bluuebunny/crossref_metadata_2025 huggingface dataset:
Atom probe microscopy of zinc isotopic enrichment in ZnO nanorods
Authors: Ironside C. N. , Saxey D. W. , Rickard W. D. A. , Gray C. , McGlynn E. , Reddy S. M. , Marks N. A.
Published: February 2017

We report on atomic probe microscopy (APM) of isotopically enriched ZnO nanorods that measures the spatial distribution of zinc isotopes in sections of ZnO nanorods for natural abundance natZnO and 64Zn and 66Zn enriched ZnO nanorods. The results demonstrate that APM can accurately quantify isotopic abundances within these nanoscale structures. Therefore the atom probe microscope is a useful tool for characterizing Zn isotopic heterostructures in ZnO. Isotopic heterostructures have been proposed for controlling thermal conductivity and also, combined with neutron transmutation doping, they could be key to a novel technology for producing p-n junctions in ZnO thin films and nanorods.
Half-metallic magnetism in Ti3Co5-xFexB2
Authors: Pathak Rohit , Ahamed Imran , Zhang W. Y. , Vallopilly Shah , Sellmyer D. J. , Skomski Ralph , Kashyap Arti
Published: February 2017

Bulk alloys and thin films of Fe-substituted Ti3Co5B2 have been investigated by first-principle density-functional calculations. The series, which is of interest in the context of alnico magnetism and spin electronics, has been experimentally realized in nanostructures but not in the bulk. Our bulk calculations predict paramagnetism for Ti3Co5B2, Ti3Co4FeB2 and Ti3CoFe4B2, whereas Ti3Fe5B2 is predicted to be ferromagnetic. The thin films are all ferromagnetic, indicating that moment formation may be facilitated at nanostructural grain boundaries. One member of the thin-film series, namely Ti3CoFe4B2, is half-metallic and exhibits perpendicular easy-axis magnetic anisotropy. The half-metallicity reflects the hybridization of the Ti, Fe and Co 3d orbitals, which causes a band gap in minority spin channel, and the limited equilibrium solubility of Fe in bulk Ti3Co5B2 may be linked to the emerging half-metallicity due to Fe substitution.
Shell-ferromagnetism in a Ni-Mn-In off-stoichiometric Heusler studied by ferromagnetic resonance
Authors: Scheibel Franziska , Spoddig Detlef , Meckenstock Ralf , Çakır Aslı , Farle Michael , Acet Mehmet
Published: February 2017

Next to the multifunctional properties of Ni-Mn-based Heusler alloys new functionalities related to shell-ferromagnetism are emerging. To understand in more detail the properties of shell-ferromagnetism we examine a decomposed Ni50.0Mn45.1In4.9 off-stoichiometric compound using magnetic resonance techniques which provides details on magnetic interactions. We find that the ferromagnetic resonance profile of the shell-ferromagnetic state is symmetric for positive and negative fields and is independent of the direction of the field-sweep except for the hysteresis observed at small fields.
Vortex spin-torque oscillator stabilized by phase locked loop using integrated circuits
Authors: Kreissig Martin , Lebrun R. , Protze F. , Merazzo K. J. , Hem J. , Vila L. , Ferreira R. , Cyrille M. C. , Ellinger F. , Cros V. , Ebels U. , Bortolotti P.
Published: February 2017

Spin-torque nano-oscillators (STO) are candidates for the next technological implementation of spintronic devices in commercial electronic systems. For use in microwave applications, improving the noise figures by efficient control of their phase dynamics is a mandatory requirement. In order to achieve this, we developed a compact phase locked loop (PLL) based on custom integrated circuits (ICs) and demonstrate that it represents an efficient way to reduce the phase noise level of a vortex based STO. The advantage of our approach to phase stabilize STOs is that our compact system is highly reconfigurable e.g. in terms of the frequency divider ratio N, RF gain and loop gain. This makes it robust against device to device variations and at the same time compatible with a large range of STOs. Moreover, by taking advantage of the natural highly non-isochronous nature of the STO, the STO frequency can be easily controlled by e.g. changing the divider ratio N.
Soilborne root disease pathogen complexes drive widespread decline of subterranean clover pastures across diverse climatic zones
Authors: Foster Kevin , You Ming Pei , Nietschke Brett , Edwards Nick , Barbetti Martin J.
Published: February 2017

