxonomic revision in the family and the identification of cryptic species.

    Science.gov (United States)

    Chang, Chia-Hao; Li, Fan; Shao, Kwang-Tsao; Lin, Yeong-Shin; Morosawa, Takahiro; Kim, Sungmin; Koo, Hyeyoung; Kim, Won; Lee, Jae-Seong; He, Shunping; Smith, Carl; Reichard, Martin; Miya, Masaki; Sado, Tetsuya; Uehara, Kazuhiko; Lavoué, Sébastien; Chen, Wei-Jen; Mayden, Richard L

    2014-12-01

    Bitterlings are relatively small cypriniform species and extremely interesting evolutionarily due to their unusual reproductive behaviors and their coevolutionary relationships with freshwater mussels. As a group, they have attracted a great deal of attention in biological studies. Understanding the origin and evolution of their mating system demands a well-corroborated hypothesis of their evolutionary relationships. In this study, we provide the most comprehensive phylogenetic reconstruction of species relationships of the group based on partitioned maximum likelihood and Bayesian methods using DNA sequence variation of nuclear and mitochondrial genes on 41 species, several subspecies and three undescribed species. Our findings support the monophyly of the Acheilognathidae. Two of the three currently recognized genera are not monophyletic and the family can be subdivided into six clades. These clades are further regarded as genera based on both their phylogenetic relationships and a reappraisal of morphological characters. We present a revised classification for the Acheilognathidae with five genera/lineages: Rhodeus, Acheilognathus (new constitution), Tanakia (new constitution), Paratanakia gen. nov., and Pseudorhodeus gen. nov. and an unnamed clade containing five species currently referred to as "Acheilognathus". Gene trees of several bitterling species indicate that the taxa are not monophyletic. This result highlights a potentially dramatic underestimation of species diversity in this family. Using our new phylogenetic framework, we discuss the evolution of the Acheilognathidae relative to classification, taxonomy and biogeography. Copyright © 2014 Elsevier Inc. All rights reserved.

  17. Quantifying type-specific reproduction numbers for nosocomial pathogens: evidence for heightened transmission of an Asian sequence type 239 MRSA clone.

    Directory of Open Access Journals (Sweden)

    Ben S Cooper

    Full Text Available An important determinant of a pathogen's success is the rate at which it is transmitted from infected to susceptible hosts. Although there are anecdotal reports that methicillin-resistant Staphylococcus aureus (MRSA clones vary in their transmissibility in hospital settings, attempts to quantify such variation are lacking for common subtypes, as are methods for addressing this question using routinely-collected MRSA screening data in endemic settings. Here we present a method to quantify the time-varying transmissibility of different subtypes of common bacterial nosocomial pathogens using routine surveillance data. The method adapts approaches for estimating reproduction numbers based on the probabilistic reconstruction of epidemic trees, but uses relative hazards rather than serial intervals to assign probabilities to different sources for observed transmission events. The method is applied to data collected as part of a retrospective observational study of a concurrent MRSA outbreak in the United Kingdom with dominant endemic MRSA clones (ST22 and ST36 and an Asian ST239 MRSA strain (ST239-TW in two linked adult intensive care units, and compared with an approach based on a fully parametric transmission model. The results provide support for the hypothesis that the clones responded differently to an infection control measure based on the use of topical antiseptics, which was more effective at reducing transmission of endemic clones. They also suggest that in one of the two ICUs patients colonized or infected with the ST239-TW MRSA clone had consistently higher risks of transmitting MRSA to patients free of MRSA. These findings represent some of the first quantitative evidence of enhanced transmissibility of a pandemic MRSA lineage, and highlight the potential value of tailoring hospital infection control measures to specific pathogen subtypes.

  18. Millennial-scale climatic variability between 340 000 and 270 000 years ago in SW Europe: evidence from a NW Iberian margin pollen sequence

    Directory of Open Access Journals (Sweden)

    S. Desprat

    2009-03-01

    Full Text Available We present a new high-resolution marine pollen record from NW Iberian margin sediments (core MD03-2697 covering the interval between 340 000 and 270 000 years ago, a time period centred on Marine Isotope Stage (MIS 9 and characterized by particular baseline climate states. This study enables the documentation of vegetation changes in the north-western Iberian Peninsula and therefore the terrestrial climatic variability at orbital and in particular at millennial scales during MIS 9, directly on a marine stratigraphy. Suborbital vegetation changes in NW Iberia in response to cool/cold events are detected throughout the studied interval even during MIS 9e ice volume minimum. However, they appear more frequent and of higher amplitude during the 30 000 years following the MIS 9e interglacial period and during the MIS 9a-8 transition, which correspond to intervals of an intermediate to high ice volume and mainly periods of ice growth. Each suborbital cold event detected in NW Iberia has a counterpart in the Southern Iberian margin SST record. High to moderate amplitude cold episodes detected on land and in the ocean appear to be related to changes in deep water circulation and probably to iceberg discharges at least during MIS 9d, the mid-MIS 9c cold event and MIS 9b. This work provides therefore additional evidence of pervasive millennial-scale climatic variability in the North Atlantic borderlands throughout past climatic cycles of the Late Pleistocene, regardless of glacial state. However, ice volume might have an indirect influence on the amplitude of the millennial climatic changes in Southern Europe.

  19. Analysis of complete genome sequences of G9P[19] rotavirus strains from human and piglet with diarrhea provides evidence for whole-genome interspecies transmission of nonreassorted porcine rotavirus.

    Science.gov (United States)

    Yodmeeklin, Arpaporn; Khamrin, Pattara; Chuchaona, Watchaporn; Kumthip, Kattareeya; Kongkaew, Aphisek; Vachirachewin, Ratchaya; Okitsu, Shoko; Ushijima, Hiroshi; Maneekarn, Niwat

    2017-01-01

    Whole genomes of G9P[19] human (RVA/Human-wt/THA/CMH-S070-13/2013/G9P[19]) and porcine (RVA/Pig-wt/THA/CMP-015-12/2012/G9P[19]) rotaviruses concurrently detected in the same geographical area in northern Thailand were sequenced and analyzed for their genetic relationships using bioinformatic tools. The complete genome sequence of human rotavirus RVA/Human-wt/THA/CMH-S070-13/2013/G9P[19] was most closely related to those of porcine rotavirus RVA/Pig-wt/THA/CMP-015-12/2012/G9P[19] and to those of porcine-like human and porcine rotaviruses reference strains than to those of human rotavirus reference strains. The genotype constellation of G9P[19] detected in human and piglet were identical and displayed as the G9-P[19]-I5-R1-C1-M1-A8-N1-T1-E1-H1 genotypes with the nucleotide sequence identities of VP7, VP4, VP6, VP1, VP2, VP3, NSP1, NSP2, NSP3, NSP4, and NSP5 at 99.0%, 99.5%, 93.2%, 97.7%, 97.7%, 85.6%, 89.5%, 93.2%, 92.9%, 94.0%, and 98.1%, respectively. The findings indicate that human rotavirus strain RVA/Human-wt/THA/CMH-S070-13/2013/G9P[19] containing the genome segments of porcine genetic backbone is most likely a human rotavirus of porcine origin. Our data provide an evidence of interspecies transmission and whole-genome transmission of nonreassorted G9P[19] porcine RVA to human occurring in nature in northern Thailand. Copyright © 2016. Published by Elsevier B.V.

  20. Private Schools, California, 2009, California Department of Education

    Data.gov (United States)

    U.S. Environmental Protection Agency — California law (California Education Code Section 33190) requires private schools offering or conducting a full-time elementary or secondary level day school for...

  1. The California Hazards Institute

    Science.gov (United States)

    Rundle, J. B.; Kellogg, L. H.; Turcotte, D. L.

    2006-12-01

    California's abundant resources are linked with its natural hazards. Earthquakes, landslides, wildfires, floods, tsunamis, volcanic eruptions, severe storms, fires, and droughts afflict the state regularly. These events have the potential to become great disasters, like the San Francisco earthquake and fire of 1906, that overwhelm the capacity of society to respond. At such times, the fabric of civic life is frayed, political leadership is tested, economic losses can dwarf available resources, and full recovery can take decades. A patchwork of Federal, state and local programs are in place to address individual hazards, but California lacks effective coordination to forecast, prevent, prepare for, mitigate, respond to, and recover from, the harmful effects of natural disasters. Moreover, we do not know enough about the frequency, size, time, or locations where they may strike, nor about how the natural environment and man-made structures would respond. As California's population grows and becomes more interdependent, even moderate events have the potential to trigger catastrophes. Natural hazards need not become natural disasters if they are addressed proactively and effectively, rather than reactively. The University of California, with 10 campuses distributed across the state, has world-class faculty and students engaged in research and education in all fields of direct relevance to hazards. For that reason, the UC can become a world leader in anticipating and managing natural hazards in order to prevent loss of life and property and degradation of environmental quality. The University of California, Office of the President, has therefore established a new system-wide Multicampus Research Project, the California Hazards Institute (CHI), as a mechanism to research innovative, effective solutions for California. The CHI will build on the rich intellectual capital and expertise of the Golden State to provide the best available science, knowledge and tools for

  2. Setting a minimum age for juvenile justice jurisdiction in California.

    Science.gov (United States)

    S Barnert, Elizabeth; S Abrams, Laura; Maxson, Cheryl; Gase, Lauren; Soung, Patricia; Carroll, Paul; Bath, Eraka

    2017-03-13

    Purpose Despite the existence of minimum age laws for juvenile justice jurisdiction in 18 US states, California has no explicit law that protects children (i.e. youth less than 12 years old) from being processed in the juvenile justice system. In the absence of a minimum age law, California lags behind other states and international practice and standards. The paper aims to discuss these issues. Design/methodology/approach In this policy brief, academics across the University of California campuses examine current evidence, theory, and policy related to the minimum age of juvenile justice jurisdiction. Findings Existing evidence suggests that children lack the cognitive maturity to comprehend or benefit from formal juvenile justice processing, and diverting children from the system altogether is likely to be more beneficial for the child and for public safety. Research limitations/implications Based on current evidence and theory, the authors argue that minimum age legislation that protects children from contact with the juvenile justice system and treats them as children in need of services and support, rather than as delinquents or criminals, is an important policy goal for California and for other national and international jurisdictions lacking a minimum age law. Originality/value California has no law specifying a minimum age for juvenile justice jurisdiction, meaning that young children of any age can be processed in the juvenile justice system. This policy brief provides a rationale for a minimum age law in California and other states and jurisdictions without one.

  3. Setting a minimum age for juvenile justice jurisdiction in California

    Science.gov (United States)

    Barnert, Elizabeth S.; Abrams, Laura S.; Maxson, Cheryl; Gase, Lauren; Soung, Patricia; Carroll, Paul; Bath, Eraka

    2018-01-01

    Purpose Despite the existence of minimum age laws for juvenile justice jurisdiction in 18 US states, California has no explicit law that protects children (i.e. youth less than 12 years old) from being processed in the juvenile justice system. In the absence of a minimum age law, California lags behind other states and international practice and standards. The paper aims to discuss these issues. Design/methodology/approach In this policy brief, academics across the University of California campuses examine current evidence, theory, and policy related to the minimum age of juvenile justice jurisdiction. Findings Existing evidence suggests that children lack the cognitive maturity to comprehend or benefit from formal juvenile justice processing, and diverting children from the system altogether is likely to be more beneficial for the child and for public safety. Research limitations/implications Based on current evidence and theory, the authors argue that minimum age legislation that protects children from contact with the juvenile justice system and treats them as children in need of services and support, rather than as delinquents or criminals, is an important policy goal for California and for other national and international jurisdictions lacking a minimum age law. Originality/value California has no law specifying a minimum age for juvenile justice jurisdiction, meaning that young children of any age can be processed in the juvenile justice system. This policy brief provides a rationale for a minimum age law in California and other states and jurisdictions without one. Paper type Conceptual paper PMID:28299968

  4. The Story of California = La Historia de California.

    Science.gov (United States)

    Bartel, Nick

    "The Story of California" is a history and geography of the state of California, intended for classroom use by limited-English-proficient, native Spanish-speaking students in California's urban middle schools. The book is designed with the left page in English and the right page in Spanish to facilitate student transition into…

  5. LLWPA: Implementation in California

    International Nuclear Information System (INIS)

    Gaynor, R.K.; Romano, S.A.

    1987-01-01

    US Ecology has been designated by the State of California to locate, develop and operate a low-level radioactive waste disposal facility. In early 1986, the firm identified eighteen desert basins in southeastern California for siting considerations. Three candidate sites were selected for detailed field characterization work in February, 1987. A preferred site for licensing purposes will be identified in late 1987. California is currently ahead of the siting milestone schedule mandated by the Low-Level Radioactive Waste Policy Amendments Act. It is likely that a license application will be filed in mid-1988, well before the 1990 milestone date. It is anticipated that the site will be constructed around that milestone date. This paper describes the process undertaken by US Ecology to identify three candidate sites for characterization, and the public involvement program supporting this decision. Future activities leading to a final site development are also described

  6. Transit performance measures in California.

    Science.gov (United States)

    2016-04-01

    This research is the result of a California Department of Transportation (Caltrans) request to assess the most commonly : available transit performance measures in California. Caltrans wanted to understand performance measures and data used by : Metr...

  7. Solar: California, not dreaming

    Energy Technology Data Exchange (ETDEWEB)

    Jones, J.

    2006-03-15

    The California Solar Initiative (CSI) was approved by the California Public Utilities Commission (PUC) in January 2006. The CSI is the largest solar programme of this kind ever in the USA and provides for $3.2 billion in incentives for solar projects between 2007 and 2017. The PUC will oversee a $2.5 billion programme to provide funding for solar installations on commercial and existing residential buildings, while the California Energy Commission (CEC) will manage a separate $350 million fund targeted at new residential building. Existing solar programmes operated by the PUC and CEC will be consolidated into the CSI. The CEC programme will use already allocated funding, but the PUC programme will be funded through revenues collected from customers of the main gas and electric utilities in California. Funds will be distributed via rebates to householders or companies that install solar. As well as solar photovoltaics (PV), rebates will also go to solar thermal power (concentrating solar power) and solar heating and cooling. CSI funding can be used in combination with existing federal tax credits. The aim is a gradual increase from installation of 40 MW of PV in 2005 to 100 MW by 2009. The CSI is also expected to create favourable market conditions for PV manufacturers in California and to encourage investment in production of solar-grade silicon in or near California. Objections from the International Brotherhood of Electrical Workers (IBEW) appear to have been overcome but a number of other potential snags remain. CSI is expected to be replicated in other US states.

  8. Higher Education in California

    Science.gov (United States)

    Public Policy Institute of California, 2016

    2016-01-01

    Higher education enhances Californians' lives and contributes to the state's economic growth. But population and education trends suggest that California is facing a large shortfall of college graduates. Addressing this short­fall will require strong gains for groups that have been historically under­represented in higher education. Substantial…

  9. California Budget Simulation

    Science.gov (United States)

    Mallinson, Daniel J.

    2018-01-01

    The California Budget Challenge produced by Next10 provides a useful and intuitive tool for instructors to introduce students to public budgeting. Students will reason through a series of budgeting decisions using information provided on the fiscal and practical implications of their choices. The Challenge is updated with each budget cycle, so it…

  10. Oak management in California

    Science.gov (United States)

    Plumb. Timothy R.; Philip M. McDonald

    1981-01-01

    Native oak species grow on 15 to 20 million acres (6 to 8 million ha) of California land, and have an estimated net volume of about 3 billion ft3 (85 million m3). This resource, valuable not only for traditional wood products, but also for wildlife habitat, watershed protection, and recreational-esthetic values, is not...

  11. California's Perfect Storm

    Science.gov (United States)

    Bacon, David

    2010-01-01

    The United States today faces an economic crisis worse than any since the Great Depression of the 1930s. Nowhere is it sharper than in the nation's schools. Last year, California saw a perfect storm of protest in virtually every part of its education system. K-12 teachers built coalitions with parents and students to fight for their jobs and their…

  12. FELLOWS ADDRESS California Dreaming

    NARCIS (Netherlands)

    Kooten, van Kees

    2017-01-01

    California was the first jurisdiction to mandate a reduction in greenhouse gas (GHG) emissions by 80% below 1990 levels by 2050. This target was subsequently endorsed by the G8 in 2009 and the European Commission in 2014, and is the guiding principle of the 2015 Paris Agreement. To achieve these

  13. NREL + Southern California Gas

    Energy Technology Data Exchange (ETDEWEB)

    Berdahl, Sonja E [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2017-10-09

    NREL and Southern California Gas Company are evaluating a new 'power-to-gas' approach - one that produces methane through a biological pathway and uses the expansive natural gas infrastructure to store it. This approach has the potential to change how the power industry approaches renewable generation and energy storage.

  14. California's Future: Higher Education

    Science.gov (United States)

    Johnson, Hans

    2015-01-01

    California's higher education system is not keeping up with the changing economy. Projections suggest that the state's economy will continue to need more highly educated workers. In 2025, if current trends persist, 41 percent of jobs will require at least a bachelor's degree and 36 percent will require some college education short of a bachelor's…

  15. Investigation of and Response to 2 Plague Cases, Yosemite National Park, California, USA, 2015.

    Science.gov (United States)

    Danforth, Mary; Novak, Mark; Petersen, Jeannine; Mead, Paul; Kingry, Luke; Weinburke, Matthew; Buttke, Danielle; Hacker, Gregory; Tucker, James; Niemela, Michael; Jackson, Bryan; Padgett, Kerry; Liebman, Kelly; Vugia, Duc; Kramer, Vicki

    2016-12-01

    In August 2015, plague was diagnosed for 2 persons who had visited Yosemite National Park in California, USA. One case was septicemic and the other bubonic. Subsequent environmental investigation identified probable locations of exposure for each patient and evidence of epizootic plague in other areas of the park. Transmission of Yersinia pestis was detected by testing rodent serum, fleas, and rodent carcasses. The environmental investigation and whole-genome multilocus sequence typing of Y. pestis isolates from the patients and environmental samples indicated that the patients had been exposed in different locations and that at least 2 distinct strains of Y. pestis were circulating among vector-host populations in the area. Public education efforts and insecticide applications in select areas to control rodent fleas probably reduced the risk for plague transmission to park visitors and staff.

  16. Investigation of and Response to 2 Plague Cases, Yosemite National Park, California, USA, 2015

    Science.gov (United States)

    Danforth, Mary; Novak, Mark; Petersen, Jeannine; Mead, Paul; Kingry, Luke; Weinburke, Matthew; Buttke, Danielle; Hacker, Gregory; Tucker, James; Niemela, Michael; Jackson, Bryan; Padgett, Kerry; Liebman, Kelly; Vugia, Duc

    2016-01-01

    In August 2015, plague was diagnosed for 2 persons who had visited Yosemite National Park in California, USA. One case was septicemic and the other bubonic. Subsequent environmental investigation identified probable locations of exposure for each patient and evidence of epizootic plague in other areas of the park. Transmission of Yersinia pestis was detected by testing rodent serum, fleas, and rodent carcasses. The environmental investigation and whole-genome multilocus sequence typing of Y. pestis isolates from the patients and environmental samples indicated that the patients had been exposed in different locations and that at least 2 distinct strains of Y. pestis were circulating among vector–host populations in the area. Public education efforts and insecticide applications in select areas to control rodent fleas probably reduced the risk for plague transmission to park visitors and staff. PMID:27870634

  17. Engaging in Argument from Evidence and the Ocean Sciences Sequence for Grades 3-5: A case study in complementing professional learning experiences with instructional materials aligned to instructional goals

    Science.gov (United States)

    Schoedinger, S. E.; Weiss, E. L.

    2016-12-01

    K-5 science teachers, who often lack a science background, have been tasked with a huge challenge in implementing NGSS—to completely change their instructional approach from one that views science as a body of knowledge to be imparted to one that is epistemic in nature. We have found that providing high-quality professional learning (PL) experiences is often not enough and that teachers must have instructional materials that align with their instructional goals. We describe a case study in which the Lawrence Hall of Science (the Hall) used the Hall-developed Ocean Sciences Sequence for Grades 3-5 (OSS 3-5) to support a rigorous PL program for grade 3-5 teachers focused on the NGSS science and engineering practice, engaging in argument from evidence. Developed prior to the release of NGSS, the Ocean Literacy Framework and the NGSS precursor, A Framework for K-12 Science Education, informed the content and instructional approaches of OSS 3-5. OSS 3-5 provides a substantial focus on making evidence-based explanations (and other science practices), while building students' ocean sciences content knowledge. From 2013-2015, the Hall engaged cohorts of teachers in a rigorous PL experience focused on engaging in argument from evidence. During the summer, teachers attended a week-long institute, in which exemplar activities from OSS 3-5 were used to model instructional practices to support arguing from evidence and related practices, e.g., developing and using models and constructing explanations. Immediately afterward, teachers enacted what they'd learned during a two-week summer school practicum. Here, they team-taught the OSS 3-5 curriculum, participated in video reflection groups, and received coaching and just-in-time input from instructors. In the subsequent academic year, many teachers began by teaching OSS 3-5 so that they could practice engaging students in argumentation in curriculum they'd already used for that purpose. Throughout the year, teachers

  18. 78 FR 77447 - California Wind Energy Association, First Solar, Inc. v. California Independent System Operator...

    Science.gov (United States)

    2013-12-23

    ... Energy Association, First Solar, Inc. v. California Independent System Operator Corporation, Southern...), California Wind Energy Association and First Solar, Inc. (collectively, Complainants) filed a formal complaint against the California Independent System Operator Corporation (CAISO) and Southern California...

  19. Biomonitoring in California Firefighters

    Science.gov (United States)

    Israel, Leslie; McNeel, Sandra; Voss, Robert; Wang, Miaomiao; Gajek, Ryszard; Park, June-Soo; Harwani, Suhash; Barley, Frank; She, Jianwen; Das, Rupali

    2015-01-01

    Objective: To assess California firefighters' blood concentrations of selected chemicals and compare with a representative US population. Methods: We report laboratory methods and analytic results for cadmium, lead, mercury, and manganese in whole blood and 12 serum perfluorinated chemicals in a sample of 101 Southern California firefighters. Results: Firefighters' blood metal concentrations were all similar to or lower than the National Health and Nutrition Examination Survey (NHANES) values, except for six participants whose mercury concentrations (range: 9.79 to 13.42 μg/L) were close to or higher than the NHANES reporting threshold of 10 μg/L. Perfluorodecanoic acid concentrations were elevated compared with NHANES and other firefighter studies. Conclusions: Perfluorodecanoic acid concentrations were three times higher in this firefighter group than in NHANES adult males. Firefighters may have unidentified sources of occupational exposure to perfluorinated chemicals. PMID:25563545

  20. SUGARLOAF ROADLESS AREA, CALIFORNIA.

    Science.gov (United States)

    Powell, Robert E.; Campbell, Harry W.

    1984-01-01

    On the basis of geologic, geochemical, and geophysical investigations and a survey of mines, quarries, and prospects the Sugarloaf Roadless Area, California, has little promise for the occurrence of metallic mineral or energy resources. Units of carbonate rock and graphitic schist have demonstrated resources of magnesian marble and graphite. Sand, gravel, and construction stone other than carbonate rock are present in the roadless area, but similar or better quality materials are abundant and more accessible outside the area.

  1. Medical marijuana: California update.

    Science.gov (United States)

    James, J S

    1996-08-23

    The Cannabis Buyers' Club in San Francisco remains closed after it was raided by the office of California Attorney General Dan Lungren. Many individuals with serious illnesses such as AIDS and cancer are without safe access to medical marijuana to relieve the symptoms of their diseases. The need for access to medicinal marijuana, the return of the confiscated confidential medical records held at the buyers' club, and the passage of California Proposition 215 in the November election, which allows for the legitimate use of marijuana for medical purposes are of immediate concern. Since the raid, the Cannabis Buyers' Club has denied charges that it sold marijuana to teenagers, saying the drug was sold to a teen's mother, an undercover narcotics officer. However, the club admitted to sales to non-medical individuals who used fraudulent documents in order to obtain the drug and acknowledges the need to tighten procedures. Individuals may be able to obtain marijuana at other buyers' clubs if they have documentation of a medical need. While literature on the medical use of marijuana is lacking, the Federal government continues to block any efforts toward medical research on this issue. A list of other cannabis buyers' clubs in California is included, as well as a list of organizations working for Proposition 215.

  2. Ecoregions of California

    Science.gov (United States)

    Griffith, Glenn E.; Omernik, James M.; Smith, David W.; Cook, Terry D.; Tallyn, Ed; Moseley, Kendra; Johnson, Colleen B.

    2016-02-23

    Ecoregions denote areas of general similarity in ecosystems and in the type, quality, and quantity of environmental resources. They are designed to serve as a spatial framework for the research, assessment, management, and monitoring of ecosystems and ecosystem components. By recognizing the spatial differences in the capacities and potentials of ecosystems, ecoregions stratify the environment by its probable response to disturbance (Bryce and others, 1999). These general purpose regions are critical for structuring and implementing ecosystem management strategies across Federal agencies, State agencies, and nongovernment organizations that are responsible for different types of resources in the same geographical areas (Omernik and others, 2000).The approach used to compile this map is based on the premise that ecological regions are hierarchical and can be identified through the analysis of the spatial patterns and the composition of biotic and abiotic phenomena that affect or reflect differences in ecosystem quality and integrity (Wiken, 1986; Omernik, 1987, 1995). These phenomena include geology, physiography, vegetation, climate, soils, land use, wildlife, and hydrology. The relative importance of each characteristic varies from one ecological region to another regardless of the hierarchical level. A Roman numeral hierarchical scheme has been adopted for different levels of ecological regions. Level I is the coarsest level, dividing North America into 15 ecological regions. Level II divides the continent into 50 regions (Commission for Environmental Cooperation Working Group, 1997, map revised 2006). At level III, the continental United States contains 105 ecoregions and the conterminous United States has 85 ecoregions (U.S. Environmental Protection Agency, 2013). Level IV, depicted here for California, is a further refinement of level III ecoregions. Explanations of the methods used to define these ecoregions are given in Omernik (1995), Omernik and others

  3. Individual variation in paternal responses of virgin male California mice (Peromyscus californicus): behavioral and physiological correlates

    NARCIS (Netherlands)

    de Jong, T.R.; Korosi, A.; Harris, B.N.; Perea-Rodriguez, J.P.; Saltzman, W.

    2012-01-01

    California mice Peromyscus californicus are a rodent species in which fathers provide extensive paternal care; however, behavioral responses of virgin males toward conspecific neonates vary from paternal behavior to tolerance to infanticide. Indirect evidence suggests that paternal responses might

  4. Pb-Sr-Nd-O isotopic characterization of Mesozoic rocks throughout the northern end of the Peninsular Ranges batholith: Isotopic evidence for the magmatic evolution of oceanic arc–continental margin accretion during the Late Cretaceous of southern California

    Science.gov (United States)

    Kistler, Ronald W.; Wooden, Joseph L.; Premo, Wayne R.; Morton, Douglas M.

    2014-01-01

    Within the duration of the U.S. Geological Survey (USGS)–based Southern California Areal Mapping Project (SCAMP), many samples from the northern Peninsular Ranges batholith were studied for their whole-rock radioisotopic systematics (rubidium-strontium [Rb-Sr], uranium-thorium-lead [U-Th-Pb], and samarium-neodymium [Sm-Nd]), as well as oxygen (O), a stable isotope. The results of three main studies are presented separately, but here we combine them (>400 analyses) to produce a very complete Pb-Sr-Nd-O isotopic profile of an arc-continent collisional zone—perhaps the most complete in the world. In addition, because many of these samples have U-Pb zircon as well as argon mineral age determinations, we have good control of the timing for Pb-Sr-Nd-O isotopic variations.The ages and isotopic variations help to delineate at least four zones across the batholith from west to east—an older western zone (126–108 Ma), a transitional zone (111–93 Ma), an eastern zone (94–91 Ma), and a much younger allochthonous thrust sheet (ca. 84 Ma), which is the upper plate of the Eastern Peninsular Ranges mylonite zone. Average initial 87Sr/86 Sr (Sri), initial 206Pb/204Pb (206 Pbi), initial 208Pb/204Pb (average 208Pbi), initial epsilon Nd (average εNdi), and δ18O signatures range from 0.704, 18.787, 38.445, +3.1, and 4.0‰–9.0‰, respectively, in the westernmost zone, to 0.7071, 19.199, 38.777, −5, and 9‰–12‰, respectively, in the easternmost zone. The older western zone is therefore the more chemically and isotopically juvenile, characterized mostly by values that are slightly displaced from a mantle array at ca. 115 Ma, and similar to some modern island-arc signatures. In contrast, the isotopic signatures in the eastern zones indicate significant amounts of crustal involvement in the magmatic plumbing of those plutons. These isotopic signatures confirm previously published results that interpreted the Peninsular Ranges batholith as a progressively

  5. California community water systems inventory dataset, 2010

    Data.gov (United States)

    California Environmental Health Tracking Program — This data set contains information about all Community Water Systems in California. Data are derived from California Office of Drinking Water (ODW) Water Quality...

  6. Pesticides and Population Declines of California Alpine Frogs

    Science.gov (United States)

    Airborne pesticides from the Central Valley of California have been implicated as a cause for population declines of several amphibian species, with the strongest evidence for the mountain yellow-legged frog complex (Rana muscosa and R. sierrae) in the Sierra Nevada. We measured ...

  7. Conservation issues: California chaparral

    Science.gov (United States)

    Halsey, Richard W.; Keeley, Jon E.

    2016-01-01

    California chaparral, a sclerophyllous shrub-dominated plant community shaped by a Mediterranean-type climate and infrequent, high-intensity fire, is one of the most biodiverse and threatened habitats on Earth. Distinct forms of chaparral, distinguished by differing species composition, geography, and edaphic characteristics, can cover thousands of hectares with dense vegetation or be restricted to smaller communities identified by the presence of endemic species. To maintain the biodiversity of chaparral, protective land management actions will be required to mitigate the loss due to the impacts of human population growth, development, climate change, and increased fire frequencies.

