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The role of uniaxial strain in armchair, T-graphene nanoribbons (ATGNRs) with symmetric and asymmetric structures is investigated using a nearest-neighbour, tight-binding (TB) model. ATGNRs with structural symmetry and two a sub-lattice structure exhibit Dirac points at zero strain. Application of uniaxial strain to these systems induces multiple Dirac points under compression (up to −20% strain), with the number of these points commensurate with the number of tetra-carbon base-units along the width of the unit cell, accounting also for the mirror symmetry of the structure. Under tensile, uniaxial strain (up to 20% extension), the induced asymmetry in the carbon tetrabond results in the number of Dirac points being reduced, although a minimum number are preserved due to the fundamental mirror-symmetry of the symmetric ATGNR. Asymmetric ATGNRs, which are semiconductors, are shown to have tunable band-gaps that decrease as a function of increasing ribbon width and uniaxial strain. Uniaxial strain induces a single Dirac point at the band edge of these systems under high compression ( $?> > 16%), with the closing of the band gap linked to symmetry-induced perturbations in the structure that override the symmetry-breaking, gap-opening mechanisms. In summary, the TB model shows ATGNRs to have suitable device features for flexible electronics applications, such as band-gap tuning, and for the strain engineering of relativistic properties.

Hydrogen peroxide is a cosubstrate for the oxidative cleavage of saccharidic substrates by copper-containing lytic polysaccharide monooxygenases (LPMOs). The rate of reaction of LPMOs with hydrogen...

This study presents the first stable isotopic and sclerochronological calibration of the bivalve Anomalocardia flexuosa (Linnaeus, 1767) in relation to environmental variables in a subtropical coastal area of southern Brazil. We investigate incremental shell growth patterns and δ18O and δ13C values of modern specimens collected alive from the Laguna Lagoonal System (LLS). Shells of Anomalocardia flexuosa are also one of the main biological components of pre-Columbian archaeological shell mounds and middens distributed along the Brazilian coastline. We therefore selected archaeological specimens from a local late Holocene shell mound (Cabecuda) to compare their stable carbon and oxygen isotope values with those of modern specimens. Shell growth increments, δ18O and δ13C values respond to a complex of environmental conditions, involving, for example, the effects of temperature and salinity. The isotopic information extracted from archaeological specimens from Cabecuda shell midden in the LLS indirectly indicates that environmental conditions during the late Holocene were different from present day. In particular, intra-shell δ18O and δ13C values of archaeological shells reveal a stronger marine influence at 3 ka cal BP, which is in contrast to the seasonal freshwater/seawater balance that currently prevails at the LLS.

© 2015 Elsevier Ltd and INQUA The marine gastropod Conomurex fasciatus (Born 1778) is the main component of thousands of shell middens on the Farasan Islands in the southern Red Sea. The middens date from 6500 to 4500 cal BP and cover the period of increased aridification over the region. No general research on C. fasciatus has been carried out before and basic information about the species is mostly speculative. To test if C. fasciatus shells can be used as a recorder of climate variability, we collected living specimens from the Farasan Islands, in Saudi Arabia, over a 1.5 year period. This area receives almost no precipitation and sea surface salinity is extremely high (38–39 psu), and sea surface temperature (SST) ranges from +26.5 °C to +34.9 °C. Raman spectroscopy results on modern C. fasciatus shell samples show these specimens to be aragonitic. Ground fragments from archaeological C. fasciatus shells used for isotope analyses were also measured by Raman spectroscopy and shown to be well preserved against diagenetic alterations leading to aragonite to calcite transformation. Measured shell-edge δ18O values range from −0.5‰ to −1.7‰. Calculated modern shell edge temperatures from these δ18O values correlate with modern SST measured on site with an error of ±2.4 °C. Two different growth rates occurred in the shells of C. fasciatus. The measurement of growth increments in the lip part of adult specimens indicates a tide-related growth rate of ∼13 mm/year. Sequential δ18O data from juvenile parts of the shell indicates a faster growth rate of ∼90 mm/year. This growth rate and the correlation of δ18O with measured temperatures allows the use of C. fasciatus shell δ18O as a palaeoclimate proxy.

