Hollow Heaps

We introduce the hollow heap, a very simple data structure with the same amortized efficiency as the classical Fibonacci heap. All heap operations except delete and delete-min take $O(1)$ time, worst case as well as amortized; delete and delete-min take $O(\log n)$ amortized time on a heap of $n$ items. Hollow heaps are by far the simplest structure to achieve this. Hollow heaps combine two novel ideas: the use of lazy deletion and re-insertion to do decrease-key operations, and the use of a dag (directed acyclic graph) instead of a tree or set of trees to represent a heap. Lazy deletion produces hollow nodes (nodes without items), giving the data structure its name.Comment: 27 pages, 7 figures, preliminary version appeared in ICALP 201

Regioselectivity of Epoxide Ring-Openings via S(N)2 Reactions Under Basic and Acidic Conditions

We have quantum chemically analyzed the ring-opening reaction of the model non-symmetrical epoxide 2,2-dimethyloxirane under basic and acidic conditions using density functional theory at OLYP/TZ2P. For the first time, our combined activation strain and Kohn-Sham molecular orbital analysis approach have revealed the interplay of physical factors that control the regioselectivity of these chemical reactions. Ring-opening under basic conditions occurs in a regime of strong interaction between the nucleophile (OH-) and the epoxide and the interaction is governed by the steric (Pauli) repulsion. The latter steers the attack preferentially towards the sterically less encumbered C-beta. Under acidic conditions, the interaction between the nucleophile (H2O) and the epoxide is weak and, now, the regioselectivity is governed by the activation strain. Protonation of the epoxide induces elongation of the weaker (CH3)(2)C-alpha-O bond, and effectively predistorts the substrate for the attack at the sterically more hindered side, which goes with a less destabilizing overall strain energy. Our quantitative analysis significantly builds on the widely accepted rationales behind the regioselectivity of these ring-opening reactions and provide a concrete framework for understanding these indispensable textbook reactions.Bio-organic Synthesi

Binding of molecules to DNA and other semiflexible polymers

A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers (e.g. DNA) represent an intermediate case between flexible polymers and stiff, rod-like ones, whose association with small molecules was previously studied. The chains are not flexible enough to actively participate in the self-assembly, yet their fluctuations induce long-range attractive interactions between bound molecules. In cases where the binding significantly affects the local chain stiffness, those interactions lead to a very sharp, cooperative association. This scenario is of relevance to the association of DNA with surfactants and compact proteins such as RecA. External tension exerted on the chain is found to significantly modify the binding by suppressing the fluctuation-induced interaction.Comment: 15 pages, 7 figures, RevTex, the published versio

Differences in bioactivity between human insulin and insulin analogues approved for therapeutic use- compilation of reports from the past 20 years

In order to provide comprehensive information on the differences in bioactivity between human insulin and insulin analogues, published in vitro comparisons of human insulin and the rapid acting analogues insulin lispro (Humalog®), insulin aspart ( NovoRapid®), insulin glulisine (Apidra®), and the slow acting analogues insulin glargine (Lantus®), and insulin detemir (Levemir®) were gathered from the past 20 years (except for receptor binding studies). A total of 50 reports were retrieved, with great heterogeneity among study methodology. However, various differences in bioactivity compared to human insulin were obvious (e.g. differences in effects on metabolism, mitogenesis, apoptosis, intracellular signalling, thrombocyte function, protein degradation). Whether or not these differences have clinical bearings (and among which patient populations) remains to be determined

Carbon implications of converting cropland to bioenergy crops or forest for climate mitigation: a global assessment

The potential for climate change mitigation by bioenergy crops and terrestrial carbon sinks has been the object of intensive research in the past decade. There has been much debate about whether energy crops used to offset fossil fuel use, or carbon sequestration in forests, would provide the best climate mitigation benefit. Most current food cropland is unlikely to be used for bioenergy, but in many regions of the world, a proportion of cropland is being abandoned, particularly marginal croplands, and some of this land is now being used for bioenergy. In this study, we assess the consequences of land-use change on cropland. We first identify areas where cropland is so productive that it may never be converted and assess the potential of the remaining cropland to mitigate climate change by identifying which alternative land use provides the best climate benefit: C4 grass bioenergy crops, coppiced woody energy crops or allowing forest regrowth to create a carbon sink. We do not present this as a scenario of land-use change – we simply assess the best option in any given global location should a land-use change occur. To do this, we use global biomass potential studies based on food crop productivity, forest inventory data and dynamic global vegetation models to provide, for the first time, a global comparison of the climate change implications of either deploying bioenergy crops or allowing forest regeneration on current crop land, over a period of 20 years starting in the nominal year of 2000 ad. Globally, the extent of cropland on which conversion to energy crops or forest would result in a net carbon loss, and therefore likely always to remain as cropland, was estimated to be about 420.1 Mha, or 35.6% of the total cropland in Africa, 40.3% in Asia and Russia Federation, 30.8% in Europe-25, 48.4% in North America, 13.7% in South America and 58.5% in Oceania. Fast growing C4 grasses such as Miscanthus and switch-grass cultivars are the bioenergy feedstock with the highest climate mitigation potential. Fast growing C4 grasses such as Miscanthus and switch-grass cultivars provide the best climate mitigation option on ≈485 Mha of cropland worldwide with ~42% of this land characterized by a terrain slope equal or above 20%. If that land-use change did occur, it would displace ≈58.1 Pg fossil fuel C equivalent (Ceq oil). Woody energy crops such as poplar, willow and Eucalyptus species would be the best option on only 2.4% (≈26.3 Mha) of current cropland, and if this land-use change occurred, it would displace ≈0.9 Pg Ceq oil. Allowing cropland to revert to forest would be the best climate mitigation option on ≈17% of current cropland (≈184.5 Mha), and if this land-use change occurred, it would sequester ≈5.8 Pg C in biomass in the 20-year-old forest and ≈2.7 Pg C in soil. This study is spatially explicit, so also serves to identify the regional differences in the efficacy of different climate mitigation options, informing policymakers developing regionally or nationally appropriate mitigation actions

