Fluorinated olefinic peptide nucleic acid: synthesis and pairing properties with complementary DNA

The fluorinated olefinic peptide nucleic acid (F-OPA) system was designed as a peptide nucleic acid (PNA) analogue in which the base carrying amide moiety was replaced by an isostructural and isoelectrostatic fluorinated C-C double bond, locking the nucleobases in one of the two possible rotameric forms. By comparison of the base-pairing properties of this analogue with its nonfluorinated analogue OPA and PNA, we aimed at a closer understanding of the role of this amide function in complementary DNA recognition. Here we present the synthesis of the F-OPA monomer building blocks containing the nucleobases A, T, and G according to the MMTr/Acyl protecting group scheme. Key steps are a selective desymmetrization of the double bond in the monomer precursor via lactonization as well as a highly regioselective Mitsunobu reaction for the introduction of the bases. PNA decamers containing single F-OPA mutations and fully modified F-OPA decamers and pentadecamers containing the bases A and T were synthesized by solid-phase peptide chemistry, and their hybridization properties with complementary parallel and antiparallel DNA were assessed by UV melting curves and CD spectroscopic methods. The stability of the duplexes formed by the decamers containing single (Z)-F-OPA modifications with parallel and antiparallel DNA was found to be strongly dependent on their position in the sequence with T(m) values ranging from +2.4 to -8.1 degrees C/modification as compared to PNA. Fully modified F-OPA decamers and pentadecamers were found to form parallel duplexes with complementary DNA with reduced stability compared to PNA or OPA. An asymmetric F-OPA pentadecamer was found to form a stable self-complex (T(m) approximately 65 degrees C) of unknown structure. The generally reduced affinity to DNA may therefore be due to an increased propensity for self-aggregation

Exploring Hoogsteen and reversed-Hoogsteen duplex and triplex formation with tricyclo-DNA purine sequences

The duplex- and triplex-formation properties of the tricyclo-DNA purine decamer 5'p-gagaaggaaa-3' as a single strand or as part of a hairpin duplex with corresponding parallel and antiparallel pyrimidine DNA and RNA complements, as well as with antiparallel purine DNA and RNA complements, were investigated by UV melting curve analysis, circular dichroism spectroscopy, and gel mobility shift experiments. It was found that tricyclo-DNA forms very stable duplexes with the pyrimidine RNA and DNA complements not only in the Watson-Crick pairing mode, but also in the Hoogsteen one. Below pH 6.0, the tc-DNA/DNA and tc-DNA/RNA Hoogsteen duplexes were found to be more stable than the corresponding Watson-Crick DNA duplexes. Triplexes of the hairpin structure with parallel pyrimidine complements revealed even stronger Hoogsteen pairing relative to the duplexes, presumably due to structural preorganization phenomena. Triplex formation with antiparallel pyrimidine and purine third strands (reversed-Hoogsteen motif) could not be observed and seem to be unstable

The elusive S2 state, the S1/S2 splitting, and the excimer states of the benzene dimer