Subterranean clover (Trifolium subterraneum L.) is an important pasture legume in many regions of Australia, and elsewhere. A survey was undertaken in 2014 to define the levels of soilborne disease and associated pathogens in annual subterranean clover pastures across southern Australia. Most of the 202 samples processed had very severe levels of taproot rot disease (disease index 60–80%) and extremely severe lateral root rot disease (disease index 80–100%). A complex of soilborne root pathogens including Aphanomyces trifolii, Phytophthora clandestina, and one or more of Pythium, Rhizoctonia and Fusarium spp. was found responsible for severe pre- and post-emergence damping-off and root disease. This is the first study to highlight the high incidence of A. trifolii across southern Australian pastures and the first to highlight the existence of natural synergistic associations in the field between Rhizoctonia and Pythium spp., Pythium and Fusarium spp., Pythium spp. and A. trifolii, and P. clandestina and A. trifolii. Nodulation was generally poor, mainly only in the 20–40% nodulation index range. There was no relationship between rainfall zone and tap or lateral root disease level, with root disease equally severe in lower (330 mm) and higher (1000 mm) rainfall zones. This dispels the previous belief that severe root disease in subterranean clover is an issue only in higher rainfall zones. Although overall the relationship between tap and lateral root disease was relatively weak, these two root-disease components were strongly positively expressed within each pathogen’s presence grouping, providing explanation for variability in this relationship across different field situations where soilborne root disease is a major problem. Most producers underestimated the levels and effect of root disease in their pastures. This study established that tap and lateral root diseases are widespread and severe, having devastating impact on the feed gap during autumn–early winter across southern Australia. Severe root disease was independent of the highly variable complex of soilborne pathogens associated with diseased roots, geographic location and rainfall zone. It is evident that soilborne root diseases are the primary factor responsible for widespread decline in subterranean clover productivity of pastures across southern Australia. Implications for disease management and options for extension are discussed.
The microhabitat preferences of Trichoptera in rivers in north-western Spain
Authors: Álvarez-Troncoso Romina , Benetti Cesar João , Sarr Amadou Babacar , Garrido Josefina
Published: February 2017

We analysed the microhabitat preferences of caddisfly species in four rivers in north-western Spain. In each river, we sampled five sites with different types of substrate. These sites were characterised in situ according to the predominant material type (macrophytes, moss, pebbles and sand). A one-way ANOVA was used to test for significant differences in species abundance among substrates, and a nested ANOVA was used to test for significant differences in physical and chemical variables among rivers and sampling sites. A similarity percentage-species contribution analysis was performed to estimate the contribution of each species to the characterisation of each substrate. We observed significant differences in the abundance of seven species (Drusus bolivari, Glossosoma privatum, Larcasia partita, Micrasema longulum, M. servatum, M. gr. moestum and Sericostoma sp.) among substrates, confirming that these species have substrate preferences. According to similarity percentage-species contribution, the species that contributed most to differences were as follows: for sand, Sericostoma sp.; for macrophytes, Rhyacophila adjuncta, Hydropsyche ambigua, Sericostoma sp.; for moss, Micrasema gr. moestum, M. servatum, M. longulum, Hydropsyche tibialis and R. adjuncta; and for pebbles, Sericostoma sp., Larcasia partita and H. tibialis. These preferences can be explained by the fact that different species use different materials from the substrate to build their cases and also as a source of stability, protection and food.
'I'm not sure it paints an honest picture of where my health's at' – identifying community health and research priorities based on health assessments within an Aboriginal and Torres Strait Islander community: a qualitative study
Authors: Spurling Geoffrey K. , Bond Chelsea J. , Schluter Philip J. , Kirk Corey I. , Askew Deborah A.
Published: February 2017

Aboriginal and Torres Strait Islander health assessments are conducted annually in Australian primary care to detect risk factors, chronic diseases and implement preventive health measures. At the Inala Indigenous Health Service, health assessment data have also been used for research purposes. This research has been investigator-driven, which risks misinterpreting or ignoring community priorities compared with community-led research. The objective of this research was to learn about the Aboriginal and Torres Strait Islander community’s health priorities that could be translated into research themes, and investigate these using health assessment data. A thematic analysis of data was conducted from 21 semi-structured interviews with purposively selected key informants from an urban Aboriginal and Torres Strait Islander community. Key informants articulated an authoritative understanding of how interrelated, inter-generational, social, cultural and environmental determinants operated in a ‘cycle’ to influence the community’s health. Key informant views supported the inclusion of these determinants in health assessments, reinforced the importance of comprehensive primary healthcare and strengthened referral pathways to community resources. Some key informants were ambivalent about Aboriginal and Torres Strait Islander health assessments because of their biomedical emphasis. This research also revealed limitations of health assessment-based research and the biomedical emphasis of the health system more broadly.
2020, sexually transmissible infections and HIV in gay, bisexual and other men who have sex with men
Authors: Fairley Christopher K. , Prestage Garett , Bernstein Kyle , Mayer Kenneth , Gilbert Mark
Published: February 2017

This editorial accompanies a series of papers dealing with this watershed period for HIV and sexually transmissible infections (STI) infections in gay, bisexual and other men who have sex with men (GBM). We are delighted to share with you the views of some international opinion leaders on what the future may hold and what challenges lie ahead. In this issue of the Journal, authors describe current HIV and STI incidence among GBM and predict the future.
H3K4me3 induces allosteric conformational changes in the DNA-binding and catalytic regions of the V(D)J recombinase
Authors: Bettridge John , Na Chan Hyun , Pandey Akhilesh , Desiderio Stephen
Published: February 2017