Structural plasticity of single chromatin fibers revealed by torsional manipulation

Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large amount of supercoiling without much change in length. This behavior is quantitatively described by a molecular model of the chromatin 3-D architecture. In this model, we assume the existence of a dynamic equilibrium between three conformations of the nucleosome, which are determined by the crossing status of the entry/exit DNAs (positive, null or negative). Torsional strain, in displacing that equilibrium, extensively reorganizes the fiber architecture. The model explains a number of long-standing topological questions regarding DNA in chromatin, and may provide the ground to better understand the dynamic binding of most chromatin-associated proteins.Comment: 18 pages, 7 figures, Supplementary information available at http://www.nature.com/nsmb/journal/v13/n5/suppinfo/nsmb1087_S1.htm

Clustering of cancer among families of cases with Hodgkin Lymphoma (HL), Multiple Myeloma (MM), Non-Hodgkin's Lymphoma (NHL), Soft Tissue Sarcoma (STS) and control subjects

<p>Abstract</p> <p>Background</p> <p>A positive family history of chronic diseases including cancer can be used as an index of genetic and shared environmental influences. The tumours studied have several putative risk factors in common including occupational exposure to certain pesticides and a positive family history of cancer.</p> <p>Methods</p> <p>We conducted population-based studies of Hodgkin lymphoma (HL), Multiple Myeloma (MM), non-Hodgkin's Lymphoma (NHL), and Soft Tissue Sarcoma (STS) among male incident case and control subjects in six Canadian provinces. The postal questionnaire was used to collect personal demographic data, a medical history, a lifetime occupational history, smoking pattern, and the information on family history of cancer. The family history of cancer was restricted to first degree relatives and included relationship to the index subjects and the types of tumours diagnosed among relatives. The information was collected on 1528 cases (HL (n = 316), MM (n = 342), NHL (n = 513), STS (n = 357)) and 1506 age ± 2 years and province of residence matched control subjects. Conditional logistic regression analyses adjusted for the matching variables were conducted.</p> <p>Results</p> <p>We found that most families were cancer free, and a minority included two or more affected relatives. HL [(OR_adj(95% CI) <b>1.79 (1.33, 2.42)]</b>, MM <b>(1.38(1.07, 1.78))</b>, NHL <b>(1.43 (1.15, 1.77)</b>), and STS cases <b>(1.30(1.00, 1.68)) </b>had higher incidence of cancer if any first degree relative was affected with cancer compared to control families. Constructing mutually exclusive categories combining "family history of cancer" (yes, no) and "pesticide exposure ≥10 hours per year" (yes, no) indicated that a positive family history was important for HL <b>(2.25(1.61, 3.15))</b>, and for the combination of the two exposures increased risk for MM <b>(1.69(1.14,2.51))</b>. Also, a positive family history of cancer both with <b>(1.72 (1.21, 2.45)) </b>and without pesticide exposure <b>(1.43(1.12, 1.83)) </b>increased risk of NHL.</p> <p>Conclusion</p> <p>HL, MM, NHL, and STS cases had higher incidence of cancer if any first degree relative affected with cancer compared to control families. A positive family history of cancer and/or shared environmental exposure to agricultural chemicals play an important role in the development of cancer.</p

Inclusive b decays to wrong sign charmed mesons

The production of wrong sign charmed mesons b → D (s)X, D (s) = (D 0, D +, D s), is studied using the data collected by the DELPHI experiment in the years 1994 and 1995. Charmed mesons in Z → bb events are exclusively reconstructed by searching for the decays D 0 → K -π +, D + → K -π +π + and D s + φπ + → K +K -π +. The wrong sign contribution is extracted by using two discriminant variables: the charge of the b-quark at decay time, estimated from the charges of identified particles, and the momentum of the charmed meson in the rest frame of the b-hadron. The inclusive branching fractions of b-hadrons into wrong sign charm mesons are measured to be: B(b → D 0X) + B(b → D -X) = (9.3 ± 1.7(stat) ± 1.3(syst) ± 0.4(B))%, B(b → D s -X) = (10.1 ± 0.4(B))%, B(b → D s -X) = (10.1 ± 1.0(stat) ± 0.6(syst) ± 2.8(B))% where the first error is statistical, the second and third errors are systematic. © 2003 Published by Elsevier Science B.V.0SCOPUS: ar.jinfo:eu-repo/semantics/publishe