  8. California quake assessed

    Science.gov (United States)

    Wuethrich, Bernice

    On January 17, at 4:31 A.M., a 6.6 magnitude earthquake hit the Los Angeles area, crippling much of the local infrastructure and claiming 51 lives. Members of the Southern California Earthquake Network, a consortium of scientists at universities and the United States Geological Survey (USGS), entered a controlled crisis mode. Network scientists, including David Wald, Susan Hough, Kerry Sieh, and a half dozen others went into the field to gather information on the earthquake, which apparently ruptured an unmapped fault.

  9. California Tiger Salamander Range - CWHR [ds588

    Data.gov (United States)

    California Natural Resource Agency — Vector datasets of CWHR range maps are one component of California Wildlife Habitat Relationships (CWHR), a comprehensive information system and predictive model for...

  10. Giant Reed Distribution - Northern California [ds333

    Data.gov (United States)

    California Natural Resource Agency — The Arundo Distribution layer is a compilation of Arundo donax observations in northern and central California, obtained from several sources, including Arundo...

  11. Herpetofauna Surveys, Northern California - 2010 [ds694

    Data.gov (United States)

    California Natural Resource Agency — We recorded all incidental herpetofauna encountered during visual encounter and dipnet surveys in northern California. Surveys took place from April 2, 2010 to...

  12. Hydrogen energy system in California

    International Nuclear Information System (INIS)

    Zweig, R.M.

    1995-01-01

    Results of experiences on the use of hydrogen as a clean burning fuel in California and results of the South Coast Air Quality Management district tests using hydrogen as a clean burning environmentally safe fuel are given. The results of Solar Hydrogen Projects in California and recent medical data documentation of human lung damage of patients living in air polluted urban areas are summarized

  13. Experts Question California's Algebra Edict

    Science.gov (United States)

    Cavanagh, Sean

    2008-01-01

    Business leaders from important sectors of the American economy have been urging schools to set higher standards in math and science--and California officials, in mandating that 8th graders be tested in introductory algebra, have responded with one of the highest such standards in the land. Still, many California educators and school…

  14. Cryptococcus gattii VGIII isolates causing infections in HIV/AIDS patients in Southern California: identification of the local environmental source as arboreal.

    Directory of Open Access Journals (Sweden)

    Deborah J Springer

    2014-08-01

    Full Text Available Ongoing Cryptococcus gattii outbreaks in the Western United States and Canada illustrate the impact of environmental reservoirs and both clonal and recombining propagation in driving emergence and expansion of microbial pathogens. C. gattii comprises four distinct molecular types: VGI, VGII, VGIII, and VGIV, with no evidence of nuclear genetic exchange, indicating these represent distinct species. C. gattii VGII isolates are causing the Pacific Northwest outbreak, whereas VGIII isolates frequently infect HIV/AIDS patients in Southern California. VGI, VGII, and VGIII have been isolated from patients and animals in the Western US, suggesting these molecular types occur in the environment. However, only two environmental isolates of C. gattii have ever been reported from California: CBS7750 (VGII and WM161 (VGIII. The incongruence of frequent clinical presence and uncommon environmental isolation suggests an unknown C. gattii reservoir in California. Here we report frequent isolation of C. gattii VGIII MATα and MATa isolates and infrequent isolation of VGI MATα from environmental sources in Southern California. VGIII isolates were obtained from soil debris associated with tree species not previously reported as hosts from sites near residences of infected patients. These isolates are fertile under laboratory conditions, produce abundant spores, and are part of both locally and more distantly recombining populations. MLST and whole genome sequence analysis provide compelling evidence that these environmental isolates are the source of human infections. Isolates displayed wide-ranging virulence in macrophage and animal models. When clinical and environmental isolates with indistinguishable MLST profiles were compared, environmental isolates were less virulent. Taken together, our studies reveal an environmental source and risk of C. gattii to HIV/AIDS patients with implications for the >1,000,000 cryptococcal infections occurring annually for which

  15. Biomass resources in California

    Energy Technology Data Exchange (ETDEWEB)

    Tiangco, V.M.; Sethi, P.S. [California Energy Commission, Sacramento, CA (United States)

    1993-12-31

    The biomass resources in California which have potential for energy conversion were assessed and characterized through the project funded by the California Energy Commission and the US Department of Energy`s Western Regional Biomass Energy Program (WRBEP). The results indicate that there is an abundance of biomass resources as yet untouched by the industry due to technical, economic, and environmental problems, and other barriers. These biomass resources include residues from field and seed crops, fruit and nut crops, vegetable crops, and nursery crops; food processing wastes; forest slash; energy crops; lumber mill waste; urban wood waste; urban yard waste; livestock manure; and chaparral. The estimated total potential of these biomass resource is approximately 47 million bone dry tons (BDT), which is equivalent to 780 billion MJ (740 trillion Btu). About 7 million BDT (132 billion MJ or 124 trillion Btu) of biomass residue was used for generating electricity by 66 direct combustion facilities with gross capacity of about 800 MW. This tonnage accounts for only about 15% of the total biomass resource potential identified in this study. The barriers interfering with the biomass utilization both in the on-site harvesting, collection, storage, handling, transportation, and conversion to energy are identified. The question whether these barriers present significant impact to biomass {open_quotes}availability{close_quotes} and {open_quotes}sustainability{close_quotes} remains to be answered.

  16. Copulation by California condors

    Science.gov (United States)

    Wilbur, S.R.; Borneman, J.C.

    1972-01-01

    Koford (Res. Rept. No. 3, Natl. Audubon Soc., 1953) observed sexual display among California Condors (Gymnogyps californianus) on more than 30 occasions, yet only once did he see what he thought was copulation. Some of the displays he watched were quite intricate, with considerable posturing and "male" aggression, but no such activity preceded this copulation. The birds sat several feet apart for over 1 hour, then one climbed onto the other's back, staying there 1/2 minute and flapping gently at the apparent moment of coition. Afterward they sat quietly 1/2 hour before flying away. This led Koford to state (p. 79) that "possibly in Gymnogyps copulation is not immediately preceded by display." We have records of 8 California Condor copulations, 5 of which are similar to that described above. The three other occasions began similarly, with the birds sitting quietly, but then the "male" displayed briefly before the "female" with wings half spread and head drooping forward. This elicited no apparent response, but the male immediately walked behind and mounted the female. The apparent moment of coition was accompanied by gentle wing flapping in all instances.

  17. biofuel development in California

    Directory of Open Access Journals (Sweden)

    Varaprasad Bandaru

    2015-07-01

    Full Text Available Biofuels are expected to play a major role in meeting California's long-term energy needs, but many factors influence the commercial viability of the various feedstock and production technology options. We developed a spatially explicit analytic framework that integrates models of plant growth, crop adoption, feedstock location, transportation logistics, economic impact, biorefinery costs and biorefinery energy use and emissions. We used this framework to assess the economic potential of hybrid poplar as a feedstock for jet fuel production in Northern California. Results suggest that the region has sufficient suitable croplands (2.3 million acres and nonarable lands (1.5 million acres for poplar cultivation to produce as much as 2.26 billion gallons of jet fuel annually. However, there are major obstacles to such large-scale production, including, on nonarable lands, low poplar yields and broad spatial distribution and, on croplands, competition with existing crops. We estimated the production cost of jet fuel to be $4.40 to $5.40 per gallon for poplar biomass grown on nonarable lands and $3.60 to $4.50 per gallon for biomass grown on irrigated cropland; the current market price is $2.12 per gallon. Improved poplar yields, use of supplementary feedstocks at the biorefinery and economic supports such as carbon credits could help to overcome these barriers.

  18. California State Waters Map Series: offshore of Santa Barbara, California

    Science.gov (United States)

    Johnson, Samuel Y.; Dartnell, Peter; Cochrane, Guy R.; Golden, Nadine E.; Phillips, Eleyne L.; Ritchie, Andrew C.; Greene, H. Gary; Krigsman, Lisa M.; Kvitek, Rikk G.; Dieter, Bryan E.; Endris, Charles A.; Seitz, Gordon G.; Sliter, Ray W.; Erdey, Mercedes D.; Gutierrez, Carlos I.; Wong, Florence L.; Yoklavich, Mary M.; Draut, Amy E.; Hart, Patrick E.; Conrad, James E.; Cochran, Susan A.; Johnson, Samuel Y.; Cochran, Susan A.

    2013-01-01

    In 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within the 3-nautical-mile limit of California’s State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow (to about 100 m) subsurface geology. The Offshore of Santa Barbara map area lies within the central Santa Barbara Channel region of the Southern California Bight. This geologically complex region forms a major biogeographic transition zone, separating the cold-temperate Oregonian province north of Point Conception from the warm-temperate California province to the south. The map area is in the southern part of the Western Transverse Ranges geologic province, which is north of the California Continental Borderland. Significant clockwise rotation—at least 90°—since the early Miocene has been proposed for the Western Transverse Ranges province, and geodetic studies indicate that the region is presently undergoing north-south shortening. Uplift rates (as much as 2.2 mm/yr) that are based on studies of onland marine terraces provide further evidence of significant shortening. The city of Santa Barbara, the main coastal population center in the map area, is part of a contiguous urban area that extends from Carpinteria to Goleta. This urban area was developed on the coalescing alluvial surfaces, uplifted marine terraces, and low hills that lie south of the east-west-trending Santa Ynez Mountains. Several beaches line the actively

  19. Seismic stratigraphy and late Quaternary shelf history, south-central Monterey Bay, California

    Science.gov (United States)

    Chin, J.L.; Clifton, H.E.; Mullins, H.T.

    1988-01-01

    The south-central Monterey Bay shelf is a high-energy, wave-dominated, tectonically active coastal region on the central California continental margin. A prominent feature of this shelf is a sediment lobe off the mouth of the Salinas River that has surface expression. High-resolution seismic-reflection profiles reveal that an angular unconformity (Quaternary?) underlies the entire shelf and separates undeformed strata above it from deformed strata below it. The Salinas River lobe is a convex bulge on the shelf covering an area of approximately 72 km2 in water depths from 10 to 90 m. It reaches a maximum thickness of 35 m about 2.5 km seaward of the river mouth and thins in all directions away from this point. Adjacent shelf areas are characterized by only a thin (2 to 5 m thick) and uniform veneer of sediment. Acoustic stratigraphy of the lobe is complex and is characterized by at least three unconformity-bounded depositional sequences. Acoustically, these sequences are relatively well bedded. Acoustic foresets occur within the intermediate sequence and dip seaward at 0.7?? to 2.0??. Comparison with sedimentary sequences in uplifted onshore Pleistocene marine-terrace deposits of the Monterey Bay area, which were presumably formed in a similar setting under similar processes, suggests that a general interpretation can be formulated for seismic stratigraphic patterns. Depositional sequences are interpreted to represent shallowing-upwards progradational sequences of marine to nonmarine coastal deposits formed during interglacial highstands and/or during early stages of falling sea level. Acoustic foresets within the intermediate sequence are evidence of seaward progradation. Acoustic unconformities that separate depositional sequences are interpreted as having formed largely by shoreface planation and may be the only record of the intervening transgressions. The internal stratigraphy of the Salinas River lobe thus suggests that at least several late Quaternary

  20. California Baseline Ozone Transport Study (CABOTS): Ozonesonde Measurements

    Science.gov (United States)

    Eiserloh, A. J., Jr.; Chiao, S.; Spitze, J.; Cauley, S.; Clark, J.; Roberts, M.

    2016-12-01

    Because the EPA recently lowered the ambient air quality standard for the 8-hr average of ozone (O3) to70 ppbv, California must continue to achieve significant reductions in ozone precursor emissions and prepare for new State Implementation Plans (SIP) to demonstrate how ground-level ambient ozone will be reduced below the new health-based standard. Prior studies suggest that background levels of ozone traveling across the Pacific Ocean can significantly influence surface ozone throughout California, particularly during the spring. Evidence has been presented indicating that background levels of ozone continue to increase in the western United States over the recent few decades, implying more ozone exceedances in the future. To better understand the contributions of the external natural and anthropogenic pollution sources as well as atmospheric processes for surface ozone concentrations in California during the spring and summer months, the California Baseline Ozone Transport Study (CABOTS) has been established. One major goal of CABOTS is to implement near daily ozonesonde measurements along the California Coast to quantify background ozone aloft before entering the State during high ozone season. CABOTS has been ongoing from May through August of 2016 launching ozonesondes from Bodega Bay and Half Moon Bay, California. The temporal progression of ozonesonde measurements and subsequent analysis of the data will be discussed with a focus on the contribution of background ozone to surface ozone sites inland as well as likely origins of layers aloft. Comparisons of current ozonesondes versus prior ozonesonde studies of California will also be performed. A few selected cases of high ozone layers moving onshore from different sources will be discussed as well.

  1. Public Schools, California, 2009, California Department of Education

    Data.gov (United States)

    U.S. Environmental Protection Agency — This set of data represents the most current public schools in the State of California as of June, 2009. Information about each public school includes: school name,...

  2. Emergence of burrowing urchins from California continental shelf sediments-A response to alongshore current reversals?

    Science.gov (United States)

    Nichols, F.H.; Cacchione, D.A.; Drake, D.E.; Thompson, J.K.

    1989-01-01

    Two sequences of bottom photographs taken every two or four hours for two months during the Coastal Ocean Dynamics Experiment (CODE) off the Russian River, California, reveal the dynamic nature of interations between the water column, the sediments, and benthic organisms in the mid-shelf silt deposit. Time-lapse photographs taken between late spring and early summer in 1981 and 1982 show that the subsurface-dwelling urchin Brisaster latifrons (one of the largest invertebrates found in shelf-depth fine sediment off the U.S. Pacific coast) occasionally emerged from the sediment, plowed the sediment surface during the course of a few hours to several days, then buried themselves again. Frame-by-frame study of the film sequences shows that the urchins typically emerged following relaxation of coastal upwelling, periods characterized by current direction reversals and increases in bottom water turbidity. Among the possible causes of the emergence of urchins and the consequent bioturbation of the upper few cm of sediment, a response to an enhanced food supply seems most plausible. Circumstantial evidence suggests the possibility that phytoplankton sedimentation during periods of upwelling relaxation could provide a new source of food at the sediment surface. ?? 1989.

  3. Invertebrate diversity in southern California

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This shapefile displays mean invertebrate diversity within 5 minute grid cells. The Shannon Index of diversity was calculated from Southern California Coastal Water...

  4. The California Fuel Tax Swap

    Science.gov (United States)

    2016-05-01

    In early 2010, California faced another of its seemingly routine budget crises, this time mostly the result of outstanding debt due on state general obligation (GO) highway and rail bonds.2 For several years, the Legislature had been diverting ...

  5. NEXRAD Rainfall Data: Eureka, California

    Data.gov (United States)

    National Aeronautics and Space Administration — Next-Generation Radar (NEXRAD) Weather Surveillance Radar 1988 (WSR-88D) measurements were used to support AMSR-E rainfall validation efforts in Eureka, California,...

  6. Pockmarks off Big Sur, California

    Science.gov (United States)

    Paull, C.; Ussler, W.; Maher, N.; Greene, H. Gary; Rehder, G.; Lorenson, T.; Lee, H.

    2002-01-01

    A pockmark field was discovered during EM-300 multi-beam bathymetric surveys on the lower continental slope off the Big Sur coast of California. The field contains ??? 1500 pockmarks which are between 130 and 260 m in diameter, and typically are 8-12 m deep located within a 560 km2 area. To investigate the origin of these features, piston cores were collected from both the interior and the flanks of the pockmarks, and remotely operated vehicle observation (ROV) video and sampling transects were conducted which passed through 19 of the pockmarks. The water column within and above the pockmarks was sampled for methane concentration. Piston cores and ROV collected push cores show that the pockmark field is composed of monotonous fine silts and clays and the cores within the pockmarks are indistinguishable from those outside the pockmarks. No evidence for either sediment winnowing or diagenetic alteration suggestive of fluid venting was obtained. 14C measurements of the organic carbon in the sediments indicate continuous sedimentation throughout the time resolution of the radiocarbon technique ( ??? 45000 yr BP), with a sedimentation rate of ??? 10 cm per 1000 yr both within and between the pockmarks. Concentrations of methane, dissolved inorganic carbon, sulfate, chloride, and ammonium in pore water extracted from within the cores are generally similar in composition to seawater and show little change with depth, suggesting low biogeochemical activity. These pore water chemical gradients indicate that neither significant accumulations of gas are likely to exist in the shallow subsurface ( ??? 100 m) nor is active fluid advection occurring within the sampled sediments. Taken together the data indicate that these pockmarks are more than 45000 yr old, are presently inactive, and contain no indications of earlier fluid or gas venting events. ?? 2002 Elsevier Science B.V. All rights reserved.

  7. ISOLATION OF THE GENOME SEQUENCE STRAIN MYCOBACTERIUM AVIUM 104 FROM MULTIPLE PATIENTS OVER A 17-YEAR PERIOD

    Science.gov (United States)

    The genome sequence strain 104 of the opportunistic pathogen Mycobacterium avium was isolated form an adult AIDS patient in Southern California in 1983. Isolates of non-paratuberculosis M. avium from 207 other patients in Southern California and elsewhere were examined for genoty...

  8. The California cogeneration success story

    International Nuclear Information System (INIS)

    Neiggemann, M.F.

    1992-01-01

    This chapter describes the involvement of Southern California Gas Company(SoCalGas) in the promotion and demonstration of the benefits of cogeneration in California. The topics covered in this chapter are market strategy, cogeneration program objectives, cogeneration program, incentive cofunding, special gas rate, special service priority, special gas pressure and main options, advertising, promotional brochures and handbooks, technical support, program accomplishments, cogeneration outlook, and reasons for success of the program

  9. California Gnatcatcher Observations - 2004-2009 [ds457

    Data.gov (United States)

    California Natural Resource Agency — In southern California, the coastal California gnatcatcher (CAGN) has become both the flagship species and an umbrella species identified with conservation, where...

  10. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  11. Fire risk in California

    Science.gov (United States)

    Peterson, Seth Howard

    Fire is an integral part of ecosystems in the western United States. Decades of fire suppression have led to (unnaturally) large accumulations of fuel in some forest communities, such as the lower elevation forests of the Sierra Nevada. Urban sprawl into fire prone chaparral vegetation in southern California has put human lives at risk and the decreased fire return intervals have put the vegetation community at risk of type conversion. This research examines the factors affecting fire risk in two of the dominant landscapes in the state of California, chaparral and inland coniferous forests. Live fuel moisture (LFM) is important for fire ignition, spread rate, and intensity in chaparral. LFM maps were generated for Los Angeles County by developing and then inverting robust cross-validated regression equations from time series field data and vegetation indices (VIs) and phenological metrics from MODIS data. Fire fuels, including understory fuels which are not visible to remote sensing instruments, were mapped in Yosemite National Park using the random forests decision tree algorithm and climatic, topographic, remotely sensed, and fire history variables. Combining the disparate data sources served to improve classification accuracies. The models were inverted to produce maps of fuel models and fuel amounts, and these showed that fire fuel amounts are highest in the low elevation forests that have been most affected by fire suppression impacting the natural fire regime. Wildland fires in chaparral commonly burn in late summer or fall when LFM is near its annual low, however, the Jesusita Fire burned in early May of 2009, when LFM was still relatively high. The HFire fire spread model was used to simulate the growth of the Jesusita Fire using LFM maps derived from imagery acquired at the time of the fire and imagery acquired in late August to determine how much different the fire would have been if it had occurred later in the year. Simulated fires were 1.5 times larger

  12. Phylogeography and genetic structure of endemic Acmispon argophyllus and A. dendroideus (Fabaceae) across the California Channel Islands.

    Science.gov (United States)

    Wallace, Lisa E; Wheeler, Gregory L; McGlaughlin, Mitchell E; Bresowar, Gerald; Helenurm, Kaius

    2017-05-01

    Taxa inhabiting the California Channel Islands exhibit variation in their degree of isolation, but few studies have considered patterns across the entire archipelago. We studied phylogeography of insular Acmispon argophyllus and A. dendroideus to determine whether infraspecific taxa are genetically divergent and to elucidate patterns of diversification across these islands. DNA sequences were collected from nuclear (ADH) and plastid genomes ( rpL16 , ndhA , psbD-trnT ) from >450 samples on the Channel Islands and California. We estimated population genetic diversity and structure, phylogenetic patterns among populations, and migration rates, and tested for population growth. Populations of northern island A. argophyllus var. niveus are genetically distinct from conspecific populations on southern islands. On the southern islands, A. argophyllus var. argenteus populations on Santa Catalina are phylogenetically distinct from populations of var. argenteus and var. adsurgens on the other southern islands. For A. dendroideus , we found the varieties to be monophyletic. Populations of A. dendroideus var. traskiae on San Clemente are genetically differentiated from other conspecific populations, whereas populations on the northern islands and Santa Catalina show varying degrees of gene flow. Evidence of population growth was found in both species. Oceanic barriers between islands have had a strong influence on population genetic structure in both Acmispon species, although the species have differing phylogeographic patterns. This study provides a contrasting pattern of dispersal on a near island system that does not follow a strict stepping-stone model, commonly found on isolated island systems. © 2017 Botanical Society of America.

  13. Identification and Characterization of Citrus tristeza virus Isolates Breaking Resistance in Trifoliate Orange in California.

    Science.gov (United States)

    Yokomi, Raymond K; Selvaraj, Vijayanandraj; Maheshwari, Yogita; Saponari, Maria; Giampetruzzi, Annalisa; Chiumenti, Michela; Hajeri, Subhas

    2017-07-01

    Most Citrus tristeza virus (CTV) isolates in California are biologically mild and symptomless in commercial cultivars on CTV tolerant rootstocks. However, to better define California CTV isolates showing divergent serological and genetic profiles, selected isolates were subjected to deep sequencing of small RNAs. Full-length sequences were assembled, annotated and trifoliate orange resistance-breaking (RB) isolates of CTV were identified. Phylogenetic relationships based on their full genomes placed three isolates in the RB clade: CA-RB-115, CA-RB-AT25, and CA-RB-AT35. The latter two isolates were obtained by aphid transmission from Murcott and Dekopon trees, respectively, containing CTV mixtures. The California RB isolates were further distinguished into two subclades. Group I included CA-RB-115 and CA-RB-AT25 with 99% nucleotide sequence identity with RB type strain NZRB-G90; and group II included CA-RB-AT35 with 99 and 96% sequence identity with Taiwan Pumelo/SP/T1 and HA18-9, respectively. The RB phenotype was confirmed by detecting CTV replication in graft-inoculated Poncirus trifoliata and transmission from P. trifoliata to sweet orange. The California RB isolates induced mild symptoms compared with severe isolates in greenhouse indexing tests. Further examination of 570 CTV accessions, acquired from approximately 1960 and maintained in planta at the Central California Tristeza Eradication Agency, revealed 16 RB positive isolates based on partial p65 sequences. Six isolates collected from 1992 to 2011 from Tulare and Kern counties were CA-RB-115-like; and 10 isolates collected from 1968 to 2010 from Riverside, Fresno, and Kern counties were CA-RB-AT35-like. The presence of the RB genotype is relevant because P. trifoliata and its hybrids are the most popular rootstocks in California.

  14. Does Deccan Volcanic Sequence contain more reversals than the three-Chron N-R-N flow magnetostratigraphy?—a palaeomagnetic evidence from the dyke-swarm near Mumbai

    Science.gov (United States)

    Basavaiah, N.; Satyanarayana, K. VV; Deenadayalan, K.; Prasad, J. N.

    2018-06-01

    .5 respectively, indicating a latitudinal drift of ˜4.4° of the sampled location between the acquisition of two magnetizations. Six lava flows sampled from the basement of the host Deccan flow sequence nearby sampled dykes yielded reverse polarity ChRM mean at Dm = 128°, Im = 47° (k = 156, α95 = 5.4°) with corresponding pole positions at 21°S, 121°E (A95 = 5.3°). This pole falls near the GII poles, indicating a probable contemporaneous time of emplacement. In the absence of radiometric dates, no magnetochron can be assigned for GII magnetization. However, on the basis of published analyses of several palaeomagnetic and geochronological data of the flows and dykes within DVP and Deccan related dykes from the neighbouring areas, it seems plausible that GII-R magnetization belongs to either Chron 30R or 31R and GII-N magnetization pertains to 31N. Conclusive evidence in support of the presence of these reversals in the DVP, however, has to wait for new geochronological data from the undated dykes investigated in this study, and fresh updating of the stratigraphy of the lowermost flow sequence in the sampled area which also remains undated. This study, however, does indicate the possible presence of two more reversals revealed by GII magnetization on the older side beyond well-established three-Chron magnetostratigraphy.

  15. Climate scenarios for California

    Science.gov (United States)

    Cayan, Daniel R.; Maurer, Ed; Dettinger, Mike; Tyree, Mary; Hayhoe, Katharine; Bonfils, Celine; Duffy, Phil; Santer, Ben

    2006-01-01

    Possible future climate changes in California are investigated from a varied set of climate change model simulations. These simulations, conducted by three state-of-the-art global climate models, provide trajectories from three greenhouse gas (GHG) emission scenarios. These scenarios and the resulting climate simulations are not “predictions,” but rather are a limited sample from among the many plausible pathways that may affect California’s climate. Future GHG concentrations are uncertain because they depend on future social, political, and technological pathways, and thus the IPCC has produced four “families” of emission scenarios. To explore some of these uncertainties, emissions scenarios A2 (a medium-high emissions) and B1 (low emissions) were selected from the current IPCC Fourth climate assessment, which provides several recent model simulations driven by A2 and B1 emissions. The global climate model simulations addressed here were from PCM1, the Parallel Climate Model from the National Center for Atmospheric Research (NCAR) and U.S. Department of Energy (DOE) group, and CM2.1 from the National Oceanic and Atmospheric Administration (NOAA) Geophysical Fluids Dynamics Laboratory (GFDL).

  16. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  17. Complete cDNA sequence of the preproform of human pregnancy-associated plasma protein-A. Evidence for expression in the brain and induction by cAMP

    DEFF Research Database (Denmark)

    Haaning, Jesper; Oxvig, Claus; Overgaard, Michael Toft

    1996-01-01

    A cDNA that encodes the prepropeptide of pregnancy-associated plasma protein-A (preproPAPP-A), a putative metalloproteinase, has been cloned and sequenced. PAPP-A is synthesized in the placenta as a 1627-residue precursor preproprotein with a putative 22-residue signal peptide and a highly basic...

  18. Fish larvae from the Gulf of California

    Directory of Open Access Journals (Sweden)

    Gerardo Aceves-Medina

    2003-03-01

    Full Text Available Taxonomic composition of fish larvae was analysed from 464 plankton samples obtained during 10 oceanographic surveys in the Gulf of California between 1984 and 1988. We identified 283 taxa: 173 species, 57 genera, and 53 families. Tropical and subtropical species predominated except during the winter, when temperate-subarctic species were dominant. The most abundant species were the mesopelagic Benthosema panamense, Triphoturus mexicanus and Vinciguerria lucetia, but the coastal pelagic species Engraulis mordax, Opisthonema spp., Sardinops caeruleus and Scomber japonicus were also prominent. The taxonomic composition of the ichthyoplankton shows the seasonality of the Gulf as well as environmental changes that occurred between the 1984-1987 warm period and the 1956-1957 cool period previously reported. The presence of E. mordax larvae as one of the most abundant species in the Gulf provides evidence of the reproduction of this species two years before the development of the northern anchovy fishery and the decline of the sardine fishery in the Gulf of California.

  19. Comparative analysis of the full genome sequence of European bat lyssavirus type 1 and type 2 with other lyssaviruses and evidence for a conserved transcription termination and polyadenylation motif in the G-L 3' non-translated region.

    Science.gov (United States)

    Marston, D A; McElhinney, L M; Johnson, N; Müller, T; Conzelmann, K K; Tordo, N; Fooks, A R

    2007-04-01

    We report the first full-length genomic sequences for European bat lyssavirus type-1 (EBLV-1) and type-2 (EBLV-2). The EBLV-1 genomic sequence was derived from a virus isolated from a serotine bat in Hamburg, Germany, in 1968 and the EBLV-2 sequence was derived from a virus isolate from a human case of rabies that occurred in Scotland in 2002. A long-distance PCR strategy was used to amplify the open reading frames (ORFs), followed by standard and modified RACE (rapid amplification of cDNA ends) techniques to amplify the 3' and 5' ends. The lengths of each complete viral genome for EBLV-1 and EBLV-2 were 11 966 and 11 930 base pairs, respectively, and follow the standard rhabdovirus genome organization of five viral proteins. Comparison with other lyssavirus sequences demonstrates variation in degrees of homology, with the genomic termini showing a high degree of complementarity. The nucleoprotein was the most conserved, both intra- and intergenotypically, followed by the polymerase (L), matrix and glyco- proteins, with the phosphoprotein being the most variable. In addition, we have shown that the two EBLVs utilize a conserved transcription termination and polyadenylation (TTP) motif, approximately 50 nt upstream of the L gene start codon. All available lyssavirus sequences to date, with the exception of Pasteur virus (PV) and PV-derived isolates, use the second TTP site. This observation may explain differences in pathogenicity between lyssavirus strains, dependent on the length of the untranslated region, which might affect transcriptional activity and RNA stability.

  20. California State Waters Map Series: offshore of Tomales Point, California

    Science.gov (United States)

    Johnson, Samuel Y.; Dartnell, Peter; Golden, Nadine E.; Hartwell, Stephen R.; Greene, H. Gary; Erdey, Mercedes D.; Cochrane, Guy R.; Watt, Janet Tilden; Kvitek, Rikk G.; Manson, Michael W.; Endris, Charles A.; Dieter, Bryan E.; Krigsman, Lisa M.; Sliter, Ray W.; Lowe, Erik N.; Chinn, John L.; Johnson, Samuel Y.; Cochran, Susan A.

    2015-01-01

    In 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within the 3-nautical-mile limit of California’s State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow (to about 200 m) subsurface geology.