Hydrogen peroxide is a cosubstrate for the oxidative cleavage of saccharidic substrates by copper-containing lytic polysaccharide monooxygenases (LPMOs). The rate of reaction of LPMOs with hydrogen peroxide is high, but it is accompanied by rapid inactivation of the enzymes, presumably through protein oxidation. Herein, we use UV–vis, CD, XAS, EPR, VT/VH-MCD, and resonance Raman spectroscopies, augmented with mass spectrometry and DFT calculations, to show that the product of reaction of an AA9 LPMO with H2O2 at higher pHs is a singlet Cu(II)–tyrosyl radical species, which is inactive for the oxidation of saccharidic substrates. The Cu(II)–tyrosyl radical center entails the formation of significant Cu(II)–(●OTyr) overlap, which in turn requires that the plane of the d(x2–y2) SOMO of the Cu(II) is orientated toward the tyrosyl radical. We propose from the Marcus cross-relation that the active site tyrosine is part of a “hole-hopping” charge-transfer mechanism formed of a pathway of conserved tyrosine and tryptophan residues, which can protect the protein active site from inactivation during uncoupled turnover.

In recent years, considerable attention has been given to assessing the value of investments in cyberinfrastructure (CI). This paper focuses on assessment of value measured in ways other than financial benefits - what might well be termed impact or outcomes. This paper is a companion to a paper presented at the PEARC'19 conference, which focused on methods for assessing financial returns on investment. In this paper we focus on methods for assessing impacts such as effect on publication production, importance of publications, and assistance with major scientific accomplishments as signified by major awards. We in particular focus on the role of humans in the loop - humanware. This includes a brief description of the roles humans play in facilitating use of research cyberinfratructure - including clouds - and then a discussion of how those impacts have been assessed. Our conclusion overall is that there has been more progress in the past very few years in developing methods for the quantitative assessment of financial returns on investment than there has been in assessing non-quantitative impacts. There are a few clear actions that many research institutions could take to start better assessing the non-financial impacts of investment in cyberinfrastructure. However, there is a great need for assessment efforts to turn more attention to the assessment of non-financial benefits of investment in cyberinfrastructure, particularly the benefits of investing in humans and the benefits to humans who are involved in supporting and using cyberinfrastructure, including clouds.

The marine gastropod Conomurex fasciatus (Born 1778) is the main component of thousands of shell middens on the Farasan Islands in the southern Red Sea. The middens date from 6500 to 4500 cal BP and cover the period of increased aridification over the region. No general research on C. fasciatus has been carried out before and basic information about the species is mostly speculative. To test if C. fasciatus shells can be used as a recorder of climate variability, we collected living specimens from the Farasan Islands, in Saudi Arabia, over a 1.5 year period. This area receives almost no precipitation and sea surface salinity is extremely high (38–39 psu), and sea surface temperature (SST) ranges from +26.5 °C to +34.9 °C. Raman spectroscopy results on modern C. fasciatus shell samples show these specimens to be aragonitic. Ground fragments from archaeological C. fasciatus shells used for isotope analyses were also measured by Raman spectroscopy and shown to be well preserved against diagenetic alterations leading to aragonite to calcite transformation. Measured shell-edge δ18O values range from −0.5‰ to −1.7‰. Calculated modern shell edge temperatures from these δ18O values correlate with modern SST measured on site with an error of ±2.4 °C. Two different growth rates occurred in the shells of C. fasciatus. The measurement of growth increments in the lip part of adult specimens indicates a tide-related growth rate of ∼13 mm/year. Sequential δ18O data from juvenile parts of the shell indicates a faster growth rate of ∼90 mm/year. This growth rate and the correlation of δ18O with measured temperatures allows the use of C. fasciatus shell δ18O as a palaeoclimate proxy.

We describe the Open Diffusion Data Derivatives (O3D) repository: an integrated collection of preserved brain data derivatives and processing pipelines, published together using a single digital-object-identifier. The data derivatives were generated using modern diffusion-weighted magnetic resonance imaging data (dMRI) with diverse properties of resolution and signal-to-noise ratio. In addition to the data, we publish all processing pipelines (also referred to as open cloud services). The pipelines utilize modern methods for neuroimaging data processing (diffusion-signal modelling, fiber tracking, tractography evaluation, white matter segmentation, and structural connectome construction). The O3D open services can allow cognitive and clinical neuroscientists to run the connectome mapping algorithms on new, user-uploaded, data. Open source code implementing all O3D services is also provided to allow computational and computer scientists to reuse and extend the processing methods. Publishing both data-derivatives and integrated processing pipeline promotes practices for scientific reproducibility and data upcycling by providing open access to the research assets for utilization by multiple scientific communities., Design Type(s)data integration objective • database creation objectiveMeasurement Type(s)brainTechnology Type(s)magnetic resonance imagingFactor Type(s)Voxel SizeSample Characteristic(s)Homo sapiens • brain Machine-accessible metadata file describing the reported data (ISA-Tab format)

