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  • 1
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    Algorithms, Vol. 9, Pages 53: Faster Force-Directed Graph Drawing with the Well-Separated Pair Decomposition (2016)
    MDPI Publishing
    Details
    Publication Date: 2016-08-05
    Description: The force-directed paradigm is one of the few generic approaches to drawing graphs. Since force-directed algorithms can be extended easily, they are used frequently. Most of these algorithms are, however, quite slow on large graphs, as they compute a quadratic number of forces in each iteration. We give a new algorithm that takes only O ( m + n log n ) time per iteration when laying out a graph with n vertices and m edges. Our algorithm approximates the true forces using the so-called well-separated pair decomposition. We perform experiments on a large number of graphs and show that we can strongly reduce the runtime, even on graphs with less than a hundred vertices, without a significant influence on the quality of the drawings (in terms of the number of crossings and deviation in edge lengths).
    Electronic ISSN: 1999-4893
    Topics: Computer Science
    Published by MDPI Publishing
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  • 2
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    Nitric acid trihydrate (NAT) in polar stratospheric clouds (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-01-11
    Description: A comprehensive investigation of polar stratospheric clouds was performed on 25 January 2000 with instruments onboard a balloon gondola flown from Kiruna, Sweden. Cloud layers were repeatedly encountered at altitudes between 20 and 24 kilometers over a wide range of atmospheric temperatures (185 to 197 kelvin). Particle composition analysis showed that a large fraction of the cloud layers was composed of nitric acid trihydrate (NAT) particles, containing water and nitric acid at a molar ratio of 3:1; this confirmed that these long-sought solid crystals exist well above ice formation temperatures. The presence of NAT particles enhances the potential for chlorine activation with subsequent ozone destruction in polar regions, particularly in early and late winter.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Voigt, C -- Schreiner, J -- Kohlmann, A -- Zink, P -- Mauersberger, K -- Larsen, N -- Deshler, T -- Kroger, C -- Rosen, J -- Adriani, A -- Cairo, F -- Di Donfrancesco, G -- Viterbini, M -- Ovarlez, J -- Ovarlez, H -- David, C -- Dornbrack, A -- New York, N.Y. -- Science. 2000 Dec 1;290(5497):1756-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Kernphysik, Division of Atmospheric Physics, Post Office Box 103 980, D-69029 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11099412" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Encapsulation of proteins in transparent porous silicate glasses prepared by the sol-gel method (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-02-28
    Description: Novel sol-gel synthetic techniques were used to immobilize copper-zinc superoxide dismutase (CuZnSOD), cytochrome c, and myoglobin (Mb) by encapsulation in stable, optically transparent, porous silica glass matrices under mild conditions such that the biomolecules retained their characteristic reactivities and spectroscopic properties. The resulting glasses allowed transport of small molecules into and out of the glasses at reasonable rates but nevertheless retained the protein molecules within their pores. Chemical reactions of the immobilized proteins could be monitored by means of changes in their visible absorption spectra. Silica glasses containing the immobilized proteins were observed to have similar reactivities and spectroscopic properties to those found for the proteins in solution. For example, encapsulated CuZnSOD was demetallated and remetallated, encapsulated ferricytochrome c was reduced and then reoxidized, and encapsulated met Mb was reduced to deoxy Mb and then reacted either with dioxygen to make oxy Mb or with carbon monoxide to make carbonyl Mb.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ellerby, L M -- Nishida, C R -- Nishida, F -- Yamanaka, S A -- Dunn, B -- Valentine, J S -- Zink, J I -- GM28222/GM/NIGMS NIH HHS/ -- T32 GM08375/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Feb 28;255(5048):1113-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, Los Angeles 90024.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1312257" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cattle ; Cytochrome c Group/chemistry ; Gels ; *Glass ; Horses ; Myoglobin/chemistry ; Proteins/*chemistry ; Solutions ; Spectrum Analysis ; Superoxide Dismutase/chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    A borna virus cDNA encoding a protein recognized by antibodies in humans with behavioral diseases (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-11-30
