Approximating the Maximum Overlap of Polygons under Translation

Let $P$ and $Q$ be two simple polygons in the plane of total complexity $n$, each of which can be decomposed into at most $k$ convex parts. We present an $(1-\varepsilon)$-approximation algorithm, for finding the translation of $Q$, which maximizes its area of overlap with $P$. Our algorithm runs in $O(c n)$ time, where $c$ is a constant that depends only on $k$ and $\varepsilon$. This suggest that for polygons that are "close" to being convex, the problem can be solved (approximately), in near linear time

The structure of a tetrameric α-carbonic anhydrase from Thermovibrio ammonificans reveals a core formed around intermolecular disulfides that contribute to its thermostability

Carbonic anhydrase enzymes catalyse the reversible hydration of carbon dioxide to bicarbonate. A thermophilic Thermovibrio ammonificans α-carbonic anhydrase (TaCA) has been expressed in Escherichia coli and structurally and biochemically characterized. The crystal structure of TaCA has been determined in its native form and in two complexes with bound inhibitors. The tetrameric enzyme is stabilized by a unique core in the centre of the molecule formed by two intersubunit disulfides and a single lysine residue from each monomer that is involved in intersubunit ionic interactions. The structure of this core protects the intersubunit disulfides from reduction, whereas the conserved intrasubunit disulfides are not formed in the reducing environment of the E. coli host cytosol. When oxidized to mimic the environment of the periplasmic space, TaCA has increased thermostability, retaining 90% activity after incubation at 70°C for 1 h, making it a good candidate for industrial carbon-dioxide capture. The reduction of all TaCA cysteines resulted in dissociation of the tetrameric molecule into monomers with lower activity and reduced thermostability. Unlike other characterized α-carbonic anhydrases, TaCA does not display esterase activity towards p-nitrophenyl acetate, which appears to result from the increased rigidity of its protein scaffold.Statoil ASAUniversity of ExeterBotechnology and Biological Sciences Research Council (BBSRC)Wellcome TrustEUEngineering and Physical Sciences Research Council (EPSRC

Biophysical and enzymatic properties of aminoglycoside adenylyltransferase AadA6 from Pseudomonas aeruginosa

AbstractThe gene coding for the aminoglycoside adenylyltransferase (aadA6) from a clinical isolate of Pseudomonas aeruginosa was cloned and expressed in Escherichia coli strain BL21(DE3)pLysS. The overexpressed enzyme (AadA6, 281 amino-acid residues) and a carboxy-terminal truncated variant molecule ([1-264]AadA6) were purified to near homogeneity and characterized. Light scattering experiments conducted under low ionic strength supported equilibrium between monomeric and homodimeric arrangements of the enzyme subunits. Circular Dichroism spectropolarimetry indicated a close structural relation to adenylate kinases. Both forms modified covalently the aminoglycosides streptomycin and spectinomycin. The enzyme required at least 5mM MgCl2 for normal Michaelis–Menten kinetics. Streptomycin exhibited a strong substrate inhibition effect at 1mM MgCl2. The truncated 17 residues at the C-terminus have little influence on protein folding, whereas they have a positive effect on the enzymic activity and stabilize dimers at high protein concentrations (>100μM). Homology modelling and docking based on known crystal structures yielded models of the central ternary complex of monomeric AadA6 with ATP and streptomycin or spectinomycin

Site 1220

Site 1220 (10°10.600´N, 142°45.503´W; 5218 meters below sea level (mbsl); Fig. F1) forms a southerly component of the 56-Ma transect drilled during Leg 199. It is situated about midway between the Clipperton and Clarion Fracture Zones in typical abyssal hill topography. On the basis of regional magnetic anomalies, we anticipated basement age at Site 1220 to be equivalent to Chron C25n (~56 Ma; Cande et al., 1989), slightly older than at Site 1219. At the outset of drilling at Site 1220, our estimate for total sediment depth was ~225 meters below seafloor (mbsf) (Fig. F2). Based upon a fixed hotspot model (Gripp and Gordon, 1990, for 0- to 5-Ma Pacific hotspot rotation pole; Engebretson et al., 1985, for older poles), Site 1220 should have been located ~3° south of the equator at 56 Ma and in an equatorial position at 40 Ma. Thus, Site 1220 should have been situated underneath the South Equatorial Current in the early Eocene. A nearby piston core (EW9709-13PC) taken during the site survey cruise recovered >16 m of red clay, with the base of the core dated as middle-early Miocene on the basis of radiolarian biostratigraphy (Lyle, 2000). Site 1220 will be used to study equatorial ocean circulation from the late Paleocene through the late Eocene during the early Cenozoic thermal maximum. Sediment records from this site will help to define the calcite compensation depth (CCD) and lysocline during the Paleocene-Eocene and Eocene-Oligocene transitions. In this and other respects, Site 1220 will act as an interesting analog to Site 1218. Both sites are thought to have been located on the equator at ~40 Ma, but the older crustal age anticipated at Site 1220 dictates a greater paleowater depth than for contemporaneous sediments accumulating at Site 1218

