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Berlin Brandenburg

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  • 1
    Language: English
    In: 2015, Vol.10(9), p.e0137935
    Keywords: Correction
    E-ISSN: 1932-6203
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  • 2
    Language: English
    In: PLoS ONE, 01 January 2015, Vol.10(3), p.e0120016
    Description: Marijuana (Cannabis sativa L.) cultivation has proliferated in northwestern California since at least the mid-1990s. The environmental impacts associated with marijuana cultivation appear substantial, yet have been difficult to quantify, in part because cultivation is clandestine and often occurs on private property. To evaluate the impacts of water diversions at a watershed scale, we interpreted high-resolution aerial imagery to estimate the number of marijuana plants being cultivated in four watersheds in northwestern California, USA. Low-altitude aircraft flights and search warrants executed with law enforcement at cultivation sites in the region helped to validate assumptions used in aerial imagery interpretation. We estimated the water demand of marijuana irrigation and the potential effects water diversions could have on stream flow in the study watersheds. Our results indicate that water demand for marijuana cultivation has the potential to divert substantial portions of streamflow in the study watersheds, with an estimated flow reduction of up to 23% of the annual seven-day low flow in the least impacted of the study watersheds. Estimates from the other study watersheds indicate that water demand for marijuana cultivation exceeds streamflow during the low-flow period. In the most impacted study watersheds, diminished streamflow is likely to have lethal or sub-lethal effects on state- and federally-listed salmon and steelhead trout and to cause further decline of sensitive amphibian species.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 3
    Language: English
    In: Madroño, 1 July 2006, Vol.53(3), pp.264-274
    Description: The conservation of peripheral plant populations is paradoxical. Populations occurring on the edge of a species' range tend to be smaller, more isolated, and more genetically and ecologically divergent than central populations. The combination of these characteristics can impart novel evolutionary potential and local ecological significance, thus heightening their conservation value, while also making them less viable and more prone to local extinction. Public policy supports the conservation of peripheral populations, despite the commonness of the species elsewhere. However, the conservation of significant peripheral populations of nonlisted plants has been arbitrary and ineffective. The absence of explicit criteria to determine the conservation value of peripheral plant populations, the lack of finer-scale data on plant distributions, and a general unawareness of their value have hindered efforts to conserve them. We review the conservation value of peripheral plant populations and, using California as an example, describe regulatory methods to improve their conservation. We also propose a scheme to assess a population's conservation value.
    Keywords: Biological sciences -- Biology -- Conservation biology ; Biological sciences -- Wildlife studies -- Wildlife management ; Biological sciences -- Biology -- Genetics ; Biological sciences -- Biology -- Botany ; Biological sciences -- Biology -- Conservation biology ; Biological sciences -- Biology -- Conservation biology ; Biological sciences -- Biology -- Conservation biology ; Biological sciences -- Ecology -- Population ecology ; Biological sciences -- Biology -- Biological taxonomies ; Social sciences -- Human geography -- Population geography
    ISSN: 00249637
    E-ISSN: 19436297
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  • 4
    Language: English
    In: Madroño, 1 April 2008, Vol.55(2), pp.93-112
    Description: We present Part II of a catalogue documenting nonnative vascular plant taxa occurring spontaneously in California beyond those addressed in The Jepson Manual: Higher Plants of California (Hickman 1993). Here we document an additional 117 taxa occurring spontaneously in California that were not accounted for in Part I (Hrusa et al. 2002) or in The Jepson Manual. The catalogue was compiled from new collections by the authors and others, previously existing herbarium specimens, peer-reviewed publications, other printed reports, and direct communications with field botanists. Only reports backed by herbarium vouchers are accepted as adequately documented. Of the 117 taxa, 42 are fully or sparingly naturalized in relatively undisturbed wildland habitats, 14 are naturalized in non-wildlands (roadsides, fallow fields, croplands, other disturbed areas), 13 are tenuously established or locally persisting, 22 are weeds of greenhouse or other horticultural environments, 7 are presumed to be non-persisting casuals (waifs), and for 19 there is no current information. Taxa recorded as already being widely naturalized and/or potentially significant pests include Brachypodium sylvatìcum, Cuscuta japónica, Danthonia decumbens, Glyceria declinata, Juncus usitatus, Melaleuca viminalis, Rytidosperma penicillatum, Verbena incompta and Zostera japonica.