  1. California State Waters Map Series: offshore of San Francisco, California

    Science.gov (United States)

    Cochrane, Guy R.; Johnson, Samuel Y.; Dartnell, Peter; Greene, H. Gary; Erdey, Mercedes D.; Golden, Nadine E.; Hartwell, Stephen R.; Endris, Charles A.; Manson, Michael W.; Sliter, Ray W.; Kvitek, Rikk G.; Watt, Janet Tilden; Ross, Stephanie L.; Bruns, Terry R.; Cochrane, Guy R.; Cochran, Susan A.

    2015-01-01

    In 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within California’s State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow (to about 100 m) subsurface geology.

  2. California State Waters Map Series: offshore of Refugio Beach, California

    Science.gov (United States)

    Johnson, Samuel Y.; Dartnell, Peter; Cochrane, Guy R.; Golden, Nadine E.; Phillips, Eleyne L.; Ritchie, Andrew C.; Krigsman, Lisa M.; Dieter, Bryan E.; Conrad, James E.; Greene, H. Gary; Seitz, Gordon G.; Endris, Charles A.; Sliter, Ray W.; Wong, Florence L.; Erdey, Mercedes D.; Gutierrez, Carlos I.; Yoklavich, Mary M.; East, Amy E.; Hart, Patrick E.; Johnson, Samuel Y.; Cochran, Susan A.

    2015-01-01

    In 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within California’s State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow (to about 100 m) subsurface geology.

  3. California State Waters Map Series: offshore of Pacifica, California

    Science.gov (United States)

    Edwards, Brian D.; Phillips, Eleyne L.; Dartnell, Peter; Greene, H. Gary; Bretz, Carrie K.; Kvitek, Rikk G.; Hartwell, Stephen R.; Johnson, Samuel Y.; Cochrane, Guy R.; Dieter, Bryan E.; Sliter, Ray W.; Ross, Stephanie L.; Golden, Nadine E.; Watt, Janet Tilden; Chinn, John L.; Erdey, Mercedes D.; Krigsman, Lisa M.; Manson, Michael W.; Endris, Charles A.; Cochran, Susan A.; Edwards, Brian D.

    2015-01-01

    In 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within the 3-nautical-mile limit of California’s State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow (to about 100 m) subsurface geology. 

  4. Learning in Baja California micro-enterprises

    Directory of Open Access Journals (Sweden)

    Michelle Texis Flores

    2011-01-01

    Full Text Available Mexico’s business structure has been characterized by the presence of microenterprises, particularly those averaging two workers, representing 65% of establishments in 2008 and 18% of employment. This makes them important for equity and welfare improvement of their members. This paper analyzes the performance of a group of 227 microenterprises in the state of Baja California, by the use of a practical application of the concept of learning curve arranged to incorporate returns to scale. The results indicate that in 48% of cases there is evidence of learning processes and 58% exhibited increasing returns to scale. This allows evaluating the development potential of these microenterprises and the design and implementation of proactive programs that encourage their learning and consolidation in the market.

  5. ASSOCIATION BETWEEN POSITIVE CANINE HEARTWORM (DIROFILARIA IMMITIS) ANTIGEN RESULTS AND PRESENCE OF ACANTHOCHEILONEMA ODENDHALI MICROFILARIA IN CALIFORNIA SEA LIONS (ZALOPHUS CALIFORNIANUS).

    Science.gov (United States)

    Krucik, David D R; Van Bonn, William; Johnson, Shawn P

    2016-03-01

    This study establishes a relationship between positive canine heartworm (Dirofilaria immitis) test results frequently observed in California sea lions (Zalophus californianus) and infection with the filarid nematode Acanthocheilonema odendhali. Four commercially available canine heartworm antigen tests were evaluated for cross-reaction with A. odendhali in California sea lions. Sera were tested from fifteen California sea lions with A. odendhali-associated microfilaremia, confirmed by blood smear, and with no evidence of D. immitis infection at necropsy. Ninety-five percent of tests were falsely positive for D. immitis. This study also determined that the prevalence of A. odendhali infection in stranded California sea lions from central California is approximately 23% by comparing the number of findings of mircofilaremia to the total number of California sea lions sampled at The Marine Mammal Center between 2005 and 2011, inclusive. Acanthocheilonema odenhali microfilaremia in California sea lions is likely to cross-react with canine heartworm antigen tests, and clinicians should interpret results with caution.

  6. California Geological Survey Geologic Map Index

    Data.gov (United States)

    California Natural Resource Agency — All the individual maps from the Geologic Atlas of California and the Regional Geologic map series have been georeferenced for display in a GIS (and viewable online...

  7. Teale Urband and rural areas of California

    Data.gov (United States)

    California Natural Resource Agency — California Spatial Information System (CaSIL) is a project designed to improve access to geo-spatial and geo-spatial related data information throughout the state of...

  8. Missing Linkages in California's Landscape [ds420

    Data.gov (United States)

    California Natural Resource Agency — The critical need for conserving landscape linkages first came to the forefront of conservation thinking in California in November 2000, when a statewide interagency...

  9. Teale California Office of Emergency Services

    Data.gov (United States)

    California Department of Resources — California Spatial Information System (CaSIL) is a project designed to improve access to geo-spatial and geo-spatial related data information throughout the state of...

  10. Teale California Office of Emergency Services

    Data.gov (United States)

    California Natural Resource Agency — California Spatial Information System (CaSIL) is a project designed to improve access to geo-spatial and geo-spatial related data information throughout the state of...

  11. Missing Linkages in California's Landscape [ds420

    Data.gov (United States)

    California Department of Resources — The critical need for conserving landscape linkages first came to the forefront of conservation thinking in California in November 2000, when a statewide interagency...

  12. Structure, organization, and sequence of alpha satellite DNA from human chromosome 17: evidence for evolution by unequal crossing-over and an ancestral pentamer repeat shared with the human X chromosome.

    Science.gov (United States)

    Waye, J S; Willard, H F

    1986-09-01

    The centromeric regions of all human chromosomes are characterized by distinct subsets of a diverse tandemly repeated DNA family, alpha satellite. On human chromosome 17, the predominant form of alpha satellite is a 2.7-kilobase-pair higher-order repeat unit consisting of 16 alphoid monomers. We present the complete nucleotide sequence of the 16-monomer repeat, which is present in 500 to 1,000 copies per chromosome 17, as well as that of a less abundant 15-monomer repeat, also from chromosome 17. These repeat units were approximately 98% identical in sequence, differing by the exclusion of precisely 1 monomer from the 15-monomer repeat. Homologous unequal crossing-over is suggested as a probable mechanism by which the different repeat lengths on chromosome 17 were generated, and the putative site of such a recombination event is identified. The monomer organization of the chromosome 17 higher-order repeat unit is based, in part, on tandemly repeated pentamers. A similar pentameric suborganization has been previously demonstrated for alpha satellite of the human X chromosome. Despite the organizational similarities, substantial sequence divergence distinguishes these subsets. Hybridization experiments indicate that the chromosome 17 and X subsets are more similar to each other than to the subsets found on several other human chromosomes. We suggest that the chromosome 17 and X alpha satellite subsets may be related components of a larger alphoid subfamily which have evolved from a common ancestral repeat into the contemporary chromosome-specific subsets.

  13. California Hydrogen Infrastructure Project

    Energy Technology Data Exchange (ETDEWEB)

    Heydorn, Edward C

    2013-03-12

    Air Products and Chemicals, Inc. has completed a comprehensive, multiyear project to demonstrate a hydrogen infrastructure in California. The specific primary objective of the project was to demonstrate a model of a real-world retail hydrogen infrastructure and acquire sufficient data within the project to assess the feasibility of achieving the nation's hydrogen infrastructure goals. The project helped to advance hydrogen station technology, including the vehicle-to-station fueling interface, through consumer experiences and feedback. By encompassing a variety of fuel cell vehicles, customer profiles and fueling experiences, this project was able to obtain a complete portrait of real market needs. The project also opened its stations to other qualified vehicle providers at the appropriate time to promote widespread use and gain even broader public understanding of a hydrogen infrastructure. The project engaged major energy companies to provide a fueling experience similar to traditional gasoline station sites to foster public acceptance of hydrogen. Work over the course of the project was focused in multiple areas. With respect to the equipment needed, technical design specifications (including both safety and operational considerations) were written, reviewed, and finalized. After finalizing individual equipment designs, complete station designs were started including process flow diagrams and systems safety reviews. Material quotes were obtained, and in some cases, depending on the project status and the lead time, equipment was placed on order and fabrication began. Consideration was given for expected vehicle usage and station capacity, standard features needed, and the ability to upgrade the station at a later date. In parallel with work on the equipment, discussions were started with various vehicle manufacturers to identify vehicle demand (short- and long-term needs). Discussions included identifying potential areas most suited for hydrogen fueling

  14. Baja California: literatura y frontera

    Directory of Open Access Journals (Sweden)

    Gabriel Trujillo Muñoz

    2014-06-01

    Baja California is a region that not only has migration problems and criminal violence because of the war of drugs or is a space of border conflicts in close neighborhood with the United States of America. Baja California is too a geographic space of culture and art, of creative writing and struggle to narrate the things and persons that here live, a plain sight, like their house, like their home, like a center of creation. This text give a cultural context of the border literature in the north of Mexico like a phenomenon in notice because his own merits, books and writers.

  15. Molecular Diversity of Trypanosoma cruzi Detected in the Vector Triatoma protracta from California, USA.

    Directory of Open Access Journals (Sweden)

    Lisa A Shender

    2016-01-01

    Full Text Available Trypanosoma cruzi, causative agent of Chagas disease in humans and dogs, is a vector-borne zoonotic protozoan parasite that can cause fatal cardiac disease. While recognized as the most economically important parasitic infection in Latin America, the incidence of Chagas disease in the United States of America (US may be underreported and even increasing. The extensive genetic diversity of T. cruzi in Latin America is well-documented and likely influences disease progression, severity and treatment efficacy; however, little is known regarding T. cruzi strains endemic to the US. It is therefore important to expand our knowledge on US T. cruzi strains, to improve upon the recognition of and response to locally acquired infections.We conducted a study of T. cruzi molecular diversity in California, augmenting sparse genetic data from southern California and for the first time investigating genetic sequences from northern California. The vector Triatoma protracta was collected from southern (Escondido and Los Angeles and northern (Vallecito California regions. Samples were initially screened via sensitive nuclear repetitive DNA and kinetoplast minicircle DNA PCR assays, yielding an overall prevalence of approximately 28% and 55% for southern and northern California regions, respectively. Positive samples were further processed to identify discrete typing units (DTUs, revealing both TcI and TcIV lineages in southern California, but only TcI in northern California. Phylogenetic analyses (targeting COII-ND1, TR and RB19 genes were performed on a subset of positive samples to compare Californian T. cruzi samples to strains from other US regions and Latin America. Results indicated that within the TcI DTU, California sequences were similar to those from the southeastern US, as well as to several isolates from Latin America responsible for causing Chagas disease in humans.Triatoma protracta populations in California are frequently infected with T. cruzi

  16. Regional variations in breast cancer among california teachers.

    Science.gov (United States)

    Reynolds, Peggy; Hurley, Susan; Goldberg, Debbie E; Anton-Culver, Hoda; Bernstein, Leslie; Deapen, Dennis; Horn-Ross, Pamela L; Peel, David; Pinder, Richard; Ross, Ronald K; West, Dee; Wright, William E; Ziogas, Argyrios

    2004-11-01

    Observed regional differences in breast cancer incidence could provide valuable clues to the etiology of this disease. The pattern of historically higher breast cancer rates among residents of California's San Francisco Bay and Southern Coastal areas is evident in the disease experience among members of the California Teachers Study. This large cohort study has followed female professional school employees for cancer incidence since 1995 and has collected extensive information on breast cancer risk factors. Between 1996 and 1999, invasive breast cancer was diagnosed in 1562 of the 115,611 cohort members who could be geocoded to a California address in 1995 and who had no previous breast cancer diagnosis. Adjusted hazard rate ratios (HRs) were estimated through multivariate Cox proportional hazards modeling. Rates were higher for cohort members in the San Francisco Bay area (HR = 1.22; 95% confidence interval = 1.06-1.40) and Southern Coastal area (1.16; 1.04-1.30) compared with those in the rest of California. The distributions of variables representing socioeconomic status, urbanization, and personal risk factors were consistent with higher risks for cohort members residing in the San Francisco Bay and Southern Coastal areas. Adjustment for these factors, however, did not explain regional differences in incidence, resulting in HRs that remained elevated for these 2 areas. Regional differences in breast cancer incidence in this large, well-defined cohort are not easily explained by known risk factors.

  17. Transhumant Ranchers in California

    Science.gov (United States)

    Sulak, A.; Forero, L.; Huntsinger, L.

    2009-04-01

    There is a strong link between some of the richest, most productive lands of the western United States, including California's oak woodlands, and the traditional "transhumance" of ranchers using public ranges. Oak woodland ranchers with government grazing leases report that about half of their income stems from using government -owned montane ranges. For many, loss of these leases reduces their ranch productive capacity to a level insufficient for sustainability, augmenting the sale of ranch lands for development. Many thousands of hectares of oak woodlands are linked to the fate of government leases in this way, and this linkage limits the opportunities for conservation of oak woodlands as "working landscapes" via conservation easements. This type of conservation is the fastest growing type in California today. The first case study shows that over the past 100 years there has been a reduction in access to the natural resources needed for transhumance from three sources: competition from use of the pastures for recreation and nature preservation, management practices that have brought about change in the character of the natural resources themselves, and urban sprawl. Ranchers are leasing other properties, purchasing feed, and transporting animals to other regions to compensate. Most had increased their privately leased land over the previous five years. Though they desire to stay on their ranches, transhumant ranching is becoming increasingly difficult because of land use changes on both public and private lands and a third of ranchers believe that they may need to sell the property for development if they lose their summer permits. There are many "line camps" on Forest Service range—cabins that families or workers would stay in during the summer to tend the cattle. However, the need to support the ranch with work in town limits the ability of the household to participate in transhumance or even travel into the mountains to check on the animals. For ranching to

  18. California State Waters Map Series: offshore of San Gregorio, California

    Science.gov (United States)

    Cochrane, Guy R.; Dartnell, Peter; Greene, H. Gary; Watt, Janet T.; Golden, Nadine E.; Endris, Charles A.; Phillips, Eleyne L.; Hartwell, Stephen R.; Johnson, Samuel Y.; Kvitek, Rikk G.; Erdey, Mercedes D.; Bretz, Carrie K.; Manson, Michael W.; Sliter, Ray W.; Ross, Stephanie L.; Dieter, Bryan E.; Chin, John L.; Cochran, Susan A.; Cochrane, Guy R.; Cochran, Susan A.

    2014-01-01

    In 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within the 3-nautical-mile limit of California's State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow (to about 100 m) subsurface geology. The Offshore of San Gregorio map area is located in northern California, on the Pacific coast of the San Francisco Peninsula about 50 kilometers south of the Golden Gate. The map area lies offshore of the Santa Cruz Mountains, part of the northwest-trending Coast Ranges that run roughly parallel to the San Andreas Fault Zone. The Santa Cruz Mountains lie between the San Andreas Fault Zone and the San Gregorio Fault system. The nearest significant onshore cultural centers in the map area are San Gregorio and Pescadero, both unincorporated communities with populations well under 1,000. Both communities are situated inland of state beaches that share their names. No harbor facilities are within the Offshore of San Gregorio map area. The hilly coastal area is virtually undeveloped grazing land for sheep and cattle. The coastal geomorphology is controlled by late Pleistocene and Holocene slip in the San Gregorio Fault system. A westward bend in the San Andreas Fault Zone, southeast of the map area, coupled with right-lateral movement along the San Gregorio Fault system have caused regional folding and uplift. The coastal area consists of high coastal bluffs and vertical sea cliffs. Coastal promontories in

  19. Analogous Three-Dimensional Constructive Interference in Steady State Sequences Enhance the Utility of Three-Dimensional Time of Flight Magnetic Resonance Angiography in Delineating Lenticulostriate Arteries in Insular Gliomas: Evidence from a Prospective Clinicoradiologic Analysis of 48 Patients.

    Science.gov (United States)

    Rao, Arun S; Thakar, Sumit; Sai Kiran, Narayanam Anantha; Aryan, Saritha; Mohan, Dilip; Hegde, Alangar S

    2018-01-01

    Three-dimensional (3D) time of flight (TOF) imaging is the current gold standard for noninvasive, preoperative localization of lenticulostriate arteries (LSAs) in insular gliomas; however, the utility of this modality depends on tumor intensity. Over a 3-year period, 48 consecutive patients with insular gliomas were prospectively evaluated. Location of LSAs and their relationship with the tumor were determined using a combination of contrast-enhanced coronal 3D TOF magnetic resonance angiography and coronal 3D constructive interference in steady state (CISS) sequences. These findings were analyzed with respect to extent of tumor resection and early postoperative motor outcome. Tumor was clearly visualized in 29 (60.4%) patients with T1-hypointense tumors using 3D TOF and in all patients using CISS sequences. Using combined 3D TOF and CISS, LSA-tumor interface was well seen in 47 patients, including all patients with T1-heterointense or T1-isointense tumors. Extent of resection was higher in the LSA-pushed group compared with the LSA-encased group. In the LSA-encased group, 6 (12.5%) patients developed postoperative hemiparesis; 2 (4.2%) cases were attributed to LSA injury. Contrast-enhanced 3D TOF can delineate LSAs in almost all insular gliomas but is limited in identifying the LSA-tumor interface. This limitation can be overcome by addition of analogous CISS sequences that delineate the LSA-tumor interface regardless of tumor intensity. Combined 3D TOF and 3D CISS is a useful tool for surgical planning and safer resections of insular tumors and may have added surgical relevance when included as an intraoperative adjunct. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Nonparametric combinatorial sequence models.

    Science.gov (United States)

    Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

    2011-11-01

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

  1. Killing tanoak in northwestern California

    Science.gov (United States)

    D. F. Roy

    1956-01-01

    Residual tanoak (Lithocarpus densiflorus (Hook. & Arn.) Rehd.) trees and tanoak sprouts often are an important component of the vegetation which competes with conifer reproduction in northwestern California. Sometimes enough tanoak is present in Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) stands to dominate the...

  2. Genetic variation in California oaks

    Science.gov (United States)

    Constance I. Millar; Diane L. Delany; Lawrence A. Riggs

    1990-01-01

    In forestry the importance of genetic variation for successful reproduction, survival and growth has been widely documented for commercial conifers; until recently, little genetic work has been done on the California oaks. Even before the nature of genetic variation was scientifically investigated, its importance was suspected in operational forestry. Many failures of...

  3. California Community Colleges Parking Survey.

    Science.gov (United States)

    McIntyre, Chuck

    In 1990, a representative sample of 25 California community colleges was contacted by telephone to determine their parking policies and practices. The colleges were sampled on the basis of location and size. Study findings included the following: (1) 17 of the colleges reported that they had insufficient numbers of on-campus parking spaces; (2)…

  4. Revamping California's Education Finance System.

    Science.gov (United States)

    McFadden, Brett

    2003-01-01

    Describes reasons for California's budget deficits and their impact on school finance. Offers five possible solutions to the school funding crises: Restructure the state's tax and revenue system, restore school district revenue-sharing abilities, initiate a top-to-bottom mandate review, provide greater fiscal and program flexibility, and revamp…

  5. The California Baseline Methane Survey

    Science.gov (United States)

    Duren, R. M.; Thorpe, A. K.; Hopkins, F. M.; Rafiq, T.; Bue, B. D.; Prasad, K.; Mccubbin, I.; Miller, C. E.

    2017-12-01

    The California Baseline Methane Survey is the first systematic, statewide assessment of methane point source emissions. The objectives are to reduce uncertainty in the state's methane budget and to identify emission mitigation priorities for state and local agencies, utilities and facility owners. The project combines remote sensing of large areas with airborne imaging spectroscopy and spatially resolved bottom-up data sets to detect, quantify and attribute emissions from diverse sectors including agriculture, waste management, oil and gas production and the natural gas supply chain. Phase 1 of the project surveyed nearly 180,000 individual facilities and infrastructure components across California in 2016 - achieving completeness rates ranging from 20% to 100% per emission sector at < 5 meters spatial resolution. Additionally, intensive studies of key areas and sectors were performed to assess source persistence and variability at times scales ranging from minutes to months. Phase 2 of the project continues with additional data collection in Spring and Fall 2017. We describe the survey design and measurement, modeling and analysis methods. We present initial findings regarding the spatial, temporal and sectoral distribution of methane point source emissions in California and their estimated contribution to the state's total methane budget. We provide case-studies and lessons learned about key sectors including examples where super-emitters were identified and mitigated. We summarize challenges and recommendations for future methane research, inventories and mitigation guidance within and beyond California.

  6. Residential Energy Efficiency Potential: California

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, Eric J [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2017-11-16

    Energy used by California single-family homes that can be saved through cost-effective improvements. Prepared by Eric Wilson and Noel Merket, NREL, and Erin Boyd, U.S. Department of Energy Office of Energy Policy and Systems Analysis.

  7. California Amusement Rides and Liability

    Science.gov (United States)

    Epstein, Adam

    2005-01-01

    Twenty-three-year-old Cristina Moreno traveled from Spain to California for her honeymoon in 2000. As part of her visit, she rode the Indiana Jones amusement ride at Disneyland with her new husband. On June 25, 2000, she suffered a brain injury, and she eventually died on September 1, 2000, as a result of injuries allegedly sustained while riding…

  8. Special Education Finance in California

    Science.gov (United States)

    Hill, Laura; Warren, Paul; Murphy, Patrick; Ugo, Iwunze; Pathak, Aditi

    2016-01-01

    California's system of special education served about 718,000 students in 2014-15, or about 11.5 percent of the K-12 population. It is expensive, consuming some $12 billion in federal, state, and local dollars annually. Special education operates within a legal framework that sets it apart from the rest of the K-12 system. The state's enactment of…

  9. California Endangered Species Resource Guide.

    Science.gov (United States)

    California State Dept. of Education, Los Angeles.

    This document was developed in response to California Senate Bill No. 885, "The Endangered Species Education Project," that called for a statewide program in which schools adopt a local endangered species, research past and current efforts to preserve the species' habitat, develop and implement an action plan to educate the community…

  10. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  11. Monomorphic pathogens: The case of Candidatus Xenohaliotis californiensis from abalone in California, USA and Baja California, Mexico.

    Science.gov (United States)

    Cicala, Francesco; Moore, James D; Cáceres-Martínez, Jorge; Del Río-Portilla, Miguel A; Hernández-Rodríguez, Mónica; Vásquez-Yeomans, Rebeca; Rocha-Olivares, Axayácatl

    2018-05-01

    Withering syndrome (WS) is a chronic wasting disease affecting abalone species attributed to the pathogen Candidatus Xenohaliotis californiensis (CXc). Wild populations of blue (Haliotis fulgens) and yellow (H. corrugata) abalone have experienced unusual mortality rates since 2009 off the peninsula of Baja California and WS has been hypothesized as a possible cause. Currently, little information is available about the genetic diversity of CXc and particularly the possible existence of strains differing in pathogenicity. In a recent phylogenetic analysis, we characterized five coding genes from this rickettsial pathogen. Here, we analyze those genes and two additional intergenic non-coding regions following multi-locus sequence typing (MLST) and multi-spacer typing (MST) approaches to assess the genetic variability of CXc and its relationship with blue, yellow and red (H. rufescens) abalone. Moreover, we used 16S rRNA pyrosequencing reads from gut microbiomes of blue and yellow abalone to complete the genetic characterization of this prokaryote. The presence of CXc was investigated in more than 150 abalone of the three species; furthermore, a total of 385 DNA sequences and 7117 16S rRNA reads from Candidatus Xenohaliotis californiensis were used to evaluate its population genetic structure. Our findings suggest the absence of polymorphism in the DNA sequences of analyzed loci and the presence of a single lineage of CXc infecting abalone from California (USA) and Baja California (Mexico). We posit that the absence of genetic variably in this marine rickettsia may be the result of evolutionary and ecological processes. Copyright © 2018 Elsevier Inc. All rights reserved.

  12. Comparison of next generation sequencing technologies for transcriptome characterization

    Directory of Open Access Journals (Sweden)

    Soltis Douglas E

    2009-08-01

    Full Text Available Abstract Background We have developed a simulation approach to help determine the optimal mixture of sequencing methods for most complete and cost effective transcriptome sequencing. We compared simulation results for traditional capillary sequencing with "Next Generation" (NG ultra high-throughput technologies. The simulation model was parameterized using mappings of 130,000 cDNA sequence reads to the Arabidopsis genome (NCBI Accession SRA008180.19. We also generated 454-GS20 sequences and de novo assemblies for the basal eudicot California poppy (Eschscholzia californica and the magnoliid avocado (Persea americana using a variety of methods for cDNA synthesis. Results The Arabidopsis reads tagged more than 15,000 genes, including new splice variants and extended UTR regions. Of the total 134,791 reads (13.8 MB, 119,518 (88.7% mapped exactly to known exons, while 1,117 (0.8% mapped to introns, 11,524 (8.6% spanned annotated intron/exon boundaries, and 3,066 (2.3% extended beyond the end of annotated UTRs. Sequence-based inference of relative gene expression levels correlated significantly with microarray data. As expected, NG sequencing of normalized libraries tagged more genes than non-normalized libraries, although non-normalized libraries yielded more full-length cDNA sequences. The Arabidopsis data were used to simulate additional rounds of NG and traditional EST sequencing, and various combinations of each. Our simulations suggest a combination of FLX and Solexa sequencing for optimal transcriptome coverage at modest cost. We have also developed ESTcalc http://fgp.huck.psu.edu/NG_Sims/ngsim.pl, an online webtool, which allows users to explore the results of this study by specifying individualized costs and sequencing characteristics. Conclusion NG sequencing technologies are a highly flexible set of platforms that can be scaled to suit different project goals. In terms of sequence coverage alone, the NG sequencing is a dramatic advance

  13. Long sequence correlation coprocessor

    Science.gov (United States)

    Gage, Douglas W.

    1994-09-01

    A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

  14. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  15. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  16. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  17. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  18. Identification of circo-like virus-Brazil genomic sequences in raw sewage from the metropolitan area of São Paulo: evidence of circulation two and three years after the first detection

    Directory of Open Access Journals (Sweden)

    Silvana Beres Castrignano

    Full Text Available BACKGROUND Two novel viruses named circo-like virus-Brazil (CLV-BR hs1 and hs2 were previously discovered in a Brazilian human fecal sample through metagenomics. CLV-BR hs1 and hs2 possess a small circular DNA genome encoding a replication initiator protein (Rep, and the two genomes exhibit 92% nucleotide identity with each other. Phylogenetic analysis based on the Rep protein showed that CLV-BRs do not cluster with circoviruses, nanoviruses, geminiviruses or cycloviruses. OBJECTIVE The aim of this study was to search for CLV-BR genomes in sewage and reclaimed water samples from the metropolitan area of São Paulo, Brazil, to verify whether the first detection of these viruses was an isolated finding. METHODS Sewage and reclaimed water samples collected concomitantly during the years 2005-2006 were purified and concentrated using methodologies designed for the study of viruses. A total of 177 treated reclaimed water samples were grouped into five pools, as were 177 treated raw sewage samples. Nucleic acid extraction, polymerase chain reaction (PCR amplification and Sanger sequencing were then performed.e FINDINGS CLV-BR genomes were detected in two pools of sewage samples, p6 and p9. Approximately 28% and 51% of the CLV-BR genome was amplified from p6 and p9, respectively, including 76% of the Rep gene. The detected genomes are most likely related to CLV-BR hs1. Comparative analysis showed several synonymous substitutions within Rep-encoding sequences, suggesting purifying selection for this gene, as has been observed for other eukaryotic circular Rep-encoding single-stranded DNA (CRESS-DNA viruses. MAIN CONCLUSION The results therefore indicated that CLV-BR has continued to circulate in Brazil two and three years after first being detected.

  19. Brain calbindin-D28k and an Mr 29,000 calcium binding protein in cerebellum are different but related proteins: Evidence obtained from sequence analysis by tandem mass spectroscopy

    International Nuclear Information System (INIS)

    Gabrielides, C.; Christakos, S.; McCormack, A.L.; Hunt, D.F.

    1991-01-01

    A calcium binding protein of M r 29,000 which cross-reacts with antibodies raised against chick calbindin-D 28k was previously reported to be present in rat cerebellum. It was suggested that the M r 29,000 protein represents another form of calbindin-D 28k . In the authors laboratory they were able to identify M r 28,000 and 29,000 proteins in rat, human, and chick cerebellum by their ability to bind 45 Ca in a 45 Ca blot assay. Two calcium binding proteins of M r 27,680 and 29,450 were isolated from rat cerebelli by the use of gel permeation chromatography and preparative gel electrophoresis. After reverse-phase high-performance liquid chromatography (HPLC) the proteins were sequenced. Sequence analysis by tandem mass spectrometry indicated only 52% identity between the rat cerebellar M r 28,000 and 29,000 proteins. Thus they are not different forms of the same protein, as previously suggested. Eighty-nine percent identity was observed between the rate cerebellar M r 29,000 protein and chick calretinin. The difference in identity between the rat cerebellar M r 29,000 protein and chick calretinin may be due to species differences, and thus this protein is most likely rat calretinin. These results suggest either posttranscriptional regulation of calretinin in cerebellum or species differences. The study also suggests that previous immunocytochemical mapping for calbindin using antisera which cross-reacted with both proteins detected brain regions that expressed not only calbindin but also calretinin or a calretinin-like protein

  20. Fire management of California shrubland landscapes

    Science.gov (United States)

    Keeley, Jon E.

