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  • Springer  (9)
  • American Association for the Advancement of Science (AAAS)  (4)
  • American Institute of Physics (AIP)  (2)
  • Periodicals Archive Online (PAO)
  • 1995-1999  (15)
  • 1985-1989
  • 1965-1969
  • 1996  (15)
  • 1
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 5626-5646 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Experimentally motivated parameters from a base-pair-level discrete DNA model are averaged to yield parameters for a continuum elastic rod with a curved unstressed shape reflecting the local DNA geometry. The continuum model permits computations with discretization lengths longer than the intrinsic discretization of the base-pair model, and, for this and other reasons, yields an efficient computational formulation. Obtaining continuum stiffnesses is straightforward, but obtaining a continuum unstressed shape is hindered by the "noisy'' small-scale structure and rapid helix twist of the discrete unstressed shape. Filtering of the discrete data and an analytic transformation from the true normal-vector field to a natural (untwisted) frame allows a stable continuum fit. Equilibrium energies of closed rings predicted by the continuum model are found to match the energies of the underlying discrete model to within 0.5%. The model is applied to a set of 11 short DNA molecules (≈ 150 bp) and properly distinguishes their cyclization probabilities (J factors) when compared both to experimental cyclization rates and to Monte Carlo simulations. The continuum model does not include entropic contributions to the free energy. However, because of its rapid and accurate computation of internal energy, the continuum model should, when combined with further work on entropic effects, be a useful method for computing experimental DNA free energies. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Woodbury, NY : American Institute of Physics (AIP)
    Applied Physics Letters 68 (1996), S. 217-219 
    ISSN: 1077-3118
    Source: AIP Digital Archive
    Topics: Physics
    Notes: We present a photoemission investigation of the interface between In and 3, 4, 9, 10 perylenetetracarboxylic dianhydride (PTCDA). The interfacial region is very wide due to an anomalously fast diffusion of In into the organic layer. In also reacts with the anhydride end groups of the molecules. The absence of metal clustering, which permits diffusion, is believed to be due to the ionization of In and ion–ion repulsion in the PTCDA matrix. Finally, the ohmicity of the In/PTCDA contact is attributed to reaction-induced electronic gap states created throughout the wide interfacial region upon formation of the interface. This study provides the first direct correlation between chemistry and electronic properties of a metal contact on an organic molecular semiconductor. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1432-1203
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract We used the fluorescence-assisted mismatch analysis (FAMA) method to screen rapidly the α-galactosidase A gene in patients with Fabry disease in order to identify unknown mutations and help define genotype-phenotype correlations in this X-linked lysosomal storage disorder. Chemical cleavage at mismatches on heteroduplex DNA end-labeled with strand-specific fluorescent dyes, reliably detects sequence changes in DNA fragments of up to 1.5 kb and locates them precisely. Exhaustive scanning of the α-galactosidase gene was accomplished on four polymerase chain reaction-generated amplicons, covering all seven exons, the exon-intron boundaries, and 700 bp of 5′-flanking sequence. Mutations were identified in each of the 15 patients studied from nine unrelated kindreds. Among the seven previously undescribed sequence changes, three are obviously pathogenic because they lead to premature protein termination. The other four, a splice-site mutation and three missense mutations, were the only changes found upon complete scanning of the gene and its promoter. In addition, FAMA also detects female heterozygous carriers more dependably than direct sequencing, and thus provides a valuable diagnostic test. In Fabry disease, this molecular criterion is especially important for genetic counseling since heterozygotes can be asymptomatic and their enzymatic values within the normal range.
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Combinatorica 16 (1996), S. 465-477 
    ISSN: 1439-6912
    Keywords: 05 A 15 ; 05 A 16 ; 05 A 20 ; 60 C 05 ; 41 A 10 ; 68 R
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract It is often required to find the probability of the union of givenn eventsA 1 ,...,A n . The answer is provided, of course, by the inclusion-exclusion formula: Pr(∪A i )=∑ i −∑ i〈j Pr(A i ∩A j )±.... Unfortunately, this formula has exponentially many terms, and only rarely does one manage to carry out the exact calculation. From a computational point of view, finding the probability of the union is an intractable, #P-hard problem, even in very restricted cases. This state of affairs makes it reasonable to seek approximate solutions that are computationally feasible. Attempts to find such approximate solutions have a long history starting already with Boole [1]. A recent step in this direction was taken by Linial and Nisan [4] who sought approximations to the probability of the union, given the probabilities of allj-wise intersections of the events forj=1,...k. The developed a method to approximate Pr(∪A i ), from the above data with an additive error of exp $$( - O(k/\sqrt n ))$$ . In the present article we develop an expression that can be computed in polynomial time, that, given the sums ∑|S|=j Pr(∩ i∈S A i ) forj=1,...k, approximates Pr(∪A i ) with an additive error of exp $$( - \bar \Omega (k^2 /n))$$ . This error is optimal, up to the logarithmic factor implicit in the $$\bar \Omega$$ notation. The problem of enumerating satisfying assignments of a boolean formula in DNF formF=v l m C i is an instance of the general problem that had been extensively studied [7]. HereA i is the set of assignments that satisfyC i , and Pr(∩ i∈S A i )=a S /2n where ∧ i∈S C i is satisfied bya S assignments. Judging from the general results, it is hard to expect a decent approximation ofF's number of satisfying assignments, without knowledge of the numbersa S for, say, all cardinalities $$1 \leqslant |S| \leqslant \sqrt m$$ . Quite surprisingly, already the numbersa S over |S|≤log(n+1)uniquely determine the number of satisfying assignments for F. We point out a connection between our work and the edge-reconstruction conjecture. Finally we discuss other special instances of the problem, e.g., computing permanents of 0,1 matrices, evaluating chromatic polynomials of graphs and for families of events whose VC dimension is bounded.