The economics of high performance computing are rapidly changing. Commercial cloud offerings, private research clouds, and pressure on the budgets of institutions of higher education and federally-funded research organizations are all contributing factors. As such, it has become a necessity that all expenses and investments be analyzed and considered carefully. In this paper we will analyze the return on investment (ROI) for three different kinds of cyberinfrastructure resources: the eXtreme Science and Engineering Discovery Environment (XSEDE); the NSF-funded Jetstream cloud system; and the Indiana University (IU) Big Red II supercomputer, funded exclusively by IU for use of the IU community and collaborators. We determined the ROI for these three resources by assigning financial values to services by either comparison with commercially available services, or by surveys of value of these resources to their users. In all three cases, the ROI for these very different types of cyberinfrastructure resources was well greater than 1 - meaning that investors are getting more than $1 in returned value for every $1 invested. While there are many ways to measure the value and impact of investment in cyberinfrastructure resources, we are able to quantify the short-term ROI and show that it is a net positive for campuses and the federal government respectively.

Polyprenol phosphate mannose (PPM) is a lipid-linked sugar donor used by extra-cytoplasmic glycosyl tranferases in bacteria. PPM is synthesized by polyprenol phosphate mannose synthase, Ppm1, and in most Actinobacteria is used as the sugar donor for protein O-mannosyl transferase, Pmt, in protein glycosylation. Ppm1 and Pmt have homologues in yeasts and humans, where they are required for protein O-mannosylation. Actinobacteria also use PPM for lipoglycan biosynthesis. Here we show that ppm1 mutants of Streptomyces coelicolor have increased susceptibility to a number of antibiotics that target cell wall biosynthesis. The pmt mutants also have mildly increased antibiotic susceptibilities, in particular to β-lactams and vancomycin. Despite normal induction of the vancomycin gene cluster, vanSRJKHAX, the pmt and ppm1 mutants remained highly vancomycin sensitive indicating that the mechanism of resistance is blocked post-transcriptionally. Differential RNA expression analysis indicated that catabolic pathways were downregulated and anabolic ones upregulated in the ppm1 mutant compared to the parent or complemented strains. Of note was the increase in expression of fatty acid biosynthetic genes in the ppm1

The role of magnetic asymmetric inhomogeneities in zigzag graphene nanoribbons is studied within the context of a generalised tight-binding model with mean-field Hubbard-U interaction. Perturbing the magnetic strength along one edge of the ribbon and adjusting the ribbonwidth are shown to tune the spin-conductance and magnetic properties as the uniaxial strain is increased. We demonstrate the closing of the spin-dependent conductance gap and spin-selective transmission at the Fermi energy for systems with reduced site-specific magnetism along the top-edge of the ribbon. Quantum mechanisms for achieving tunable spin-conductance as a function of strain are revealed as energy minimisation mechanisms in the model. Such mechanisms may be key in the design of future nanoribbon spintronic devices. (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

A family of spin-switching, inhomogeneous, Hubbard-type systems is proposed consisting of finite chains of nonmagnetic N -atoms separated by a magnetic M -atom spacer. Due to the extended N -atom region, multiple spin-switching events can be activated upon application of an external magnetic field and as a function of the electron filling. Varying the external magnetic field strength enables spin-switching to be triggered by the addition of a single electron. Extended Coulomb interactions are used to produce a greater range of spin-switching signals. The potential to tune the spin-switching as a function of the N/M atom ratio and model parameterization is also demonstrated.

