bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystal structure, equation of state and elasticity of phase H (MgSiO4H2) at Earth’s lower mantle pressures
Authors: Tsuchiya Jun , Mookherjee Mainak 
Published: October 2015

AbstractDense hydrous magnesium silicate (DHMS) phases play a crucial role in transporting water in to the Earth’s interior. A newly discovered DHMS, phase H (MgSiO4H2), is stable at Earth’s lower mantle, i.e., at pressures greater than 30 GPa. Here we report the crystal structure and elasticity of phase H and its evolution upon compression. Using first principles simulations, we have explored the relative energetics of the candidate crystal structures with ordered and disordered configurations of magnesium and silicon atoms in the octahedral sites. At conditions relevant to Earth’s lower mantle, it is likely that phase H is able to incorporate a significant amount of aluminum, which may enhance the thermodynamic stability of phase H. The sound wave velocities of phase H are ~2–4% smaller than those of isostructural δ-AlOOH. The shear wave impedance contrast due to the transformation of phase D to a mixture of phase H and stishovite at pressures relevant to the upper part of the lower mantle could partly explain the geophysical observations. The calculated elastic wave velocities and anisotropies indicate that phase H can be a source of significant seismic anisotropy in the lower mantle.
Great influence of geographic isolation on the genetic differentiation of Myriophyllum spicatum under a steep environmental gradient
Authors: Wu Zhigang , Yu Dan , Wang Zhong , Li Xing , Xu Xinwei 
Published: October 2015

AbstractUnderstanding how natural processes affect population genetic structures is an important issue in evolutionary biology. One effective method is to assess the relative importance of environmental and geographical factors in the genetic structure of populations. In this study, we examined the spatial genetic variation of thirteen Myriophyllum spicatum populations from the Qinghai-Tibetan Plateau (QTP) and adjacent highlands (Yunnan-Guizhou Plateau, YGP) by using microsatellite loci and environmental and geographical factors. Bioclim layers, hydrological properties and elevation were considered as environmental variables and reduced by principal component analysis. The genetic isolation by geographic distance (IBD) was tested by Mantel tests and the relative importance of environmental variables on population genetic differentiation was determined by a partial Mantel test and multiple matrix regression with randomization (MMRR). Two genetic clusters corresponding to the QTP and YGP were identified. Both tests and MMRR revealed a significant and strong correlation between genetic divergence and geographic isolation under the influence of environmental heterogeneity at the overall and finer spatial scales. Our findings suggested the dominant role of geography on the evolution of M. spicatum under a steep environmental gradient in the alpine landscape as a result of dispersal limitation and genetic drift.
One-step large-scale deposition of salt-free DNA origami nanostructures
Authors: Linko Veikko , Shen Boxuan , Tapio Kosti , Toppari J. Jussi , Kostiainen Mauri A. , Tuukkanen Sampo 
Published: October 2015

AbstractDNA origami nanostructures have tremendous potential to serve as versatile platforms in self-assembly -based nanofabrication and in highly parallel nanoscale patterning. However, uniform deposition and reliable anchoring of DNA nanostructures often requires specific conditions, such as pre-treatment of the chosen substrate or a fine-tuned salt concentration for the deposition buffer. In addition, currently available deposition techniques are suitable merely for small scales. In this article, we exploit a spray-coating technique in order to resolve the aforementioned issues in the deposition of different 2D and 3D DNA origami nanostructures. We show that purified DNA origamis can be controllably deposited on silicon and glass substrates by the proposed method. The results are verified using either atomic force microscopy or fluorescence microscopy depending on the shape of the DNA origami. DNA origamis are successfully deposited onto untreated substrates with surface coverage of about 4 objects/mm2. Further, the DNA nanostructures maintain their shape even if the salt residues are removed from the DNA origami fabrication buffer after the folding procedure. We believe that the presented one-step spray-coating method will find use in various fields of material sciences, especially in the development of DNA biochips and in the fabrication of metamaterials and plasmonic devices through DNA metallisation.
Inverse relationship between chitobiase and transglycosylation activities of chitinase-D from Serratia proteamaculans revealed by mutational and biophysical analyses
Authors: Madhuprakash Jogi , Bobbili Kishore Babu , Moerschbacher Bruno M. , Singh Tej Pal , Swamy Musti J. , Podile Appa Rao 
Published: October 2015