Site 1216

Site 1216 (21°27.16´N, 139°28.79´W; 5152 meters below sea level [mbsl]; Fig. F1) is situated in abyssal hill topography south of the Molokai Fracture Zone and two small associated unnamed parasitic fracture zones (Fig. F2). Based on magnetic lineations, Site 1216 appears to be situated on normal ocean crust formed during the C25r magnetic anomaly (~57 Ma; Atwater and Severinghaus, 1989). Site 1216 was chosen for drilling because it is near the thickest section of lower Eocene sediments along the 56-Ma transect, which was based upon the seismic stratigraphy of seismic reflection data acquired on site survey cruise EW9709 during transits between the proposed drill sites (Lyle et al., this volume; Moore et al., 2002). The Cenozoic history of sedimentation in this region was poorly constrained prior to Leg 199, being largely based on two Deep Sea Drilling Project (DSDP) drill sites (40 and 41) and piston core data (EW9709-3PC) from ~1.5° in latitude to the south. Based on data from these drill sites, we expected the sedimentary sequence at Site 1216 to comprise red clays (a mixture of wind-blown dust and authigenic precipitates) overlying a biogenic sediment section composed of an upper middle Eocene radiolarian ooze and lower carbonate ooze deposited when the site was near the ridge crest in the late Paleocene and early Eocene. The broad paleoceanographic objectives of drilling the sedimentary sequence anticipated at Site 1216 are as follows: (1) to help define the shift in the Intertropical Convergence Zone through the Paleogene by following the change in eolian-dust composition and flux through time (red clays) and (2) to help define the latitudinal extent, composition, and mass accumulation of plankton communities in the north equatorial Pacific region thereby constraining ocean circulation patterns and the extent of the equatorial high-productivity belt in the Eocene ocean. Results from Site 1216 will also provide important information to test whether there was significant motion of the Hawaiian hotspot with respect to the Earth's spin axis during the early Cenozoic. At 56 Ma, the backtracked location of Site 1216 based upon a hotspot reference frame (Gripp and Gordon, 1990, for 0- to 5-Ma Pacific hotspot rotation pole; Engebretson et al., 1985, for older poles) is about 9°N, 108°W. If significant hotspot motion or true polar wander occurred since 57 Ma (Petronotis et al., 1994), this drill site could have been much nearer to the equator

Site 1222

Site 1222 (13°48.98´N, 143°53.35´W; 4989 meters below sea level [mbsl]; Fig. F1) forms a south-central component of the 56-Ma transect drilled during Leg 199 and is situated ~2° south of the Clarion Fracture Zone in typical abyssal hill topography. On the basis of regional magnetic anomalies, we anticipated basement age at Site 1222 to be equivalent to Chron C25r or Chron C25n (~56-57 Ma) (Cande et al., 1989), which is slightly older than at Site 1219. At the outset of drilling at Site 1222, our estimate for total sediment thickness was ~115 m (Fig. F2). Based upon a fixed hotspot model (Gripp and Gordon, 1990, for 0- to 5-Ma Pacific hotspot rotation pole; Engebretson et al., 1985, for older poles) Site 1222 should have been located ~1° north of the equator at 56 Ma and ~4°N at 40 Ma. A nearby gravity core (EW9709-17GC), taken during the site survey cruise, recovered >5 m of red clay with a late-middle Miocene age on the basis of radiolarian biostratigraphy (Lyle, 2000). Deep Sea Drilling Project (DSDP) Site 42 located ~4° east of Site 1222, was not drilled to basement but contains a thin sedimentary section (~100 m thick) of upper Oligocene nannofossil ooze through middle Eocene radiolarian nannofossil ooze. In turn, DSDP Site 162 lies ~1° north of DSDP Site 42 and is situated on young crust (49 Ma) that contains ~150 m of clayey radiolarian and nannofossil oozes of early Oligocene-middle Eocene age. Site 1222 will be used to study the position of the Intertropical Convergence Zone in the late Eocene and Oligocene, to sample late Paleocene and early Eocene sediments in the central tropical Pacific Ocean, and to help determine whether or not there has been significant southward movement of the hotspots with respect to the spin axis prior to 40 Ma

