bluuebunny/crossref_metadata_2025_split huggingface dataset:
CRISPR/Cas9 cleavage of viral DNA efficiently suppresses hepatitis B virus
Authors: Ramanan Vyas , Shlomai Amir , Cox David B.T. , Schwartz Robert E. , Michailidis Eleftherios , Bhatta Ankit , Scott David A. , Zhang Feng , Rice Charles M. , Bhatia Sangeeta N. 
Published: June 2015

AbstractChronic hepatitis B virus (HBV) infection is prevalent, deadly and seldom cured due to the persistence of viral episomal DNA (cccDNA) in infected cells. Newly developed genome engineering tools may offer the ability to directly cleave viral DNA, thereby promoting viral clearance. Here, we show that the CRISPR/Cas9 system can specifically target and cleave conserved regions in the HBV genome, resulting in robust suppression of viral gene expression and replication. Upon sustained expression of Cas9 and appropriately chosen guide RNAs, we demonstrate cleavage of cccDNA by Cas9 and a dramatic reduction in both cccDNA and other parameters of viral gene expression and replication. Thus, we show that directly targeting viral episomal DNA is a novel therapeutic approach to control the virus and possibly cure patients.
Maskless inverted pyramid texturization of silicon
Authors: Wang Yan , Yang Lixia , Liu Yaoping , Mei Zengxia , Chen Wei , Li Junqiang , Liang Huili , Kuznetsov Andrej , Xiaolong Du 
Published: June 2015

AbstractWe discovered a technical solution of such outstanding importance that it can trigger new approaches in silicon wet etching processing and, in particular, photovoltaic cell manufacturing. The so called inverted pyramid arrays, outperforming conventional pyramid textures and black silicon because of their superior light-trapping and structure characteristics, can currently only be achieved using more complex techniques involving lithography, laser processing, etc. Importantly, our data demonstrate a feasibility of inverted pyramidal texturization of silicon by maskless Cu-nanoparticles assisted etching in Cu(NO3)2 / HF / H2O2 / H2O solutions and as such may have significant impacts on communities of fellow researchers and industrialists.
The role of basic residues in the adsorption of blood proteins onto the graphene surface
Authors: Gu Zonglin , Yang Zaixing , Wang Lingle , Zhou Hong , Jimenez-Cruz Camilo A. , Zhou Ruhong 
Published: June 2015

AbstractWith its many unique properties, graphene has shown great potential in various biomedical applications, while its biocompatibility has also attracted growing concerns. Previous studies have shown that the formation of protein-graphene corona could effectively reduce its cytotoxicity; however, the underlying molecular mechanism remains not well-understood. Herein, we use extensive molecular dynamics simulations to demonstrate that blood proteins such as bovine fibrinogen (BFG) can absorb onto the graphene surface quickly and tightly to form a corona complex. Aromatic residues contributed significantly during this adsorption process due to the strong π−π stacking interactions between their aromatic rings and the graphene sp2-carbons. Somewhat surprisingly, basic residues like arginine, also played an equally or even stronger role during this process. The strong dispersion interactions between the sidechains of these solvent-exposed basic residues and the graphene surface provide the driving force for a tight binding of these basic residues. To the best of our knowledge, this is the first study with blood proteins to show that, in addition to the aromatic residues, the basic residues also play an important role in the formation of protein-graphene corona complexes.
Analysis of bibliometric indicators to determine citation bias
Authors: Simko Ivan 
Published: June 2015