AbstractSerratia proteamaculans chitinase-D (SpChiD) has a unique combination of hydrolytic and transglycosylation (TG) activities. The TG activity of SpChiD can be used for large-scale production of chito-oligosaccharides (CHOS). The multiple activities (hydrolytic and/or chitobiase activities and TG) of SpChiD appear to be strongly influenced by the substrate-binding cleft. Here, we report the unique property of SpChiD substrate-binding cleft, wherein, the residues Tyr28, Val35 and Thr36 control chitobiase activity and the residues Trp160 and Trp290 are crucial for TG activity. Mutants with reduced (V35G and T36G/F) or no (SpChiDΔ30–42 and Y28A) chitobiase activity produced higher amounts of the quantifiable even-chain TG product with degree of polymerization (DP)-6, indicating that the chitobiase and TG activities are inversely related. In addition to its unprecedented catalytic properties, unlike other chitinases, the single modular SpChiD showed dual unfolding transitions. Ligand-induced thermal stability studies with the catalytically inactive mutant of SpChiD (E153A) showed that the transition temperature increased upon binding of CHOS with DP2–6. Isothermal titration calorimetry experiments revealed the exceptionally high binding affinities for E153A to CHOS with DP2–6. These observations strongly support that the architecture of SpChiD substrate-binding cleft adopted to control chitobiase and TG activities, in addition to usual chitinase-mediated hydrolysis.
Graphene-supported Pd catalyst for highly selective hydrogenation of resorcinol to 1, 3-cyclohexanedione through giant π-conjugate interactions
Authors: Wei Zuojun , Pan Ruofei , Hou Yaxin , Yang Yao , Liu Yingxin 
Published: October 2015

AbstractThe selective hydrogenation of resorcinol (RES) to 1, 3-cyclohexanedione (1,3-CHD) without the addition of alkali is a big challenge. In this article, a novel reduced graphene oxide (rGO) supported Pd catalyst was prepared through co-reduction method, over which we obtained 99.9% of resorcinol conversion and 94.2% of the ever-reported highest 1,3-cyclohexanedione selectivity at 25 °C in only CH2Cl2 solvent. The excellent selectivity was contributed to the strong π-π and p-π interactions between the graphene nanosheet and the benzene ring as well as hydroxyl in RES molecule. The followed adsorption experiment and Raman analysis also showed the existence of aromatic graphite structures in rGO, which exhibited stronger adsorption towards RES than towards 1,3-CHD.
Testicular expression of the Lin28/let-7 system: Hormonal regulation and changes during postnatal maturation and after manipulations of puberty
Authors: Sangiao-Alvarellos S. , Manfredi-Lozano M. , Ruiz-Pino F. , León S. , Morales C. , Cordido F. , Gaytán F. , Pinilla L. , Tena-Sempere M. 
Published: October 2015

AbstractThe Lin28/let-7 system, which includes the RNA-binding proteins, Lin28a/Lin28b and let-7 miRNAs, has emerged as putative regulator of puberty and male gametogenesis; yet, its expression pattern and regulation in postnatal testis remain ill defined. We report herein expression profiles of Lin28 and let-7 members and related mir-145 and mir-132, in rat testis during postnatal maturation and in models of altered puberty and hormonal deregulation. Neonatal expression of Lin28a and Lin28b was low and rose markedly during the infantile period; yet, expression patterns diverged thereafter, with persistently elevated levels only for Lin28b, which peaked at puberty. Let-7a, let-7b, mir-132 and mir-145 showed profiles opposite to Lin28b. In fact, let-7b and mir-145 were abundant in pachytene spermatocytes, but absent in elongating spermatids, where high expression of Lin28b was previously reported. Perturbation of puberty by neonatal estrogenization reverted the Lin28/let-7 expression ratio; expression changes were also detected in other models of delayed puberty, due to early photoperiod or nutritional manipulations. In addition, hypophysectomy or growth hormone (GH) deficiency revealed regulation of this system by gonadotropins and GH. Our data document the expression profiles of the Lin28/let-7 system in rat testis along postnatal/pubertal maturation and their perturbation in models of pubertal and hormonal manipulation.
The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7
Authors: Klähn Stephan , Schaal Christoph , Georg Jens , Baumgartner Desirée , Knippen Gernot , Hagemann Martin , Muro-Pastor Alicia M. , Hess Wolfgang R. 
Published: October 2015