    2002-01-01

    Fire management of California shrublands has been heavily influenced by policies designed for coniferous forests, however, fire suppression has not effectively excluded fire from chaparral and coastal sage scrub landscapes and catastrophic wildfires are not the result of unnatural fuel accumulation. There is no evidence that prescribed burning in these shrublands provides any resource benefit and in some areas may negatively impact shrublands by increasing fire frequency. Therefore, fire hazard reduction is the primary justification for prescription burning, but it is doubtful that rotational burning to create landscape age mosaics is a cost effective method of controlling catastrophic wildfires. There are problems with prescription burning in this crown-fire ecosystem that are not shared by forests with a natural surface-fire regime. Prescription weather conditions preclude burning at rotation intervals sufficient to effect the control of fires ignited under severe weather conditions. Fire management should focus on strategic placement of prescription burns to both insure the most efficient fire hazard reduction and to minimize the amount of landscape exposed to unnaturally high fire frequency. A major contributor to increased fire suppression costs and increased loss of property and lives is the continued urban sprawl into wildlands naturally subjected to high intensity crown fires. Differences in shrubland fire history suggest there may be a need for different fire management tactics between central coastal and southern California. Much less is known about shrubland fire history in the Sierra Nevada foothills and interior North Coast Ranges, and thus it would be prudent to not transfer these ideas too broadly across the range of chaparral until we have a clearer understanding of the extent of regional variation in shrubland fire regimes.

  1. Hierarchically nested river landform sequences

    Science.gov (United States)

    Pasternack, G. B.; Weber, M. D.; Brown, R. A.; Baig, D.

    2017-12-01

    River corridors exhibit landforms nested within landforms repeatedly down spatial scales. In this study we developed, tested, and implemented a new way to create river classifications by mapping domains of fluvial processes with respect to the hierarchical organization of topographic complexity that drives fluvial dynamism. We tested this approach on flow convergence routing, a morphodynamic mechanism with different states depending on the structure of nondimensional topographic variability. Five nondimensional landform types with unique functionality (nozzle, wide bar, normal channel, constricted pool, and oversized) represent this process at any flow. When this typology is nested at base flow, bankfull, and floodprone scales it creates a system with up to 125 functional types. This shows how a single mechanism produces complex dynamism via nesting. Given the classification, we answered nine specific scientific questions to investigate the abundance, sequencing, and hierarchical nesting of these new landform types using a 35-km gravel/cobble river segment of the Yuba River in California. The nested structure of flow convergence routing landforms found in this study revealed that bankfull landforms are nested within specific floodprone valley landform types, and these types control bankfull morphodynamics during moderate to large floods. As a result, this study calls into question the prevailing theory that the bankfull channel of a gravel/cobble river is controlled by in-channel, bankfull, and/or small flood flows. Such flows are too small to initiate widespread sediment transport in a gravel/cobble river with topographic complexity.

  2. Age and paleoenvironment of the imperial formation near San Gorgonio Pass, Southern California

    Science.gov (United States)

    McDougall, K.; Poore, R.Z.; Matti, J.

    1999-01-01

    Microfossiliferous marine sediments of the Imperial Formation exposed in the Whitewater and Cabazon areas, near San Gorgonio Pass, southern California, are late Miocene in age and were deposited at intertidal to outer neritic depths, and possibly upper bathyal depths. A late Miocene age of 7.4 to >6.04 Ma is based on the ranges of age-diagnostic benthic foraminifers (Cassidulina delicata and Uvigerina peregrina), planktic foraminifers (Globigerinoides obliquus, G. extremus, and Globigerina nepenthes; zones N17-N19), and calcareous nannoplankton (Discoaster brouweri, D. aff. D. surculus, Reticulofenestra pseudoumbilicata, Sphenolithus abies, and S. neoabies; zones CN9a-CN11) coupled with published K/Ar dates from the underlying Coachella Formation (10.1 ?? 1.2 Ma; Peterson, 1975) and overlying Painted Hill Formation (6.04 ?? 0.18 and 5.94 ?? 0.18 Ma; J. L. Morton in Matti and others, 1985 and Matti and Morton, 1993). Paleoecologic considerations (sea-level fluctuations and paleotemperature) restrict the age of the Imperial Formation to 6.5 through 6.3 Ma. Benthic foraminiferal assemblages indicate that the Imperial Formation in the Whitewater and Cabazon sections accumulated at inner neritic to outer neritic (0-152 m) and possibly upper bathyal (152-244 m) depths. Shallowing to inner neritic depths occurred as the upper part of the section was deposited. This sea-level fluctuation corresponds to a global highstand at 6.3 Ma (Haq and others, 1987). Planktic foraminifers suggest an increase in surface-water temperatures upsection. A similar increase in paleotemperatures is interpreted for the North Pacific from 6.5 to 6.3 Ma (warm interval W10 of Barron and Keller, 1983). Environmental contrasts between the Whitewater and Cabazon sections of the Imperial Formation provide evidence for right-lateral displacements on the Banning fault, a late Miocene strand of the San Andreas fault system. The Cabazon section lies south of the Banning fault, and has been displaced west

  3. Native peoples’ relationship to the California chaparral

    Science.gov (United States)

    Anderson, M. Kat; Keeley, Jon E.; Underwood, Emma C.; Safford, Hugh D.; Molinari, Nicole A.; Keeley, Jon E.

    2018-01-01

    Ethnographic interviews and historical literature reviews provide evidence that for many tribes of California, chaparral plant communities were a rich source of food, medicines, and technologies and that they supplemented natural fires with deliberate burning of chaparral to maximize its ability to produce useful products. Many of the most important chaparral plant species used in the food and material culture have strong adaptations to fire. Particularly useful were many annual and perennial herbs, which proliferate after fire from seed and bulb banks, shrub resprouts that made superb cordage and basketry material, as well as animals that were more readily caught in postfire environments. The reasons for burning in chaparral are grouped into seven ecological categories, each relying on a known response to fire of the chaparral community. The authors posit that tribes employed intentional burning to maintain chaparral in different ages and size classes to meet diverse food and material needs, tracking the change in plant and animal abundance and diversity, and shifts in shrub architecture and habitat structure during the recovery of the chaparral community. Areas were burned in ways designed to create a mosaic of open grassland and recently burned, young and mature stands of chaparral with different combinations of species and densities. This management conferred on chaparral plant communities a degree of spatial, structural, successional, and biotic diversity that exceeded what would have been the case in the absence of human intervention. These impacts are still evident on contemporary landscapes.

  4. Geographic proximity not a prerequisite for invasion: Hawaii not the source of California invasion by light brown apple moth (Epiphyas postvittana.

    Directory of Open Access Journals (Sweden)

    Daniel Rubinoff

    Full Text Available BACKGROUND: The light brown apple moth (LBAM, Epiphyas postvittana (Walker, is native to Australia but invaded England, New Zealand, and Hawaii more than 100 years ago. In temperate climates, LBAM can be a major agricultural pest. In 2006 LBAM was discovered in California, instigating eradication efforts and quarantine against Hawaiian agriculture, the assumption being that Hawaii was the source of the California infestation. Genetic relationships among populations in Hawaii, California, and New Zealand are crucial to understanding LBAM invasion dynamics across the Pacific. METHODOLOGY/PRINCIPAL FINDINGS: We sequenced mitochondrial DNA (mtDNA from 1293 LBAM individuals from California (695, Hawaii (448, New Zealand (147, and Australia (3 to examine haplotype diversity and structure among introduced populations, and evaluate the null hypothesis that invasive populations are from a single panmictic source. However, invasive populations in California and New Zealand harbor deep genetic diversity, whereas Hawaii shows low level, shallow diversity. CONCLUSIONS/SIGNIFICANCE: LBAM recently has established itself in California, but was in Hawaii and New Zealand for hundreds of generations, yet California and New Zealand show similar levels of genetic diversity relative to Hawaii. Thus, there is no clear relationship between duration of invasion and genetic structure. Demographic statistics suggest rapid expansion occurring in California and past expansions in New Zealand; multiple introductions of diverse, genetically fragmented lineages could contribute to these patterns. Hawaii and California share no haplotypes, therefore, Hawaii is not the source of the California introduction. Paradoxically, Hawaii and California share multiple haplotypes with New Zealand. New Zealand may be the source for the California and Hawaii infestations, but the introductions were independent, and Hawaii was invaded only once. This has significant implications for

  5. Perception Enhancement using Visual Attributes in Sequence Motif Visualization

    OpenAIRE

    Oon, Yin; Lee, Nung; Kok, Wei

    2016-01-01

    Sequence logo is a well-accepted scientific method to visualize the conservation characteristics of biological sequence motifs. Previous studies found that using sequence logo graphical representation for scientific evidence reports or arguments could seriously cause biases and misinterpretation by users. This study investigates on the visual attributes performance of a sequence logo in helping users to perceive and interpret the information based on preattentive theories and Gestalt principl...

  6. Channel Responses and Hydromodification in Southern California

    Science.gov (United States)

    Hawley, R. J.; Dust, D. W.; Bledsoe, B. P.

    2007-12-01

    Hydromodification (changes in watershed hydrologic characteristics, and the resulting hydraulics and channel forms due to urbanization) is ubiquitous in Southern California. In this region, the effects of hydromodification are driven and compounded by the arid/semiarid climate, high relief, erodible soils, high urbanization rates, and relatively low frequency of retention/detention. We conducted a preliminary survey of over 50 stream reaches along a gradient from least disturbed to fully urbanized. All stages of the Channel Evolution Model (CEM) of Schumm et al. (1984) were observed, from stable to degrading, widening, aggrading, and quasi-equilibrium channels. Several sites have CEM stages II through V in close proximity due to headcutting, hardpoints, and infrastructure. We also observed channels in undeveloped watersheds impacted by downstream urbanization via headcutting. A range of intervention measures was observed, with the frequent evolutionary endpoint as a concrete engineered flood control channel. We also observed multiple channel evolution sequences that deviate from the CEM for single-thread, incising channels. An alternative channel response, particularly on smaller urbanized streams is a stabilized, vegetation encroached low-flow channel with regular baseflow supplied by residential irrigation runoff. The limited cases of unimpacted streams that remain tend to be high gradient, high energy systems that are naturally proximate to the transition between braided and meandering form for a given sediment size.

  7. Pandemic H1N1 influenza isolated from free-ranging Northern Elephant Seals in 2010 off the central California coast.

    Directory of Open Access Journals (Sweden)

    Tracey Goldstein

    Full Text Available Interspecies transmission of influenza A is an important factor in the evolution and ecology of influenza viruses. Marine mammals are in contact with a number of influenza reservoirs, including aquatic birds and humans, and this may facilitate transmission among avian and mammalian hosts. Virus isolation, whole genome sequencing, and hemagluttination inhibition assay confirmed that exposure to pandemic H1N1 influenza virus occurred among free-ranging Northern Elephant Seals (Mirounga angustirostris in 2010. Nasal swabs were collected from 42 adult female seals in April 2010, just after the animals had returned to the central California coast from their short post-breeding migration in the northeast Pacific. Swabs from two seals tested positive by RT-PCR for the matrix gene, and virus was isolated from each by inoculation into embryonic chicken eggs. Whole genome sequencing revealed greater than 99% homology with A/California/04/2009 (H1N1 that emerged in humans from swine in 2009. Analysis of more than 300 serum samples showed that samples collected early in 2010 (n = 100 were negative and by April animals began to test positive for antibodies against the pH1N1 virus (HI titer of ≥1∶40, supporting the molecular findings. In vitro characterizations studies revealed that viral replication was indistinguishable from that of reference strains of pH1N1 in canine kidney cells, but replication was inefficient in human epithelial respiratory cells, indicating these isolates may be elephant seal adapted viruses. Thus findings confirmed that exposure to pandemic H1N1 that was circulating in people in 2009 occurred among free-ranging Northern Elephant Seals in 2010 off the central California coast. This is the first report of pH1N1 (A/Elephant seal/California/1/2010 in any marine mammal and provides evidence for cross species transmission of influenza viruses in free-ranging wildlife and movement of influenza viruses between humans and wildlife.

  8. Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: further evidence from a nuclear gene of the systematic chaos in the family.

    Science.gov (United States)

    He, Shunping; Mayden, Richard L; Wang, Xuzheng; Wang, Wei; Tang, Kevin L; Chen, Wei-Jen; Chen, Yiyu

    2008-03-01

    The family Cyprinidae is the largest freshwater fish group in the world, including over 200 genera and 2100 species. The phylogenetic relationships of major clades within this family are simply poorly understood, largely because of the overwhelming diversity of the group; however, several investigators have advanced different hypotheses of relationships that pre- and post-date the use of shared-derived characters as advocated through phylogenetic systematics. As expected, most previous investigations used morphological characters. Recently, mitochondrial DNA (mtDNA) sequences and combined morphological and mtDNA investigations have been used to explore and advance our understanding of species relationships and test monophyletic groupings. Limitations of these studies include limited taxon sampling and a strict reliance upon maternally inherited mtDNA variation. The present study is the first endeavor to recover the phylogenetic relationships of the 12 previously recognized monophyletic subfamilies within the Cyprinidae using newly sequenced nuclear DNA (nDNA) for over 50 species representing members of the different previously hypothesized subfamily and family groupings within the Cyprinidae and from other cypriniform families as outgroup taxa. Hypothesized phylogenetic relationships are constructed using maximum parsimony and Basyesian analyses of 1042 sites, of which 971 sites were variable and 790 were phylogenetically informative. Using other appropriate cypriniform taxa of the families Catostomidae (Myxocyprinus asiaticus), Gyrinocheilidae (Gyrinocheilus aymonieri), and Balitoridae (Nemacheilus sp. and Beaufortia kweichowensis) as outgroups, the Cyprinidae is resolved as a monophyletic group. Within the family the genera Raiamas, Barilius, Danio, and Rasbora, representing many of the tropical cyprinids, represent basal members of the family. All other species can be classified into variably supported and resolved monophyletic lineages, depending upon analysis

  9. Discussing epigenetics in Southern California

    Science.gov (United States)

    2012-01-01

    With the goal of discussing how epigenetic control and chromatin remodeling contribute to the various processes that lead to cellular plasticity and disease, this symposium marks the collaboration between the Institut National de la Santé et de la Recherche Médicale (INSERM) in France and the University of California, Irvine (UCI). Organized by Paolo Sassone-Corsi (UCI) and held at the Beckman Center of the National Academy of Sciences at the UCI campus December 15–16, 2011, this was the first of a series of international conferences on epigenetics dedicated to the scientific community in Southern California. The meeting also served as the official kick off for the newly formed Center for Epigenetics and Metabolism at the School of Medicine, UCI (http://cem.igb.uci.edu). PMID:22414797

  10. Absolute gravity measurements in California

    Science.gov (United States)

    Zumberge, M. A.; Sasagawa, G.; Kappus, M.

    1986-08-01

    An absolute gravity meter that determines the local gravitational acceleration by timing a freely falling mass with a laser interferometer has been constructed. The instrument has made measurements at 11 sites in California, four in Nevada, and one in France. The uncertainty in the results is typically 10 microgal. Repeated measurements have been made at several of the sites; only one shows a substantial change in gravity.

  11. Fumigation success for California facility.

    Science.gov (United States)

    Hacker, Robert

    2010-02-01

    As Robert Hacker, at the time director of facilities management at the St John's Regional Medical Center in Oxnard, California, explains, the hospital, one of the area's largest, recently successfully utilised a new technology to eliminate mould, selecting a cost and time-saving fumigation process in place of the traditional "rip and tear" method. Although hospital managers knew the technology had been used extremely effectively in other US buildings, this was reportedly among the first ever healthcare applications.

  12. Global climate change and California

    International Nuclear Information System (INIS)

    Knox, J.B.; Scheuring, A.F.

    1991-01-01

    In the fall of 1988 the University of California organized a new public-service initiative on global climate change in response to inquiries and requests from members of Congress and the Department of Energy (DOE). This new systemwide initiative involved all of the University of California campuses and the University's three national laboratories at Berkeley, Los Alamos, and Livermore. The goal of this Greenhouse Initiative was to focus the multidisciplinary resources of the UC campuses and the team-oriented research capabilities of the laboratories on the prospect of global warming and its associated effects on the planet and its nations. In consultation with the DOE, the organizers proposed a series of workshops to focus University of California research resources on the issue of global warming, to contribute to the congressionally mandated DOE studies on options for the US to reduce carbon dioxide emissions by 20% by the year 2000, and to begin building a long-term research base contributing to an improved understanding of global change in all of its complexity and diverse discipline implications. This volume contains papers from the first of these workshops. Individual papers are processed separately for inclusion in the appropriate data bases

  13. In-source laser spectroscopy of $^{75, 77, 78}$Cu Direct evidence for a change in the quasiparticle energy sequence in $^{75, 77}$Cu and an absence of longer-lived isomers in $^{78}$Cu

    CERN Document Server

    Koster, U; Serot, O; Fedosseev, V N; Kratz, K L; Stone, N J; Sjodin, A M; Materna, T; Flanagan, K T; Molkanov, P L; Stone, J R; Seliverstov, M D; Mathieu, L; Marsh, B A

    2011-01-01

    This paper describes measurements on the isotopes (75,77,78)Cu by the technique of in-source laser spectroscopy, at the ISOLDE facility, CERN. The role of this technique is briefly discussed in the context of this and other, higher resolution, methods applied to copper isotopes in the range (57-78)Cu. The data, analyzed in comparison with previous results on the lighter isotopes (59,63)Cu, establish the ground-state nuclear spin of (75,77)Cu as 5/2 and yield their magnetic dipole moments as +1.01(5)mu(N) and +1.61(5)mu(N), respectively. The results on (78)Cu show no evidence for long-lived isomerism at this mass number and are consistent with a spin in the range 3-6 and moment of 0.0(4) mu(N)

  14. Accessing northern California earthquake data via Internet

    Science.gov (United States)

    Romanowicz, Barbara; Neuhauser, Douglas; Bogaert, Barbara; Oppenheimer, David

    The Northern California Earthquake Data Center (NCEDC) provides easy access to central and northern California digital earthquake data. It is located at the University of California, Berkeley, and is operated jointly with the U.S. Geological Survey (USGS) in Menlo Park, Calif., and funded by the University of California and the National Earthquake Hazard Reduction Program. It has been accessible to users in the scientific community through Internet since mid-1992.The data center provides an on-line archive for parametric and waveform data from two regional networks: the Northern California Seismic Network (NCSN) operated by the USGS and the Berkeley Digital Seismic Network (BDSN) operated by the Seismographic Station at the University of California, Berkeley.

  15. California commercial building energy benchmarking

    Energy Technology Data Exchange (ETDEWEB)

    Kinney, Satkartar; Piette, Mary Ann

    2003-07-01

    Building energy benchmarking is the comparison of whole-building energy use relative to a set of similar buildings. It provides a useful starting point for individual energy audits and for targeting buildings for energy-saving measures in multiple-site audits. Benchmarking is of interest and practical use to a number of groups. Energy service companies and performance contractors communicate energy savings potential with ''typical'' and ''best-practice'' benchmarks while control companies and utilities can provide direct tracking of energy use and combine data from multiple buildings. Benchmarking is also useful in the design stage of a new building or retrofit to determine if a design is relatively efficient. Energy managers and building owners have an ongoing interest in comparing energy performance to others. Large corporations, schools, and government agencies with numerous facilities also use benchmarking methods to compare their buildings to each other. The primary goal of Task 2.1.1 Web-based Benchmarking was the development of a web-based benchmarking tool, dubbed Cal-Arch, for benchmarking energy use in California commercial buildings. While there were several other benchmarking tools available to California consumers prior to the development of Cal-Arch, there were none that were based solely on California data. Most available benchmarking information, including the Energy Star performance rating, were developed using DOE's Commercial Building Energy Consumption Survey (CBECS), which does not provide state-level data. Each database and tool has advantages as well as limitations, such as the number of buildings and the coverage by type, climate regions and end uses. There is considerable commercial interest in benchmarking because it provides an inexpensive method of screening buildings for tune-ups and retrofits. However, private companies who collect and manage consumption data are concerned that the

  16. California's experience with alternative fuel vehicles

    International Nuclear Information System (INIS)

    Sullivan, C.

    1993-01-01

    California is often referred to as a nation-state, and in many aspects fits that description. The state represents the seventh largest economy in the world. Most of California does not have to worry about fuel to heat homes in the winter. What we do worry about is fuel for our motor vehicles, approximately 24 million of them. In fact, California accounts for ten percent of new vehicle sales in the United States each year, much of it used in the transportation sector. The state is the third largest consumer of gasoline in the world, only exceeded by the United States as a whole and the former Soviet Union. California is also a leader in air pollution. Of the nine worst ozone areas in the country cited in the 1990 Clean Air Act Amendments, two areas the Los Angeles Basin and San Diego are located in California. Five of California's cities made the top 20 smoggiest cities in the United States. In reality, all of California's major metropolitan areas have air quality problems. This paper will discuss the beginnings of California's investigations of alternative fuels use in vehicles; the results of the state's demonstration programs; and future plans to improve California's air quality and energy security in the mobile sector

  17. California Attorney General opines: California's nuclear legislation unconstitutional

    International Nuclear Information System (INIS)

    Gabin, V.

    1979-01-01

    The California Attorney General found three sections of the state's nuclear regulation code to be in violation of Federal authority and the State Constitution. Legislation and court cases since 1946 are quoted to support the Attorney General's position. The Warren--Alquist Act, which requires a demonstrated technology for reprocessing fuel rods or disposing of high-level wastes before a nuclear plant can be licensed, is unconstitutional because it usurps Federal control and allows the state to permanently block nuclear facility construction and certification. States' rights in the area of radiological health and safety are supplanted by the Federal government

  18. California's 2002 Clean Water Act Section 303(d) - Impaired Waterbodies

    Data.gov (United States)

    California Natural Resource Agency — This dataset contains California's 2002 Clean Water Act Section 303(d) list which is submitted by the California State Water Resources Control Board. The layer has...

  19. Vegetation (MCV / NVCS) Mapping Projects - California [ds515

    Data.gov (United States)

    California Natural Resource Agency — This metadata layer shows the footprint of vegetation mapping projects completed in California that have used the Manual California of Vegetation ( MCV 1st edition)...

  20. SWFSC/MMTD/CCE: California Harbor Porpoise Survey (CAHPS) 1995

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A ship-based marine mammal survey in California from Point Conception, California to the California-Oregon border, with the survey extent limited to waters from the...

  1. LiDAR data for the Delta Area of California

    Data.gov (United States)

    California Natural Resource Agency — LiDAR data for the Delta Area of California from the California Department of Water Resources. Bare earth grids from LiDAR.This data is in ESRI Grid format with 2...

  2. Impacts of Phytophthora ramorum on oaks and tanoaks in Marin County, California forests since 2000

    Science.gov (United States)

    Brice A. McPherson; David L. Wood; Maggi Kelly; Sylvia R. Mori; Pavel Svihra; Andrew J. Storer; Richard B. Standiford

    2010-01-01

    The forests of Marin County were among the first in coastal California to be affected by the Phytophthora ramorum epidemic. Although initially observed in 1994 in tanoaks (Lithocarpus densiflorus) and 1995 in coast live oaks (Quercus agrifolia), it is evident from studies of disease progression that the...

  3. Survival of fishers in the southern Sierra Nevada region of California

    Science.gov (United States)

    Richard A. Sweitzer; Craig M. Thompson; Rebecca E. Green; Reginald H. Barrett; Kathryn L. Purcell

    2015-01-01

    Fishers in the western United States were recently proposed for listing under the U.S. Endangered Species Act because of concerns for loss of suitable habitat and evidence of a diversity of mortality risks that reduce survival. One of 2 remnant populations of fishers in California is in the southern Sierra Nevada region, where we studied them at 2 research sites in the...

  4. Walking the California County Lines with Pesticides on the Mind - A Tale of Two Cities

    Science.gov (United States)

    California has numerous aquatic threatened and endangered species and there is evidence that these species may be affected by non-target pesticide runoff. Modeling can play an important role in assessing the impact of pesticides but it requires complete data on pesticide use, mo...

  5. Providing Educationally Related Mental Health Services in California Schools: The Roles of School Psychologists

    Science.gov (United States)

    Sosa-Estrella, Olga

    2017-01-01

    Although there is a great need for school-based mental health services (SBMH), these needs are not adequately met in California's public schools. To meet these needs better, evidence-based methods have been used, including multi-tiered systems of support, training and workforce development, cultural competence, and family and youth engagement and…

  6. California's hardwood resource: history and reasons for lack of a sustained hardwood industry

    Science.gov (United States)

    Dean W. Huber; Philip M. McDonald

    1992-01-01

    Interest in utilizing California's forest-zone hardwoods for lumber and wood products has waxed and waned for more than 140 years. In spite of many unsuccessful ventures, strong interest is once again evident from landowners, processors, consumers, and policy makers. Their interest suggests a need to know past pitfalls, to recognize some realities of hardwood...

  7. 3000 years of environmental change at Zaca Lake, California, USA

    Directory of Open Access Journals (Sweden)

    Theodore eDingemans

    2014-07-01

    Full Text Available Climatic variations of the last few millennia can reveal patterns of variability beyond that recorded by the instrumental record. In this study we use pollen and sediments to generate a high resolution 3000 year record of vegetation and climate along the southern California coast. An increase in Pinus and Quercus pollen found in the top 100 years of the record is a result of known planting and fire suppression by the forest service. In the pre-historic record, a period of high Salix percentages and high pollen concentration from 500-250 cal yr BP represents the wettest period of the record and coincides with the Little Ice Age. We also find evidence for 3 warm periods between 1350 and 650 cal yr BP which are identified in the record by the presence of Pediastrum boryanum var. boryanum. The latter two of these periods, dating from 1070-900 and 700–650 cal yr BP correspond to Medieval Climatic Anomaly droughts identified in other records. In addition to these events, we identify a multi-centennial scale drought between 2700 and 2000 cal yr BP in Zaca Lake, corroborating evidence from across the Great Basin and extending the regional spread of this multi-centennial drought to southern California. Corresponding wetter conditions in the northwest indicate that the modern ENSO precipitation dipole also occurred during this persistent drought. Today this dipole is associated with La Niña conditions and we note a coincidence with intriguing evidence for a change in ENSO dynamics from marine records in the tropical Pacific. This dry period is remarkably persistent and has important implications for understanding the possible durations of drought conditions in the past in California.

  8. From continental to oceanic rifting in the Gulf of California

    Science.gov (United States)

    Ferrari, Luca; Bonini, Marco; Martín, Arturo

    2017-11-01

    The continental margin of northwestern Mexico is the youngest example of the transition from a convergent plate boundary to an oblique divergent margin that formed the Gulf of California rift. Subduction of the Farallon oceanic plate during the Cenozoic progressively brought the East Pacific Rise (EPR) toward the North America trench. In this process increasingly younger and buoyant oceanic lithosphere entered the subduction zone until subduction ended just before most of the EPR could collide with the North America continental lithosphere. The EPR segments bounding the unsubducted parts of the Farallón plate remnants (Guadalupe and Magdalena microplates) also ceased spreading (Lonsdale, 1991) and a belt of the North American plate (California and Baja California Peninsula) became coupled with the Pacific Plate and started moving northwestward forming the modern Gulf of California oblique rift (Nicholson et al., 1994; Bohannon and Parsons, 1995). The timing of the change from plate convergence to oblique divergence off western Mexico has been constrained at the middle Miocene (15-12.5 Ma) by ocean floor morphology and magnetic anomalies as well as plate tectonic reconstructions (Atwater and Severinghaus, 1989; Stock and Hodges, 1989; Lonsdale, 1991), although the onset of transtensional deformation and the amount of right lateral displacement within the Gulf region are still being studied (Oskin et al., 2001; Fletcher et al., 2007; Bennett and Oskin, 2014). Other aspects of the formation of the Gulf of California remain not well understood. At present the Gulf of California straddles the transition from continental transtension in the north to oceanic spreading in the south. Seismic reflection-refraction data indicate asymmetric continent-ocean transition across conjugate margins of rift segments (González-Fernández et al., 2005; Lizarralde et al., 2007; Miller and Lizarralde, 2013; Martín-Barajas et al., 2013). The asymmetry may be related to crustal

  9. Deconstructing the Rosenfeld curve: Making sense of California's low electricity intensity

    International Nuclear Information System (INIS)

    Sudarshan, Anant

    2013-01-01

    Regulatory regimes that have increased household energy efficiency are of widespread interest to policymakers today. A prominent example is the state of California where electricity intensities in the residential sector have stayed near constant since the 1970s in sharp contrast to nationwide trends in the United States. A structural model of residential energy consumption is used to show that the use of energy intensities alone to evaluate the success of California efficiency programs is misleading and glosses over important policy independent factors. We quantify important effects of price, climate conditions and demographic characteristics on energy consumption in California. We also provide evidence of split incentive considerations in residential energy consumption patterns. We conclude that while state policy may have had some effect on efficiency, caution needs to be exercised in using the California example to inform expectations from similar measures in other regions. - Highlights: • We model electricity and heating fuel consumption in US households. • We use the structural model to estimate price elasticities. • California energy intensities are strongly influenced by policy independent factors. • The role of energy efficiency policy in lowering intensities is limited. • Evidence of split incentive considerations in energy demand

  10. The carbon budget of California

    International Nuclear Information System (INIS)

    Potter, Christopher

    2010-01-01

    The carbon budget of a region can be defined as the sum of annual fluxes of carbon dioxide (CO 2 ) and methane (CH 4 ) greenhouse gases (GHGs) into and out of the regional surface coverage area. According to the state government's recent inventory, California's carbon budget is presently dominated by 115 MMTCE per year in fossil fuel emissions of CO 2 (>85% of total annual GHG emissions) to meet energy and transportation requirements. Other notable (non-ecosystem) sources of carbon GHG emissions in 2004 were from cement- and lime-making industries (7%), livestock-based agriculture (5%), and waste treatment activities (2%). The NASA-CASA (Carnegie Ames Stanford Approach) simulation model based on satellite observations of monthly vegetation cover (including those from the Moderate Resolution Imaging Spectroradiometer, MODIS) was used to estimate net ecosystem fluxes and vegetation biomass production over the period 1990-2004. California's annual NPP for all ecosystems in the early 2000s (estimated by CASA at 120 MMTCE per year) was roughly equivalent to its annual fossil fuel emission rates for carbon. However, since natural ecosystems can accumulate only a small fraction of this annual NPP total in long-term storage pools, the net ecosystem sink flux for atmospheric carbon across the state was estimated at a maximum rate of about 24 MMTCE per year under favorable precipitation conditions. Under less favorable precipitation conditions, such as those experienced during the early 1990s, ecosystems statewide were estimated to have lost nearly 15 MMTCE per year to the atmosphere. Considering the large amounts of carbon estimated by CASA to be stored in forests, shrublands, and rangelands across the state, the importance of protection of the natural NPP capacity of California ecosystems cannot be overemphasized.