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Astrophysics and space science 245 (1996), S. iii 
    ISSN: 1572-946X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Mammalian genome 7 (1996), S. 803-809 
    ISSN: 1432-1777
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract. Upstream stimulatory factors (USF/MLTF) belong to the c-myc family of transcription factors. Through binding to target DNA as dimers, the ubiquitous USF proteins regulate a variety of genes. USF proteins are encoded by two genes, USF1 and USF2. Protein sequences of USF1 and 2 are highly homologous across species, suggesting functional conservation. To determine whether the genomic organization was conserved between USF1 and USF2, we isolated the murine USF1 gene and characterized its genomic structure. Both genes are similarly organized in 10 exons spanning over 10 kbp. By the 5′-rapid amplification of cDNA ends and S1 nuclease mapping methods, exon 1 was defined and the transcription initiation sites were mapped. The sequence of 8 kb of the gene, including 1.75 kb of 5′-flanking DNA, was determined. The promoter region is GC rich and lacks a typical TATA or CCAAT element. Strikingly, a comparison of the murine and human untranslated sequences reveals regions that exhibit greater than 73% sequence identity. A genomic alignment of the dimerization and DNA binding domains is presented for five genes of the c-myc family, suggesting a hypothetical common ancestor gene.
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    International journal of peptide research and therapeutics 3 (1996), S. 25-30 
    ISSN: 1573-3904
    Keywords: Secondary structure templates ; Solid-phase synthesis ; Combinatorial libraries ; Vaccines ; Pharmaceuticals
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Nature has used a ‘library approach’ to constructing ligands for specific receptors and enzymes by combining a limited functional diversity of 20 amino acid side chains with a small array of secondary structure motifs — reverse turns, α-helices and β-strands. The dissection of multidomain proteins into small synthetic conformationally restricted components is an important step in the design of low-molecular-weight nonpeptides that mimic the activity of the native protein. Mimetics of critical functional domains might possess beneficial properties with regard to specificity and therapeutic potential compared to the intact proteinaceous species. Combinatorial secondary-structure-templated libraries provide a powerful engine for the development of novel vaccines and pharmaceuticals.
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  • 8
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-10-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kahn, P -- New York, N.Y. -- Science. 1996 Oct 25;274(5287):496-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8928001" target="_blank"〉PubMed〈/a〉
    Keywords: Asthma/genetics ; BRCA2 Protein ; Breast Neoplasms/*genetics ; Diabetes Mellitus, Type 1/genetics ; Female ; *Genes, BRCA1 ; Genetic Counseling ; Genetic Predisposition to Disease ; Genetic Research ; Genetic Services ; *Genetic Testing ; Heterozygote ; Humans ; National Institutes of Health (U.S.) ; Neoplasm Proteins/*genetics ; Ovarian Neoplasms/genetics ; Registries ; Risk Assessment ; Transcription Factors/*genetics ; United States
    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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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-08-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kahn, P -- New York, N.Y. -- Science. 1996 Aug 2;273(5275):570-1.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8701304" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Genome ; Germany ; *Human Genome Project/economics/organization & administration ; Humans ; Research Support as Topic ; *Sequence Analysis, DNA/economics
    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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  • 10
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-03-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kahn, P -- New York, N.Y. -- Science. 1996 Mar 29;271(5257):1798-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8596944" target="_blank"〉PubMed〈/a〉
    Keywords: *Base Sequence ; Genome, Fungal ; *Human Genome Project ; Humans ; *Intellectual Property ; Patents as Topic ; Saccharomyces cerevisiae/genetics ; Sequence Analysis, DNA
    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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