Significance
A key enzyme in inorganic nitrogen assimilation, glutamine synthetase, is the target of multiple regulatory mechanisms. Here we describe the nitrogen stress-induced RNA 4 (NsiR4), a small regulatory RNA that reduces the expression of inactivating factor 7 (IF7), an inhibitory factor of glutamine synthetase in cyanobacteria. The expression of NsiR4 is under positive control through the nitrogen control transcription factor (NtcA). NtcA also induces the transcription of the glutamine synthetase gene and represses the gene encoding IF7. Therefore, NsiR4 is a new player in the NtcA-mediated regulation of nitrogen assimilation, which is important for adaptations to rapid changes in available nitrogen sources and concentrations.
The bar involution for quantum symmetric pairs
Authors: Balagović Martina , Kolb Stefan 
Published: October 2015

We construct a bar involution for quantum symmetric pair coideal subalgebras

B

c

,

s

B_{\mathbf {c},\mathbf {s}}

corresponding to involutive automorphisms of the second kind of symmetrizable Kac-Moody algebras. To this end we give unified presentations of these algebras in terms of generators and relations, extending previous results by G. Letzter and the second-named author. We specify precisely the set of parameters

c

\mathbf {c}

for which such an intrinsic bar involution exists.
Relative Citation Ratio (RCR): A new metric that uses citation rates to measure influence at the article level
Authors: Ian Hutchins B. , Yuan Xin , Anderson James M. , Santangelo George M. 
Published: October 2015

AbstractDespite their recognized limitations, bibliometric assessments of scientific productivity have been widely adopted. We describe here an improved method that makes novel use of the co-citation network of each article to field-normalize the number of citations it has received. The resulting Relative Citation Ratio is article-level and field-independent, and provides an alternative to the invalid practice of using Journal Impact Factors to identify influential papers. To illustrate one application of our method, we analyzed 88,835 articles published between 2003 and 2010, and found that the National Institutes of Health awardees who authored those papers occupy relatively stable positions of influence across all disciplines. We demonstrate that the values generated by this method strongly correlate with the opinions of subject matter experts in biomedical research, and suggest that the same approach should be generally applicable to articles published in all areas of science. A beta version of iCite, our web tool for calculating Relative Citation Ratios of articles listed in PubMed, is available athttps://icite.od.nih.gov.
SiteOut: an online tool to design binding site-free DNA sequences
Authors: Estrada Javier , Ruiz-Herrero Teresa , Scholes Clarissa , Wunderlich Zeba , DePace Angela H. 
Published: October 2015

AbstractDNA-binding proteins control many fundamental biological processes such as transcription, recombination and replication. A major goal is to decipher the role that DNA sequence plays in orchestrating the binding and activity of such regulatory proteins. To address this goal, it is useful to rationally design DNA sequences with desired numbers, affinities and arrangements of protein binding sites. However, removing binding sites from DNA is computationally non-trivial since one risks creating new sites in the process of deleting or moving others. Here we present an online binding site removal tool, SiteOut, that enables users to design arbitrary DNA sequences that entirely lack binding sites for factors of interest. SiteOut can also be used to delete sites from a specific sequence, or to introduce site-free spacers between functional sequences without creating new sites at the junctions. In combination with commercial DNA synthesis services, SiteOut provides a powerful and flexible platform for synthetic projects that interrogate regulatory DNA. Here we describe the algorithm and illustrate the ways in which SiteOut can be used; it is publicly available athttps://depace.med.harvard.edu/siteout/.
RapMap: A Rapid, Sensitive and Accurate Tool for Mapping RNA-seq Reads to Transcriptomes
Authors: Srivastava Avi , Sarkar Hirak , Gupta Nitish , Patro Rob 
Published: October 2015