Significance

Accessibility of antigen receptor gene segments to recombination-activating gene (RAG), the V(D)J recombinase, is correlated with marks of active chromatin. One mark, histone H3 at lysine 4 (H3K4me3), binds to a plant homeodomain (PHD) in the RAG-2 subunit; mutations that abolish binding of the PHD to H3K4me3 also impair V(D)J recombination. Engagement of H3K4me3 by RAG-2 enhances substrate binding and catalysis, which are functions of RAG-1. We show that H3K4me3 acts through the PHD to induce conformational changes in an autoinhibitory domain residing within RAG-2 as well as in substrate-binding and catalytic regions of RAG-1. Our data suggest that H3K4me3 promotes displacement of the autoinhibitory domain as well as concomitant conformational alterations in RAG-1 that favor increased substrate affinity and catalytic rate.
A statics-dynamics equivalence through the fluctuation–dissipation ratio provides a window into the spin-glass phase from nonequilibrium measurements
Authors: Baity-Jesi Marco , Calore Enrico , Cruz Andres , Fernandez Luis Antonio , Gil-Narvión José Miguel , Gordillo-Guerrero Antonio , Iñiguez David , Maiorano Andrea , Marinari Enzo , Martin-Mayor Victor , Monforte-Garcia Jorge , Muñoz Sudupe Antonio , Navarro Denis , Parisi Giorgio , Perez-Gaviro Sergio , Ricci-Tersenghi Federico , Ruiz-Lorenzo Juan Jesus , Schifano Sebastiano Fabio , Seoane Beatriz , Tarancón Alfonso , Tripiccione Raffaele , Yllanes David
Published: February 2017

Significance

The unifying feature of glass formers (such as polymers, supercooled liquids, colloids, granulars, spin glasses, superconductors, etc.) is a sluggish dynamics at low temperatures. Indeed, their dynamics are so slow that thermal equilibrium is never reached in macroscopic samples: in analogy with living beings, glasses are said to age. Here, we show how to relate experimentally relevant quantities with the experimentally unreachable low-temperature equilibrium phase. This relation is made quantitative via a statics-dynamics dictionary, established for spin glasses. In our dictionary, the aging response to a magnetic field is related to the spin-glass order parameter as obtained on samples small enough to equilibrate. We remark that all of the observables we consider can be measured with current experimental methods.
Impersonal clauses in Chinese
Authors: Wang Yong
Published: February 2017

This article deals with impersonal clauses in Chinese (ICiCs) (e.g. Táishàng chàngzhe xì, 台上唱着戏). These are called pseudo-existentials in the literature, as they resemble typical existentials both in form and in meaning. I argue that ICiCs are impersonal, ergatively oriented, and existential. They are impersonal in that the actor of the process is typically demoted to the end position or completely omitted; ergatively oriented in that they express the meaning of happening instead of doing, and existential in that they present the existence of events with reference to some location realized by the initial locative nominal group. These three semantic aspects are in tune with each other and are realized by the structure NGL ^ VG ^ NG, in which VG ^ NG constitutes the event, whose existence is expressed through its configuration with the initial NGL.
Bidirectional cross-linguistic influence in late bilingualism
Authors: Azaz Mahmoud , Frank Joshua
Published: February 2017

The container-content relation represents a set of nominal configurations unexplored in the acquisition literature. Whereas in English the switch from a noun-noun compound (water bottle) to a noun-prepositional phrase (bottle of water) is associated with a semantic shift from container to content, Spanish and Arabic adopt single canonical configurations for both conditions, noun-prepositional phrase and noun phrase, respectively. Importantly, Spanish, Arabic, and English display structural overlap in the content condition maintained by head-first isomorphic strings. In the container condition, they show structural dissimilarity; whereas English uses a head-final construction, Arabic and Spanish consistently use head-first constructions. Results from an elicited sentence-reordering task demonstrate that advanced late learners pattern native speakers when tested in Spanish but not when tested in English. Additionally, when tested in English, Arabic-speaking and Spanish-speaking learners overextend their L1 canonical configurations to both conditions. Furthermore, bilingual native speakers do not perform at ceiling, suggesting bidirectional cross-linguistic influence.
Identification of bilingual children with Specific Language Impairment in France
Authors: Almeida Laetitia de , Ferré Sandrine , Morin Eléonore , Prévost Philippe , Santos Christophe dos , Tuller Laurie , Zebib Racha , Barthez Marie-Anne
Published: February 2017

We report on the usefulness of three LITMUS tools in distinguishing bilingual children with SLI (Bi-SLI) from bilingual children with typical development (Bi-TD), in France: LITMUS-NWR-FR (non-word repetition), LITMUS-SR-FR (sentence repetition), and LITMUS-PABIQ (parental questionnaire). 82 bilingual children, aged 5–8, who had all been exposed to both French and either Arabic, Portuguese or Turkish, recruited both in ordinary schools and in SLP practices, were divided into Bi-TD (n = 61) and Bi-SLI (n = 21) groups based on parental questionnaire (LITMUS-PABIQ) information and standardized language scores in each language. Monolingual controls included 17 children with SLI and 37 TD children. NWR and SR significantly distinguished between the Bi-TD and the Bi-SLI children, and there was minimal impact of different factors related to bilingual development on children’s performance.
Glimpses of semantic restructuring of English emotion-laden words of American English L1 users residing outside the USA
Authors: Dewaele Jean-Marc
Published: February 2017