Site 1217

Site 1217 (16°52.02´N, 138°06.00´W; 5342 meters below sea level [mbsl]; Fig. F1) is one of seven sites drilled to target upper Paleocene crust along a latitudinal transect during Leg 199 and will be used to investigate paleoceanographic processes in the northern tropical early Eocene Pacific Ocean. Site 1217 is situated ~1° north of the Clarion Fracture Zone on abyssal hill topography typical of the central Pacific. Based on magnetic lineations, basement age at Site 1217 should be in magnetic Anomaly C25r or ~57 Ma (Cande et al., 1989; timescale of Cande and Kent, 1995). The Cenozoic history of sedimentation in this region was poorly constrained prior to Leg 199 drilling because the nearest drill site (Deep Sea Drilling Project [DSDP] Site 162) is situated ~300 km south and west on 48-Ma crust. Based on data from this early rotary-cored hole, magnetic anomaly maps, a shallow-penetration piston core near Site 1217 (EW9709-4PC), and seismic profiling (Fig. F2), we expected the sedimentary sequence at Site 1217 to comprise a relatively thick (25 to 35 m thick) section of red clays overlying a radiolarian ooze and a basal carbonate section with possible chert near basement (estimated total depth ~125-150 meters below seafloor [mbsf]) deposited when the site was near the ridge crest in the late Paleocene and early Eocene. Site 1217 was chosen because it is anticipated to have been located just outside of the equatorial region at 56 Ma, ~5°N, 106°W based upon a fixed hotspot model (Gripp and Gordon, 1990, for 0- to 5-Ma Pacific hotspot rotation pole; Engebretson et al., 1985, for older poles). On the same basis at 40 Ma, the site was located at ~8°N, 111°W. Thus, Site 1217 should help define the paleoceanography of the northern tropical Pacific, in particular locating the ancient North Equatorial Countercurrent (NECC) region. General circulation-model experiments for the early Eocene (see Huber, this volume) suggest that the NECC was a well-developed current during this time period. Other paleoceanographic and paleoclimatic objectives of drilling the sedimentary sequence anticipated at Site 1217 are as follows: (1) to help define the shift in the Intertropical Convergence Zone through the Paleogene by following the change in eolian dust composition and flux through time (red clays); (2) to help constrain the middle-late Eocene calcite compensation depth (CCD); and (3) to sample the Paleocene/Eocene (P/E) boundary, one of the most climatologically critical intervals of Cenozoic time. Recovery of deep-sea sediments from this time interval during Leg 199 is a high priority because the P/E boundary has never before been sampled in the central tropical Pacific Ocean. Results from Site 1217 will also provide important information to test whether there was significant motion of the Hawaiian hotspot, with respect to the Earth's spin axis during the early Cenozoic. At 56 Ma, the backtracked location based upon a hotspot reference frame is ~5°N, 106°W, and at 40 Ma is ~8°N, 106°W. If significant hotspot motion or true polar wander occurred since 57 Ma (Petronotis et al., 1994), this drill site could have been much nearer to the equator

Geochemical analysis of bulk marine sediment by Inductively Coupled Plasma–Atomic Emission Spectroscopy on board the JOIDES Resolution

Geochemical analyses on board the JOIDES Resolution have been enhanced with the addition of a Jobin-Yvon Ultrace inductively coupled plasma-atomic emission spectrometer (ICP-AES) as an upgrade from the previous X-ray fluorescence facility. During Leg 199, we sought to both challenge and utilize the capabilities of the ICP-AES in order to provide an extensive bulk-sediment geochemical database during the cruise. These near real-time analyses were then used to help characterize the recovered sedimentary sequences, calculate mass accumulation rates of the different sedimentary components, and assist with cruise and postcruise sampling requests. The general procedures, sample preparation techniques, and basic protocol for ICP-AES analyses on board ship are outlined by Murray et al. (2000) in Ocean Drilling Program Tech Note, 29. We expand on those concepts and offer suggestions for ICP-AES methodology, calibration by standard reference materials, data reduction procedures, and challenges that are specific to the analysis of bulk-sediment samples. During Leg 199, we employed an extensive bulk-sediment analytical program of ~600 samples of varying lithologies, thereby providing several opportunities for refinement of techniques. We also discuss some difficulties and challenges that were faced and suggest how to alleviate such occurrences for sedimentary chemical analyses during future legs

Steady state solutions of hydrodynamic traffic models

We investigate steady state solutions of hydrodynamic traffic models in the absence of any intrinsic inhomogeneity on roads such as on-ramps. It is shown that typical hydrodynamic models possess seven different types of inhomogeneous steady state solutions. The seven solutions include those that have been reported previously only for microscopic models. The characteristic properties of wide jam such as moving velocity of its spatiotemporal pattern and/or out-flux from wide jam are shown to be uniquely determined and thus independent of initial conditions of dynamic evolution. Topological considerations suggest that all of the solutions should be common to a wide class of traffic models. The results are discussed in connection with the universality conjecture for traffic models. Also the prevalence of the limit-cycle solution in a recent study of a microscopic model is explained in this approach.Comment: 9 pages, 6 figure

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types