  11. California energy flow in 1993

    Energy Technology Data Exchange (ETDEWEB)

    Borg, I.Y.; Briggs, C.K.

    1995-04-01

    Energy consumption in the state of California decreased about 3% in 1993 reflecting continuation of the recession that was manifest in a moribund construction industry and a high state unemployment that ran counter to national recovery trends. Residential/commercial use decreased slightly reflecting a mild winter in the populous southern portion of the state, a decrease that was offset to some extent by an increase in the state population. Industrial consumption of purchased energy declined substantially as did production of self-generated electricity for in-house use. Consumption in the transportation sector decreased slightly. The amount of power transmitted by the utilities was at 1992 levels; however a smaller proportion was produced by the utilities themselves. Generation of electricity by nonutilities, primarily cogenerators and small power producers, was the largest of any state in the US. The growth in the number of private power producers combined with increased amounts of electricity sold to the public utilities set the stage for the sweeping proposals before the California Public Utility Commission to permit direct sales from the nonutilities to retail customers. California production of both oil and natural gas declined; however, to meet demand only the imports of natural gas increased. A break in the decade-long drought during the 1992--1993 season resulted in a substantial increase in the amount of hydroelectricity generated during the year. Geothermal energy`s contribution increased substantially because of the development of new resources by small power producers. Decline in steam production continued at The Geysers, the state`s largest field, principally owned and managed by a public utility. Increases in windpower constituted 1--1/2% of the total electric supply--up slightly from 1992. Several solar photo voltaic demonstration plants were in operation, but their contribution remained small.

  12. Chemical composition of fogwater collected along the California coast

    Energy Technology Data Exchange (ETDEWEB)

    Jacob, D.J.; Waldman, J.M.; Munger, J.W.; Hoffman, M.R.

    1985-01-01

    Fogwater collected at both urban and nonurban coastal sites in California ws found to be consistently acidic. Millimolar concentrations of NO/sub 3//sup -/, and fogwater pH values below 3, were observed at sites downwind of the Los Angeles basin. Fogwater composition at remote sites showed evidence of substantial continental and anthropogenic contributions. Acid-neutralizing capacities in coastal air were found to be very low and insufficient to neutralize even small acid inputs. Chloride loss relative to its sea salt contribution was observed at sites furthest from anthropogenic sources.

  13. BENTON RANGE ROADLESS AREA, CALIFORNIA.

    Science.gov (United States)

    McKee, Edwin H.; Rains, Richard L.

    1984-01-01

    On the basis of a mineral survey, two parts of the Benton Range Roadless Area, California are considered to have mineral-resource potential. The central and southern part of the roadless area, near several nonoperating mines, has a probable potential for tungsten and gold-silver mineralization in tactite zones. The central part of the area has a substantiated resource potential for gold and silver in quartz veins. Detailed mapping and geochemical sampling for tungsten, gold, and silver in the central and southern part of the roadless area might indicate targets for shallow drilling exploration.

  14. CACTUS SPRING ROADLESS AREA, CALIFORNIA.

    Science.gov (United States)

    Matti, Jonathan C.; Kuizon, Lucia

    1984-01-01

    Geologic, geochemical, and geophysical studies together with a review of historic mining and prospecting activities indicate that the Cactus Spring Roadless Area in California has little promise for the occurrence of mineral or energy resources. Marble bodies occur in the northern part of the roadless area and are possible resources for building stone, crushed and quarried aggregate, and lime and magnesium for Portland cement and industrial applications. It is recommended that the terrane of marble be mapped and sampled carefully in order to evaluate the quantity and quality of the carbonate resources.

  15. Sequences for Student Investigation

    Science.gov (United States)

    Barton, Jeffrey; Feil, David; Lartigue, David; Mullins, Bernadette

    2004-01-01

    We describe two classes of sequences that give rise to accessible problems for undergraduate research. These problems may be understood with virtually no prerequisites and are well suited for computer-aided investigation. The first sequence is a variation of one introduced by Stephen Wolfram in connection with his study of cellular automata. The…

  16. California Red-Legged Frog Range - CWHR [ds587

    Data.gov (United States)

    California Natural Resource Agency — Vector datasets of CWHR range maps are one component of California Wildlife Habitat Relationships (CWHR), a comprehensive information system and predictive model for...

  17. Sonoma Ecology Center Northern California Arundo Distribution Data

    Data.gov (United States)

    California Natural Resource Agency — The Arundo Distribution layer is a compilation of Arundo donax observations in northern and central California, obtained from numerous sources, including Arundo...

  18. Light at Night and Breast Cancer Risk Among California Teachers

    Science.gov (United States)

    Hurley, Susan; Goldberg, Debbie; Nelson, David; Hertz, Andrew; Horn-Ross, Pamela L.; Bernstein, Leslie; Reynolds, Peggy

    2014-01-01

    Background There is convincing evidence that circadian disruption mediated by exposure to light at night promotes mammary carcinogenesis in rodents. The role that light at night plays in human breast cancer etiology remains unknown. We evaluated the relationship between estimates of indoor and outdoor light at night and the risk of breast cancer among members of the California Teachers Study. Methods Indoor light-at-night estimates were based on questionnaire data regarding sleep habits and use of night time lighting while sleeping. Estimates of outdoor light at night were derived from imagery data obtained from the U.S. Defense Meteorological Satellite Program assigned to geocoded addresses of study participants. Analyses were conducted among 106,731 California Teachers Study members who lived in California, had no prior history of breast cancer, and provided information on lighting while sleeping. 5,095 cases of invasive breast cancer diagnosed 1995–2010 were identified via linkage to the California Cancer Registry. We used age-stratified Cox proportional hazard models to calculate hazard ratios (HRs) with 95% confidence intervals (CIs), adjusting for breast cancer risk factors and neighborhood urbanization and socioeconomic class. Results An increased risk was found for women living in areas with the highest quintile of outdoor light at night exposure estimates (HR=1.12 [95% CI=1.00 – 1.26], test for trend, P=0.06). While more pronounced among premenopausal women (HR=1.34 [95% CI=1.07 – 1.69], test for trend, P=0.04), the associations did not differ statistically by menopausal status (test for interaction, P=0.34). Conclusions Women living in areas with high levels of ambient light at night may be at an increased risk of breast cancer. Future studies that integrate quantitative measurements of indoor and outdoor light at night are warranted. PMID:25061924

  19. Sequence History Update Tool

    Science.gov (United States)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  20. Foreshocks and aftershocks of the Great 1857 California earthquake

    Science.gov (United States)

    Meltzner, A.J.; Wald, D.J.

    1999-01-01

    The San Andreas fault is the longest fault in California and one of the longest strike-slip faults anywhere in the world, yet we know little about many aspects of its behavior before, during, and after large earthquakes. We conducted a study to locate and to estimate magnitudes for the largest foreshocks and aftershocks of the 1857 M 7.9 Fort Tejon earthquake on the central and southern segments of the fault. We began by searching archived first-hand accounts from 1857 through 1862, by grouping felt reports temporally, and by assigning modified Mercalli intensities to each site. We then used a modified form of the grid-search algorithm of Bakum and Wentworth, derived from empirical analysis of modern earthquakes, to find the location and magnitude most consistent with the assigned intensities for each of the largest events. The result confirms a conclusion of Sieh that at least two foreshocks ('dawn' and 'sunrise') located on or near the Parkfield segment of the San Andreas fault preceded the mainshock. We estimate their magnitudes to be M ~ 6.1 and M ~ 5.6, respectively. The aftershock rate was below average but within one standard deviation of the number of aftershocks expected based on statistics of modern southern California mainshock-aftershock sequences. The aftershocks included two significant events during the first eight days of the sequence, with magnitudes M ~ 6.25 and M ~ 6.7, near the southern half of the rupture; later aftershocks included a M ~ 6 event near San Bernardino in December 1858 and a M ~ 6.3 event near the Parkfield segment in April 1860. From earthquake logs at Fort Tejon, we conclude that the aftershock sequence lasted a minimum of 3.75 years.

  1. Case study : The California Digital Library

    OpenAIRE

    Ober, John

    2002-01-01

    The California Digital Library was founded in 1997 as a digital “co-library” of the 10 Universities of California campuses. Responses to crisis in scholarly communication and the opportunity presented by digital technologies and the Web. Charged to create a comprehensive system for the management of digital scholarly information.

  2. Outlook for California's electric utility industry

    International Nuclear Information System (INIS)

    Frank, S.E.

    1996-01-01

    This article describes how the Southern California Edison Company deals with revolutionary change as the state's electricity industry reinvents itself. The topics of the article include how competition has make things better for SCEC's employees, customers, and shareholders, and an outline of the principal features of the electric utility industry in California

  3. Quercus kelloggii Newb., California black oak

    Science.gov (United States)

    P.M. McDonald

    1990-01-01

    California black oak (Quercus kelloggii) exceeds all other California oaks in volume, distribution, and altitudinal range. Yet this deciduous hardwood has had little sustained commercial use and almost no management, even though its wood closely resembles that of its valuable, managed, and heavily used counterpart-northern red oak (...

  4. A Brief History of California School Funding

    Science.gov (United States)

    Canfield, Jacquie

    2013-01-01

    In January 2013, the governor proposed a new funding model for California school districts called the Local Control Funding Formula. As the Legislature debates the proposed new funding model for schools, which is expected to start in the 2013-14 fiscal year, the author thought it would be a good time for a history lesson in California school…

  5. Inequalities in School Climate in California

    Science.gov (United States)

    Jain, Sonia; Cohen, Alison K.; Huang, Kevin; Hanson, Thomas L.; Austin, Gregory

    2015-01-01

    Purpose: School climate, or the physical and social conditions of the learning environment, has implications for academic achievement. The paper aims to discuss this issue. Design/Methodology/Approach: The authors examine how school climate varies by school-level characteristics in California using administrative data and the California School…

  6. California Indian ethnomycology and associated forest management

    Science.gov (United States)

    Kat M. Anderson; Frank K. Lake

    2013-01-01

    Many California Indian tribes utilized mushrooms for food, medicine, and/or technological purposes. This paper summarizes which mushrooms were important to different California Indian tribes in historic and modern times and how they were harvested, prepared, and stored. Oral interviews were conducted and the ethnographic literature reviewed to detail the extent and...

  7. Home range characteristics of fishers in California

    Science.gov (United States)

    W. J. Zielinski; R. L. Truex; G. A. Schmidt; F. V. Schlexer; K. N. Schmidt; R. H. Barrett

    2004-01-01

    The fisher (Martes pennanti) is a forest mustelid that historically occurred in California from the mixed conifer forests of the north coast, east to the southern Cascades, and south throughout the Sierra Nevada. Today fishers in California occur only in 2 disjunct populations in the northwestern mountains and the...

  8. California Contradictions: Creating Your Own Crisis.

    Science.gov (United States)

    Roth, Robert A.

    1988-01-01

    California state policies and regulations that force teacher education programs to limit enrollment because of insufficient resources, and discourage immigration of out-of-state teachers contribute to California's critical shortage of teachers. In addition, the quality of elementary instruction is jeopardized by regulations that diminish…

  9. Collaborative monitoring in Walnut Creek, California

    Science.gov (United States)

    Heidi Ballard; Ralph Kraetsch; Lynn Huntsinger

    2002-01-01

    In 1995 and 2000, a monitoring program was designed and implemented to track oak regeneration and native grass populations in target management areas in the four Open Space Preserves of the City of Walnut Creek, California. The program resulted from a collaboration of scientists at the University of California, Berkeley, a group of interested citizens known as the...

  10. Supporting Continuous Improvement in California's Education System

    Science.gov (United States)

    Darling-Hammond, Linda; Plank, David N.

    2015-01-01

    California's new accountability system originated in the radical decentralization of power and authority from Sacramento to local schools and their communities brought about by the Legislature's adoption of the Local Control Funding Formula (LCFF) in 2013. Under California's previous accountability policies and the federal "No Child Left…

  11. California-Mexico gas exports eyed

    International Nuclear Information System (INIS)

    Anon.

    1992-01-01

    This paper reports that two California utilities have proposed providing natural gas transportation services to Mexico. The arrangement would provide a second U.S. export sales point at the U.S.-Mexico border and perhaps help alleviate an expected surplus of gas pipeline capacity available to California. Mexico currently imports about 200 MMcfd of U.S. gas via pipelines in Texas

  12. Discovery of viruses and virus-like pathogens in pistachio using high-throughput sequencing

    Science.gov (United States)

    Pistachio (Pistacia vera L.) trees from the National Clonal Germplasm Repository (NCGR) and orchards in California were surveyed for viruses and virus-like agents by high-throughput sequencing (HTS). Analyses of 60 trees including clonal UCB-1 hybrid rootstock (P. atlantica × P. integerrima) identif...

  13. California energy flow in 1979

    Science.gov (United States)

    Briggs, C. K.; Borg, I. Y.

    1981-03-01

    Energy use in California during 1979 differed significantly from 1978. Overall use of natural gas in the state increased substantially (14.3%) due principally to greater use for electrical power production; 4% more gas was used for electrical power generation in 1979 than in 1978 and 21% more than in 1977. Use of fuel oil for electrical generation remained at the 1978 level but below the high 1977 level, which reflected substitution of oil for hydroelectric power during the 1976 to 1977 drought. Together, oil and gas accounted for 80% of the fuels used to generate electricity. Crude-oil imports principally from Indonesia fell substantially; however, use of Alaskan North Slope oil increased so that the net increase in crude oil use was up about 4%. The transportation end-use sector consumed about as much as in 1978 despite shortages in early 1979 associated with the Iranian revolution. While sales fell slightly, sales of high-sulfur residual oils (Bunker C) increased markedly. Transportation represents 38% of total energy consumption in California.

  14. Transport woes threaten California production

    International Nuclear Information System (INIS)

    Anon.

    1994-01-01

    California oil producers face a loss of production this year because of constraints on pipeline and tanker transportation to Los Angeles area refineries. The potential bottleneck is occurring at a time when Outer Continental Shelf production is near capacity from Chevron Corp.'s Point Arguello project at the same time production is increasing from Exxon Corp.'s nearby Santa Ynex Unit (SYU) expansion. Both megaprojects must compete for pipeline space with onshore crude producers, notably in California's San Joaquin Valley (SJV). Recent development limiting transportation options include: An indefinite shutdown of Four Corners Pipe Line Co.'s 50,000 b/d Line No. 1, damaged by the Jan. 17 earthquake; Loss of a tanker permit by Chevron and partners for offshore Point Arguello production; Permanent shutdown of Exxon's offshore storage and treatment (OST) facility, which since 1981 has used tankers to transport about 20,000 b/d of SYU production from the Santa Barbara Channel to Los Angeles. The OST, the first commercial floating production system in the US -- placed in the Santa Barbara Channel in 1981 after a decade of precedent setting legal and political battles -- was shut down Apr. 4. The paper discusses these production concerns, available options, the OST shutdown, and the troubled history of the OST

  15. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  16. Mapping sequences by parts

    Directory of Open Access Journals (Sweden)

    Guziolowski Carito

    2007-09-01

    Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

  17. The morphology of strike-slip faults - Examples from the San Andreas Fault, California

    Science.gov (United States)

    Bilham, Roger; King, Geoffrey

    1989-01-01

    The dilatational strains associated with vertical faults embedded in a horizontal plate are examined in the framework of fault kinematics and simple displacement boundary conditions. Using boundary element methods, a sequence of examples of dilatational strain fields associated with commonly occurring strike-slip fault zone features (bends, offsets, finite rupture lengths, and nonuniform slip distributions) is derived. The combinations of these strain fields are then used to examine the Parkfield region of the San Andreas fault system in central California.

  18. Paleohydrogeology of the San Joaquin basin, California

    Science.gov (United States)

    Wilson, A.M.; Garven, G.; Boles, J.R.

    1999-01-01

    Mass transport can have a significant effect on chemical diagenetic processes in sedimentary basins. This paper presents results from the first part of a study that was designed to explore the role of an evolving hydrodynamic system in driving mass transport and chemical diagenesis, using the San Joaquin basin of California as a field area. We use coupled hydrogeologic models to establish the paleohydrogeology, thermal history, and behavior of nonreactive solutes in the basin. These models rely on extensive geological information and account for variable-density fluid flow, heat transport, solute transport, tectonic uplift, sediment compaction, and clay dehydration. In our numerical simulations, tectonic uplift and ocean regression led to large-scale changes in fluid flow and composition by strengthening topography-driven fluid flow and allowing deep influx of fresh ground water in the San Joaquin basin. Sediment compaction due to rapid deposition created moderate overpressures, leading to upward flow from depth. The unusual distribution of salinity in the basin reflects influx of fresh ground water to depths of as much as 2 km and dilution of saline fluids by dehydration reactions at depths greater than ???2.5 km. Simulations projecting the future salinity of the basin show marine salinities persisting for more than 10 m.y. after ocean regression. Results also show a change from topography-to compaction-driven flow in the Stevens Sandstone at ca. 5 Ma that coincides with an observed change in the diagenetic sequence. Results of this investigation provide a framework for future hydrologic research exploring the link between fluid flow and diagenesis.

  19. Tulelake, California: The last 3 million years

    Science.gov (United States)

    Adam, D.P.; Sarna-Wojcicki, A. M.; Rieck, Hugh J.; Bradbury, J.P.; Dean, W.E.; Forester, R.M.

    1989-01-01

    The Tulelake basin, formed by east-west extension and faulting during the past several million years, contains at least 550 m of lacustrine sediment. Interdisciplinary studies of a 334 m-long cored section from the town of Tulelake, California, near the center of the basin, document a 3-m.y. record of environmental changes. The core consists of a thick sequence of diatomaceous clayey, silty, and marly lacustrine sediments interbedded with numerous tephra layers. Paleomagnetic study puts the base of the core at about 3.0 Ma. Twelve widespread silicic tephra units provide correlations with other areas and complement age control provided by magnetostratigraphy; mafic and silicic tephra units erupted from local sources are also common in the core. Widespread tephra units include the Llao Rock pumice (=Tsoyawata, 7 ka), the Trego Hot Springs Bed (23 ka), and the Rockland (0.40 Ma), Lava Creek (0.62 Ma), and Rio Dell (1.5 Ma) ash beds, as well as several ash beds also found at Summer Lake, Oregon, and an ash bed originally recognized in DSDP hole 173 in the northeastern Pacific. Several tephra layers found in the core also occur in lacustrine beds exposed around the margins of the basin and elsewhere in the ancestral lacustrine system. Diatoms are present throughout the section. Pollen is present in most of the section, but some barren zones are found in the interval between 50 and 140 m; the greatest change in behavior of the pollen record takes place just above the top of the Olduvai Normal-Polarity Subchronozone. Ostracodes are present only in high-carbonate (>10% CaCO3) intervals. Evolutionary changes are found in the diatom and ostracode records. Bulk geochemical analyses show significant changes in elemental composition of the sediment through time. ?? 1989.

  20. Exploration of noncoding sequences in metagenomes.

    Directory of Open Access Journals (Sweden)

    Fabián Tobar-Tosse

    Full Text Available Environment-dependent genomic features have been defined for different metagenomes, whose genes and their associated processes are related to specific environments. Identification of ORFs and their functional categories are the most common methods for association between functional and environmental features. However, this analysis based on finding ORFs misses noncoding sequences and, therefore, some metagenome regulatory or structural information could be discarded. In this work we analyzed 23 whole metagenomes, including coding and noncoding sequences using the following sequence patterns: (G+C content, Codon Usage (Cd, Trinucleotide Usage (Tn, and functional assignments for ORF prediction. Herein, we present evidence of a high proportion of noncoding sequences discarded in common similarity-based methods in metagenomics, and the kind of relevant information present in those. We found a high density of trinucleotide repeat sequences (TRS in noncoding sequences, with a regulatory and adaptive function for metagenome communities. We present associations between trinucleotide values and gene function, where metagenome clustering correlate with microorganism adaptations and kinds of metagenomes. We propose here that noncoding sequences have relevant information to describe metagenomes that could be considered in a whole metagenome analysis in order to improve their organization, classification protocols, and their relation with the environment.

  1. The Colliding Beams Sequencer

    International Nuclear Information System (INIS)

    Johnson, D.E.; Johnson, R.P.

    1989-01-01

    The Colliding Beam Sequencer (CBS) is a computer program used to operate the pbar-p Collider by synchronizing the applications programs and simulating the activities of the accelerator operators during filling and storage. The Sequencer acts as a meta-program, running otherwise stand alone applications programs, to do the set-up, beam transfers, acceleration, low beta turn on, and diagnostics for the transfers and storage. The Sequencer and its operational performance will be described along with its special features which include a periodic scheduler and command logger. 14 refs., 3 figs

  2. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  3. California sea lions (Zalophus californianus californianus) have lower chlorinated hydrocarbon contents in northern Baja California, Mexico, than in California, USA

    Energy Technology Data Exchange (ETDEWEB)

    Del Toro, Ligeia [Universidad Autonoma de Baja California (UABC), Facultad de Ciencias Marinas, Ensenada, Baja California (Mexico); Investigacion y Conservacion de Mamiferos Marinos de Ensenada, A.C., Placido Mata 2309 Depto. D-5, Condominio Las Fincas, Ensenada, Baja California 22810 (Mexico); Heckel, Gisela [Investigacion y Conservacion de Mamiferos Marinos de Ensenada, A.C., Placido Mata 2309 Depto. D-5, Condominio Las Fincas, Ensenada, Baja California 22810 (Mexico) and Centro de Investigacion Cientifica y de Educacion Superior de Ensenada, B.C. Km 107 Carretera Tijuana-Ensenada, Ensenada, Baja California 22860 (Mexico)]. E-mail: gheckel@cicese.mx; Camacho-Ibar, Victor F. [Instituto de Investigaciones Oceanologicas, UABC, Apdo. Postal 453, Ensenada, Baja California 22860 (Mexico); Schramm, Yolanda [Universidad Autonoma de Baja California (UABC), Facultad de Ciencias Marinas, Ensenada, Baja California (Mexico); Investigacion y Conservacion de Mamiferos Marinos de Ensenada, A.C., Placido Mata 2309 Depto. D-5, Condominio Las Fincas, Ensenada, Baja California 22810 (Mexico)

    2006-07-15

    Chlorinated hydrocarbons (CHs) were determined in blubber samples of 18 California sea lions (Zalophus californianus californianus) that stranded dead along Todos Santos Bay, Ensenada, Baja California, Mexico, January 2000-November 2001. {sigma}DDTs were the dominant group (geometric mean 3.8 {mu}g/g lipid weight), followed by polychlorinated biphenyls ({sigma}PCBs, 2.96 {mu}g/g), chlordanes (0.12 {mu}g/g) and hexachlorocyclohexanes (0.06 {mu}g/g). The {sigma}DDTs/{sigma}PCBs ratio was 1.3. We found CH levels more than one order of magnitude lower than those reported for California sea lion samples collected along the California coast, USA, during the same period as our study. This sharp north-south gradient suggests that Z. californianus stranded in Ensenada (most of them males) would probably have foraged during the summer near rookeries 500-1000 km south of Ensenada and the rest of the year migrate northwards, foraging along the Baja California peninsula, including Ensenada, and probably farther north. - Results suggest that sea lion prey must also have lower hydrocarbons in Baja California than in California in the USA.

  4. California sea lions (Zalophus californianus californianus) have lower chlorinated hydrocarbon contents in northern Baja California, Mexico, than in California, USA

    International Nuclear Information System (INIS)

    Del Toro, Ligeia; Heckel, Gisela; Camacho-Ibar, Victor F.; Schramm, Yolanda

    2006-01-01

    Chlorinated hydrocarbons (CHs) were determined in blubber samples of 18 California sea lions (Zalophus californianus californianus) that stranded dead along Todos Santos Bay, Ensenada, Baja California, Mexico, January 2000-November 2001. ΣDDTs were the dominant group (geometric mean 3.8 μg/g lipid weight), followed by polychlorinated biphenyls (ΣPCBs, 2.96 μg/g), chlordanes (0.12 μg/g) and hexachlorocyclohexanes (0.06 μg/g). The ΣDDTs/ΣPCBs ratio was 1.3. We found CH levels more than one order of magnitude lower than those reported for California sea lion samples collected along the California coast, USA, during the same period as our study. This sharp north-south gradient suggests that Z. californianus stranded in Ensenada (most of them males) would probably have foraged during the summer near rookeries 500-1000 km south of Ensenada and the rest of the year migrate northwards, foraging along the Baja California peninsula, including Ensenada, and probably farther north. - Results suggest that sea lion prey must also have lower hydrocarbons in Baja California than in California in the USA

  5. California State Waters Map Series—Offshore of Monterey, California

    Science.gov (United States)

    Johnson, Samuel Y.; Dartnell, Peter; Hartwell, Stephen R.; Cochrane, Guy R.; Golden, Nadine E.; Watt, Janet T.; Davenport, Clifton W.; Kvitek, Rikk G.; Erdey, Mercedes D.; Krigsman, Lisa M.; Sliter, Ray W.; Maier, Katherine L.; Johnson, Samuel Y.; Cochran, Susan A.

    2016-08-18

    IntroductionIn 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within the 3-nautical-mile limit of California’s State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath bathymetry data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow subsurface geology.The Offshore of Monterey map area in central California is located on the Pacific Coast, about 120 km south of San Francisco. Incorporated cities in the map area include Seaside, Monterey, Marina, Pacific Grove, Carmel-by-the-Sea, and Sand City. The local economy receives significant resources from tourism, as well as from the Federal Government. Tourist attractions include the Monterey Bay Aquarium, Cannery Row, Fisherman’s Wharf, and the many golf courses near Pebble Beach, and the area serves as a gateway to the spectacular scenery and outdoor activities along the Big Sur coast to the south. Federal facilities include the Army’s Defense Language Institute, the Naval Postgraduate School, and the Fleet Numerical Meteorology and Oceanography Center (operated by the Navy). In 1994, Fort Ord army base, located between Seaside and Marina, was closed; much of former army base land now makes up the Fort Ord National Monument, managed by the U.S. Bureau of Land Management as part of the National Landscape Conservation System. In addition, part of the old Fort Ord is now occupied by California State University, Monterey Bay.The offshore part of the map area lies entirely within the Monterey Bay National

  6. California State Waters Map Series--Offshore of Ventura, California

    Science.gov (United States)

    Johnson, Samuel Y.; Dartnell, Peter; Cochrane, Guy R.; Golden, Nadine E.; Phillips, Eleyne L.; Ritchie, Andrew C.; Kvitek, Rikk G.; Greene, H. Gary; Krigsman, Lisa M.; Endris, Charles A.; Seitz, Gordon G.; Gutierrez, Carlos I.; Sliter, Ray W.; Erdey, Mercedes D.; Wong, Florence L.; Yoklavich, Mary M.; Draut, Amy E.; Hart, Patrick E.; Johnson, Samuel Y.; Cochran, Susan A.

    2013-01-01

    In 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within the 3-nautical-mile limit of California’s State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow (to about 100 m) subsurface geology. The Offshore of Ventura map area lies within the Santa Barbara Channel region of the Southern California Bight. This geologically complex region forms a major biogeographic transition zone, separating the cold-temperate Oregonian province north of Point Conception from the warm-temperate California province to the south. The map area is in the Ventura Basin, in the southern part of the Western Transverse Ranges geologic province, which is north of the California Continental Borderland. Significant clockwise rotation—at least 90°—since the early Miocene has been proposed for the Western Transverse Ranges, and the region is presently undergoing north-south shortening. The city of Ventura is the major cultural center in the map area. The Ventura River cuts through Ventura, draining the Santa Ynez Mountains and the coastal hills north of Ventura. Northwest of Ventura, the coastal zone is a narrow strip containing highway and railway transportation corridors and a few small residential clusters. Rincon Island, an island constructed for oil and gas production, lies offshore of Punta Gorda. Southeast of Ventura, the coastal zone consists of the mouth and broad, alluvial plains of the Santa Clara River

  7. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  8. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  9. Dynamic Sequence Assignment.

    Science.gov (United States)

    1983-12-01

    D-136 548 DYNAMIIC SEQUENCE ASSIGNMENT(U) ADVANCED INFORMATION AND 1/2 DECISION SYSTEMS MOUNTAIN YIELW CA C A 0 REILLY ET AL. UNCLSSIIED DEC 83 AI/DS...I ADVANCED INFORMATION & DECISION SYSTEMS Mountain View. CA 94040 84 u ,53 V,..’. Unclassified _____ SCURITY CLASSIFICATION OF THIS PAGE REPORT...reviews some important heuristic algorithms developed for fas- ter solution of the sequence assignment problem. 3.1. DINAMIC MOGRAMUNIG FORMULATION FOR

  10. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  11. General LTE Sequence

    OpenAIRE

    Billal, Masum

    2015-01-01

    In this paper,we have characterized sequences which maintain the same property described in Lifting the Exponent Lemma. Lifting the Exponent Lemma is a very powerful tool in olympiad number theory and recently it has become very popular. We generalize it to all sequences that maintain a property like it i.e. if p^{\\alpha}||a_k and p^\\b{eta}||n, then p^{{\\alpha}+\\b{eta}}||a_{nk}.