AbstractMotivation:The alignment of sequencing reads to a transcriptome is a common and important step in many RNA-seq analysis tasks. When aligning RNA-seq reads directly to a transcriptome (as is common in thede novosetting or when a trusted reference annotation is available), care must be taken to report the potentially large number of multi-mapping locations per read. This can pose a substantial computational burden for existing aligners, and can considerably slow downstream analysis.Results:We introduce a novel concept, quasi-mapping, and an efficient algorithm implementing this approach for mapping sequencing reads to a transcriptome. By attempting only to report the potential loci of origin of a sequencing read, and not the base-to-base alignment by which it derives from the reference,RapMap— our tool implementing quasi-mapping— is capable ofmappingsequencing reads to a target transcriptome substantially faster than existing alignment tools. The algorithm we employ to implement quasi-mapping uses several efficient data structures and takes advantage of the special structure of shared sequence prevalent in transcriptomes to rapidly provide highly-accurate mapping information. We demonstrate how quasi-mapping can be successfully applied to the problems of transcript-level quantification from RNA-seq reads and the clustering of contigs fromde novoassembled transcriptomes into biologically-meaningful groups.Availability:RapMapis implemented inC++11and is available as open-source software, under GPL v3, athttps://github.com/COMBINE-lab/RapMap.Contact:rob.patro@cs.stonybrook.edu
Firm characteristics and intellectual capital disclosure in IPO prospectuses
Authors: Alcaniz Leire , Gomez-Bezares Fernando , Ugarte Jose Vicente 
Published: October 2015

PurposeInitial Public Offerings (IPOs) have been studied from different perspectives. The purpose of this paper is to analyse the type of intellectual capital (IC) information provided in the Spanish IPO prospectuses and the characteristics of the firms that go public and supply more information. The paper also compares the results with similar previous studies carried out in different countries.Design/methodology/approachThe database gathers Spanish IPOs from 1996 to 2007 (after which the number of IPOs in Spain plummeted due to the crisis). Content analysis is used to obtain information about IC from the IPO prospectuses and, afterwards, the authors apply different statistical methods to analyse any relation between IC disclosure and firms’ characteristics.FindingsThe paper concludes that the companies that provide more information about IC in IPO prospectuses are high-tech companies, larger firms and those whose previous shareholders do not retain the majority after the IPO.Originality/valueThe authors have created an original database with the Spanish data. Moreover, this is the first study with these characteristics carried out in Spain, and some original conclusions are obtained, such as the importance of retained share percentage by previous shareholders. The authors have developed a statistical methodology suitable for the data. Both, the conclusions and the methodology will be especially useful for markets such as the Latin American ones, which are not as developed as Anglo-Saxon markets.
The country-brand in the wine industry: how important is variety specialization?
Authors: Berríos Rodrigo , Saens Rodrigo 
Published: October 2015

Purpose
The purpose of this paper is to analyze whether or not the reputation of a region/country in the international wine market depends on a region/country’s efforts to specialize in a specific grape variety.

Design/methodology/approach
Data on 19,959 bottles of wine corresponding to six vintages across ten wine producing regions worldwide are used to estimate a hedonic price model that measures consumer valuations of the different wine attributes.

Findings
The results of this study show that although variety specialization has successfully underpinned the reputation of some New World regions, such as the Napa Valley (with its Cabernet Sauvignon) or Oregon (with its Pinot Noir); in others, such as Australia (with its Shiraz), this has not been successful.

Practical implications
Over the last ten years, the exponential growth of Australian bulk wine exports has seriously harmed the reputation of Australian wine. With respect to the Napa Valley wines, price discount received by Australian wines increases between the 1997 and 2007 vintage from 33 to 61 percent. Thus, in order to successfully build a collective reputation of an entrant (New World) country, an institutional framework that mediates differences of interest between the large and small vineyards and, above all, that regulates the free-rider problem in the wine market is required.