The present exploratory study focuses on the effect of living outside the USA on the understanding of the meaning, the perceived offensiveness and the self-reported frequency of use of four English emotion-laden words of British origin and four English emotion-laden words of American origin among 556 first (L1) users of American English. Statistical analyses revealed that the scores of the Americans living in the UK or in non-English-speaking countries differed significantly from those of compatriots living in the USA. Positive relationships emerged between multilingualism and scores on the dependent variables for the four British words, but no link emerged between languages known and the dependent variables for the American words. This is interpreted as an indication that semantic representations of emotion-laden words originating from another variety of the L1 are relatively weaker and are more likely to shift as a result of exposure to their use in other varieties, and the knowledge of other languages.
“Communication is a two-way street”
Authors: Cheng Dongmei
Published: February 2017

Speech act studies are increasingly likely to use retrospective verbal protocols to record the thoughts of participants who produced targeted speech acts (e.g., Cohen & Olshtain, 1993). However, although communication is always a two-way street, little is known about the recipients’ perceptions of speech acts. In academic communication at universities, it is critical for students to gain awareness of the socio-cultural norms as well as knowledge of appropriate linguistic forms in interacting with instructors. Therefore, gathering perceptual information from instructors, the recipients of many speech acts such as apologies, serves an important role in realizing successful student-instructor communication. Targeting instructors’ perceptions, two forms of an online survey were created via surveygizmo.com, with one including 12 spoken apologies and the other including 12 emailed apologies. An equal number of native (NS) and nonnative English speaking (NNS) students produced these apologies. The 150 instructors who responded to the survey gave significantly higher ratings to apologies made by NS students than to those made by NNS students. An analysis of instructors’ explanations after the ratings showed that both sociopragmatic and pragmalinguistic knowledge (Thomas, 1983) were valued in the successful realization of apologies, with the majority of instructor explanations addressing the sociopragmatic aspects of apology productions. In their comments on highly-rated student apologies, instructors appreciated the fact that students took responsibility in apologizing, offered worthy explanations, and delivered the messages with minimum grammatical mistakes. Poorly rated apology messages did not contain sufficient or valid evidence, inconvenienced the instructors through inappropriate requests, and usually had multiple grammatical mistakes. This study provides useful source of information to be used in university classrooms that can orientate novice learners towards socio-cultural expectations and appropriate lexical markers to be employed in making successful apologies in academic settings.
Going beyond address forms
Authors: Serrano María José
Published: February 2017

The cognitive properties of morphosyntactic choices are at the base of any usage, patterns and tendencies they could possibly reveal; thus, by means of the cognitive properties of salience and informativeness, variation in second-person tú and usted must be considered as inherently meaningful, implying that each form conveys a different meaning that is used to pursue concrete communicative goals in discursive interaction. A qualitative and quantitative analysis of tú and usted and their syntactic variants (preverbal, postverbal and omitted) reveals that these forms are unevenly distributed across different textual genres and socioprofessional affiliations of speakers. It may be concluded that tú and usted contribute toward shaping the different communicative styles on the basis of the cognitive dimensions of objectivity and subjectivity, respectively. Considering these pronouns as meaningful choices by themselves, this study attempts to go beyond the traditional approach that treats them as terms of address, delving into the discursive and cognitive traits which underlie such a variation.
The environmental impacts of home and community gardening.
Authors: Wang XianZhong Wang XianZhong , Clark P. B.
Published: February 2017

Gardening has been practiced by humans for food and aesthetic purposes for thousands of years. As urbanization intensifies globally, gardening is increasing in both popularity and extent in urban and suburban regions of the world, thus increasing its impact on the environments. Here we discuss the health benefits and risks of home-grown vegetables followed by an in-depth examination of how home and community gardening impacts the biological and physical environments of the world with a focus on North America. In addition to offering multiple health benefits, gardens may promote biodiversity by providing critical habitats for a variety of native plant and animal species. At the same time, gardening has the potential to alter cycles of carbon, nutrients and water in urban and suburban areas, consequently contributing to global environmental changes. Conversely, gardening may have a range of adverse impacts on the environment, for instance, higher nutrient runoff and increased risk of eutrophication in aquatic ecosystems. Intensive lawn care, particularly in North America because of its large lawn areas, could divert essential resources, such as manpower, fertilizers and water, away from more ecologically and economically important activities. Exotic plants commonly grown in home gardens could escape cultivation and become noxious in their non-native habitats as already demonstrated by an increasing number of ornamental species, such as Callery pear and non-native honeysuckle, in the USA. As the world becomes more and more urbanized, the increasingly popular gardening will have greater impact on the abiotic and biotic environments of the world.
Integration and Evaluation of Substance Abuse Research Education Training (SARET) into a Master of Social Work Program
Authors: Tuchman Ellen , Hanley Kathleen , Naegle Madeline , More Frederick , Bereket Sewit , Gourevitch Marc N.
Published: February 2017

