bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geochemistry of Lower Jurassic Sandstones of Shemshak Formation, Kerman Basin, Central Iran: Provenance, Source Weathering and Tectonic Setting
Authors: Moosavirad S. M. , Janardhana M. R. , Sethumadhav M. S. , Prakash Narasimha K. N. 
Published: May 2012

Abstract
Lower Jurassic sandstones of Shemshak Formation of Kerman basin, central Iran were analyzed for major and select trace elements to infer their provenance, palaeoweathering of source rocks and tectonic setting. Average modal framework components (Qt: F: L= 67.25: 2.41: 30.48) and chemical composition of the sandstones classify them as litharenites. The sandstones are quartz-rich (∼ 67% quartz; 75.34 wt.% SiO2) and derived from a recycled orogen composed of quartzose sedimentary rocks. Average CIA, PIA and CIW values (69%, 76% and 80%, respectively) indicate moderate to intense chemical weathering of the source material. The inferred index of weathering/alteration is the sum total of intensities of weathering witnessed by the lithocomponents during atleast two cycles of sedimentation involving (1) chemical weathering of the source rocks («ultimate» granodiorite source and «proximal» quartzose sedimentary source), (2) chemical weathering during fluvial transport of the detritus, (3) chemical weathering of the detritus in depocenters, and (4) chemical weathering during diagenesis. Sandstones exhibit moderate maturity and were deposited under humid climatic conditions. Plots of the chemical analyses data on tectonic setting discrimination diagrams indicate active continental margin setting, which is in agreement with the tectonic evolutionary history of the Central Iran during Jurassic period.
Numerical Model of Antecedent Rainfall Effect on Slope Stability at a Hillslope of Weathered Granitic Soil Formation
Authors: Mukhlisin Muhammad , Taha Mohd Raihan 
Published: May 2012

Abstract
Modeling rainwater infiltration in slopes is vital to the analysis of slope failure induced by heavy rainfall. Although the significance of rainwater infiltration in causing landslides is widely recognized, there have been different conclusions as to the relative roles of antecedent rainfall to slope failure. In this study, a numerical model was developed to estimate the effect of antecedent rainfall on an unsaturated slope, the formation of a saturated zone, and the change in slope stability under weak rainfall and rainstorm event. Results showed that under a rainstorm event, slope failure occurred at comparably similar time although the antecedent rainfall drainage periods prior to the major rainfall were different (i.e., 24-h, 48-h and 96-h). However, under weak rainfall condition, differences of the antecedent rainfall drainage periods have significant effect on development of pore-water pressure. A higher initial soil moisture conditions caused faster increase in pore water pressure and thus decreasing the safety factor of the slope eventually increasing likelihood of slope failure.
The electronic spectrum of Si3 I: Triplet D3h system
Authors: Reilly N. J. , Kokkin D. L. , Zhuang X. , Gupta V. , Nagarajan R. , Fortenberry R. C. , Maier J. P. , Steimle T. C. , Stanton J. F. , McCarthy M. C. 
Published: May 2012

We report the measurement of a jet-cooled electronic spectrum of the silicon trimer. Si3 was produced in a pulsed discharge of silane in argon, and the excitation spectrum examined in the 18 000–20 800 cm−1 region. A combination of resonant two-color two-photon ionization (R2C2PI) time-of-flight mass spectroscopy, laser-induced fluorescence/dispersed fluorescence, and equation-of-motion coupled-cluster calculations have been used to establish that the observed spectrum is dominated by the \documentclass[12pt]{minimal}\begin{document}$1\sideset{^{3}}{_{1}^{\prime \prime }}{A}$\end{document}1A1″3 – \documentclass[12pt]{minimal}\begin{document}$\tilde{a}$\end{document}ã \documentclass[12pt]{minimal}\begin{document}$\sideset{^{3}}{_{2}^{\prime }}{A}$\end{document}A2′3 transition of the D3h isomer. The spectrum has an origin transition at 18 600± 4 cm−1 and a short progression in the symmetric stretch with a frequency of ∼445 cm−1, in good agreement with a predicted vertical transition energy of 2.34 eV for excitation to the \documentclass[12pt]{minimal}\begin{document}$1\sideset{^{3}}{_{1}^{\prime \prime }}{A}$\end{document}1A1″3 state, which has a calculated symmetric stretching frequency of 480 cm−1. In addition, a ∼505 cm−1 ground state vibrational frequency determined from sequence bands and dispersed fluorescence is in agreement with an earlier zero-electron kinetic energy study of the lowest D3h state and with theory. A weaker, overlapping band system with a ∼360 cm−1 progression, observed in the same mass channel (m/z = 84) by R2C2PI but under different discharge conditions, is thought to be due to transitions from the (more complicated) singlet C2v ground state (1A1) state of Si3. Evidence of emission to this latter state in the triplet dispersed fluorescence spectra suggests extensive mixing in the excited triplet and singlet manifolds. Prospects for further spectroscopic characterization of the singlet system and direct measurement of the energy separation between the lowest singlet and triplet states are discussed.
Structure of the phage TP901-1 1.8 MDa baseplate suggests an alternative host adhesion mechanism
Authors: Veesler David , Spinelli Silvia , Mahony Jennifer , Lichière Julie , Blangy Stéphanie , Bricogne Gérard , Legrand Pierre , Ortiz-Lombardia Miguel , Campanacci Valérie , van Sinderen Douwe , Cambillau Christian 
Published: May 2012