    Description: Borna disease virus (BDV) causes a rare neurological disease in horses and sheep. The virus has not been classified because neither an infectious particle nor a specific nucleic acid had been identified. To identify the genome of BDV, a subtractive complementary DNA expression library was constructed with polyadenylate-selected RNA from a BDV-infected MDCK cell line. A clone (B8) was isolated that specifically hybridized to RNA isolated from BDV-infected brain tissue and BDV-infected cell lines. This clone hybridized to four BDV-specific positive strand RNAs (10.5, 3.6, 2.1, and 0.85 kilobases) and one negative strand RNA (10.5 kilobases) in BDV-infected rat brain. Nucleotide sequence analysis of the clone suggested that it represented a full-length messenger RNA which contained several open reading frames. In vitro transcription and translation of the clone resulted in the synthesis of the 14- and 24-kilodalton BDV-specific proteins. The 24-kilodalton protein, when translated in vitro from the clone, was recognized by antibodies in the sera of patients (three of seven) with behavioral disorders. This BDV-specific clone will provide the means to isolate the other BDV-specific nucleic acids and to identify the virus responsible for Borna disease. In addition, the significance of BDV or a BDV-related virus as a human pathogen can now be more directly examined.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉VandeWoude, S -- Richt, J A -- Zink, M C -- Rott, R -- Narayan, O -- Clements, J E -- RR00130/RR/NCRR NIH HHS/ -- RR07002/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1990 Nov 30;250(4985):1278-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Colorado State University, Lab Animal Resources, Fort Collins 80532.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2244211" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antibodies, Viral/*blood ; Borna Disease/*microbiology ; Borna disease virus/*genetics/immunology ; Brain/microbiology ; Cloning, Molecular ; DNA/*genetics ; Fluorescent Antibody Technique ; Humans ; Immunoblotting ; Mental Disorders/*microbiology ; Molecular Sequence Data ; Molecular Weight ; Nucleic Acid Hybridization ; RNA, Messenger/analysis/genetics ; RNA, Viral/analysis/genetics ; Rats ; Transcription, Genetic ; Viral Proteins/*genetics/immunology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Advancing translational research (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-03-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bolon, Brad -- Altrock, Bruce -- Barthold, Stephen W -- Baumgarth, Nicole -- Besselsen, David -- Boivin, Gregory -- Boyd, Kelli L -- Brayton, Cory -- Cardiff, Robert D -- Couto, Suzana -- Eaton, Kathryn A -- Foreman, Oded -- Griffey, Stephen M -- La Perle, Krista -- Lairmore, Michael D -- Liu, Chen -- Meyerholz, David K -- Nikitin, Alexander Yu -- Schoeb, Trenton R -- Schwahn, Denise -- Sellers, Rani S -- Sundberg, John P -- Tolwani, Ravi -- Valli, Victor E -- Zink, M Christine -- U01 CA141582/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2011 Mar 25;331(6024):1516-7. doi: 10.1126/science.331.6024.1516-b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21436422" target="_blank"〉PubMed〈/a〉
    Keywords: National Institutes of Health (U.S.)/*organization & administration ; Translational Medical Research/*organization & administration ; United States
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Electrical or photocontrol of the rotary motion of a metallacarborane (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-20
    Description: Rotary motion around a molecular axis has been controlled by simple electron transfer processes and by photoexcitation. The basis of the motion is intramolecular rotation of a carborane cage ligand (7,8-dicarbollide) around a nickel axle. The Ni(III) metallacarborane structure is a transoid sandwich with two pairs of carbon vertices reflected through a center of symmetry, but that of the Ni(IV) species is cisoid. The interconversion of the two provides the basis for controlled, rotational, oscillatory motion. The energies of the Ni(III) and Ni(IV) species are calculated as a function of the rotation angle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hawthorne, M Frederick -- Zink, Jeffrey I -- Skelton, Johnny M -- Bayer, Michael J -- Liu, Chris -- Livshits, Ester -- Baer, Roi -- Neuhauser, Daniel -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1849-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095-1569, USA. mfh@chem.ucla.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15031500" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Neurobiological substrates of dread (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-05-06
    Description: Given the choice of waiting for an adverse outcome or getting it over with quickly, many people choose the latter. Theoretical models of decision-making have assumed that this occurs because there is a cost to waiting-i.e., dread. Using functional magnetic resonance imaging, we measured the neural responses to waiting for a cutaneous electric shock. Some individuals dreaded the outcome so much that, when given a choice, they preferred to receive more voltage rather than wait. Even when no decision was required, these extreme dreaders were distinguishable from those who dreaded mildly by the rate of increase of neural activity in the posterior elements of the cortical pain matrix. This suggests that dread derives, in part, from the attention devoted to the expected physical response and not simply from fear or anxiety. Although these differences were observed during a passive waiting procedure, they correlated with individual behavior in a subsequent choice paradigm, providing evidence for a neurobiological link between the experienced disutility of dread and subsequent decisions about unpleasant outcomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820741/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820741/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berns, Gregory S -- Chappelow, Jonathan -- Cekic, Milos -- Zink, Caroline F -- Pagnoni, Giuseppe -- Martin-Skurski, Megan E -- DA00367/DA/NIDA NIH HHS/ -- DA016434/DA/NIDA NIH HHS/ -- K08 DA000367/DA/NIDA NIH HHS/ -- R01 DA016434/DA/NIDA NIH HHS/ -- New York, N.Y. -- Science. 