Background: The Substance Abuse Research and Education Training (SARET) program is funded by the National Institutes of Drug Abuse in 2006 as a novel approach to spark interest in substance abuse research among medical, dental, nursing, and social work graduate students through a Web-based curriculum and research mentorships. This report presents the initial integration of the intervention in a Master of Social Work (MSW) program, the components of the program, and the mixed-methods evaluation of its effect on students’ attitudes towards substance abuse research and treatment. Methods: SARET comprises 2 main components: stipend-supported research mentorships and a Web-based module series, consisting of 6 interactive, multimedia modules addressing core SA research topics, delivered via course curricula and in the research mentorships. An initial evaluation was designed to assess SARET's acceptability and short-term impact on participants’ interest in SA research. The components of this Web-based curriculum evaluation include focus group feedback on the relevance of the modules to SW students, number of courses into which the modules were integrated with number of module completions, changes in interest in SA research associated with module completion. Results: The full series of Web-based modules has been integrated across several courses in the social work curriculum, and social work students have become integral participants in the summer mentored research experience. One hundred eighteen students completed at least 1 module and 42 students completed all 6 modules. Neurobiology, Screening, and Epidemiology were the most widely viewed modules. Students reported positive impact on their vision of SA-related clinical care, more positive attitudes about conducting research, and in some cases, change in career. Conclusions: The SARET program's modules and summer mentored research increased clinical and research interest related to SUDs, as well as interprofessional attitudes among social work students. Participants have shown some early research success. Longer-term follow-up will enable us to continue to assess the effectiveness of the program.
Potential Reservoirs and Risk Factors for VHSV IVb in an Enzootic System: Budd Lake, Michigan
Authors: Throckmorton Elizabeth , Brenden Travis , Peters Amber K. , Newcomb Tammy J. , Whelan Gary E. , Faisal Mohamed
Published: February 2017

Viral hemorrhagic septicemia virus genotype IVb (VHSV IVb) has caused major, sporadic fish die-offs in the Laurentian Great Lakes region of North America since 2005. Presently, factors affecting VHSV IVb persistence in enzootic systems are not well understood. Even with annual surveillance, the virus can go undetected for several years after an outbreak before again re-emerging, which suggests that the virus is maintained in the system either below detectable levels or in untested reservoirs. The aim of this study was to identify potential reservoirs of VHSV IVb in Budd Lake, Michigan; VHSV IVb was first detected in Budd Lake in 2007 but remained undetected until 2011. Additionally, we explored the susceptibility of naive fish introduced into a water body enzootic for VHSV IVb by stocking age-0 Largemouth Bass Micropterus salmoides at varying densities into enclosures in the lake. The virus was not detected among samples of the fishes Notropis spp. and Lepomis spp., cylindrical papershell mussels Anodontoides ferussacianus, leeches (subclass Hirudinea), sediment, or water. However, the virus was successfully isolated from amphipods (family Hyalellidae) and Largemouth Bass held in the enclosures. Our finding of VHSV IVb in Hyalellidae amphipods in combination with other research that has detected the virus in Diporeia spp., a large benthic amphipod important as a food resource to Great Lake fishes, suggests that benthic macroinvertebrates are a reservoir for VHSV IVb in infected systems. If there are environmental reservoirs for VHSV IVb in infected systems, they are likely unevenly distributed. Findings of this study add to our understanding of the seemingly complex ecology of this deadly and economically detrimental virus.

Received February 22, 2016; accepted October 16, 2016 Published online February 6, 2017
Biochemical synthesis of uniformly 13C-labeled diterpene hydrocarbons and their bioconversion to diterpenoid phytoalexins in planta
Authors: Ye Zhongfeng , Nakagawa Kazuya , Natsume Masahiro , Nojiri Hideaki , Kawaide Hiroshi , Okada Kazunori
Published: February 2017

Phytocassanes and momilactones are the major diterpenoid phytoalexins inductively produced in rice as bioactive substances. Regardless of extensive studies on the biosynthetic pathways of these phytoalexins, bioconversion of diterpene hydrocarbons is not shown in planta. To elucidate the entire biosynthetic pathways of these phytoalexins, uniformly 13C-labeled ent-cassadiene and syn-pimaradiene were enzymatically synthesized with structural verification by GC–MS and 13C-NMR. Application of the 13C-labeled substrates on rice leaves led to the detection of 13C-labeled metabolites using LC-MS/MS. Further application of this method in the moss Hypnum plumaeforme and the nearest out-group of Oryza species Leersia perrieri, respectively, resulted in successful bioconversion of these labeled substrates into phytoalexins in these plants. These results demonstrate that genuine biosynthetic pathways from these diterpene hydrocarbons to the end product phytoalexins occur in these plants and that enzymatically synthesized [U-13C20] diterpene substrates are a powerful tool for chasing endogenous metabolites without dilution with naturally abundant unlabeled compounds.
Performing Prudence: Barack Obama’s Defense of NSA Surveillance Programs
Authors: Trifonov Svilen Veselinov
Published: February 2017