Phages of the
Caudovirales
order possess a tail that recognizes the host and ensures genome delivery upon infection. The X-ray structure of the approximately 1.8 MDa host adsorption device (baseplate) from the lactococcal phage TP901-1 shows that the receptor-binding proteins are pointing in the direction of the host, suggesting that this organelle is in a conformation ready for host adhesion. This result is in marked contrast with the lactococcal phage p2 situation, whose baseplate is known to undergo huge conformational changes in the presence of Ca
2+
to reach its active state. In vivo infection experiments confirmed these structural observations by demonstrating that Ca
2+
ions are required for host adhesion among p2-like phages (936-species) but have no influence on TP901-1-like phages (P335-species). These data suggest that these two families rely on diverse adhesion strategies which may lead to different signaling for genome release.
Topographical and electrochemical nanoscale imaging of living cells using voltage-switching mode scanning electrochemical microscopy
Authors: Takahashi Yasufumi , Shevchuk Andrew I. , Novak Pavel , Babakinejad Babak , Macpherson Julie , Unwin Patrick R. , Shiku Hitoshi , Gorelik Julia , Klenerman David , Korchev Yuri E. , Matsue Tomokazu 
Published: May 2012

We describe voltage-switching mode scanning electrochemical microscopy (VSM-SECM), in which a single SECM tip electrode was used to acquire high-quality topographical and electrochemical images of living cells simultaneously. This was achieved by switching the applied voltage so as to change the faradaic current from a hindered diffusion feedback signal (for distance control and topographical imaging) to the electrochemical flux measurement of interest. This imaging method is robust, and a single nanoscale SECM electrode, which is simple to produce, is used for both topography and activity measurements. In order to minimize the delay at voltage switching, we used pyrolytic carbon nanoelectrodes with 6.5–100 nm radii that rapidly reached a steady-state current, typically in less than 20 ms for the largest electrodes and faster for smaller electrodes. In addition, these carbon nanoelectrodes are suitable for convoluted cell topography imaging because the RG value (ratio of overall probe diameter to active electrode diameter) is typically in the range of 1.5–3.0. We first evaluated the resolution of constant-current mode topography imaging using carbon nanoelectrodes. Next, we performed VSM-SECM measurements to visualize membrane proteins on A431 cells and to detect neurotransmitters from a PC12 cells. We also combined VSM-SECM with surface confocal microscopy to allow simultaneous fluorescence and topographical imaging. VSM-SECM opens up new opportunities in nanoscale chemical mapping at interfaces, and should find wide application in the physical and biological sciences.
The role of randomised controlled trials in developing an evidence‐base for counselling and psychotherapy
Authors: Cooper Mick , Reeves Andrew 
Published: May 2012