  12. Community exposure to tsunami hazards in California

    Science.gov (United States)

    Wood, Nathan J.; Ratliff, Jamie; Peters, Jeff

    2013-01-01

    Evidence of past events and modeling of potential events suggest that tsunamis are significant threats to low-lying communities on the California coast. To reduce potential impacts of future tsunamis, officials need to understand how communities are vulnerable to tsunamis and where targeted outreach, preparedness, and mitigation efforts may be warranted. Although a maximum tsunami-inundation zone based on multiple sources has been developed for the California coast, the populations and businesses in this zone have not been documented in a comprehensive way. To support tsunami preparedness and risk-reduction planning in California, this study documents the variations among coastal communities in the amounts, types, and percentages of developed land, human populations, and businesses in the maximum tsunami-inundation zone. The tsunami-inundation zone includes land in 94 incorporated cities, 83 unincorporated communities, and 20 counties on the California coast. According to 2010 U.S. Census Bureau data, this tsunami-inundation zone contains 267,347 residents (1 percent of the 20-county resident population), of which 13 percent identify themselves as Hispanic or Latino, 14 percent identify themselves as Asian, 16 percent are more than 65 years in age, 12 percent live in unincorporated areas, and 51 percent of the households are renter occupied. Demographic attributes related to age, race, ethnicity, and household status of residents in tsunami-prone areas demonstrate substantial range among communities that exceed these regional averages. The tsunami-inundation zone in several communities also has high numbers of residents in institutionalized and noninstitutionalized group quarters (for example, correctional facilities and military housing, respectively). Communities with relatively high values in the various demographic categories are identified throughout the report. The tsunami-inundation zone contains significant nonresidential populations based on 2011 economic

  13. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  14. Review of research to inform California's climate scoping plan: Agriculture and working lands

    Directory of Open Access Journals (Sweden)

    Ryan Byrnes

    2017-09-01

    Full Text Available Agriculture in California contributes 8% of the state's greenhouse gas (GHG emissions. To inform the state's policy and program strategy to meet climate targets, we review recent research on practices that can reduce emissions, sequester carbon and provide other co-benefits to producers and the environment across agriculture and rangeland systems. Importantly, the research reviewed here was conducted in California and addresses practices in our specific agricultural, socioeconomic and biophysical environment. Farmland conversion and the dairy and intensive livestock sector are the largest contributors to GHG emissions and offer the greatest opportunities for avoided emissions. We also identify a range of other opportunities including soil and nutrient management, integrated and diversified farming systems, rangeland management, and biomass-based energy generation. Additional research to replicate and quantify the emissions reduction or carbon sequestration potential of these practices will strengthen the evidence base for California climate policy.

  15. Regeneration of native California oaks in the forest zone [Abstract

    Science.gov (United States)

    P.M. McDonald

    1999-01-01

    The two native California oaks in the forest zone of California are California black oak (Quercus kelloggii Newb.) and tanoak (Lithocarpus densiflorus [Hook. and Arn.] Rehd.). Both are ancient species with many adaptations to withstand California's Mediterranean climate, but some weaknesses as well. Both sprout vigorously...

  16. Memory for sequences of events impaired in typical aging

    Science.gov (United States)

    Allen, Timothy A.; Morris, Andrea M.; Stark, Shauna M.; Fortin, Norbert J.

    2015-01-01

    Typical aging is associated with diminished episodic memory performance. To improve our understanding of the fundamental mechanisms underlying this age-related memory deficit, we previously developed an integrated, cross-species approach to link converging evidence from human and animal research. This novel approach focuses on the ability to remember sequences of events, an important feature of episodic memory. Unlike existing paradigms, this task is nonspatial, nonverbal, and can be used to isolate different cognitive processes that may be differentially affected in aging. Here, we used this task to make a comprehensive comparison of sequence memory performance between younger (18–22 yr) and older adults (62–86 yr). Specifically, participants viewed repeated sequences of six colored, fractal images and indicated whether each item was presented “in sequence” or “out of sequence.” Several out of sequence probe trials were used to provide a detailed assessment of sequence memory, including: (i) repeating an item from earlier in the sequence (“Repeats”; e.g., ABADEF), (ii) skipping ahead in the sequence (“Skips”; e.g., ABDDEF), and (iii) inserting an item from a different sequence into the same ordinal position (“Ordinal Transfers”; e.g., AB3DEF). We found that older adults performed as well as younger controls when tested on well-known and predictable sequences, but were severely impaired when tested using novel sequences. Importantly, overall sequence memory performance in older adults steadily declined with age, a decline not detected with other measures (RAVLT or BPS-O). We further characterized this deficit by showing that performance of older adults was severely impaired on specific probe trials that required detailed knowledge of the sequence (Skips and Ordinal Transfers), and was associated with a shift in their underlying mnemonic representation of the sequences. Collectively, these findings provide unambiguous evidence that the

  17. From Drought to Recovery: a GRACE-Based Assessment of Groundwater Storage Variations in California

    Science.gov (United States)

    McEvoy, A.; Famiglietti, J. S.; Liu, P. W.; Reager, J. T., II

    2017-12-01

    The 2011-2015 drought in California was the most severe on record and significantly depleted state water reserves. However, after the consecutive wet winters of 2015-16 and 2016-17, water storage in reservoirs, soil, snowpack, and aquifers began recovering and the state government lifted the drought emergency for all California counties except four. But is the drought really "over"? Quantifiable metrics of groundwater storage are necessary to provide such evidence, yet in situ measurements are sparse at best. Here we holistically test whether California state water resources have fully recovered in the Sacramento, San Joaquin, and Tulare Lake basins of California, using remote sensing satellite observations, in situ measurements, and numerical models. Specifically, we partition water storage into four components of the terrestrial water cycle: soil moisture, snow water equivalent, surface water, and groundwater. We derive soil moisture and snow water equivalent from the North American Land Data Assimilation System (NLDAS) and we use the California Data Exchange Center (CDEC) network to measure in situ reservoir storage. To estimate changes in groundwater storage, we subtract these three components from the total water storage derived from the Gravity Recovery and Climate Experiment (GRACE) satellite. Preliminary results show that the groundwater storage plummeted to a record low during the 2011-2015 drought. The results also show a rapid recovery in total water storage from 2015-2017. Moreover, we find that groundwater accounts for, on average, 60% of the total water storage variations in the study basins. Our results hold social significance when placed in the context of arid California: Did the groundwater recover? Is this the largest recovery that California can expect? Finally, our results have implications for the utility of remote sensing to inform water resource management decisions.

  18. Mortality among California highway workers.

    Science.gov (United States)

    Maizlish, N; Beaumont, J; Singleton, J

    1988-01-01

    Standardized proportional mortality ratios (PMR) were computed for a population of highway workers. Hazards of highway maintenance work include exposure to solvents, herbicides, asphalt and welding fumes, diesel and auto exhaust, asbestos, abrasive dusts, hazardous material spills, and moving motor vehicles. Underlying cause of death was obtained for 1,570 workers who separated from the California Department of Transportation between 1970 and 1983, and who died in California between 1970 and 1983 (inclusive). Among 1,260 white males, the major findings were statistically significant excesses of cancers of digestive organs (PMR = 128), skin (PMR = 218), lymphopoietic cancer (PMR = 157), benign neoplasms (PMR = 343), motor vehicle accidents (PMR = 141), and suicide (PMR = 154). Black males (N = 66) experienced nonsignificant excesses of cancer of the digestive organs (PMR = 191) and arteriosclerotic heart disease (PMR = 143). Among 168 white females, deaths from lung cancer (PMR = 189) and suicide (PMR = 215) were elevated. White male retirees, a subgroup with 5 or more years of service, experienced excess mortality due to cancers of the colon (PMR = 245), skin (PMR = 738), brain (PMR = 556), and lymphosarcomas and reticulosarcomas (PMR = 514). Deaths from external causes (PMR = 135) and cirrhosis of the liver (PMR = 229) were elevated among white males with a last job in landscape maintenance. White males whose last job was highway maintenance experienced a deficit in mortality from circulatory diseases (PMR = 83) and excess mortality from emphysema (PMR = 250) and motor vehicle accidents (PMR = 196). Further epidemiologic and industrial hygiene studies are needed to confirm the apparent excess mortality and to quantify occupational and nonoccupational exposures. However, reduction of recognized hazards among highway maintenance workers is a prudent precautionary measure.

  19. The california electricity reform debacle

    International Nuclear Information System (INIS)

    Jaccard, M.

    2001-01-01

    In 1998, California launched a dramatic reform of its electricity sector, vertically de-integrating its major utilities and establishing a competitive generation market, with separate entities responsible for grid control and power exchange. After two uneventful years, wholesale prices rose dramatically in the summer of 2000 and have remained high into 2001. An imbalance between the high wholesale prices and frozen retail rates caused a financial crisis for the electric utilities and power shortages have been a chronic threat. Several factors contributed to this crisis: capacity has not expanded in step with demand either in California or its larger trading region; extreme weather and poorly timed plant outages further increased demand and decreased supply; market design flaws allowed significant suppliers to influence the market while frozen retail rates limited the demand response that would have mitigated the supply-demand imbalance. State and federal agencies have taken corrective action but the situation may remain critical for some time. Longer term solutions involve recognizing the special characteristics of electricity in designing marking reform. Because electricity supply and demand must be instantaneously balanced at all times, market reform must ensure that someone has the responsibility and effective tools to ensure that this occurs, in spite of unforeseen circumstances, and to prevent the exercise of market power. Because a competitive commodity market must work in concert with a monopoly delivery system, someone must be responsible and have the means to develop and operate the grid in ways that are amenable to effective competition. Finally, reform design must ensure that the cyclical investment and price patterns of normal commodity markets are minimized in the electricity market and that when they do occur, market volatility does not compromise reliability and price stability for those who value these highly and would pay a premium for them

  20. Range and Frequency of Africanized Honey Bees in California (USA)

    Science.gov (United States)

    Kono, Yoshiaki; Kohn, Joshua R.

    2015-01-01

    Africanized honey bees entered California in 1994 but few accounts of their northward expansion or their frequency relative to European honey bees have been published. We used mitochondrial markers and morphometric analyses to determine the prevalence of Africanized honeybees in San Diego County and their current northward progress in California west of the Sierra Nevada crest. The northernmost African mitotypes detected were approximately 40 km south of Sacramento in California’s central valley. In San Diego County, 65% of foraging honey bee workers carry African mitochondria and the estimated percentage of Africanized workers using morphological measurements is similar (61%). There was no correlation between mitotype and morphology in San Diego County suggesting Africanized bees result from bidirectional hybridization. Seventy percent of feral hives, but only 13% of managed hives, sampled in San Diego County carried the African mitotype indicating that a large fraction of foraging workers in both urban and rural San Diego County are feral. We also found a single nucleotide polymorphism at the DNA barcode locus COI that distinguishes European and African mitotypes. The utility of this marker was confirmed using 401 georeferenced honey bee sequences from the worldwide Barcode of Life Database. Future censuses can determine whether the current range of the Africanized form is stable, patterns of introgression at nuclear loci, and the environmental factors that may limit the northern range of the Africanized honey bee. PMID:26361047

  1. California State Waters Map Series: offshore of Carpinteria, California

    Science.gov (United States)

    Johnson, Samuel Y.; Dartnell, Peter; Cochrane, Guy R.; Golden, Nadine E.; Phillips, Eleyne L.; Ritchie, Andrew C.; Kvitek, Rikk G.; Greene, H. Gary; Endris, Charles A.; Seitz, Gordon G.; Sliter, Ray W.; Erdey, Mercedes D.; Wong, Florence L.; Gutierrez, Carlos I.; Krigsman, Lisa M.; Draut, Amy E.; Hart, Patrick E.; Johnson, Samuel Y.; Cochran, Susan A.

    2013-01-01

    In 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within the 3-nautical-mile limit of California’s State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow (to about 100 m) subsurface geology. The Offshore of Carpinteria map area lies within the central Santa Barbara Channel region of the Southern California Bight. This geologically complex region forms a major biogeographic transition zone, separating the cold-temperate Oregonian province north of Point Conception from the warm-temperate California province to the south. The map area is in the southern part of the Western Transverse Ranges geologic province, which is north of the California Continental Borderland. Significant clockwise rotation—at least 90°—since the early Miocene has been proposed for the Western Transverse Ranges province, and the region is presently undergoing north-south shortening. The small city of Carpinteria is the most significant onshore cultural center in the map area; the smaller town of Summerland lies west of Carpinteria. These communities rest on a relatively flat coastal piedmont that is surrounded on the north, east, and west by hilly relief on the flanks of the Santa Ynez Mountains. El Estero, a salt marsh on the coast west of Carpinteria, is an ecologically important coastal estuary. Southeast of Carpinteria, the coastal zone is narrow strip containing highway and railway transportation corridors

  2. California Geothermal Forum: A Path to Increasing Geothermal Development in California

    Energy Technology Data Exchange (ETDEWEB)

    Young, Katherine R. [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2017-01-01

    The genesis of this report was a 2016 forum in Sacramento, California, titled 'California Geothermal Forum: A Path to Increasing Geothermal Development in California.' The forum was held at the California Energy Commission's (CEC) headquarters in Sacramento, California with the primary goal being to advance the dialogues for the U.S. Department of Energy's Geothermal Technologies Office (GTO) and CEC technical research and development (R&D) focuses for future consideration. The forum convened a diverse group of stakeholders from government, industry, and research to lay out pathways for new geothermal development in California while remaining consistent with critical Federal and State conservation planning efforts, particularly at the Salton Sea.

  3. Bear phalanx traumatically introduced into a living human: Prehistoric evidence.

    Science.gov (United States)

    Richards, Gary D; Ojeda, Hillary M; Jabbour, Rebecca S; Ibarra, Caitlin L; Horton, Caroline F

    2013-03-01

    Traumatically induced skeletal injuries are common and can be ascribed to a normal range of events occurring in an individual's lifetime. A subset of these trauma-induced injuries provides enhanced insight into cultural history. Such cases might include those referable to medico-surgical and religious/ritualistic practices. We describe prehistoric evidence and cultural implications of the traumatic insertion of an Ursus manual phalanx into the elbow of a living human. The injury healed and the phalanx remained in situ until death. The individual derives from the Ellis Landing shellmound and dates to a subphase of the Middle Period (≈500BC-300AD) in the California cultural sequence. The remains are of a 30-40 year-old female. Comparative data on arm morphology and pathological conditions present were collected (n=159). Three Ursus subspecies (n=15) were examined to identify the taxon represented by the phalanx. The described individual was probably wearing bear paw ornaments at the time she was crushed by a heavy object. During this event, a bear claw was driven into her cubital fossa, the basal phalangeal tubercle being impressed into the humerus. The wound healed completely. The presence of Ursus body parts indicates an elevated societal role for this female; most likely she was a shaman or healer. Copyright © 2013 Elsevier Inc. All rights reserved.

  4. Aftershocks and triggered events of the Great 1906 California earthquake

    Science.gov (United States)

    Meltzner, A.J.; Wald, D.J.

    2003-01-01

    The San Andreas fault is the longest fault in California and one of the longest strike-slip faults in the world, yet little is known about the aftershocks following the most recent great event on the San Andreas, the Mw 7.8 San Francisco earthquake on 18 April 1906. We conducted a study to locate and to estimate magnitudes for the largest aftershocks and triggered events of this earthquake. We examined existing catalogs and historical documents for the period April 1906 to December 1907, compiling data on the first 20 months of the aftershock sequence. We grouped felt reports temporally and assigned modified Mercalli intensities for the larger events based on the descriptions judged to be the most reliable. For onshore and near-shore events, a grid-search algorithm (derived from empirical analysis of modern earthquakes) was used to find the epicentral location and magnitude most consistent with the assigned intensities. For one event identified as far offshore, the event's intensity distribution was compared with those of modern events, in order to contrain the event's location and magnitude. The largest aftershock within the study period, an M ???6.7 event, occurred ???100 km west of Eureka on 23 April 1906. Although not within our study period, another M ???6.7 aftershock occurred near Cape Mendocino on 28 October 1909. Other significant aftershocks included an M ???5.6 event near San Juan Bautista on 17 May 1906 and an M ???6.3 event near Shelter Cove on 11 August 1907. An M ???4.9 aftershock occurred on the creeping segment of the San Andreas fault (southeast of the mainshock rupture) on 6 July 1906. The 1906 San Francisco earthquake also triggered events in southern California (including separate events in or near the Imperial Valley, the Pomona Valley, and Santa Monica Bay), in western Nevada, in southern central Oregon, and in western Arizona, all within 2 days of the mainshock. Of these trigerred events, the largest were an M ???6.1 earthquake near Brawley

  5. Evidence logics with relational evidence

    DEFF Research Database (Denmark)

    Baltag, Alexandru; Occhipinti, Andrés

    2017-01-01

    We introduce a family of logics for reasoning about relational evidence: evidence that involves an ordering of states in terms of their relative plausibility. We provide sound and complete axiomatizations for the logics. We also present several evidential actions and prove soundness...

  6. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

    2012-01-01

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  7. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  8. Contraceptive use and risk of unintended pregnancy in California

    OpenAIRE

    Foster, Diana; Bley, Julia; Mikanda, John; Induni, Marta; Arons, Abigail; Baumrind, Nikki; Darney, Philip D.; Stewart, Felicia

    2004-01-01

    Abstract California is home to more than one out of eight American women of reproductive age. Because California has a large, diverse and growing population, national statistics do not necessarily describe the reproductive health of California women. This article presents risk for pregnancy and sexually transmitted infections among women in California based on the California Women’s Health Survey. Over 8900 women of reproductive age who participated in this survey between 1998 and 2001 pr...

  9. California Ocean Uses Atlas: Industrial sector

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset is a result of the California Ocean Uses Atlas Project: a collaboration between NOAA's National Marine Protected Areas Center and Marine Conservation...

  10. Gravity Data for California and Southern Nevada

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The gravity data (88,514 records) were compiled largely from a state-wide regional gravity study program organized by the California Division of Mines and Geology in...

  11. Pneumocystosis in wild small mammals from California

    Science.gov (United States)

    Laakkonen, Juha; Fisher, Robert N.; Case, Ted J.

    2001-01-01

    Cyst forms of the opportunistic fungal parasite Pneumocystis carinii were found in the lungs of 34% of the desert shrew, Notiosorex crawfordi (n = 59), 13% of the ornate shrew, Sorex ornatus (n = 55), 6% of the dusky-footed wood rat, Neotoma fuscipes (n = 16), 2.5% of the California meadow vole,Microtus californicus (n = 40), and 50% of the California pocket mouse, Chaetodipus californicus (n= 2) caught from southern California between February 1998 and February 2000. Cysts were not found in any of the harvest mouse, Reithrodontomys megalotis (n = 21), California mouse,Peromyscus californicus (n = 20), brush mouse, Peromyscus boylii (n = 7) or deer mouse, Peromyscus maniculatus (n = 4) examined. All infections were mild; extrapulmonary infections were not observed. Other lung parasites detected were Hepatozoon sp./spp. from M. californicus andNotiosorex crawfordi, Chrysosporium sp. (Emmonsia) from M. californicus, and a nematode from S. ornatus.

  12. California Ocean Uses Atlas: Fishing sector

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset is a result of the California Ocean Uses Atlas Project: a collaboration between NOAA's National Marine Protected Areas Center and Marine Conservation...

  13. Humboldt Bay, California Benthic Habitats 2009 Geodatabase

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Humboldt Bay is the largest estuary in California north of San Francisco Bay and represents a significant resource for the north coast region. Beginning in 2007 the...

  14. Humboldt, California 1 arc-second DEM

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The 1-second Humboldt, California Elevation Grid provides bathymetric data in ASCII raster format of 1-second resolution in geographic coordinates. This grid is...

  15. Coccidioidomycosis among Prison Inmates, California, USA, 2011

    Centers for Disease Control (CDC) Podcasts

    2015-02-26

    Dr. Charlotte Wheeler discusses Coccidioidomycosis among Prison Inmates in California.  Created: 2/26/2015 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 2/26/2015.

  16. Culicoides variipennis (Diptera: Ceratopogonidae) complex in California.

    Science.gov (United States)

    Holbrook, F R; Tabachnick, W J

    1995-07-01

    Genetic relationships were examined among 24 collections, representing 23 populations of Culicoides variipennis (Coquillett) using isozyme electrophoresis of 11 protein encoding loci. The populations were collected from alkaline or fresh water larval habitats in California. Distance analysis demonstrated that C. v. occidentalis Wirth and Jones and C. v. sonorensis Wirth and Jones are genetically distinct. All C. v. occidentalis were geographically isolated from each other in highly alkaline or saline larval habitats, whereas C. v. sonorensis populations were collected from artificial freshwater habitats that were polluted with organic wastes. Higher levels of gene flow were found between C. v. sonorensis populations than from C. v. sonorensis populations to nearby C. v. occidentalis populations, indicative of genetic isolation between subspecies. Northern California C. v. sonorensis were genetically distinguishable from southern California C. v. sonorensis. The relationship between this variation and bluetongue disease epidemiology in California is discussed.

  17. Humboldt Bay, California Benthic Habitats 2009 Substrate

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Humboldt Bay is the largest estuary in California north of San Francisco Bay and represents a significant resource for the north coast region. Beginning in 2007 the...

  18. Historical Fire Perimeters - Southern California [ds384

    Data.gov (United States)

    California Natural Resource Agency — CDF, USDA Forest Service Region 5, BLM, NPS, Contract Counties and other agencies jointly maintain a comprehensive fire perimeter GIS layer for public and private...

  19. Programs that work : California case examples

    Energy Technology Data Exchange (ETDEWEB)

    Rodgrigues, G. [Southern California Edison, Rosemead, CA (United States)

    2007-07-01

    Examples of programs that work in California with respect to greenhouse gas emissions were discussed. Specifically, Southern California Edison (SCE) was noted as one of the country's largest investor-owned utilities that has provided environmental leadership in this area. Energy, environment, economy, and community were mentioned as being the four value propositions for demand side management (DSM) programs. The environmental benefits of California investor-owned utilities programs were also discussed. Customer participation in SCE's energy efficiency programs was defined as an important measure of success. Other topics that were addressed in the presentation included energy efficiency in the long-term resource plan; ratcheting codes and standards; effective marketing and outreach; residential and non-residential programs; partnership programs; and competitively-selected programs. Measurement, verification and evaluation were noted as being real savings. Initiatives on the horizon such as the California solar initiative and Edison smartconnect were presented. tabs., figs.

  20. Humboldt Bay, California Benthic Habitats 2009 Geoform

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Humboldt Bay is the largest estuary in California north of San Francisco Bay and represents a significant resource for the north coast region. Beginning in 2007 the...

  1. Northern California 6 arc-second DEM

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The 6-second Northern California Elevation Grid provides bathymetric data in ASCII raster format of 6-second resolution in geographic coordinates. This grid is...

  2. Ecosystems past: prehistory of California vegetation

    Science.gov (United States)

    C.I. Millar; W.B. Woolfenden

    2016-01-01

    The history of California's vegetation, from origins in the Mesozoic through Quaternary is outlined. Climatic and geologic history and the processes driving changes in vegetation over time are also described. 

  3. Programs that work : California case examples

    International Nuclear Information System (INIS)

    Rodgrigues, G.

    2007-01-01

    Examples of programs that work in California with respect to greenhouse gas emissions were discussed. Specifically, Southern California Edison (SCE) was noted as one of the country's largest investor-owned utilities that has provided environmental leadership in this area. Energy, environment, economy, and community were mentioned as being the four value propositions for demand side management (DSM) programs. The environmental benefits of California investor-owned utilities programs were also discussed. Customer participation in SCE's energy efficiency programs was defined as an important measure of success. Other topics that were addressed in the presentation included energy efficiency in the long-term resource plan; ratcheting codes and standards; effective marketing and outreach; residential and non-residential programs; partnership programs; and competitively-selected programs. Measurement, verification and evaluation were noted as being real savings. Initiatives on the horizon such as the California solar initiative and Edison smartconnect were presented. tabs., figs

  4. Northern California 36 arc-second DEM

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The 36-second Northern California Elevation Grid provides bathymetric data in ASCII raster format of 36-second resolution in geographic coordinates. This grid is...

  5. Botaanikud Chamisso ja Eschscholtz Californias / Tiiu Speek

    Index Scriptorium Estoniae

    Speek, Tiiu, 1958-

    2012-01-01

    Loodusteadlaste A. von Chamisso ja J. Fr. Eschscholtzi osalemisest O. von Kotzebue ekspeditsioonidel (1815-1818 ning 1823-1826); reisidel kogutud ja kirjeldatud USA lääneosa ja California taimeliikidest ning neist koostatud herbaariumite saatusest

  6. On calculating the probability of a set of orthologous sequences

    Directory of Open Access Journals (Sweden)

    Junfeng Liu

    2009-02-01

    Full Text Available Junfeng Liu1,2, Liang Chen3, Hongyu Zhao4, Dirk F Moore1,2, Yong Lin1,2, Weichung Joe Shih1,21Biometrics Division, The Cancer, Institute of New Jersey, New Brunswick, NJ, USA; 2Department of Biostatistics, School of Public Health, University of Medicine and Dentistry of New Jersey, Piscataway, NJ, USA; 3Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA; 4Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, USAAbstract: Probabilistic DNA sequence models have been intensively applied to genome research. Within the evolutionary biology framework, this article investigates the feasibility for rigorously estimating the probability of a set of orthologous DNA sequences which evolve from a common progenitor. We propose Monte Carlo integration algorithms to sample the unknown ancestral and/or root sequences a posteriori conditional on a reference sequence and apply pairwise Needleman–Wunsch alignment between the sampled and nonreference species sequences to estimate the probability. We test our algorithms on both simulated and real sequences and compare calculated probabilities from Monte Carlo integration to those induced by single multiple alignment.Keywords: evolution, Jukes–Cantor model, Monte Carlo integration, Needleman–Wunsch alignment, orthologous

  7. Characteristics of Southern California coastal aquifer systems

    Science.gov (United States)

    Edwards, B.D.; Hanson, R.T.; Reichard, E.G.; Johnson, T.A.

    2009-01-01

    Most groundwater produced within coastal Southern California occurs within three main types of siliciclastic basins: (1) deep (>600 m), elongate basins of the Transverse Ranges Physiographic Province, where basin axes and related fluvial systems strike parallel to tectonic structure, (2) deep (>6000 m), broad basins of the Los Angeles and Orange County coastal plains in the northern part of the Peninsular Ranges Physiographic Province, where fluvial systems cut across tectonic structure at high angles, and (3) shallow (75-350 m), relatively narrow fluvial valleys of the generally mountainous southern part of the Peninsular Ranges Physiographic Province in San Diego County. Groundwater pumped for agricultural, industrial, municipal, and private use from coastal aquifers within these basins increased with population growth since the mid-1850s. Despite a significant influx of imported water into the region in recent times, groundwater, although reduced as a component of total consumption, still constitutes a significant component of water supply. Historically, overdraft from the aquifers has caused land surface subsidence, flow between water basins with related migration of groundwater contaminants, as well as seawater intrusion into many shallow coastal aquifers. Although these effects have impacted water quality, most basins, particularly those with deeper aquifer systems, meet or exceed state and national primary and secondary drinking water standards. Municipalities, academicians, and local water and governmental agencies have studied the stratigraphy of these basins intensely since the early 1900s with the goals of understanding and better managing the important groundwater resource. Lack of a coordinated effort, due in part to jurisdictional issues, combined with the application of lithostratigraphic correlation techniques (based primarily on well cuttings coupled with limited borehole geophysics) have produced an often confusing, and occasionally conflicting

  8. Main sequence mass loss

    International Nuclear Information System (INIS)

    Brunish, W.M.; Guzik, J.A.; Willson, L.A.; Bowen, G.

    1987-01-01

    It has been hypothesized that variable stars may experience mass loss, driven, at least in part, by oscillations. The class of stars we are discussing here are the δ Scuti variables. These are variable stars with masses between about 1.2 and 2.25 M/sub θ/, lying on or very near the main sequence. According to this theory, high rotation rates enhance the rate of mass loss, so main sequence stars born in this mass range would have a range of mass loss rates, depending on their initial rotation velocity and the amplitude of the oscillations. The stars would evolve rapidly down the main sequence until (at about 1.25 M/sub θ/) a surface convection zone began to form. The presence of this convective region would slow the rotation, perhaps allowing magnetic braking to occur, and thus sharply reduce the mass loss rate. 7 refs

  9. Digital evidence

    Directory of Open Access Journals (Sweden)

    Lukić Tatjana

    2012-01-01

    Full Text Available Although computer makes human activities faster and easier, innovating and creating new forms of work and other kinds of activities, it also influenced the criminal activity. The development of information technology directly affects the development of computer forensics without which, it can not even imagine the discovering and proving the computer offences and apprehending the perpetrator. Information technology and computer forensic allows us to detect and prove the crimes committed by computer and capture the perpetrators. Computer forensics is a type of forensics which can be defined as a process of collecting, preserving, analyzing and presenting digital evidence in court proceedings. Bearing in mind, that combat against crime, in which computers appear as an asset or object of the offense, requires knowledge of digital evidence as well as specific rules and procedures, the author in this article specifically addresses the issues of digital evidence, forensic (computer investigation, specific rules and procedures for detecting, fixing and collecting digital evidence and use of this type of evidence in criminal proceedings. The author also delas with international standards regarding digital evidence and cyber-space investigation.

  10. Hydrogeophysical investigations at Hidden Dam, Raymond, California

    Science.gov (United States)

    Minsley, Burke J.; Burton, Bethany L.; Ikard, Scott; Powers, Michael H.

    2011-01-01

    Self-potential and direct current resistivity surveys are carried out at the Hidden Dam site in Raymond, California to assess present-day seepage patterns and better understand the hydrogeologic mechanisms that likely influence seepage. Numerical modeling is utilized in conjunction with the geophysical measurements to predict variably-saturated flow through typical two-dimensional dam cross-sections as a function of reservoir elevation. Several different flow scenarios are investigated based on the known hydrogeology, as well as information about typical subsurface structures gained from the resistivity survey. The flow models are also used to simulate the bulk electrical resistivity in the subsurface under varying saturation conditions, as well as the self-potential response using petrophysical relationships and electrokinetic coupling equations.The self-potential survey consists of 512 measurements on the downstream area of the dam, and corroborates known seepage areas on the northwest side of the dam. Two direct-current resistivity profiles, each approximately 2,500 ft (762 m) long, indicate a broad sediment channel under the northwest side of the dam, which may be a significant seepage pathway through the foundation. A focusing of seepage in low-topography areas downstream of the dam is confirmed from the numerical flow simulations, which is also consistent with past observations. Little evidence of seepage is identified from the self-potential data on the southeast side of the dam, also consistent with historical records, though one possible area of focused seepage is identified near the outlet works. Integration of the geophysical surveys, numerical modeling, and observation well data provides a framework for better understanding seepage at the site through a combined hydrogeophysical approach.