AbstractCitations of research papers and citation-related indicators are frequently used factors in determining research priorities, allocating funding, and deciding appointments, promotions and tenures. The main problem with using citations for a variety of evaluations is a substantial difference in the average number of citations received by papers in different research fields and subfields. A large number of species are subjects of biological research, but the distributions of their citations have not been studied in detail. The key objective of the present work was to determine whether the choice of experimental subjects influence bias in citations. A case study was performed on papers from 108 plant species and five research fields. Funnel plot analyses and computer simulations identified species-related citation bias within all research fields. Relationships between bibliometric indicators imply that species with a fast growing number of publications in recent years (for example, new model organisms) generally have a higher average number of citations per paper than is the overall mean for the research field. In contrast, the average number of citations received by the five most prominent papers of the species was strongly correlated with the total number of published papers from laboratories working with the species. The current study indicates that despite the high frequency of cross-species citations, citations of species show a pattern similar to separate subfields. Although these analyses were performed on plant research papers, the findings have relevance for other areas of research where experimental subjects tend to form separate subfields. To reliably compare citations across subfields, a new type of bibliometric indicator is needed. In the meantime committees evaluating quality of research should take into consideration that citations of papers within a research field might be biased due to the experimental subjects used in the studies.
Imaging transient melting of a nanocrystal using an X-ray laser
Authors: Clark Jesse N. , Beitra Loren , Xiong Gang , Fritz David M. , Lemke Henrik T. , Zhu Diling , Chollet Matthieu , Williams Garth J. , Messerschmidt Marc M. , Abbey Brian , Harder Ross J. , Korsunsky Alexander M. , Wark Justin S. , Reis David A. , Robinson Ian K. 
Published: June 2015

Significance
Despite phase transitions, such as melting, being ubiquitous in nature, understanding what occurs at the nanoscale (such as in nanocrystals) has so far remained challenging. With ensemble studies of nanocrystals it is often difficult to discriminate between intrinsic size-dependent properties and effects due to sample size and shape dispersity. Here, using an X-ray free electron laser we image the reversible melting of an individual nanocrystal induced by an ultrashort laser. It is revealed that the melting occurs transiently, repeatably, and inhomogeneously. This is consistent with a core-shell model where the exterior is melted and a solid core remains. These findings reveal, unambiguously, that core-shell melting occurs, which has important implications for understanding nanoscale phenomena.
New approaches narrow global species estimates for beetles, insects, and terrestrial arthropods
Authors: Stork Nigel E. , McBroom James , Gely Claire , Hamilton Andrew J. 
Published: June 2015

Significance
Many suggest we are approaching a sixth mass extinction event, and yet estimates of how many species exist, and thus how many might become extinct, vary by as much as an order of magnitude. There are few statistically robust methods to estimate global species richness, and here we introduce several new methods, including one that builds on the observation that larger species are often described before smaller species. We combine these, giving equal weight to each, to provide mean global species estimates for the most speciose order, class, and phylum on Earth, beetles, insects, and arthropods (terrestrial). We attempt to aid conservation planning by broadening the range of methods used and bringing greater stability to global estimates for these taxa.
The influence of performance level, age and gender on pacing strategy during a 100‐km ultramarathon
Authors: Renfree Andrew , Crivoi do Carmo Everton , Martin Louise 
Published: June 2015

AbstractThe aim of this study is to analyse the influence of performance level, age and gender on pacing during a 100‐km ultramarathon. Results of a 100‐km race incorporating the World Masters Championships were used to identify differences in relative speeds in each 10‐km segment between participants finishing in the first, second, third and fourth quartiles of overall positions (Groups 1, 2, 3 and 4, respectively). Similar analyses were performed between the top and bottom 50% of finishers in each age category, as well as within male and female categories. Pacing varied between athletes achieving different absolute performance levels. Group 1 ran at significantly lower relative speeds than all other groups in the first three 10‐km segments (all P < 0.01), and significantly higher relative speeds than Group 4 in the 6th and 10th (both P < 0.01), and Group 2 in the 8th (P = 0.04). Group 4 displayed significantly higher relative speeds than Group 2 and 3 in the first three segments (all P < 0.01). Overall strategies remained consistent across age categories, although a similar phenomenon was observed within each category whereby ‘top’ competitors displayed lower relative speeds than ‘bottom’ competitors in the early stages, but higher relative speeds in the later stages. Females showed lower relative starting speeds and higher finishing speeds than males. ‘Top’ and ‘bottom’ finishing males displayed differing strategies, but this was not the case within females. Although pacing remained consistent across age categories, it differed with level of performance within each, possibly suggesting strategies are anchored on direct competitors. Strategy differs between genders and differs depending on performance level achieved in males but not females.
FourCSeq: analysis of 4C sequencing data
Authors: Klein Felix A. , Pakozdi Tibor , Anders Simon , Ghavi-Helm Yad , Furlong Eileen E. M. , Huber Wolfgang 
Published: June 2015