With this essay, I present an argument about the performative and perceptual nature of prudence. I support my argument through a case study in which I examine Barack Obama’s response to Edward Snowden’s unauthorized disclosures about NSA surveillance programs as a way to observe prudence in practice. In my analysis, I identify three ways in which Obama performed prudence. First, he established his image as a prudent and informed leader. Second, he established surveillance as a prudent and historically effective practice ensuring national security. Third, he established the contemporary policy of surveillance as a prudent and deliberate choice reached through discussion and participation by all citizens.
Jeannette Rankin’s Democratic Errand to Washington
Authors: Stob Paul
Published: February 2017

In this essay, I argue that Jeannette Rankin’s 1917 address at Carnegie Hall recast a religious rhetorical form—the Puritan errand—for the democratic needs of the early twentieth century. Rankin’s “democratic errand” positioned the American West as a place that nurtured the truths of democracy and could help purge the nation of its political sins.
Video Stabilization Using Feature Point Matching
Authors: Kulkarni Shamsundar , Bormane D.S , Nalbalwar S.L
Published: February 2017

Video capturing by non-professionals will lead to unanticipated effects. Such as image distortion, image blurring etc. Hence, many researchers study such drawbacks to enhance the quality of videos. In this paper an algorithm is proposed to stabilize jittery videos. A stable output video will be attained without the effect of jitter which is caused due to shaking of handheld camera during video recording. Firstly, salient points from each frame from the input video is identified and processed followed by optimizing and stabilize the video. Optimization includes the quality of the video stabilization. This method has shown good result in terms of stabilization and it discarded distortion from the output videos recorded in different circumstances.
Individual S-acylated cysteines differentially contribute to H-Ras endomembrane trafficking and acylation/deacylation cycles
Authors: Pedro Maria P. , Vilcaes Aldo A. , Gomez Guillermo A. , Daniotti Jose L.
Published: February 2017

S-acylation/deacylation cycles and vesicular transport are critical for an adequate subcellular distribution of S-acylated Ras proteins. H-Ras is dually acylated on cysteines 181 and 184, but it is unknown how these residues individually contribute to H-Ras trafficking. In this study, we characterized the acylation and deacylation rates and membrane trafficking of monoacylated H-Ras mutants to analyze their contributions to H-Ras plasma membrane and endomembrane distribution. We demonstrated that dually acylated H-Ras interacts with acyl-protein thioesterases (APTs) 1 and 2 at the plasma membrane. Moreover, single-acylation mutants of H-Ras differed not only in their subcellular distribution, where both proteins localized to different extents at both the Golgi complex and plasma membrane, but also in their deacylation rates, which we showed to be due to different sensitivities to APT1 and APT2. Fluorescence photobleaching and photoactivation experiments also revealed that 1) although S-acylated, single-acylation mutants are incorporated with different efficiencies into Golgi complex to plasma membrane vesicular carriers, and 2) the different deacylation rates of single-acylated H-Ras influence differentially its overall exchange between different compartments by nonvesicular transport. Taken together, our results show that individual S-acylation sites provide singular information about H-Ras subcellular distribution that is required for GTPase signaling.
RelExplain—integrating data and networks to explain biological processes
Authors: Berchtold Evi , Csaba Gergely , Zimmer Ralf
Published: February 2017

Motivation

The goal of many genome-wide experiments is to explain the changes between the analyzed conditions. Typically, the analysis is started with a set of differential genes DG and the first step is to identify the set of relevant biological processes BP. Current enrichment methods identify the involved biological process via statistically significant overrepresentation of differential genes in predefined sets, but do not further explain how the differential genes interact with each other or which other genes might be important for the enriched process. Other network-based methods determine subnetworks of interacting genes containing many differential genes, but do not employ process knowledge for a more focused analysis.

Results

RelExplain is a method to analyze a given biological process bp (e.g. identified by enrichment) in more detail by computing an explanation using the measured DG and a given network. An explanation is a subnetwork that contains the differential genes in the process bp and connects them in the best way given the experimental data using also genes that are not differential or not in bp. RelExplain takes into account the functional annotations of nodes and the edge consistency of the measurements. Explanations are compact networks of the relevant part of the bp and additional nodes that might be important for the bp. Our evaluation showed that RelExplain is better suited to retrieve manually curated subnetworks from unspecific networks than other algorithms. The interactive RelExplain tool allows to compute and inspect sub-optimal and alternative optimal explanations.

Availability and Implementation

A webserver is available at https://services.bio.ifi.lmu.de/relexplain.

Supplementary information

Supplementary data are available at Bioinformatics online.
An efficient concordant integrative analysis of multiple large-scale two-sample expression data sets
Authors: Lai Yinglei , Zhang Fanni , Nayak Tapan K , Modarres Reza , Lee Norman H , McCaffrey Timothy A
Published: February 2017

Motivation

We have proposed a mixture model based approach to the concordant integrative analysis of multiple large-scale two-sample expression datasets. Since the mixture model is based on the transformed differential expression test P-values (z-scores), it is generally applicable to the expression data generated by either microarray or RNA-seq platforms. The mixture model is simple with three normal distribution components for each dataset to represent down-regulation, up-regulation and no differential expression. However, when the number of datasets increases, the model parameter space increases exponentially due to the component combination from different datasets.