    Keywords: Biological sciences -- Biology -- Botany ; Biological sciences -- Agriculture -- Agricultural sciences ; Biological sciences -- Biology -- Biological taxonomies ; Biological sciences -- Biology -- Biological taxonomies ; Biological sciences -- Agriculture -- Agricultural sciences ; Biological sciences -- Biology -- Botany ; Physical sciences -- Earth sciences -- Geography ; Biological sciences -- Ecology -- Aquatic ecology ; Biological sciences -- Biology -- Botany ; Biological sciences -- Ecology -- Ecological processes
    ISSN: 00249637
    E-ISSN: 19436297
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  • 5
    Language: English
    In: Madroño, 1 April 2002, Vol.49(2), pp.61-98
    Description: A catalogue of 315 non-native vascular plant taxa documented as occurring spontaneously in California beyond those addressed in The Jepson Manual: Higher Plants of California is presented. The catalogue was compiled from new collections by the authors and others, previously existing herbarium specimens, formal publications, other printed reports, and direct communications with field botanists. Only reports backed by herbarium vouchers are accepted as adequately documented. Of the 315 species, 58 are fully or sparingly naturalized in relatively undisturbed wildland habitats, 53 are naturalized in disturbed areas, 34 are tenuously established or locally persisting, 13 are non-escaped weeds of greenhouse or similarly cultivated environments, 43 are presumed to be non-persisting casuals (waifs), for 110 there is no current information or observations available, and 4 have likely been extirpated. In addition, 13 reported taxa are here specifically excluded as based on erroneous information. Taxa highlighted as already being fully naturalized or potential pests are Amaranthus rudis, Brassica fruticulosa, Boehmeria cylindrica, Calystegia silvática subsp. disjuncta, Cabomba caroliniana, Cotoneaster lacteus, Crataegus monogyna, Dittrichia graveolens, Fumaria capreolata, Geranium purpureum, Geranium rotundifolium, Hederá canariensis, Limnobium laevigatum, Maytenus boaria, Pyracantha crenatoserrata, Salvinia molesta, Trifolium tomentosum, and Verbascum olympicum.
    Keywords: Biological sciences -- Biology -- Botany ; Physical sciences -- Earth sciences -- Geography ; Biological sciences -- Biology -- Biological taxonomies ; Applied sciences -- Engineering -- Civil engineering ; Biological sciences -- Agriculture -- Agricultural sciences ; Biological sciences -- Biology -- Botany ; Biological sciences -- Agriculture -- Agricultural sciences ; Biological sciences -- Biology -- Biological taxonomies ; Environmental studies -- Environmental social sciences -- Landscape architecture ; Physical sciences -- Earth sciences -- Geography
    ISSN: 00249637
    E-ISSN: 19436297
    Source: Archival Journals (JSTOR)
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  • 6
    In: The New England Journal of Medicine, 2012, Vol.367(14), pp.1321-1331
    Description: Background Some copy-number variants are associated with genomic disorders with extreme phenotypic heterogeneity. The cause of this variation is unknown, which presents challenges in genetic diagnosis, counseling, and management. Methods We analyzed the genomes of 2312 children known to carry a copy-number variant associated with intellectual disability and congenital abnormalities, using array comparative genomic hybridization. Results Among the affected children, 10.1% carried a second large copy-number variant in addition to the primary genetic lesion. We identified seven genomic disorders, each defined by a specific copy-number variant, in which the affected children were more likely to carry multiple copy-number variants than were controls. We found that syndromic disorders could be distinguished from those with extreme phenotypic heterogeneity on the basis of the total number of copy-number variants and whether the variants are inherited or de novo. Children who carried two large copy-number variants of unknown clinical significance were eight times as likely to have developmental delay as were controls (odds ratio, 8.16; 95% confidence interval, 5.33 to 13.07; P=2.11×10 −38 ). Among affected children, inherited copy-number variants tended to co-occur with a second-site large copy-number variant (Spearman correlation coefficient, 0.66; P〈0.001). Boys were more likely than girls to have disorders of phenotypic heterogeneity (P〈0.001), and mothers were more likely than fathers to transmit second-site copy-number variants to their offspring (P=0.02). Conclusions Multiple, large copy-number variants, including those of unknown pathogenic significance, compound to result in a severe clinical presentation, and secondary copy-number variants are preferentially transmitted from maternal carriers. (Funded by the Simons Foundation Autism Research Initiative and the National Institutes of Health.) Most chromosomal deletions and duplications (copy-number variants) that are associated with neurodevelopmental disorders are known to result in a wide variation of clinical phenotypes. This study describes a genetic mechanism for such variation. Genomic rearrangements are an important source of genetic and phenotypic variation. Rare, recurrent copy-number variants of pathogenic significance, termed genomic disorders, were originally identified in persons with a characteristic set of clinically recognizable features, such as the Smith–Magenis syndrome, the Sotos syndrome, and the Williams–Beuren syndrome. Although unexplained phenotypic variation and differences in severity have long been recognized among patients with the same genomic disorder,1–5 comparatively recent discoveries of potentially pathogenic copy-number variants have broadened the phenotypic range associated with a given variant to include entirely distinct diseases. High-throughput analyses of patient populations have implicated the same copy-number variants . . .
    Keywords: Medicine;
    ISSN: 0028-4793
    E-ISSN: 1533-4406
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  • 7
    In: Molecular Genetics & Genomic Medicine, March 2017, Vol.5(2), pp.122-129
    Description: Genetic testing has multigenerational and familial repercussions, but the “trickle down effects” of testing a family network are poorly understood. Three probands were identified during the pharmacogenetics research phase of eMERGEII (electronic MEdical Record and GEnomics) to have unanticipated variants in genes associated with autosomal dominant disorders determined to be actionable by the American College of Medical Genetics (ACMG) and had additional family members cared for by the same healthcare system. We describe our experience of contacting patients at risk for a familial pathogenic variant in three families and the ramifications for offering genetic testing to extended family members including ethical, legal, and social issues around issues of genetic testing.