We observe the weak S 0 → S 2 transitions of the T-shaped benzene dimers (Bz)2 and (Bz-d 6)2 about 250 cm−1 and 220 cm−1 above their respective S 0 → S 1 electronic origins using two-color resonant two-photon ionization spectroscopy. Spin-component scaled (SCS) second-order approximate coupled-cluster (CC2) calculations predict that for the tipped T-shaped geometry, the S 0 → S 2 electronic oscillator strength f el (S 2) is ∼10 times smaller than f el (S 1) and the S 2 state lies ∼240 cm−1 above S 1, in excellent agreement with experiment. The S 0 → S 1 (ππ ∗) transition is mainly localized on the “stem” benzene, with a minor stem → cap charge-transfer contribution; the S 0 → S 2 transition is mainly localized on the “cap” benzene. The orbitals, electronic oscillator strengths f el (S 1) and f el (S 2), and transition frequencies depend strongly on the tipping angle ω between the two Bz moieties. The SCS-CC2 calculated S 1 and S 2 excitation energies at different T-shaped, stacked-parallel and parallel-displaced stationary points of the (Bz)2 ground-state surface allow to construct approximate S 1 and S 2 potential energy surfaces and reveal their relation to the “excimer” states at the stacked-parallel geometry. The f el (S 1) and f el (S 2) transition dipole moments at the C 2v -symmetric T-shape, parallel-displaced and stacked-parallel geometries are either zero or ∼10 times smaller than at the tipped T-shaped geometry. This unusual property of the S 0 → S 1 and S 0 → S 2 transition-dipole moment surfaces of (Bz)2 restricts its observation by electronic spectroscopy to the tipped and tilted T-shaped geometries; the other ground-state geometries are impossible or extremely difficult to observe. The S 0 → S 1/S 2 spectra of (Bz)2 are compared to those of imidazole ⋅ (Bz)2, which has a rigid triangular structure with a tilted (Bz)2 subunit. The S 0 → S 1/ S 2 transitions of imidazole-(benzene)2 lie at similar energies as those of (Bz)2, confirming our assignment of the (Bz)2 S 0 → S 2 transition.

Expanding cities and expanding waistlines: Urban sprawl and its impact on obesity, how the adoption of smart growth statutes can build healthier and more active communities

For decades, American towns and cities have expanded from their established cores into the surrounding rural areas. U.S. population has grown but the land that we use has grown at an even faster pace, and our country has now become a largely suburban nation. Americans moved and continue to move out to the suburbs in search of better lives – for clean and healthy living, for larger homes, and for better resources. In many ways and for many Americans, the suburban lifestyle has been a great success. However, there are some unintended public health consequences of urban sprawl that must be recognized. As most Americans no longer walk or bicycle, increasingly sedentary lifestyles now contribute to greater levels of obesity, diabetes and other associated chronic diseases. This thesis reviewed the impacts of urban sprawl on the public's health specifically, as sprawl relates to decreased physical activity rates and increased obesity rates. The health effects and their connection with sprawl were identified, and available evidence was reviewed. Finally, this thesis described legal and policy solutions for addressing the health effect through improving the design of our built environment and by recommending that governments adopt and implement Smart Growth statutes that incorporate a public health component and require public health involvement. ^

Anisotropy and acoustic properties at DSDP Holes 62-463 and 62-465A

Variations of acoustic properties within the sediment column may significantly affect the propagation of acoustic energy in the upper portion of the oceanic crust. Moreover, the acoustic properties of sediments reflect their mineral compositions, fabrics, and degrees of compaction and cementation. Hence, the physical properties of indurated deep-sea sediments are of considerable geophysical and geological interest. Chalks and limestones are particularly important because substantial accumulations of biogenic carbonates are generally present at the base of the deep-sea sediment column, and high-standing features such as Hess Rise are capped by calcareous deposits. This paper constitutes a preliminary report of the compressional-wave velocities and densities of 31 indurated calcareous sediment samples recovered at DSDP Sites 463 and 465, in the Mid-Pacific Mountains and on Hess Rise, respectively. The sample set includes nine pairs of samples in which velocities were measured parallel and perpendicular to bedding to determine the velocity anisotropy of the sediment. This research is part of an ongoing study of the seismic properties of indurated deep-sea carbonates.

Growth rates and biometric measurements of coccolithophores (Coccolithus pelagicus, Coccolithus braarudii, Emiliania huxleyi) during experiments

Coccolithophores, a diverse group of phytoplankton, make important contributions to pelagic calcite production and export, yet the comparative biogeochemical role of species other than the ubiquitous Emiliania huxleyi is poorly understood. Here we examined the relative importance of E. huxleyi and two Coccolithus species (Coccolithus pelagicus and Coccolithus braarudii), in terms of daily calcite production, by culturing E. huxleyi and Coccolithus in parallel, and comparing growth rates and biometrically determined cellular carbon calcite quotas. Biometric measurements of Coccolithus species, and E. huxleyi cell diameters, were performed using polarised light microscopy. Scanning electron microscopy was used for all other biometric measurements of E. huxleyi.