Results

In this study, motivated by the well-known generalized estimating equations (GEEs) for longitudinal data analysis, we focus on the concordant components and assume that the proportions of non-concordant components follow a special structure. We discuss the exchangeable, multiset coefficient and autoregressive structures for model reduction, and their related expectation-maximization (EM) algorithms. Then, the parameter space is linear with the number of datasets. In our previous study, we have applied the general mixture model to three microarray datasets for lung cancer studies. We show that more gene sets (or pathways) can be detected by the reduced mixture model with the exchangeable structure. Furthermore, we show that more genes can also be detected by the reduced model. The Cancer Genome Atlas (TCGA) data have been increasingly collected. The advantage of incorporating the concordance feature has also been clearly demonstrated based on TCGA RNA sequencing data for studying two closely related types of cancer.

Availability and Implementation

Additional results are included in a supplemental file. Computer program R-functions are freely available at http://home.gwu.edu/∼ylai/research/Concordance.

Supplementary information

Supplementary data are available at Bioinformatics online.
cooccurNet: an R package for co-occurrence network construction and analysis
Authors: Zou Yuanqiang , Wu Zhiqiang , Deng Lizong , Wu Aiping , Wu Fan , Li Kenli , Jiang Taijiao , Peng Yousong
Published: February 2017

Motivation

Previously, we developed a computational model to identify genomic co-occurrence networks that was applied to capture the coevolution patterns within genomes of influenza viruses. To facilitate easy public use of this model, an R package ‘cooccurNet’ is presented here.

Results

‘cooccurNet’ includes functionalities of construction and analysis of residues (e.g. nucleotides, amino acids and SNPs) co-occurrence network. In addition, a new method for measuring residues coevolution, defined as residue co-occurrence score (RCOS), is proposed and implemented in ‘cooccurNet’ based on the co-occurrence network.

Availability and Implementation

‘cooccurNet’ is publicly available on CRAN repositories under the GPL-3 Open Source License (http://cran.r-project.org/package=cooccurNet)

Supplementary information

Supplementary data are available at Bioinformatics online.
CPSS 2.0: a computational platform update for the analysis of small RNA sequencing data
Authors: Wan Changlin , Gao Jianing , Zhang Huan , Jiang Xiaohua , Zang Qiguang , Ban Rongjun , Zhang Yuanwei , Shi Qinghua
Published: February 2017

Next-generation sequencing has been widely applied to understand the complexity of non-coding RNAs (ncRNAs) in the last decades. Here, we present CPSS 2.0, an updated version of CPSS 1.0 for small RNA sequencing data analysis, with the following improvements: (i) a substantial increase of supported species from 10 to 48; (ii) improved strategies applied to detect ncRNAs; (iii) more ncRNAs can be detected and profiled, such as lncRNA and circRNA; (iv) identification of differentially expressed ncRNAs among multiple samples; (v) enhanced visualization interface containing graphs and charts in detailed analysis results. The new version of CPSS is an efficient bioinformatics tool for users in non-coding RNA research.

Availability and implementation

CPSS 2.0 is implemented in PHP + Perl + R and can be freely accessed at http://114.214.166.79/cpss2.0/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Genome sequence of a rice pest, the white-backed planthopper (Sogatella furcifera)
Authors: Wang Lin , Tang Nan , Gao Xinlei , Chang Zhaoxia , Zhang Liqin , Zhou Guohui , Guo Dongyang , Zeng Zhen , Li Wenjie , Akinyemi Ibukun A. , Yang Huanming , Wu Qingfa
Published: February 2017

Background:  Sogatella furcifera is an important phloem sap-sucking and plant virus-transmitting migratory insect of rice. Because of its high reproductive potential, dispersal capability and transmission of plant viral diseases, S. furcifera causes considerable damage to rice grain production and has great economical and agricultural impacts. Comprehensive studies into ecological aspects and virus–host interactions of S. furcifera have been limited because of the lack of a well-assembled genome sequence.

Findings: A total of 241.3 Gb of raw reads from the whole genome of S. furcifera were generated by Illumina sequencing using different combinations of mate-pair and paired-end libraries from 17 insert libraries ranging between 180 bp and 40 kbp. The final genome assembly (0.72 Gb), with average N50 contig size of 70.7 kb and scaffold N50 of 1.18 Mb, covers 98.6 % of the estimated genome size of S. furcifera. Genome annotation, assisted by eight different developmental stages (embryos, 1st-5th instar nymphs, 5-day-old adults and 10-day-old adults), generated 21 254 protein-coding genes, which captured 99.59 % (247/248) of core CEGMA genes and 91.7 % (2453/2675) of BUSCO genes.