Originality/value
This paper empirically illustrates how cooperative (and non-cooperative) behavior between firms can help to build (and to destroy) collective reputation of wines that come from the same region or country.
A decade of supply chain collaboration and directions for future research
Authors: Soosay Claudine Antoinette , Hyland Paul 
Published: October 2015

Purpose– This paper aims to conduct a systematic review of the literature on supply chain collaboration published over a 10-year period from 2005 to 2014. It explores the nature and extent of research undertaken to identify key themes emerging in the field and gaps that need to be addressed.Design/methodology/approach– The authors review a sample of 207 articles from 69 journals, after using an iterative cycle of defining appropriate search keywords, searching the literature and conducting the analysis.Findings– Key themes include the meaning of collaboration; considerations for supply chain collaboration theory; emerging areas in collaboration for sustainability, technology-enabled supply chains and humanitarian supply chains; and the need for a more holistic approach, multi-tier perspectives and research into B2C collaborations.Research limitations/implications– The paper provides discussion and scope for future research into the area which would contribute to the field tremendously.Originality/value– There have been very few reviews in the past on supply chain collaboration, and this is one of the first extensive reviews conducted to address how well the body of knowledge on supply chain collaboration corresponds with our contemporary society.
Foraging and growth responses of cotton armyworm Spodoptera litura to the biophysical characteristics of five cotton varieties
Authors: Amin Md Ruhul , Roy Miltan Chandra , Rahman Md Mahbubar , Miah Md Giashuddin , Kwon Yong Jung , Suh Sang Jae 
Published: October 2015

AbstractThis study investigated the morphological and biochemical characteristics of the CB1, CB3, CB5, CB8 and CB12 cotton varieties and evaluated their effects on third instar larval movement, and body weight of the cotton armyworm Spodoptera litura at different developmental stages. The cotton varieties differed in their plant architecture, branching, stem color and hairiness, leaf color and hairiness, leaf trichome density, flower color, numbers of leaves and bolls per plant, concentrations of protein and starch, and boll length, width and weight. The CB1 and CB3 varieties possessed significantly higher trichome densities, while CB8 produced larger and heavier bolls. Boll bearing was found to be highest in CB1 and lowest in CB8. Biochemical analyses indicated the highest percentage of protein in CB5, and of starch in CB8; concentrations of both were lowest in CB12. Cotton varieties did not affect larval foraging, but their abundance on leaflet, mature and square differed significantly. Analysis of the growth response parameters of S. litura as a result of feeding on the tested varieties revealed that larval instars, pupae and adult moths attained the highest body weight on CB8, followed by CB5, and the lowest weight on CB12. Collectively, the results of this study show that the CB5 and CB8 varieties are favorable host‐plants for cotton armyworms; therefore, these varieties are the least suitable for cultivation.
New insights into desert kites in Armenia: the fringes of the Ararat Depression
Authors: Nadel Dani , Bar‐Oz Guy , Malkinson Dan , Spivak Polina , Langgut Dafna , Porat Naomi , Khechoyan Anna , Nachmias Amnon , Crater‐Gershtein Eli , Katinaa Amir , Bermatov‐Paz Gal , Nahapetyan Samvel , Gasparyan Boris 
Published: October 2015

The Armenian kites are the northernmost known kites in south‐west Asia. In contrast to those in the deserts further south, their research has only recently begun. The Armenian kites are situated at high elevations, mostly between 900 and 1500 m above mean sea level, in steppic conditions whereArtemisiais at present the dominant shrub on the landscape. In our ongoing project we excavated three V‐shaped kites and one enclosure kite. The two kinds are similar in construction details, but they differ in size and location: the former run down into gullies, while the latter were placed on the plateau. SixOSLages suggest terminal Late Bronze Age and Early Iron Age construction dates, while geomorphological considerations and surface artefacts suggest earlier dates. A preliminary palynological study suggests a gradual increase in grazing‐resistant vegetation since the mid‐Holocene, probably reflecting human impact on the natural vegetation through the herding of grazing animals.