Seismic velocities and elastic properties of gabbroic rocks from ODP Hole 118-735B

The nearly continuous recovery of 0.5 km of generally fresh, layer 3 gabbroic rocks at Hole 735B, especially near the bottom of the section, presents scientists an unusual opportunity to study the detailed elastic properties of the lower oceanic crust. Extending compressional-wave and density shipboard measurements at room pressure, Vp and Vs were measured at pressures from 20 to 200 MPa using the pulse transmission method. All of the rocks exhibit significant increases in velocity with increasing pressure up to about 150 MPa, a feature attributed to the closing of microcrack porosity. Measured velocities reflect the mineralogical makeup and microstructures acquired during the tectonic history of Hole 735B. Most of the undeformed and unaltered gabbros are approximately 65:35 plagioclase/clinopyroxene rocks plus olivine or oxide minerals, and the observed densities and velocities are fully consistent with the Voigt-Reuss-Hill (VRH) averages of the component minerals and their proportions. Depending on their olivine content, the predominant olivine gabbros at 200 MPa have average Vp = 7.1 ± 0.2 km/s, Vs = 3.9 ± 0.1 km/s, and grain densities of 2.95 ± 0.5 g/cm3. The less abundant iron-titanium (Fe-Ti) oxide gabbros average Vp = 6.75 ± 0.15 km/s, Vs = 3.70 ± 0.1 km/s, and grain densities of 3.22 ± 0.05 g/cm3, reflecting the higher densities and lower velocities of oxide minerals compared to olivine. About 30% of the core is plastically deformed, and the densities and directionally averaged velocities of these shear-zone tectonites are generally consistent with those of the gabbros, their protoliths. Three sets of observations indicate that the shear-zone metagabbros are elastically anisotropic: (1) directional variations in Vp, both vertical and horizontal and with respect to foliation and lineation; (2) discrepancies among Vp values for the horizontal cores and the VRH averages of the component minerals and their mineral proportions, suggesting preferred crystallographic orientations of anisotropic minerals; and (3) variations of Vs of up to 7%, with polarization directions parallel and perpendicular to foliation. Optical inspection of thin sections of the same samples indicates that plagioclase feldspar, clinopyroxene, and amphibole typically display crystallographic-preferred orientations, and this, plus the elastic anisotropy of these minerals, suggests that preferred orientations are responsible for much of the observed anisotropy, particularly at high pressure. Alteration tends to be localized to brittle faults and brecciated zones, and typical alteration minerals are amphibole and secondary plagioclase, which do not significantly change the velocity-density relationships.

Major and trace element data for the Mehmetalan (ME), Mollatopuz (MO), and Alabayir (C) diabase dykes in turkey

The diabases cut across the ophiolites as parallel and variably thick dyke-swarms. Geochemistry of the diabases reveals three distinct groups, including a) supra-subduction zone (SSZ) type, which is characterized by marked Nb-anomaly and normal mid-ocean ridge basalt (N-MORB) like HFSE distribution, b) enriched MORB (E-MORB) type, showing some degree of enrichment relative to N-MORB, c) oceanic-island basalt (OIB) type with characteristic hump-backed trace element patterns, coupled with fractionated REE distribution.

FDI inflows and outflows, intellectual property rights, and productivity growth

Using panel data of 57 countries during the period of 1995-2012, this study investigates the impact of intellectual property rights (IPR) processes on productivity growth. The IPR processes are decomposed into three stages, innovation process, commercialization process, and IPR protection process. Our results suggest that better IPR protection is directly associated with productivity improvement only in developed economies. In addition, the contribution of IPR processes on growth through foreign direct investment (FDI) appears to be very limited. Only FDI inflows in developed countries which help to create a better innovative capability lead to a higher growth. And in connection with FDI outflows, only IPR protection and commercialization processes are proven to improve productivity in the case of developing countries, particularly when the country acts as the investing country.