Polyprenol phosphate mannose (PPM) is a lipid-linked sugar donor used by extra-cytoplasmic glycosyl tranferases in bacteria. PPM is synthesiszed by polyprenol phosphate mannose synthase, Ppm1, and in most Actinobacteria is used as the sugar donor for protein O-mannosyl transferase, Pmt, in protein glycosylation. Ppm1 and Pmt have homologues in yeasts and humans, where they are required for protein O-mannosylation. Actinobacteria also use PPM for lipoglycan biosynthesis. Here we show that ppm1 mutants of Streptomyces coelicolor have increased susceptibility to a number of antibiotics that target cell wall biosynthesis. The pmt mutants also have mildly increased antibiotic susceptibilities, in particular to β-lactams and vancomycin. Despite normal induction of the vancomycin gene cluster, vanSRJKHAX, the pmt and ppm1 mutants remained highly vancomycin sensitive indicating that the mechanism of resistance is blocked post-transcriptionally. Differential RNA expression analysis indicated that catabolic pathways were downregulated and anabolic ones upregulated in the ppm1 mutant compared to the parent or complemented strains. Of note was the increase in expression of fatty acid biosynthetic genes in the ppm1- mutant. A change in lipid composition was confirmed using Raman spectroscopy, which showed that the ppm1- mutant had a greater relative proportion of unsaturated fatty acids compared to the parent or the complemented mutant. Taken together, these data suggest that an inability to synthesize PPM (ppm1) and loss of the glycoproteome (pmt- mutant) can detrimentally affect membrane or cell envelope functions leading to loss of intrinsic and, in the case of vancomycin, acquired antibiotic resistance.

The thermal expansion of a synthetic single-crystal sample of magnetite (Fe3O4) in the [111] direction has been investigated for the temperature range of 4.2–300 K using three-terminal capacitance dilatometry. The strain results and corresponding thermal expansion curve show the Verwey transition to be first-order with T v = 120 ± 2 K. At T = 4.2–70 K, the sample shows Invar-like behaviour.

The Hubbard Model has been used to study the local and interfacial magnetic properties of finite inhomogeneous cluster systems. These are generally of the type, NMMMMMN , where N and M , respectively, refer to non-magnetic and magnetic atoms, of a 7-site finite chain. The applicability of the Hartree–Fock (HF) approximation is gauged via direct comparison of the ground state magnetization results derived from exact diagonalization methods. The underlying HF and exact mechanisms are compared as a function of the model parameters, with particular attention being paid to the local and interfacial ( N / M interface) magnetic properties. Regimes, which exhibit favourable comparison between HF and exact results are found. Detailed inspection of the HF prediction is made and general trends established as a function of system size and model parameters.

Shell beads appear to have been one of the earliest examples of personal adornments. Marine shells identified far from the shore evidence long-distance transport and imply networks of exchange and negotiation. However, worked beads lose taxonomic clues to identification, and this may be compounded by taphonomic alteration. Consequently, the significance of this key early artefact may be underestimated. We report the use of bulk amino acid composition of the stable intra-crystalline proteins preserved in shell biominerals and the application of pattern recognition methods to a large dataset (777 samples) to demonstrate that taxonomic identification can be achieved at genus level. Amino acid analyses are fast (

Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize: (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) the first evidence of ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, “red-complex” pathogens, and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental calculus permits the simultaneous investigation of pathogen activity, host immunity, and diet, thereby extending the direct investigation of common diseases into the human evolutionary past.

Ab initio methods are used to study the spin-resolved transport properties of graphene nanoribbons (GNRs) that have both chemical and structural edge disorder. Oxygen edge adsorbates on ideal and protruded ribbons are chosen as representative examples, with the protrusions forming the smallest possible structural disorder consistent with the edge geometry. The impact of the oxygen adsorbate dominates the transport properties of armchair nanoribbons. For zigzag nanoribbons, the transmission properties are markedly affected by the protrusion alone, leading to spin-polarized transport and a smaller perturbation from the oxygen adsorbate. Armchair nanoribbons also exhibit, as a function of their width and the threefold family structure, a repeating pattern related to the existence of the spin polarization and to the variation in the width of the band gap.

An extended tight-binding model that includes up to third-nearest-neighbor hopping and a Hubbard mean-field interaction term is tested against ab initio local spin-density approximation results of band structures for armchair- and zigzag-edged graphene nanoribbons. A single tight-binding parameter set is found to accurately reproduce the ab initio results for both the armchair and zigzag cases. Transport calculations based on the extended tight-binding model faithfully reproduce the results of ab initio transport calculations of graphene nanoribbon-based systems.