    Keywords: Electronic Medical Record And Genomics ; Family Network ; Ldlr ; Ryr 1 ; Scn 5a
    ISSN: 2324-9269
    E-ISSN: 2324-9269
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  • 8
    Language: English
    In: Genome Medicine, July 3, 2015, Vol.7(1)
    Description: Background In an effort to return actionable results from variant data to electronic health records (EHRs), participants in the Electronic Medical Records and Genomics (eMERGE) Network are being sequenced with the targeted Pharmacogenomics Research Network sequence platform (PGRNseq). This cost-effective, highly-scalable, and highly-accurate platform was created to explore rare variation in 84 key pharmacogenetic genes with strong drug phenotype associations. Methods To return Clinical Laboratory Improvement Amendments (CLIA) results to our participants at the Group Health Cooperative, we sequenced the DNA of 900 participants (61 % female) with non-CLIA biobanked samples. We then selected 450 of those to be re-consented, to redraw blood, and ultimately to validate CLIA variants in anticipation of returning the results to the participant and EHR. These 450 were selected using an algorithm we designed to harness data from self-reported race, diagnosis and procedure codes, medical notes, laboratory results, and variant-level bioinformatics to ensure selection of an informative sample. We annotated the multi-sample variant call format by a combination of SeattleSeq and SnpEff tools, with additional custom variables including evidence from ClinVar, OMIM, HGMD, and prior clinical associations. Results We focused our analyses on 27 actionable genes, largely driven by the Clinical Pharmacogenetics Implementation Consortium. We derived a ranking system based on the total number of coding variants per participant (75.2[+ or -]14.7), and the number of coding variants with high or moderate impact (11.5[+ or -]3.9). Notably, we identified 11 stop-gained (1 %) and 519 missense (20 %) variants out of a total of 1785 in these 27 genes. Finally, we prioritized variants to be returned to the EHR with prior clinical evidence of pathogenicity or annotated as stop-gain for the following genes: CACNA1S and RYR1 (malignant hyperthermia); SCN5A, KCNH2, and RYR2 (arrhythmia); and LDLR (high cholesterol). Conclusions The incorporation of genetics into the EHR for clinical decision support is a complex undertaking for many reasons including lack of prior consent for return of results, lack of biospecimens collected in a CLIA environment, and EHR integration. Our study design accounts for these hurdles and is an example of a pilot system that can be utilized before expanding to an entire health system.
    Keywords: Evidence-Based Medicine – Analysis ; Arrhythmia – Genetic Aspects ; Arrhythmia – Analysis ; Medical Records – Analysis ; Electronic Records – Analysis ; Electronic Records – Rankings ; Pharmacogenomics – Analysis ; Biomedical Laboratories – Analysis ; Algorithms – Analysis ; Medical Schools – Analysis
    ISSN: 1756-994X
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  • 9
    Language: English
    In: American journal of human genetics, 05 September 2019, Vol.105(3), pp.526-533
    Description: As clinical testing for Mendelian causes of colorectal cancer (CRC) is largely driven by recognition of family history and early age of onset, the rates of such findings among individuals with prevalent CRC not recognized to have these features is largely unknown. We evaluated actionable genomic findings...
    Keywords: Actionable Variant ; Cancer Risk ; Clinical Sequencing ; Colorectal Cancer ; Genetic Testing ; Incidental Finding ; Panel Sequencing ; Polyp
    ISSN: 00029297
    E-ISSN: 1537-6605
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  • 10
    In: Clinical Pharmacology & Therapeutics, October 2014, Vol.96(4), pp.482-489
    Description: We describe here the design and initial implementation of the eMERGE‐PGx project. eMERGE‐PGx, a partnership of the Electronic Medical Records and Genomics Network and the Pharmacogenomics Research Network, has three objectives: (i) to deploy PGRNseq, a next‐generation sequencing platform assessing sequence variation in 84 proposed pharmacogenes, in nearly 9,000 patients likely to be prescribed drugs of interest in a 1‐ to 3‐year time frame across several clinical sites; (ii) to integrate well‐established clinically validated pharmacogenetic genotypes into the electronic health record with associated clinical decision support and to assess process and clinical outcomes of implementation; and (iii) to develop a repository of pharmacogenetic variants of unknown significance linked to a repository of electronic health record–based clinical phenotype data for ongoing pharmacogenomics discovery. We describe site‐specific project implementation and anticipated products, including genetic variant and phenotype data repositories, novel variant association studies, clinical decision support modules, clinical and process outcomes, approaches to managing incidental findings, and patient and clinician education methods. (2014); 4, 482–489. doi:
    Keywords: Pharmacy, Therapeutics, & Pharmacology;
    ISSN: 0009-9236
    E-ISSN: 1532-6535
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