2006 May 5;312(5774):754-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, 101 Woodruff Circle, Suite 4000, Atlanta, GA 30322, USA. gberns@emory.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16675703" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; *Anxiety ; Brain Mapping ; Cerebral Cortex/*physiology ; Cues ; *Decision Making ; Electroshock ; *Emotions ; *Fear ; Female ; Humans ; Magnetic Resonance Imaging ; Male ; Models, Psychological ; Pain/physiopathology ; Time Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Characterizing mutagenic effects of recombination through a sequence-level genetic map (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Description: 〈p〉Genetic diversity arises from recombination and de novo mutation (DNM). Using a combination of microarray genotype and whole-genome sequence data on parent-child pairs, we identified 4,531,535 crossover recombinations and 200,435 DNMs. The resulting genetic map has a resolution of 682 base pairs. Crossovers exhibit a mutagenic effect, with overrepresentation of DNMs within 1 kilobase of crossovers in males and females. In females, a higher mutation rate is observed up to 40 kilobases from crossovers, particularly for complex crossovers, which increase with maternal age. We identified 35 loci associated with the recombination rate or the location of crossovers, demonstrating extensive genetic control of meiotic recombination, and our results highlight genes linked to the formation of the synaptonemal complex as determinants of crossovers.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    Water, Vol. 8, Pages 161: Development of Ecogeomorphological (EGM) Stream Design and Assessment Tools for the Piedmont of Alabama, USA (2016)
    MDPI Publishing
    In: Water
    Details
    Publication Date: 2016-04-21
    Description: Regional data needed for effective stream restoration include hydraulic geometry relationships (i.e., regional curves) and reference channel morphology parameters. Increasingly ecological conditions are being considered when designing, implementing, and assessing restoration efforts. We provide morphology relationships and associated ecological endpoint curves for reference streams in the Alabama piedmont. Twenty-one reference stream reaches were identified in the Tallapoosa drainage of Alabama, ranging from 0.2 to 242 km2 drainage area. Geomorphic surveys were conducted in each stream to measure riffle cross-sections and longitudinal profiles and related to drainage area to develop regional curves. Fish, crayfish, and benthic macroinvertebrates were collected from each surveyed reach and related to drainage area and geomorphic data to provide associated biological community endpoints. Bankfull channel cross-section area, width, mean depth, and estimated discharge were strongly correlated to watershed drainage area, similar to efforts in other areas of the Piedmont ecoregion. Multiple measures of fish assemblages and crayfish size were strongly predicted by drainage area and geomorphic dimensions. Macroinvertebrates showed no taxonomic and limited functional relationships with drainage area and geomorphic dimension. These tools, which integrate geomorphological and ecological conditions, can result in improved stream evaluations and designs increasing the effectiveness of stream restoration projects.
    Electronic ISSN: 2073-4441
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by MDPI Publishing
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  • 10
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    Ancient genome-wide analyses infer kinship structure in an Early Medieval Alemannic graveyard (2018)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2018-09-06
    Description: From historical and archeological records, it is posited that the European medieval household was a combination of close relatives and recruits. However, this kinship structure has not yet been directly tested at a genomic level on medieval burials. The early 7th century CE burial at Niederstotzingen, discovered in 1962, is the most complete and richest example of Alemannic funerary practice in Germany. Excavations found 13 individuals who were buried with an array of inscribed bridle gear, jewelry, armor, and swords. These artifacts support the view that the individuals had contact with France, northern Italy, and Byzantium. This study analyzed genome-wide sequences recovered from the remains, in tandem with analysis of the archeological context, to reconstruct kinship and the extent of outside contact. Eleven individuals had sufficient DNA preservation to genetically sex them as male and identify nine unique mitochondrial haplotypes and two distinct Y chromosome lineages. Genome-wide analyses were performed on eight individuals to estimate genetic affiliation to modern west Eurasians and genetic kinship at the burial. Five individuals were direct relatives. Three other individuals were not detectably related; two of these showed genomic affinity to southern Europeans. The genetic makeup of the individuals shares no observable pattern with their orientation in the burial or the cultural association of their grave goods, with the five related individuals buried with grave goods associated with three diverse cultural origins. These findings support the idea that not only were kinship and fellowship held in equal regard: Diverse cultural appropriation was practiced among closely related individuals as well.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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