  11. Interpretation of shallow crustal structure of the Imperial Valley, California, from seismic reflection profiles

    Energy Technology Data Exchange (ETDEWEB)

    Severson, L.K.

    1987-05-01

    Eight seismic reflection profiles (285 km total length) from the Imperial Valley, California, were provided to CALCRUST for reprocessing and interpretation. Two profiles were located along the western margin of the valley, five profiles were situated along the eastern margin and one traversed the deepest portion of the basin. These data reveal that the central basin contains a wedge of highly faulted sediments that thins to the east. Most of the faulting is strike-slip but there is evidence for block rotations on the scale of 5 to 10 kilometers within the Brawley Seismic Zone. These lines provide insight into the nature of the east and west edges of the Imperial Valley. The basement at the northwestern margin of the valley, to the north of the Superstition Hills, has been normal-faulted and blocks of basement material have ''calved'' into the trough. A blanket of sediments has been deposited on this margin. To the south of the Superstition Hills and Superstition Mountain, the top of the basement is a detachment surface that dips gently into the basin. This margin is also covered by a thick sequence sediments. The basement of the eastern margin consists of metamorphic rocks of the upper plate of the Chocolate Mountain Thrust system underlain by the Orocopia Schist. These rocks dip to the southeast and extend westward to the Sand Hills Fault but do not appear to cross it. Thus, the Sand Hills Fault is interpreted to be the southern extension of the San Andreas Fault. North of the Sand Hills Fault the East Highline Canal seismicity lineament is associated with a strike-slip fault and is probably linked to the Sand Hills Fault. Six geothermal areas crossed by these lines, in agreement with previous studies of geothermal reservoirs, are associated with ''faded'' zones, Bouguer gravity and heat flow maxima, and with higher seismic velocities than surrounding terranes.

  12. Theseus Assembly Sequence #2

    Science.gov (United States)

    1996-01-01

    Crew members are seen here assembling the tail of the Theseus prototype research aircraft at NASA's Dryden Flight Research Center, Edwards, California, in May of 1996. The Theseus aircraft, built and operated by Aurora Flight Sciences Corporation, Manassas, Virginia, was a unique aircraft flown at NASA's Dryden Flight Research Center, Edwards, California, under a cooperative agreement between NASA and Aurora. Dryden hosted the Theseus program, providing hangar space and range safety for flight testing. Aurora Flight Sciences was responsible for the actual flight testing, vehicle flight safety, and operation of the aircraft. The Theseus remotely piloted aircraft flew its maiden flight on May 24, 1996, at Dryden. During its sixth flight on November 12, 1996, Theseus experienced an in-flight structural failure that resulted in the loss of the aircraft. As of the beginning of the year 2000, Aurora had not rebuilt the aircraft. Theseus was built for NASA under an innovative, $4.9 million fixed-price contract by Aurora Flight Sciences Corporation and its partners, West Virginia University, Morgantown, West Virginia, and Fairmont State College, Fairmont, West Virginia. The twin-engine, unpiloted vehicle had a 140-foot wingspan, and was constructed largely of composite materials. Powered by two 80-horsepower, turbocharged piston engines that drove twin 9-foot-diameter propellers, Theseus was designed to fly autonomously at high altitudes, with takeoff and landing under the active control of a ground-based pilot in a ground control station 'cockpit.' With the potential ability to carry 700 pounds of science instruments to altitudes above 60,000 feet for durations of greater than 24 hours, Theseus was intended to support research in areas such as stratospheric ozone depletion and the atmospheric effects of future high-speed civil transport aircraft engines. Instruments carried aboard Theseus also would be able to validate satellite-based global environmental change

  13. Theseus Assembly Sequence #3

    Science.gov (United States)

    1996-01-01

    The Theseus prototype research aircraft being assembled at NASA's Dryden Flight Research Center, Edwards, California, in May of 1996. The Theseus aircraft, built and operated by Aurora Flight Sciences Corporation, Manassas, Virginia, was a unique aircraft flown at NASA's Dryden Flight Research Center, Edwards, California, under a cooperative agreement between NASA and Aurora. Dryden hosted the Theseus program, providing hangar space and range safety for flight testing. Aurora Flight Sciences was responsible for the actual flight testing, vehicle flight safety, and operation of the aircraft. The Theseus remotely piloted aircraft flew its maiden flight on May 24, 1996, at Dryden. During its sixth flight on November 12, 1996, Theseus experienced an in-flight structural failure that resulted in the loss of the aircraft. As of the beginning of the year 2000, Aurora had not rebuilt the aircraft. Theseus was built for NASA under an innovative, $4.9 million fixed-price contract by Aurora Flight Sciences Corporation and its partners, West Virginia University, Morgantown, West Virginia, and Fairmont State College, Fairmont, West Virginia. The twin-engine, unpiloted vehicle had a 140-foot wingspan, and was constructed largely of composite materials. Powered by two 80-horsepower, turbocharged piston engines that drove twin 9-foot-diameter propellers, Theseus was designed to fly autonomously at high altitudes, with takeoff and landing under the active control of a ground-based pilot in a ground control station 'cockpit.' With the potential ability to carry 700 pounds of science instruments to altitudes above 60,000 feet for durations of greater than 24 hours, Theseus was intended to support research in areas such as stratospheric ozone depletion and the atmospheric effects of future high-speed civil transport aircraft engines. Instruments carried aboard Theseus also would be able to validate satellite-based global environmental change measurements. Dryden's Project Manager was

  14. Theseus Assembly Sequence #1

    Science.gov (United States)

    1996-01-01

    The Theseus prototype research aircraft being assembled at NASA's Dryden Flight Research Center, Edwards, California, in May of 1996. The Theseus aircraft, built and operated by Aurora Flight Sciences Corporation, Manassas, Virginia, was a unique aircraft flown at NASA's Dryden Flight Research Center, Edwards, California, under a cooperative agreement between NASA and Aurora. Dryden hosted the Theseus program, providing hangar space and range safety for flight testing. Aurora Flight Sciences was responsible for the actual flight testing, vehicle flight safety, and operation of the aircraft. The Theseus remotely piloted aircraft flew its maiden flight on May 24, 1996, at Dryden. During its sixth flight on November 12, 1996, Theseus experienced an in-flight structural failure that resulted in the loss of the aircraft. As of the beginning of the year 2000, Aurora had not rebuilt the aircraft. Theseus was built for NASA under an innovative, $4.9 million fixed-price contract by Aurora Flight Sciences Corporation and its partners, West Virginia University, Morgantown, West Virginia, and Fairmont State College, Fairmont, West Virginia. The twin-engine, unpiloted vehicle had a 140-foot wingspan, and was constructed largely of composite materials. Powered by two 80-horsepower, turbocharged piston engines that drove twin 9-foot-diameter propellers, Theseus was designed to fly autonomously at high altitudes, with takeoff and landing under the active control of a ground-based pilot in a ground control station 'cockpit.' With the potential ability to carry 700 pounds of science instruments to altitudes above 60,000 feet for durations of greater than 24 hours, Theseus was intended to support research in areas such as stratospheric ozone depletion and the atmospheric effects of future high-speed civil transport aircraft engines. Instruments carried aboard Theseus also would be able to validate satellite-based global environmental change measurements. Dryden's Project Manager was

  15. Tobacco Use In California 1990-1991

    OpenAIRE

    University of California, San Diego; California Department of Health Services; Westat, Inc.; Los Angels County Department of Health Services

    1991-01-01

    Summary This report presents data from a survey of cigarette smoking behaviors and attitudes among Californians conducted between June, 1990 and July, 1991. The prevalence of current smoking among adults in California was 22.2%, with males (25.5%) smoking more than females (19.1%). This represents a sharp decline in smoking following the increase in the tobacco excise tax and implementation of a comprehensive tobacco control program by the State of California. The decline in preva...

  16. Southern California Coastal Processes Annotated Bibliography.

    Science.gov (United States)

    1985-12-01

    05/01/71 TITLE : Avalon Transportation Wharf CITATION : Journal of Waterways, Harbors and Coastal Engineering Division, ASCE, N. Y., Vol. 97, No. WW2 ...105, No. WW2 ; ASCE, N. Y., pp. 131-147 DESCRIPTION s Effect of various offshore structures as significant barriers to normal wave progress...California, 33 pp. DESCRIPTION Infrared satellite images are shown for each of two areas near +- the California coast, Cape Mendocino and Point

  17. Electricity sequence control

    International Nuclear Information System (INIS)

    Shin, Heung Ryeol

    2010-03-01

    The contents of the book are introduction of control system, like classification and control signal, introduction of electricity power switch, such as push-button and detection switch sensor for induction type and capacitance type machinery for control, solenoid valve, expression of sequence and type of electricity circuit about using diagram, time chart, marking and term, logic circuit like Yes, No, and, or and equivalence logic, basic electricity circuit, electricity sequence control, added condition, special program control about choice and jump of program, motor control, extra circuit on repeat circuit, pause circuit in a conveyer, safety regulations and rule about classification of electricity disaster and protective device for insulation.

  18. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    , Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...... information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity...

  19. Energy subsidies in California's electricity market deregulation

    International Nuclear Information System (INIS)

    Ritschel, Alexander; Smestad, G.P.

    2003-01-01

    Deregulation and re-regulation of California's electricity market not only failed in terms of anticipated cost reductions, improved customer service and higher competition, it also led to the introduction of various additional energy subsidies. This paper analyzes California's electricity market deregulation process from a subsidy viewpoint. Under deregulation in California, investor-owned utilities were not allowed to pass their energy procurement costs fully on to their customers, and therefore subsequently, and inevitably, ran into severe financial problems. Such retail price regulation is an energy subsidy that is both economically and environmentally unfavorable, because it veils true price signals to electricity consumers and, in this way, discourages energy conservation. Other policies implemented in California that represent perverse energy subsidies are the purchase of power by the state of California, the suspension of retail competition, and the potential misuse of money from the recovery of stranded costs. Many interventions implemented by the state to smooth out the impacts of the energy crisis insulated electricity consumers from market realities, supported the existing structure of California's electricity market, which is predominantly based on fossil fuels, and suppressed market incentives to improve energy conservation

  20. Depredation of the California Ridgway’s rail: Causes and distribution

    Science.gov (United States)

    Casazza, Michael L.; Overton, Cory T.; Bui, Thuy-Vy D.; Takekawa, John Y.; Merritt, Angela M.; Hull, J.M.

    2016-01-01

    We studied the causes of mortality for the California Ridgway’s rail at multiple tidal marshes in the San Francisco Bay Estuary, California. We radio-marked 196 individual rails and examined the evidence from 152 recovered California Ridgway’s rail mortalities from our radio-marked sample and determined plausible cause of death from a wide array of evidence. We also included 10 additional California Ridgway’s rail mortalities (unmarked) that we encountered during our normal field operations. We assigned a likely cause of death to 130 of the recoveries, of which 127 were determined to be caused by predation. Of those, 103 could be divided into class of cause (avian or mammalian), and avian predators were responsible for 64% of those events. Primary predators identified include domestic or feral cats, red fox, owl, and northern harrier. We did find seasonal differences between avian and mammalian predation rates, with higher proportions of avian predation in the winter and early spring. Time of day and tide height

  1. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene...

  2. THE RHIC SEQUENCER

    International Nuclear Information System (INIS)

    VAN ZEIJTS, J.; DOTTAVIO, T.; FRAK, B.; MICHNOFF, R.

    2001-01-01

    The Relativistic Heavy Ion Collider (RHIC) has a high level asynchronous time-line driven by a controlling program called the ''Sequencer''. Most high-level magnet and beam related issues are orchestrated by this system. The system also plays an important task in coordinated data acquisition and saving. We present the program, operator interface, operational impact and experience

  3. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak

  4. simple sequence repeat (SSR)

    African Journals Online (AJOL)

    In the present study, 78 mapped simple sequence repeat (SSR) markers representing 11 linkage groups of adzuki bean were evaluated for transferability to mungbean and related Vigna spp. 41 markers amplified characteristic bands in at least one Vigna species. The transferability percentage across the genotypes ranged ...

  5. Benefits and Economic Costs of Managed Aquifer Recharge in California

    Directory of Open Access Journals (Sweden)

    Debra Perrone

    2016-07-01

    Full Text Available doi: http://dx.doi.org/10.15447/sfews.2016v14iss2art4Groundwater management is important and challenging, and nowhere is this more evident than in California. Managed aquifer recharge (MAR projects can play an important role in ensuring California manages its groundwater sustainably. Although the benefits and economic costs of surface water storage have been researched extensively, the benefits and economic costs of MAR have been little researched. Historical groundwater data are sparse or proprietary within the state, often impairing groundwater analyses. General obligation bonds from ballot propositions offer a strategic means of mining information about MAR projects, because the information is available publicly. We used bond-funding applications to identify anticipated MAR project benefits and proposed economic costs. We then compared these costs with actual project costs collected from a survey, and identified factors that promote or limit MAR. Our analysis indicates that the median proposed economic cost for MAR projects in California is $410 per acre-foot per year ($0.33 per cubic meter per year. Increasing Water Supply, Conjunctive Use, and Flood Protection are the most common benefits reported. Additionally, the survey indicates that (1 there are many reported reasons for differences between proposed and actual costs ($US 2015 and (2 there is one primary reason for differences between proposed recharge volumes and actual recharge volumes (AFY: availability of source water for recharge. Although there are differences between proposed and actual costs per recharge volume ($US 2015/AFY, the ranges for proposed costs per recharge volume and actual costs per recharge volume for the projects surveyed generally agree. The two most important contributions to the success of a MAR project are financial support and good communication with stakeholders.

  6. Genetic Variation at Exon 2 of the MHC Class II DQB Locus in Blue Whale (Balaenoptera musculus from the Gulf of California.

    Directory of Open Access Journals (Sweden)

    Diana D Moreno-Santillán

    Full Text Available The genes of the Major Histocompatibility Complex (MHC play an important role in the vertebrate immune response and are among the most polymorphic genes known in vertebrates. In some marine mammals, MHC genes have been shown to be characterized by low levels of polymorphism compared to terrestrial taxa; this reduction in variation is often explained as a result of lower pathogen pressures in marine habitats. To determine if this same reduction in variation applies to the migratory population of blue whales (Balaenoptera musculus that occurs in the Gulf of California, we genotyped a 172 bp fragment of exon 2 of the MHC Class II DQB locus for 80 members of this population. Twenty-two putatively functional DQB allotypes were identified, all of which were homologous with DQB sequences from other cetacean species. Up to 5 putative alleles per individual were identified, suggesting that gene duplication has occurred at this locus. Rates of non-synonymous to synonymous substitutions (ω and maximum likelihood analyses of models of nucleotide variation provided potential evidence of ongoing positive selection at this exon. Phylogenetic analyses of DQB alleles from B. musculus and 16 other species of cetaceans revealed trans-specific conservation of MHC variants, suggesting that selection has acted on this locus over prolonged periods of time. Collectively our findings reveal that immunogenic variation in blue whales is comparable to that in terrestrial mammals, thereby providing no evidence that marine taxa are subject to reduced pathogen-induced selective pressures.

  7. Identification of two novel coccidian species shed by California sea lions (Zalophus californianus).

    Science.gov (United States)

    Carlson-Bremer, Daphne; Johnson, Christine K; Miller, Robin H; Gulland, Frances M D; Conrad, Patricia A; Wasmuth, James D; Colegrove, Kathleen M; Grigg, Michael E

    2012-04-01

    Routine fecal examination revealed novel coccidian oocysts in asymptomatic California sea lions (Zalophus californianus) in a rehabilitation facility. Coccidian oocysts were observed in fecal samples collected from 15 of 410 California sea lions admitted to The Marine Mammal Center between April 2007 and October 2009. Phylogenetic analysis using the full ITS-1 region, partial small subunit 18S rDNA sequence, and the Apicomplexa rpoB region identified 2 distinct sequence clades, referred to as Coccidia A and Coccidia B, and placed them in the Sarcocystidae, grouped with the tissue-cyst-forming coccidia. Both sequence clades resolved as individual taxa at ITS-1 and rpoB and were most closely related to Neospora caninum. Coccidia A was identified in 11 and Coccidia B in 4 of 12 sea lion oocyst samples successfully sequenced (3 of those sea lions were co-infected with both parasites). Shedding of Coccidia A oocysts was not associated with age class, sex, or stranding location, but yearlings represented the majority of shedders (8/15). This is the first study to use molecular phylogenetics to identify and describe coccidian parasites shed by a marine mammal.

  8. Serologic and molecular evidence for testudinid herpesvirus 2 infection in wild Agassiz’s desert tortoise, Gopherus agassizii

    Science.gov (United States)

    Jacobson, Elliott R.; Berry, Kristin H.; Wellehan, James F. X.; Origgi, Francesco; Childress, April L.; Braun, Josephine; Schrenzel, Mark; Yee, Julie; Rideout, Bruce

    2012-01-01

    Following field observations of wild Agassiz’s desert tortoises (Gopherus agassizii) with oral lesions similar to those seen in captive tortoises with herpesvirus infection, we measured the prevalence of antibodies to Testudinid herpesvirus (TeHV) 3 in wild populations of desert tortoises in California. The survey revealed 30.9% antibody prevalence. In 2009 and 2010, two wild adult male desert tortoises, with gross lesions consistent with trauma and puncture wounds, respectively, were necropsied. Tortoise 1 was from the central Mojave Desert and tortoise 2 was from the northeastern Mojave Desert. We extracted DNA from the tongue of tortoise 1 and from the tongue and nasal mucosa of tortoise 2. Sequencing of polymerase chain reaction products of the herpesviral DNA-dependent DNA polymerase gene and the UL39 gene respectively showed 100% nucleotide identity with TeHV2, which was previously detected in an ill captive desert tortoise in California. Although several cases of herpesvirus infection have been described in captive desert tortoises, our findings represent the first conclusive molecular evidence of TeHV2 infection in wild desert tortoises. The serologic findings support cross-reactivity between TeHV2 and TeHV3. Further studies to determine the ecology, prevalence, and clinical significance of this virus in tortoise populations are needed.

  9. Surface circulation patterns in the Gulf of California derived from MODIS Aqua 250 m

    Science.gov (United States)

    Martínez-Flores, G.; Salinas-González, F.; Gutiérrez de Velasco-Sanromán, G.; Godínez-Orta, L.

    2009-04-01

    The Gulf of California (GC) is a marginal elongated and semi-enclosed sea located at northwest of Mexico, between the Peninsula of Baja California and the mainland Mexico. The considered area average 150 km in width and 1500 km in length, from the mouth of the Colorado River to Cabo Corrientes, Jalisco. It has a maximum depth of 3600 m at the southern inlet and the northern region average 200 m in deep. The study of superficial circulation patterns in the GC is of interest because its relevance to the mechanisms of transport for distribution of a variety of materials -plankton, contaminants, microalgae, etc.- and its association with areas of sedimentary deposits, zones where there is a higher probability for fishing or related to the presence of certain species of marine life. Recent studies explain the circulation of the GC as a result of the Pacific Ocean's forcing, wind, heat fluxes on the sea surface and the interaction between the flow produced by these agents and bathymetry. The objective of this work was to obtain evidence of the patterns of surface circulation using a spatial resolution of 250 m over a period of two to seven days (depending on cloud cover), which offered images from the MODIS Level 1B. This essay is an attempt to contribute with more information to the understanding of the regional dynamics of the GC and its local influence on the zones bordering the coast. Thus, MODIS Aqua 250 m data was used, to which algorithms were applied in order to enhance the contrast of reflectance levels of these bands (0.620-0.670 and 0.841-0.876 µm) within the marine environment. The results are associated with suspended particulate matter (SPM), which we used as tracers of the surface circulation, using a sequence of images from January 2004 to December 2008. Algorithms for dust and cloud detection were used and incorporated with thermal band images, in which zones of terrigenous contribution by eolian transport were identified. Furthermore, pluvial

  10. 75 FR 69910 - Revisions to the California State Implementation Plan, California Air Resources Board-Consumer...

    Science.gov (United States)

    2010-11-16

    ...'s national Consumer Products rule. The TSD has more information on our evaluation. C. Public Comment... the California State Implementation Plan, California Air Resources Board--Consumer Products AGENCY... revisions concern volatile organic compound (VOC) emissions from consumer products. We are approving a local...

  11. 76 FR 62004 - Revisions to the California State Implementation Plan, California Air Resources Board-Consumer...

    Science.gov (United States)

    2011-10-06

    ... Organic Compound Emission Standards for Consumer Products. B. Does the rule meet the evaluation criteria... the California State Implementation Plan, California Air Resources Board--Consumer Products AGENCY... revisions concern volatile organic compound (VOC) emissions from consumer products. We are approving a local...

  12. The Story of California. Teacher's Guide = Guia del Maestro de La Historia de California.

    Science.gov (United States)

    Gray (Naomi) Associates, Inc., San Francisco, CA.

    The teacher's guide is designed to accompany "The Story of California," a Spanish-English bilingual history and geography of the state intended for classroom use by limited-English-proficient, native Spanish-speaking students in California's urban middle schools. The guide describes classroom activities coordinated with the student's…

  13. 77 FR 50500 - California State Nonroad Engine Pollution Control Standards; California Nonroad Compression...

    Science.gov (United States)

    2012-08-21

    ... ENVIRONMENTAL PROTECTION AGENCY [AMS-FRL 9716-8] California State Nonroad Engine Pollution Control Standards; California Nonroad Compression Ignition Engines--In-Use Fleets; Authorization Request... emissions control of new engines not listed under section 209(e)(1). The section 209(e) rule and its...

  14. Silviculture-ecology of three native California hardwoods on high sites in north central California

    Science.gov (United States)

    Philip M. McDonald

    1978-01-01

    Pacific madrone, tanoak, and California black oak are the most economically promising native California hardwoods. Volume and value data indicate upward trends in growing stock levels and prices received for their products. These trends are likely to continue. They suggest research is particularly needed for: (1) seed fall and regeneration, (2) sprout growth and...

  15. Transfer and Articulation Issues between California Community Colleges and California State University

    Science.gov (United States)

    Tucker, Linda

    2013-01-01

    Purpose: The primary purpose of this study was to discover common transfer and articulation practices and to determine what practices aid in the implementation of the STAR Act between California Community Colleges and the California State University. The review of literature revealed a lack of research on the application of practices in transfer…

  16. Targeted sequencing of plant genomes

    Science.gov (United States)

    Mark D. Huynh

    2014-01-01

    Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, wholegenome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-...

  17. Almost convergence of triple sequences

    OpenAIRE

    Ayhan Esi; M.Necdet Catalbas

    2013-01-01

    In this paper we introduce and study the concepts of almost convergence and almost Cauchy for triple sequences. Weshow that the set of almost convergent triple sequences of 0's and 1's is of the first category and also almost everytriple sequence of 0's and 1's is not almost convergent.Keywords: almost convergence, P-convergent, triple sequence.

  18. A few Smarandache Integer Sequences

    OpenAIRE

    Ibstedt, Henry

    2010-01-01

    This paper deals with the analysis of a few Smarandache Integer Sequences which first appeared in Properties or the Numbers, F. Smarandache, University or Craiova Archives, 1975. The first four sequences are recurrence generated sequences while the last three are concatenation sequences.

  19. Analysis of Neuronal Sequences Using Pairwise Biases

    Science.gov (United States)

    2015-08-27

    semantic memory (knowledge of facts) and implicit memory (e.g., how to ride a bike ). Evidence for the participation of the hippocampus in the formation of...hippocampal formation in an attempt to be cured of severe epileptic seizures. Although the surgery was successful in regards to reducing the frequency and...very different from each other in many ways including duration and number of spikes. Still, these sequences share a similar trend in the general order

  20. California State Waters Map Series—Offshore of Gaviota, California

    Science.gov (United States)

    Johnson, Samuel Y.; Dartnell, Peter; Cochrane, Guy R.; Hartwell, Stephen R.; Golden, Nadine E.; Kvitek, Rikk G.; Davenport, Clifton W.; Johnson, Samuel Y.; Cochran, Susan A.

    2018-04-20

    IntroductionIn 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within the 3-nautical-mile limit of California’s State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow subsurface geology.The map area is in the southern part of the Western Transverse Ranges geologic province, which is north of the California Continental Borderland. Significant clockwise rotation—at least 90°—since the early Miocene has been proposed for the Western Transverse Ranges province, and the region is presently undergoing north-south shortening. The offshore part of the map area lies south of the steep south flank of the Santa Ynez Mountains. The crest of the range, which has a maximum elevation of about 760 m in the map area, lies about 4 km north of the shoreline.Gaviota is an unincorporated community that has a sparse population (less than 100), and the coastal zone is largely open space that is locally used for cattle grazing. The Union Pacific railroad tracks extend westward along the coast through the entire map area, within a few hundred meters of the shoreline. Highway 101 crosses the eastern part of the map area, also along the coast, then turns north (inland) and travels through Cañada de la Gaviota and Gaviota Pass en route to Buellton. Gaviota State Park lies at the mouth of Cañada de la Gaviota. West of Gaviota, the onland coastal zone is occupied by the Hollister Ranch, a privately owned

  1. Perceptions of randomness in binary sequences: Normative, heuristic, or both?

    Science.gov (United States)

    Reimers, Stian; Donkin, Chris; Le Pelley, Mike E

    2018-03-01

    When people consider a series of random binary events, such as tossing an unbiased coin and recording the sequence of heads (H) and tails (T), they tend to erroneously rate sequences with less internal structure or order (such as HTTHT) as more probable than sequences containing more structure or order (such as HHHHH). This is traditionally explained as a local representativeness effect: Participants assume that the properties of long sequences of random outcomes-such as an equal proportion of heads and tails, and little internal structure-should also apply to short sequences. However, recent theoretical work has noted that the probability of a particular sequence of say, heads and tails of length n, occurring within a larger (>n) sequence of coin flips actually differs by sequence, so P(HHHHH) rational norms based on limited experience. We test these accounts. Participants in Experiment 1 rated the likelihood of occurrence for all possible strings of 4, 5, and 6 observations in a sequence of coin flips. Judgments were better explained by representativeness in alternation rate, relative proportion of heads and tails, and sequence complexity, than by objective probabilities. Experiments 2 and 3 gave similar results using incentivized binary choice procedures. Overall the evidence suggests that participants are not sensitive to variation in objective probabilities of a sub-sequence occurring; they appear to use heuristics based on several distinct forms of representativeness. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Continuous Online Sequence Learning with an Unsupervised Neural Network Model.

    Science.gov (United States)

    Cui, Yuwei; Ahmad, Subutar; Hawkins, Jeff

    2016-09-14

    The ability to recognize and predict temporal sequences of sensory inputs is vital for survival in natural environments. Based on many known properties of cortical neurons, hierarchical temporal memory (HTM) sequence memory recently has been proposed as a theoretical framework for sequence learning in the cortex. In this letter, we analyze properties of HTM sequence memory and apply it to sequence learning and prediction problems with streaming data. We show the model is able to continuously learn a large number of variableorder temporal sequences using an unsupervised Hebbian-like learning rule. The sparse temporal codes formed by the model can robustly handle branching temporal sequences by maintaining multiple predictions until there is sufficient disambiguating evidence. We compare the HTM sequence memory with other sequence learning algorithms, including statistical methods: autoregressive integrated moving average; feedforward neural networks-time delay neural network and online sequential extreme learning machine; and recurrent neural networks-long short-term memory and echo-state networks on sequence prediction problems with both artificial and real-world data. The HTM model achieves comparable accuracy to other state-of-the-art algorithms. The model also exhibits properties that are critical for sequence learning, including continuous online learning, the ability to handle multiple predictions and branching sequences with high-order statistics, robustness to sensor noise and fault tolerance, and good performance without task-specific hyperparameter tuning. Therefore, the HTM sequence memory not only advances our understanding of how the brain may solve the sequence learning problem but is also applicable to real-world sequence learning problems from continuous data streams.

  3. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  4. Addressing the Sustainability of Groundwater Extraction in California Using Hydrochronology

    Science.gov (United States)

    Moran, J. E.; Visser, A.; Singleton, M. J.; Esser, B. K.

    2017-12-01

    In urban and agricultural settings in California, intense pressure on water supplies has led to extensive managed aquifer recharge and extensive overdraft in these areas, respectively. The California Sustainable Groundwater Management Act (SGMA) includes criteria for pumping that maintains groundwater levels and basin storage, and avoids stream depletion and degradation of water quality. Most sustainability plans will likely use water level monitoring and water budget balancing based on integrated flow models as evidence of compliance. However, hydrochronology data are applicable to several of the criteria, and provide an independent method of addressing questions related to basin turnover time, recharge rate, surface water-groundwater interaction, and the age distribution at pumping wells. We have applied hydrochronology (mainly tritium-helium groundwater age dating and extrinsic tracers) in urban areas to delineate flowpaths of artificially recharged water, to identify stagnant zones bypassed by the engineered flow system, and to predict vulnerability of drinking water sources to contamination. In agricultural areas, we have applied multi-tracer hydrochronology to delineate groundwater stratigraphy, to identify paleowater, and to project future nitrate concentrations in long-screened wells. This presentation will describe examples in which groundwater dating and other tracer methods can be applied to directly address the SGMA criteria for sustainable groundwater pumping.

  5. Some comments on reconstructing the historical climate of California, USA

    International Nuclear Information System (INIS)

    Mock, C.J.