AbstractBackground: Representatives of counselling and person‐centred organisations indicate many of their members feel their profession and orientation is under threat, with counselling services being decommissioned in NHS settings. Aims: To understand the views of key figures in the psychological therapies field (policy makers, researchers and representatives of the counselling community) towards randomised controlled trials (RCTs), and their present and future role in developing the evidence‐base for counselling and psychotherapy. Method: Interviews (phone, Skype or face‐to‐face) were conducted with 24 authorities in the field. Relevant practitioner and academic networks were also contacted and key documents in the field were reviewed. Results: Key figures believe that RCTs will continue to play a decisive role in determining which psychological interventions are recommended and commissioned within the NHS for the foreseeable future. Other methods are seen as having some validity, but are generally considered supplementary to RCTs and not a replacement for them. Discussion: Although many members of the counselling community are critical of RCTs, they are likely to remain the mainstay of commissioning policy for some years to come. This means, in the coming years, members of the counselling community may face difficult choices in how to promote their work, while maintaining their core principles and values.
PyKnot: a PyMOL tool for the discovery and analysis of knots in proteins
Authors: Lua Rhonald C. 
Published: May 2012

Abstract
Summary: Understanding the differences between knotted and unknotted protein structures may offer insights into how proteins fold. To characterize the type of knot in a protein, we have developed PyKnot, a plugin that works seamlessly within the PyMOL molecular viewer and gives quick results including the knot's invariants, crossing numbers and simplified knot projections and backbones. PyKnot may be useful to researchers interested in classifying knots in macromolecules and provides tools for students of biology and chemistry with which to learn topology and macromolecular visualization.
Availability: PyMOL is available at http://www.pymol.org. The PyKnot module and tutorial videos are available at http://youtu.be/p95aif6xqcM.
Contact: rhonald.lua@gmail.com
Efficient RNA pairwise structure comparison by SETTER method
Authors: Hoksza David , Svozil Daniel 
Published: May 2012

AbstractMotivation: Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their 3D structures. Although a structural alignment of short RNAs is achievable in a reasonable amount of time, large structures represent much bigger challenge. However, the growth of the number of large RNAs deposited in the PDB database calls for the development of fast and accurate methods for analyzing their structures, as well as for rapid similarity searches in databases.Results: In this article a novel algorithm for an RNA structural comparison SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) is introduced. SETTER uses a pairwise comparison method based on 3D similarity of the so-called generalized secondary structure units. For each pair of structures, SETTER produces a distance score and an indication of its statistical significance. SETTER can be used both for the structural alignments of structures that are already known to be homologous, as well as for 3D structure similarity searches and functional annotation. The algorithm presented is both accurate and fast and does not impose limits on the size of aligned RNA structures.Availability: The SETTER program, as well as all datasets, is freely available from http://siret.cz/hoksza/projects/setter/.Contact: hoksza@ksi.mff.cuni.cz, or svozild@vscht.czSupplementary information: Supplementary data are available at Bioinformatics online.
A prey-related shift in the abundance of small pelagic fish in eastern Tasmania?
Authors: McLeod David J. , Hobday Alistair J. , Lyle Jeremy M. , Welsford Dirk C. 
Published: May 2012

Abstract
McLeod, D. J., Hobday, A. J., Lyle, J. M., and Welsford, D. C. 2012. A prey-related shift in abundance of small pelagic fish in eastern Tasmania? – ICES Journal of Marine Science, 69: 953–960. Shifts in the relative abundance of small pelagic fish species have signalled a change in the ocean environment in a number of locations. Here we show that the replacement of jack mackerel, Trachurus declivis, with redbait, Emmelichthys nitidus, as the dominant small pelagic species from eastern Tasmania, following a period of high fishing pressure on jack mackerel, is consistent with altered zooplankton communities and long-term climate change. Stomach contents analysis and morphology measurements were conducted on both species to determine if they were functionally equivalent with regard to zooplankton prey. Diet varied between species and with fish size. Krill (Nyctiphanes australis) was consumed by both species, with redbait feeding more heavily on small copepods. The diet overlap and morphometric characteristics indicated that these species are not equivalent with regard to prey and therefore changes in prey availability may have contributed to the observed shifts in relative abundance. The continued poleward extension of the East Australian Current is expected to favour small warm-water copepods; thus, redbait may have an advantage over jack mackerel due to prey preferences. An increase in relative abundance of redbait has decreased effort in surface fisheries and may impact on surface-feeding higher predators in this region.
Abundance, composition, and development of zooplankton in the Subarctic Iceland Sea in 2006, 2007, and 2008
Authors: Gislason Astthor , Silva Teresa 
Published: May 2012