Conclusions: We report the first assembled and annotated whole genome sequence and transcriptome of S. furcifera. The assembled draft genome of S. furcifera will be a valuable resource for ecological and virus–host interaction studies of this pest.
Constitutional Antecedents
Authors: De Rohit
Published: February 2017

This chapter focuses on the antecedents of the Indian Constitution. It first examines the various charters and laws that established the structure of power in colonial India from 1600 to 1947. It then considers the attempts by Indian groups during the freedom struggle to draw up constitutions or articulate claims against the State, before turning to a discussion of constitutional practice in colonial India. The article treats the Indian Constitution as a set of interactions between constitutional texts, constitutional aspirations, and the quotidian practice of constitutional law, rather than a succession of legislation. This approach shifts from the idea that the Constitution was a product of grand ‘consensus underwritten by nationalism’ to that of the Constitution as a product of a series of conflicts.
Language
Authors: Choudhry Sujit
Published: February 2017

This chapter examines the constitutional politics of official language status in India. It gives an overview of the debates in the Indian Constituent Assembly over issues such as the official language of the Central Government and the Indian Constitution’s distinction between the language of parliamentary deliberations and the language of legislation. It considers the disaggregation of official language status into different linguistic states within the context of the relationship between federalism and language. It also discusses the implications of linguistic federalism for linguistic minorities in India and the legal controversy regarding the extent to which Article 30(1) of the Indian Constitution grants linguistic minorities the right to exclude instruction in the regional language.
Judicial Architecture and Capacity
Authors: Robinson Nick
Published: February 2017

This chapter examines the structure of the Indian judiciary, which includes the different types of courts and judges as well as the hierarchies and relations between them. In particular, it considers the appeal and stare decisis, along with the system of internal administrative control through which the Indian judiciary coordinates its behaviour. The discussion begins with an overview of India’s judicial system and the relevant provisions of the Indian Constitution. The chapter then discusses the functioning of the Indian Supreme Court, the High Courts, and subordinate judiciary. It comments on the top-heaviness of the Indian judiciary and its impact on the judicial system’s performance.
Judicial Independence
Authors: Srikrishna B. N.
Published: February 2017

This chapter focuses on the independence of the Indian judiciary and how judicial independence has been interpreted and secured in the country’s constitutional law. In particular, it considers the balance between judicial independence and judicial accountability, along with various concerns and goals that have shaped constitutional doctrine in this area. The chapter begins with and primarily focuses upon a study of the appointment of judges to the higher judiciary and its relevance to the debate over judicial independence in India. It then describes the conditions of service of officers and servants of the Indian Supreme Court and the High Courts as spelled out in the Indian Constitution. It also discusses the approach towards disciplinary action against judges, including their impeachment, and concludes by looking at issues that are integral to the question of judicial independence, especially those relating to salaries, tenure, transfers, and removal.
Inter-State Trade, Commerce, and Intercourse
Authors: Datar Arvind
Published: February 2017

This chapter examines the trade, commerce, and intercourse clauses in the Indian Constitution. Part XIII of the Indian Constitution consists of Articles 301 to 305 and encompasses ‘Trade, Commerce and Intercourse within the territory of India’. The focus of this chapter is on the controversy surrounding compensatory taxes. It first compares the Indian framework with Australian law on trade, commerce, and intercourse, before discussing the controversy over compensatory tax that began with Section 3 of the Assam Taxation (On Goods Carried by Roads or Inland Waterways) Act 1954 and whether the concept of compensatory tax has a place in Indian constitutional law. It then considers the Indian Supreme Court ruling in the Atiabari and Automobile Transport cases and concludes by analysing unresolved questions, such as whether the imposition of entry tax levied under Entry 52, List II, violates Article 301.
Inter-State River Water Disputes
Authors: Salve Harish
Published: February 2017

This chapter examines the constitutional framework for the resolution of inter-State river water disputes in India, considering whether water disputes are best resolved through political negotiation or through adjudication, how political agreements can be enforced and implemented, and how disputes are tackled substantively and procedurally. It discusses Article 262 of the Indian Constitution and the vesting of power in Parliament to adjudicate disputes regarding inter-State rivers or river valleys. It then provides a historical perspective on inter-State river water dispute resolution, starting from the Government of India Act 1919, and reviews two pieces of legislation enacted in 1956 to deal with inter-State river waters: the River Boards Act 1956 and the Inter-State River Water Disputes Act 1956. It looks at some of the major constitutional and legal debates that have surrounded inter-State river water disputes in India and analyses the Indian Supreme Court’s ruling in the Mullaperiyar Dam case.
Writs and Remedies
Authors: Subramanium Gopal
Published: February 2017

This chapter examines the relevant provisions of the Indian Constitution regarding the power of courts to issue writs and grant remedies, with particular emphasis on Articles 32 and 226. It considers these two provisions and how they empower the Indian Supreme Court and High Courts to issue directions, orders, or writs to any person or authority, and to enforce the fundamental rights. It then considers a number of issues relating to Article 226, such as whether it is confined to governmental institutions and statutory public bodies, along with the question of cause of action and territoriality. It also discusses the Supreme Court’s position on the nature of writ jurisdiction in India, including the writ of mandamus, habeas corpus, certiorari, prohibition, and quo warranto. Finally, the chapter explores the procedural aspects of constitutional remedies by focusing on res judicata, questions of fact, and political questions.