Lock-free Parallel Dynamic Programming

We show a method for parallelizing top down dynamic programs in a straightforward way by a careful choice of a lock-free shared hash table implementation and randomization of the order in which the dynamic program computes its subproblems. This generic approach is applied to dynamic programs for knapsack, shortest paths, and RNA structure alignment, as well as to a state-of-the-art solution for minimizing the máximum number of open stacks. Experimental results are provided on three different modern multicore architectures which show that this parallelization is effective and reasonably scalable. In particular, we obtain over 10 times speedup for 32 threads on the open stacks problem.

A Novel Scalable Deblocking-Filter Architecture for H.264/AVC and SVC Video Codecs

A highly parallel and scalable Deblocking Filter (DF) hardware architecture for H.264/AVC and SVC video codecs is presented in this paper. The proposed architecture mainly consists on a coarse grain systolic array obtained by replicating a unique and homogeneous Functional Unit (FU), in which a whole Deblocking-Filter unit is implemented. The proposal is also based on a novel macroblock-level parallelization strategy of the filtering algorithm which improves the final performance by exploiting specific data dependences. This way communication overhead is reduced and a more intensive parallelism in comparison with the existing state-of-the-art solutions is obtained. Furthermore, the architecture is completely flexible, since the level of parallelism can be changed, according to the application requirements. The design has been implemented in a Virtex-5 FPGA, and it allows filtering 4CIF (704 × 576 pixels @30 fps) video sequences in real-time at frequencies lower than 10.16 Mhz.

Non-strict independent and-parallelism

This paper presents and develops a generalized concept of Non-Strict Independent And Parallelism (NSIAP). NSIAP extends the applicability of Independent And- Parallelism (IAP) by enlarging the class of goals which are eligible for parallel execution. At the same time it maintains IAP's ability to run non-deterministic goals in parallel and to preserve the computational complexity expected in the execution of the program by the programmer. First, a parallel execution framework is defined and some fundamental correctness results, in the sense of equivalence of solutions with the sequential model, are discussed for this framework. The issue of efficiency is then considered. Two new definitions of NSI are given for the cases of puré and impure goals respectively and efficiency results are provided for programs parallelized under these definitions which include treatment of the case of goal failure: not only is reduction of execution time guaranteed (modulo run-time overheads) in the absence of failure but it is also shown that in the worst case of failure no speed-down will occur. In addition to applying to NSI, these results carry over and complete previous results shown in the context of IAP which did not deal with the case of goal failure. Finally, some practical examples of the application of the NSIAP concept to the parallelization of a set of programs are presented and performance results, showing the advantage of using NSI, are given.

Some techniques for automated, resource-aware distributed and mobile computing in a multi-paradigm programming system

Distributed parallel execution systems speed up applications by splitting tasks into processes whose execution is assigned to different receiving nodes in a high-bandwidth network. On the distributing side, a fundamental problem is grouping and scheduling such tasks such that each one involves sufñcient computational cost when compared to the task creation and communication costs and other such practical overheads. On the receiving side, an important issue is to have some assurance of the correctness and characteristics of the code received and also of the kind of load the particular task is going to pose, which can be specified by means of certificates. In this paper we present in a tutorial way a number of general solutions to these problems, and illustrate them through their implementation in the Ciao multi-paradigm language and program development environment. This system includes facilities for parallel and distributed execution, an assertion language for specifying complex programs properties (including safety and resource-related properties), and compile-time and run-time tools for performing automated parallelization and resource control, as well as certification of programs with resource consumption assurances and efñcient checking of such certificates.

Divided we stand: Parallel distributed stack memory management

We present an overview of the stack-based memory management techniques that we used in our non-deterministic and-parallel Prolog systems: &-Prolog and DASWAM. We believe that the problems associated with non-deterministic and-parallel systems are more general than those encountered in or-parallel and deterministic and-parallel systems, which can be seen as subsets of this more general case. We develop on the previously proposed "marker scheme", lifting some of the restrictions associated with the selection of goals while keeping (virtual) memory consumption down. We also review some of the other problems associated with the stack-based management scheme, such as handling of forward and backward execution, cut, and roll-backs.