Abstract
Gislason, A., and Silva, T. 2012. Abundance, composition, and development of zooplankton in the Subarctic Iceland Sea in 2006, 2007, and 2008. – ICES Journal of Marine Science, 69: . A large-scale study of zooplankton from surface waters and depth-stratified sampling at selected sites in the Iceland Sea was conducted during the years 2006–2008. The abundance of mesozooplankton was low during winter, when animals were mostly confined to the colder (∼0°C) and deeper (∼200–1000 m) layers, and peaked during late summer (∼11–18 g dry weight m−2, ∼300 000–400 000 ind. m−2), when animals resided mainly above the 50–100-m depth range. Diversity was greatest near the shelf edges and least in the central Iceland Sea. Around 32% of mesozooplankton variability was explained by six variables [longitude, year 2008, temperature, bottom depth, chlorophyll a (Chl a), and salinity]. Three main mesozooplankton communities were identified: (i) an Atlantic community in the east, with Calanus finmarchicus and Pseudocalanus spp. most abundant, (ii) an Arctic community at high latitudes, with large numbers of C. hyperboreus and C. glacialis, and (iii) a community with coastal affinities at lower latitudes, with large numbers of Temora longicornis and Acartia spp. Longitude and Chl a explained ∼43% of macrozooplankton variability (euphausiids and amphipods). Results show that the region is a meeting place of Arctic and Atlantic species, with the copepods C. finmarchicus and C. hyperboreus, the amphipod Themisto abyssorum, and the euphausiid Thysanoessa longicaudata the key players.
Interannual changes in zooplankton on the West Spitsbergen Shelf in relation to hydrography and their consequences for the diet of planktivorous seabirds
Authors: Kwasniewski Slawomir , Gluchowska Marta , Walkusz Wojciech , Karnovsky Nina J. , Jakubas Dariusz , Wojczulanis-Jakubas Katarzyna , Harding Ann M. A. , Goszczko Ilona , Cisek Malgorzata , Beszczynska-Möller Agnieszka , Walczowski Waldemar , Weslawski Jan M. , Stempniewicz Lech 
Published: May 2012

AbstractKwasniewski, S., Gluchowska, M., Walkusz, W., Karnovsky, N. J., Jakubas, D., Wojczulanis-Jakubas, K., Harding, A. M. A., Goszczko, I., Cisek, M., Beszczynska-Möller, A., Walczowski, W., Weslawski, J. M., and Stempniewicz, L. 2012. Interannual changes in zooplankton on the West Spitsbergen Shelf in relation to hydrography and their consequences for the diet of planktivorous seabirds. – ICES Journal of Marine Science, 69: 890–901. The purpose of the work was to determine how atmospheric and oceanic processes (the North Atlantic Oscillation (NAO) and the Arctic Ocean Oscillation (AOO)) influence hydrography and zooplankton on the West Spitsbergen Shelf (WSS), and the impacts of the processes on chick meals of zooplanktivorous little auks Alle alle. There were distinct Atlantic and Arctic oceanographic domains on the shelf resulting from the presence of the West Spitsbergen Current and the Sørkapp Current, which contain different proportions of Calanus finmarchicus and C. glacialis. The abundance of warm- and cold-water species varied as a result of an interplay between processes in the atmosphere and ocean. In the Arctic domain, on which the study focused, the NAO impacted oceanography, zooplankton, and consequently little auk chick meals, with time-lags of 4–7 years. The diet of little auk chicks was more energy-rich when C. glacialis stage 5 in the Arctic community were more easily available. To date, the changes in zooplankton abundance on the WSS have not posed a threat to the ability of little auks to feed their chicks lipid-rich Arctic copepods.
Half a century of decadal symposia by NAFO and ICES
Authors: Mälkki Pentti 
Published: May 2012