    2006-01-01

    This paper describes some examples of historical climate reconstruction pertaining to California, USA, focusing mostly on winter climate given the expected strongest teleconnection signals for this season. Climatic data consist of early instrumental data from the US Army Surgeon General at military forts, observers of the Smithsonian Institution, the Signal Service, and some private observers. Documentary (non-instrumental) data were also used in assessing extreme events. Original daily records of these data were carefully assessed for discontinuities from examining diurnal temperature ranges and daily precipitation amounts. The climatic reconstructions conducted were as follows: 1) winter precipitation time series for selected locations since 1850, particularly for Sacramento and San Francisco, 2) winter temperature time series for selected locations since 1850, and 3) analyses of an extreme flooding event in January 1862 and a landfalling tropical cyclone of September 1939. Results indicate distinctive wetter winters for central and northern California in the late nineteenth century, and some of these wetter years correspond to well-known very strong El Ni no events. Connections to weaker El Nino and La Nina events, however, are not clearly evident. The flood of January 1862 is considered unprecedented when compared to other floods of the last 130 years. The reconstruction of a landfalling tropical cyclone for September 1939 near Los Angeles suggests its intensity at just below hurricane strength

  6. Air quality and acute deaths in California, 2000-2012.

    Science.gov (United States)

    Young, S Stanley; Smith, Richard L; Lopiano, Keneth K

    2017-08-01

    Many studies have shown an association between air quality and acute deaths, and such associations are widely interpreted as causal. Several factors call causation and even association into question, for example multiple testing and multiple modeling, publication bias and confirmation bias. Many published studies are difficult or impossible to reproduce because of lack of access to confidential data sources. Here we make publically available a dataset containing daily air quality levels, PM 2.5 and ozone, daily temperature levels, minimum and maximum and daily maximum relative humidity levels for the eight most populous California air basins, thirteen years, >2M deaths, over 37,000 exposure days. The data are analyzed using standard time series analysis, and a sensitivity analysis is computed varying model parameters, locations and years. Our analysis finds little evidence for association between air quality and acute deaths. These results are consistent with those for the widely cited NMMAPS dataset when the latter are restricted to California. The daily death variability was mostly explained by time of year or weather variables; Neither PM 2.5 nor ozone added appreciably to the prediction of daily deaths. These results call into question the widespread belief that association between air quality and acute deaths is causal/near-universal. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Evaluation of the Geothermal Public Power Utility Workshops in California

    Energy Technology Data Exchange (ETDEWEB)

    Farhar, B. C.

    2004-10-01

    The federal government devotes significant resources to educating consumers and businesses about geothermal energy. Yet little evidence exists for defining the kinds of information needed by the various audiences with specialized needs. This paper presents the results of an evaluation of the Geothermal Municipal Utility Workshops that presented information on geothermal energy to utility resource planners at customer-owned utilities in California. The workshops were sponsored by the Western Area Power Administration and the U.S. Department of Energy's GeoPowering the West Program and were intended to qualitatively assess the information needs of municipal utilities relative to geothermal energy and get feedback for future workshops. The utility workshop participants found the geothermal workshops to be useful and effective for their purposes. An important insight from the workshops is that utilities need considerable lead-time to plan a geothermal project. They need to know whether it is better to own a project or to purchase geothermal electricity from another nonutility owner. California customer-owned utilities say they do not need to generate more electricity to meet demand, but they do need to provide more electricity from renewable resources to meet the requirements of the state's Renewable Portfolio Standard.

  8. Late Neogene marine incursions and the ancestral Gulf of California

    Science.gov (United States)

    McDougall, K.

    2008-01-01

    The late Neogene section in the Salton Trough, California, and along the lower Colorado River in Arizona is composed of marine units bracketed by nonmarine units. Microfossils from the marine deposits indicate that a marine incursion inundated the Salton Trough during the late Miocene. Water depths increased rapidly in the Miocene and eventually flooded the region now occupied by the Colorado River as far north as Parker, Arizona. Marine conditions were restricted in the Pliocene as the Colorado River filled the Salton Trough with sediments and the Gulf of California assumed its present configuration. Microfossils from the early part of this incursion include a diverse assemblage of benthic foraminifers (Amphistegina gibbosa, Uvigerina peregrina, Cassidulina delicata, and Bolivina interjuncta), planktic foraminifers (Globigerinoides obliquus, G. extremus, and Globigerina nepenthes), and calcareous nannoplankton (Discoaster brouweri, Discoaster aff. Discoaster surculus, Sphenolithus abies, and S. neoabies), whereas microfossils in the final phase contain a less diverse assemblage of benthic foraminifers that are diagnostic of marginal shallow-marine conditions (Ammonia, Elphidium, Bolivina, Cibicides, and Quinqueloculina). Evidence of an earlier middle Miocene marine incursion comes from reworked microfossils found near Split Mountain Gorge in the Fish Creek Gypsum (Sphenolithus moriformis) and near San Gorgonio Pass (Cyclicargolithus floridanus and Sphenolithus heteromorphus and planktic foraminifers). The middle Miocene incursion may also be represented by the older marine sedimentary rocks encountered in the subsurface near Yuma, Arizona, where rare middle Miocene planktic foraminifers are found. ?? 2008 The Geological Society of America.

  9. Work satisfaction among California registered nurses: a longitudinal comparative analysis.

    Science.gov (United States)

    Tellez, Michelle

    2012-01-01

    California's minimum nurse-to-patient staffing ratio law, the nation's first, was implemented in 2004. This study had two aims: (a) to evaluate the effect of the nurse-to-patient ratios law on nurse job satisfaction in order to advance the debate over the merits of nurse staffing law, and (b) to compare California nurses who were satisfied against those who were not, in order to facilitate the development targeted retention interventions based on empirical evidence. The sample's overall job satisfaction increased significantly as the years passed, suggesting the nurse-to-patient ratios law was associated with improvements in nurse satisfaction. Satisfied RNs were more likely to have a balanced and financially secure life that included a partner, children living at home, higher hourly wages, and higher income from sources other than a nursing job. Nurses working in direct patient care positions remained dissatisfied in larger proportions than those working in other types of positions, even after the nurse-to-patient ratios were implemented. More nurses are satisfied today than before the ratios; nevertheless, far too many nurses (18.5%) have job satisfaction scores that are neutral or worse.

  10. The timing of sediment transport down Monterey Submarine Canyon, offshore California

    Science.gov (United States)

    Stevens, Thomas; Paull, Charles K.; Ussler, William III; McGann, Mary; Buylaert, Jan-Pieter; Lundsten, Eve M.

    2013-01-01

    While submarine canyons are the major conduits through which sediments are transported from the continents out into the deep sea, the time it takes for sediment to pass down through a submarine canyon system is poorly constrained. Here we report on the first study to couple optically stimulated luminescence (OSL) ages of quartz sand deposits and accelerator mass spectrometry 14C ages measured on benthic foraminifera to examine the timing of sediment transport through the axial channel of Monterey Submarine Canyon and Fan, offshore California. The OSL ages date the timing of sediment entry into the canyon head while the 14C ages of benthic foraminifera record the deposition of hemipelagic sediments that bound the sand horizons. We use both single-grain and small (∼2 mm area) single-aliquot regeneration approaches on vibracore samples from fining-upward sequences at various water depths to demonstrate relatively rapid, decadal-scale sand transport to at least 1.1 km depth and more variable decadal- to millennial-scale transport to a least 3.5 km depth on the fan. Significant differences between the time sand was last exposed at the canyon head (OSL age) and the timing of deposition of the sand (from 14C ages of benthic foraminifera in bracketing hemipelagic sediments) are interpreted as indicating that the sand does not pass through the entire canyon instantly in large individual events, but rather moves multiple times before emerging onto the fan. The increased spread in single-grain OSL dates with water depth provides evidence of mixing and temporary storage of sediment as it moves through the canyon system. The ages also indicate that the frequency of sediment transport events decreases with distance down the canyon channel system. The amalgamated sands near the canyon head yield OSL ages that are consistent with a sub-decadal recurrence frequency while the fining-upward sand sequences on the fan indicate that the channel is still experiencing events with a 150

  11. Transformation of the genital epithelial tract occurs early in California sea lion development

    Science.gov (United States)

    Barragán-Vargas, Cecilia; Montano-Frías, Jorge; Ávila Rosales, Germán; Godínez-Reyes, Carlos R.; Acevedo-Whitehouse, Karina

    2016-01-01

    An unusually high prevalence of metastatic urogenital carcinoma has been observed in free-ranging California sea lions stranded off the coast of California in the past two decades. No cases have been reported for sea lions in the relatively unpolluted Gulf of California. We investigated occurrence of genital epithelial transformation in 60 sea lions (n=57 pups and 3 adult females) from the Gulf of California and examined whether infection by a viral pathogen previously found to be associated with urogenital carcinoma accounted for such alterations. We also explored the contribution of MHC class II gene expression on transformation. Cellular alterations, such as squamous cell atypia (ASC), atypical squamous cells of undetermined significance (ASCUS) and low-grade squamous intraepithelial lesions were observed in 42% of the pups and in 67% of the adult females. Normal genital epithelium was more common in male than female pups. ASC was five times more likely to occur in older pups. Epithelial alterations were unrelated to infection by the potentially oncogenic otarine type I gammaherpesvirus (OtHV-1), but ASCUS was more common in pups with marked and severe inflammation. Expression of MHC class II DRB loci (Zaca DRB-D) by peripheral antigen-presenting leucocytes showed a slightly ‘protective’ effect for ASC. We propose that transformation of the California sea lion genital epithelium is relatively common in young animals, increases with age and is probably the result of infection by an unidentified pathogen. Expression of a specific MHC class II gene, suggestive of presentation of specific antigenic peptides to immune effectors, appears to lower the risk of transformation. Our study provides the first evidence that epithelial transformation of the California sea lion genital tract is relatively common, even from an early age, and raises questions regarding differences in sea lion cancer-detection and -repair success between geographical regions. PMID:27069641

  12. Multilocus Sequence Typing

    OpenAIRE

    Belén, Ana; Pavón, Ibarz; Maiden, Martin C.J.

    2009-01-01

    Multilocus sequence typing (MLST) was first proposed in 1998 as a typing approach that enables the unambiguous characterization of bacterial isolates in a standardized, reproducible, and portable manner using the human pathogen Neisseria meningitidis as the exemplar organism. Since then, the approach has been applied to a large and growing number of organisms by public health laboratories and research institutions. MLST data, shared by investigators over the world via the Internet, have been ...

  13. Achalasia Carcinoma Sequence

    OpenAIRE

    Makmun, Dadang

    2001-01-01

    We report a case of carcinoma of the esophagus in a 58 years old woman with achalasia, who has been diagnosed since 30 years ago, which initiated by surgical treatment (myotomy) and the symptoms recurred since 3 years ago. According to the progress of the disease, Malignancy was strongly suspected due to prolonged stasis and mucosal irritation caused by achalasia (achalasia carcinoma sequence). Because of these contributing factors for the development of serious complications such as Malignan...

  14. Fogwater chemistry at Riverside, California

    Science.gov (United States)

    Munger, J. William; Collett, Jeff; Daube, Bruce; Hoffmann, Michael R.

    Fog, aerosol, and gas samples were collected during the winter of 1986 at Riverside, California. The dominant components of the aerosol were NH 4+, NO 3-, and SO 42-. Gaseous NH 3 was frequently present at levels equal to or exceeding the aerosol NH 4+. Maximum level were 3800, 3100, 690 and 4540 neq m -3 for NH 4+, NO 32- and NH 3(g), respectively. The fogwater collected at Riverside had very high concentrations, particularly of the major aerosol components. Maximum concentrations were 26,000 29,000 and 6200 μM for NH 4+, NO 3- and SO 42-, respectively. pH values in fogwater ranged from 2.3 to 5.7. Formate and acetate concentrations as high as 1500 and 580 μM, respectively, were measured. The maximum CH 2O concentration was 380 μM. Glyoxal and methylglyoxal were found in all the samples; their maximum concentrations were 280 and 120 μM, respectively. Comparison of fogwater and aerosol concentrations indicates that scavenging of precursor aerosol by fog droplets under the conditions at Riverside is less than 100% efficient. The chemistry at Riverside is controlled by the balance between HNO 3 production from NO x emitted throughout the Los Angeles basin and NH 3 emitted from dairy cattle feedlots just west of Riverside. The balance is controlled by local mixing. Acid fogs result at Riverside when drainage flows from the surrounding mountains isolate the site from the NH 3 source. Continued formation of HNO 3(g) in this air mass eventually depletes the residual NH 3(g). A simple box model that includes deposition, fog scavenging, and dilution is used to assess the effect of curtailing the dairy cattle feedlot operations. The calculations suggest that the resulting reduction of NH 3 levels would decrease the total NO 3- in the atmosphere, but nearly all remaining NO 3- would exist as HNO 3. Fogwater in the basin would be uniformly acidic.

  15. The least-cost hydrogen for Southern California

    International Nuclear Information System (INIS)

    Lin, Zhenhong; Chen, Chien-Wei; Ogden, Joan; Fan, Yueyue

    2008-01-01

    Optimization is applied to identify the least-cost sequence of hydrogen infrastructure build-up in Southern California during 2010-2060. Given an exogenous demand, the model generates temporal and spatial decisions for building a hydrogen infrastructure, in terms of when, where, at what sizes and by what technologies, that minimize the net present value of technology, environment, and fuel accessibility costs. The least-cost sequence is then analyzed with respect to technology deployment, delivered hydrogen cost, capital requirements, subsidy need, subsidy capacity, and CO 2 mitigation. It is found that industrial hydrogen could play a critical role in initiating hydrogen transition, temporally bridged by onsite SMR to central production dominated at first by biomass gasification and later by coal gasification with carbon dioxide capture and storage (CCS). While a non-discounted capital investment of $24.43 billion is needed for the 50-year build-up, a hydrogen price below 3$/kg could pay back the costs in 20 years earning a 10% IRR. If hydrogen is purchased at the current equivalent gasoline price (2.517 $/gallon), the hydrogen industry could potentially provide $4715 as subsidy for each new FCV purchase. With CCS, 50% of 50-year CO 2 emissions could be avoided. (author)

  16. Changes in and Factors Affecting Second-hand Smoke Exposure in Nonsmoking Korean Americans in California: A Panel Study

    Directory of Open Access Journals (Sweden)

    Hyeongsu Kim, MD, PhD

    2014-12-01

    Conclusions: We showed that SHS exposure increased among Korean American nonsmokers in California, and the most important variables explaining the change in SHS exposure involved smoking among others with whom the subject is associated. These findings could be used as objective evidence for developing public health policies to reduce SHS exposure.

  17. Airborne Pesticides as an Unlikely Cause for Population Declines of Alpine Frogs in the Sierra Nevada, California

    Science.gov (United States)

    Airborne pesticides from the Central Valley of California have been implicated as a cause for population declines of several amphibian species, with the strongest evidence for the mountain yellow-legged frog complex (Rana muscosa and R. sierrae) in the Sierra Nevada. We measured...

  18. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

    Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

    2016-03-02

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  19. Sequencing BPS spectra

    International Nuclear Information System (INIS)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-01-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  20. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  1. Organochloride pesticides in California sea lions revisited

    Directory of Open Access Journals (Sweden)

    Tanabe Shinsuke

    2002-12-01

    Full Text Available Abstract Background Dichlorodiphenyltrichloroethane (DDT and polychlorinated biphenyls (PCBs are ubiquitous environmental contaminants that have been banned in most countries, but considerable amounts continue to cycle the ecosphere. Top trophic level predators, like sea birds and marine mammals, bioaccumulate these lipophilic compounds, reflecting their presence in the environment. Results We measured concentrations of tDDT (p,p' - DDT + p,p' - DDD + p,p' - DDE and PCBs in the blubber of dead California sea lions stranded along the California coast. tDDT and PCB concentrations were 150 ± 257 ug/g lipid weight (mean ± SD and 44 ± 78 ug/g lipid weight, respectively. There were no differences in tDDT or PCB concentrations between animal categories varying in sex or age. There was a trend towards a decrease in tDDT and PCB concentrations from northern to southern California. The lipid content of the blubber was negatively correlated with levels of tDDT and PCBs. tDDT concentrations were approximately 3 times higher than PCB concentrations. Conclusions tDDT levels in the blubber of California sea lions decreased by over one order of magnitude from 1970 to 2000. PCB level changes over time were unclear owing to a paucity of data and analytical differences over the years. Current levels of these pollutants in California sea lions are among the highest among marine mammals and exceed those reported to cause immunotoxicity or endocrine disruption.

  2. Industrial Physics---Southern California Style

    Science.gov (United States)

    Leslie, Stuart

    2013-03-01

    Only in Southern California did space-age style really come into its own as a unique expression of Cold War scientific culture. The corporate campuses of General Atomic in San Diego and North American Aviation in Los Angeles perfectly expressed the exhilarating spirit of Southern California's aerospace era, scaling up the residential version of California modernism to industrial proportion. Architects William Pereira and A.C. Martin Jr., in collaboration with their scientific counterparts, fashioned military-industrial `dream factories' for industrial physics that embodied the secret side of the space-age zeitgeist, one the public could only glimpse of in photographs, advertisements, and carefully staged open houses. These laboratories served up archetypes of the California dream for a select audience of scientists, engineers, and military officers, live-action commercials for a lifestyle intended to lure the best and brightest to Southern California. Paradoxically, they hid in plain sight, in the midst of aerospace suburbs, an open secret, at once visible and opaque, the public face of an otherwise invisible empire. Now, at the end of the aerospace era, these places have become an endangered species, difficult to repurpose, on valuable if sometimes highly polluted land. Yet they offer an important reminder of a more confident time when many physicists set their sights on the stars.

  3. Uta stansburiana and Elgaria multicarinata on the California Channel Islands: Natural dispersal or artificial introduction?

    Science.gov (United States)

    Mahoney, Meredith J.; Parks, Duncan S.M.; Fellers, Gary M.

    2003-01-01

    Uta stansburiana and Elgaria multicarinata occur on several California Channel Islands, and recent introduction of some populations has been suggested because of similarity in life-history traits and body size to mainland populations. We sequenced representatives of each species from mainland southern California and some of the islands on which they occur. For each species, cytochrome bsequence divergence is low across the narrow geographic area sampled. Analyses of 14 haplotypes of U. stansburiana suggest long-established residency on Santa Catalina and San Clemente Islands but more recent arrival on San Nicolas and Santa Cruz Islands. Analyses of eight haplotypes of E. multicarinata suggest these lizards may have been recently transported to San Nicolas Island.

  4. A Unique Sequence of Financial Accounting Courses Featuring Team Teaching, Linked Courses, Challenging Assignments, and Instruments for Evaluation and Assessment

    Science.gov (United States)

    Lundblad, Heidemarie; Wilson, Barbara A.

    2008-01-01

    The Department of Accounting at California State University Northridge (CSUN) has developed a unique sequence of courses designed to ensure that accounting students are trained not only in technical accounting, but also acquire critical thinking, research and communication skills. The courses have proven effective and have embedded assessment…

  5. A refined ecological risk assessment for California red-legged frog, Delta smelt, and California tiger salamander exposed to malathion.

    Science.gov (United States)

    Clemow, Yvonne H; Manning, Gillian E; Breton, Roger L; Winchell, Michael F; Padilla, Lauren; Rodney, Sara I; Hanzas, John P; Estes, Tammara L; Budreski, Katherine; Toth, Brent N; Hill, Katie L; Priest, Colleen D; Teed, R Scott; Knopper, Loren D; Moore, Dwayne Rj; Stone, Christopher T; Whatling, Paul

    2018-03-01

    The California red-legged frog (CRLF), Delta smelt (DS), and California tiger salamander (CTS) are 3 species listed under the United States Federal Endangered Species Act (ESA), all of which inhabit aquatic ecosystems in California. The US Environmental Protection Agency (USEPA) has conducted deterministic screening-level risk assessments for these species potentially exposed to malathion, an organophosphorus insecticide and acaricide. Results from our screening-level analyses identified potential risk of direct effects to DS as well as indirect effects to all 3 species via reduction in prey. Accordingly, for those species and scenarios in which risk was identified at the screening level, we conducted a refined probabilistic risk assessment for CRLF, DS, and CTS. The refined ecological risk assessment (ERA) was conducted using best available data and approaches, as recommended by the 2013 National Research Council (NRC) report "Assessing Risks to Endangered and Threatened Species from Pesticides." Refined aquatic exposure models including the Pesticide Root Zone Model (PRZM), the Vegetative Filter Strip Modeling System (VFSMOD), the Variable Volume Water Model (VVWM), the Exposure Analysis Modeling System (EXAMS), and the Soil and Water Assessment Tool (SWAT) were used to generate estimated exposure concentrations (EECs) for malathion based on worst-case scenarios in California. Refined effects analyses involved developing concentration-response curves for fish and species sensitivity distributions (SSDs) for fish and aquatic invertebrates. Quantitative risk curves, field and mesocosm studies, surface-water monitoring data, and incident reports were considered in a weight-of-evidence approach. Currently, labeled uses of malathion are not expected to result in direct effects to CRLF, DS or CTS, or indirect effects due to effects on fish and invertebrate prey. Integr Environ Assess Manag 2018;14:224-239. © 2017 The Authors. Integrated Environmental Assessment and

  6. Deregulation of the California electric power industry: An analysis of electric and natural gas corporate mergers and their effect on the California electric power market

    Science.gov (United States)

    Hornbuckle, James Dixon

    Deregulation of the electric utility industry in California is moving in a direction that places greater reliance on the market forces of competition. Investor owned utilities (IOU's) are using mergers and acquisitions to improve their ability to compete in this new environment. Two large mergers were proposed in 1996 that could affect the California market. The first is between Enron Corporation, a large power marketer and Portland General Corporation, owner of Portland General Electric. The second is between Pacific Enterprises Inc., owner of Southern California Gas Company, the largest natural gas utility in the U. S., and Enova Corporation, owner of San Diego Gas and Electric Company. Understanding the impact of these mergers on the California electric power market is the focus of this study. This study examines hypotheses dealing with: (1) Merger Strategy, (2) Efficiency, and (3) Market Power. Using the Miles and Snow (1978) typology, I develop a strategic orientation model for the merger participants and their competitors. The results suggest a two-stage strategic orientation: (1) regulated core business stage, where the firms follow a Defender strategy, and (2) unregulated business stage, where the firms follow a Prospector strategy. Further, the results show the mergers are consistent with the strategy of Enron and Pacific Enterprises. Event study methodology, dollar gains/losses and market value weighted returns are used to determine if the mergers support the efficiency hypothesis. The evidence suggests the mergers lead to increased competitive advantage through improved efficiency for the participants. The results also suggest the mergers do not harm the rivals. The results of structural changes made by the California Public Utilities Commission (CPUC) in deregulation of the California market and analysis of the mergers by the CPUC and the Public Utility Commission of Oregon suggest that the exercise of market power is not a significant issue. Finally

  7. Geologic structure in California: Three studies with ERTS-1 imagery

    Science.gov (United States)

    Lowman, P. D., Jr.

    1974-01-01

    Results are presented of three early applications of imagery from the NASA Earth Resources Technology Satellite to geologic studies in California. In the Coast Ranges near Monterey Bay, numerous linear drainage features possibly indicating unmapped fracture zones were mapped within one week after launch of the satellite. A similar study of the Sierra Nevada near Lake Tahoe revealed many drainage features probably formed along unmapped joint or faults in granitic rocks. The third study, in the Peninsular Ranges, confirmed existence of several major faults not shown on published maps. One of these, in the Sawtooth Range, crosses in Elsinore fault without lateral offset; associated Mid-Cretaceous structures have also been traced continuously across the fault without offset. It therefore appears that displacement along the Elsinore fault has been primarily of a dip-slip nature, at least in this area, despite evidence for lateral displacement elsewhere.

  8. Pesticide occurrence and distribution in fog collected near Monterey, California

    Energy Technology Data Exchange (ETDEWEB)

    Schomburg, C.J.; Glotfelty, D.E. (Department of Agriculture, Beltsville, MD (USA)); Seiber, J.N. (Univ. of California, Davis (USA))

    1991-01-01

    The authors analyzed pesticides in air and fog in several fog events sampled near Monterey, CA, to determine whether the uptake of pesticides in advected oceanic fog was different from uptake in fog forming under stagnant inversion conditions in California's Central Valley in the winter. Data for several pesticides common to both ares showed that the pesticide content and distribution were remarkable similar in the two locations. The conversion of organophosphorus insecticides to their corresponding oxons, and aqueous-phase enrichment factors, were also very similar. Evidence is presented to support the hypothesis that enhanced pesticide concentration in fogwater is caused by strongly sorptive nonfilterable particles and colloids in the fog liquid that are derived from atmospheric particles.

  9. Current depression among women in California according to residence in the California-Mexico border region.

    Science.gov (United States)

    Ryan-Ibarra, Suzanne; Epstein, Joan Faith; Induni, Marta; Wright, Michael A

    2012-05-01

    To estimate the prevalence of current depression; examine the relationship between current depression and immigration, health status, health care access, and health behaviors; and assess differences by California-Mexico border region (Imperial and San Diego Counties) among women in California. Using a cross-sectional, representative sample of adult women from the California Women's Health Survey (n = 13 454), a statewide telephone survey, prevalence of current depression and predictors of depression were examined in California and according to border region residence. Depression was assessed with the eight-item Patient Health Questionnaire. The prevalence of current depression for women in California was 12.0%. It was similar in the border (13.0%) and the nonborder (11.9%) regions. Odds of current depression in women were lower among recent immigrants (depression and health status, health care access, and binge drinking were larger in the border region than outside the border region. Similar prevalences of current depression were observed among those who live in the border region of California and in those who do not, but the relationship between depression and health status, health care access, and binge drinking varied by border region residence. Ideally, future surveillance of depression and its predictors along the Mexico-California border will be conducted binationally to inform interventions and tracking such as the Healthy Border Program's objectives.

  10. Overview of the Inland California Translational Consortium

    Science.gov (United States)

    Malkas, Linda H.

    2017-05-01

    The mission of the Inland California Translational Consortium (ICTC), an independent research consortium comprising a unique hub of regional institutions (City of Hope [COH], California Institute of Technology [Caltech], Jet Propulsion Laboratory [JPL], University of California Riverside [UCR], and Claremont Colleges Keck Graduate Institute [KGI], is to institute a new paradigm within the academic culture to accelerate translation of innovative biomedical discoveries into clinical applications that positively affect human health and life. The ICTC actively supports clinical translational research as well as the implementation and advancement of novel education and training models for the translation of basic discoveries into workable products and practices that preserve and improve human health while training and educating at all levels of the workforce using innovative forward-thinking approaches.

  11. The optimal gas tax for California

    International Nuclear Information System (INIS)

    Lin, C.-Y. Cynthia; Prince, Lea

    2009-01-01

    This paper calculates the optimal gasoline tax for the state of California. According to our analysis, the optimal gasoline tax in California is $1.37/gal, which is over three times the current California tax when excluding sales taxes. The Pigovian tax is the largest part of this tax, comprising $0.85/gal. Of this, the congestion externality is taxed the most heavily, at $0.27, followed by oil security, accident externalities, local air pollution, and finally global climate change. The other major component, a Ramsey tax, comprises a full $0.52 of this tax, reflecting the efficiency in raising revenues from a tax on gasoline consumption due to the inelastic demand of this consumption good.

  12. What went wrong in California's electricity market?

    International Nuclear Information System (INIS)

    Chikeung Woo

    2001-01-01

    The California electricity market reform promised to deliver reliable service at low and stable prices. Frequent capacity shortages and the ensuing rolling black-outs, price spikes, and large price volatility since Summer 2000 raise a simple but substantive question: what went wrong? The answer to this question will help countries contemplating electricity market reform not to commit similar mistakes. We find the answer by identifying the major factors that have turned the California dream into a nightmare. Such factors include poor market design, market power, sustained demand growth not matched by new capacity, rising marginal cost, and financial insolvency. Proposed remedies include an alternative market settlement process, long-term contract, fast licensing and siting process for new generation and transmission, conservation and energy-efficiency, distributed resources, rate options, and debt restructuring. The California experience suggests that a reversible regulatory reform is a safe alternative to an irreversible market reform. (Author)

  13. The optimal gas tax for California

    Energy Technology Data Exchange (ETDEWEB)

    Lin, C.-Y. Cynthia; Prince, Lea [Department of Agricultural and Resource Economics, University of California, Davis, CA 95616 (United States)

    2009-12-15

    This paper calculates the optimal gasoline tax for the state of California. According to our analysis, the optimal gasoline tax in California is USD1.37/gal, which is over three times the current California tax when excluding sales taxes. The Pigovian tax is the largest part of this tax, comprising USD0.85/gal. Of this, the congestion externality is taxed the most heavily, at USD0.27, followed by oil security, accident externalities, local air pollution, and finally global climate change. The other major component, a Ramsey tax, comprises a full USD0.52 of this tax, reflecting the efficiency in raising revenues from a tax on gasoline consumption due to the inelastic demand of this consumption good. (author)

  14. Fire Perimeters - Southern California, Fall 2007 [ds385

    Data.gov (United States)

    California Natural Resource Agency — Southern Callifornia fire perimeters for the Fall 2007 wildfires. The perimeters were assembled from various sources by California Department of Fish and Game (DFG)...

  15. California community water systems quarterly indicators dataset, 1999-2008

    Data.gov (United States)

    California Environmental Health Tracking Program — This data set contains quarterly measures of arsenic and nitrates in public drinking water supplies. Data are derived from California Office of Drinking Water (ODW)...

  16. The potential of energy farming in the southeastern California desert

    Science.gov (United States)

    Lew, V.

    1980-04-01

    The use of energy forms to provide future sources of energy for California is considered. Marginal desert lands in southeastern California are proposed for the siting of energy farms using acacia, eucalyptus, euphorbia, guayule, jojoba, mesquite, or tamarisk.

  17. The Class of 2014 Preserving Access to California Higher Education

    National Research Council Canada - National Science Library

    Park, George

    1998-01-01

    For over 35 years, California's policy of providing a college education to all citizens who could benefit from it has enabled California to lead the nation in making public higher education available...

  18. California community water systems annual indicators dataset, 1999-2008

    Data.gov (United States)

    California Environmental Health Tracking Program — This data set contains annual measures of arsenic and nitrates in public drinking water supplies. Data are derived from California Office of Drinking Water (ODW)...

  19. Williamson Act - The California Land Conservation Act of 1965

    Data.gov (United States)

    California Natural Resource Agency — The California Land Conservation Act of 1965 - commonly referred to as the Williamson Act - is the State's primary program for the conservation of private land in...

  20. Foundations of Sequence-to-Sequence Modeling for Time Series

    OpenAIRE

    Kuznetsov, Vitaly; Mariet, Zelda

    2018-01-01

    The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series forecasting. We provide the first theoretical analysis of this time series forecasting framework. We include a comparison of sequence-to-sequence modeling to classical time series models, and as such our theory can serve as a quantitative guide for practiti...