Abstract
Mälkki, P. 2012. Half a century of decadal symposia by NAFO and ICES – ICES Journal of Marine Science, 69: 703–705. During the establishment of ICES, it was stated “that in all researches, whether hydrographical or biological … it be recognized as a primary object to estimate the quantity of fish available for the use of man, to record the variations in its amount from place to place and from time to time, to ascribe natural variations to their natural causes, and to determine whether or how far variations in the available stock are caused by the operation of man.” ICES addressed these obligations, among others, by publishing annual volumes of Annales Biologiques, a series terminated in 1987, and in 1988 replaced by symposia on decadal variability of hydrobiological conditions. A corresponding series was started by ICNAF (later NAFO) in 1964. A brief summary of these events is presented and a comparison made of the two series.
Regional-scale benthic monitoring for ecosystem-based fisheries management (EBFM) using an autonomous underwater vehicle (AUV)
Authors: Smale Dan A. , Kendrick Gary A. , Harvey Euan S. , Langlois Timothy J. , Hovey Renae K. , Van Niel Kimberly P. , Waddington Kris I. , Bellchambers Lynda M. , Pember Matthew B. , Babcock Russ C. , Vanderklift Mathew A. , Thomson Damian P. , Jakuba Michael V. , Pizarro Oscar , Williams Stefan B. 
Published: May 2012

Abstract
Smale, D. A., Kendrick, G. A., Harvey, E. S., Langlois, T. J., Hovey, R. K., Van Niel, K. P., Waddington, K. I., Bellchambers, L. M., Pember, M. B., Babcock, R. C., Vanderklift, M. A., Thomson, D. P., Jakuba, M. V., Pizarro, O., and Williams, S. B. 2012. Regional-scale benthic monitoring for ecosystem-based fisheries management (EBFM) using an autonomous underwater vehicle (AUV). – ICES Journal of Marine Science, 69: 1108–1118. Monitoring marine habitats and biodiversity is critical for understanding ecological processes, conserving natural resources, and achieving ecosystem-based fisheries management (EBFM). Here, we describe the application of autonomous underwater vehicle (AUV) technology to conduct ongoing monitoring of benthic habitats at two key locations in Western Australia. Benthic assemblages on rocky reefs were sampled with an AUV, which captured >200 000 geo-referenced images. Surveys were designed to obtain 100% coverage of 25 × 25 m patches of benthic habitat. In 2010, multiple patches were surveyed at 15–40-m depths at three reference sites at the Houtman Abrolhos Islands and at six reference sites at Rottnest Island. The following year, repeat surveys of the same geo-referenced patches were conducted. Benthic assemblages at the Houtman Abrolhos Islands were varied in that one reference site was dominated by hard corals, whereas the other two were macroalgae dominated. Conversely, assemblages at Rottnest Island were dominated by the kelp Ecklonia radiata. The AUV resurveyed each patch with high precision and demonstrated adequate power to detect change. Repeated observations at the reference sites will track natural variability in benthic habitat structure, which in turn will facilitate the detection of ecological change and ultimately feed back into EBFM processes.
Treatment With Pamidronate for Osteoporosis Complicating Long‐term Intestinal Failure
Authors: Pastore S. , Londero M. , Barbieri F. , Di Leo G. , Paparazzo R. , Ventura A. 
Published: May 2012

ABSTRACTLong‐term home parenteral nutrition (PN) is a potential risk for developing osteoporosis. Various attempts have been made to treat bone disease both by modifying the composition of PN and by administering hormones, such as calcitonin, parathyroid hormone, and sexual hormones. Bisphosphonates are recognized as a medication useful for the treatment of several bone disorders associated with excessive reabsorption. Nevertheless, there have been no paediatric studies on bisphosphonates use for intestinal failure–associated bone disease. Our study includes 6 paediatric patients receiving extremely long‐term home PN (at least 3 years) who showed radiological and clinical signs of osteoporosis. Diagnosis of bone disease was made after a median period of 127.5 PN months. Treatment consisted in 2 cycles of intravenous pamidronate, 30 mg/m2 once per month for 6 months consecutively. They all showed a significant improvement in bone mineral density, evaluated after 6 and 12 months of pamidronate treatment. In our sample anthropometrical variables (weight, height, and body mass index) are not related with the z‐score trend. Our patients had normal levels of calcium, phosphorus, and vitamin D, and proper nutrient intake. At the last follow‐up, dual‐energy x‐ray absorptiometry scan showed that no patients had a z‐score lower than −2.5; moreover, nobody developed bone fractures during the 108‐month follow‐up. The patients did not have any prominent adverse effect. Finally, in our experience, pamidronate is effective for improving bone mineral density and safe in patients with intestinal failure–associated bone disease.