AbstractMotivation: Circularized Chromosome Conformation Capture (4C) is a powerful technique for studying the spatial interactions of a specific genomic region called the ‘viewpoint’ with the rest of the genome, both in a single condition or comparing different experimental conditions or cell types. Observed ligation frequencies typically show a strong, regular dependence on genomic distance from the viewpoint, on top of which specific interaction peaks are superimposed. Here, we address the computational task to find these specific peaks and to detect changes between different biological conditions.Results: We model the overall trend of decreasing interaction frequency with genomic distance by fitting a smooth monotonically decreasing function to suitably transformed count data. Based on the fit, z-scores are calculated from the residuals, and high z-scores are interpreted as peaks providing evidence for specific interactions. To compare different conditions, we normalize fragment counts between samples, and call for differential contact frequencies using the statistical method DESeq2 adapted from RNA-Seq analysis.Availability and implementation: A full end-to-end analysis pipeline is implemented in the R package FourCSeq available at www.bioconductor.org.Contact: felix.klein@embl.de or whuber@embl.deSupplementary information: Supplementary data are available at Bioinformatics online.
Mango: a bias-correcting ChIA-PET analysis pipeline
Authors: Phanstiel Douglas H. , Boyle Alan P. , Heidari Nastaran , Snyder Michael P. 
Published: June 2015

AbstractMotivation: Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) is an established method for detecting genome-wide looping interactions at high resolution. Current ChIA-PET analysis software packages either fail to correct for non-specific interactions due to genomic proximity or only address a fraction of the steps required for data processing. We present Mango, a complete ChIA-PET data analysis pipeline that provides statistical confidence estimates for interactions and corrects for major sources of bias including differential peak enrichment and genomic proximity.Results: Comparison to the existing software packages, ChIA-PET Tool and ChiaSig revealed that Mango interactions exhibit much better agreement with high-resolution Hi-C data. Importantly, Mango executes all steps required for processing ChIA-PET datasets, whereas ChiaSig only completes 20% of the required steps. Application of Mango to multiple available ChIA-PET datasets permitted the independent rediscovery of known trends in chromatin loops including enrichment of CTCF, RAD21, SMC3 and ZNF143 at the anchor regions of interactions and strong bias for convergent CTCF motifs.Availability and implementation: Mango is open source and distributed through github at https://github.com/dphansti/mango.Contact: mpsnyder@standford.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Recent changes in Antarctic Sea Ice
Authors: Turner John , Hosking J. Scott , Bracegirdle Thomas J. , Marshall Gareth J. , Phillips Tony 
Published: June 2015

In contrast to the Arctic, total sea ice extent (SIE) across the Southern Ocean has increased since the late 1970s, with the annual mean increasing at a rate of 186×10
3
km
2
per decade (1.5% per decade;
p
<0.01) for 1979–2013. However, this overall increase masks larger regional variations, most notably an increase (decrease) over the Ross (Amundsen–Bellingshausen) Sea. Sea ice variability results from changes in atmospheric and oceanic conditions, although the former is thought to be more significant, since there is a high correlation between anomalies in the ice concentration and the near-surface wind field. The Southern Ocean SIE trend is dominated by the increase in the Ross Sea sector, where the SIE is significantly correlated with the depth of the Amundsen Sea Low (ASL), which has deepened since 1979. The depth of the ASL is influenced by a number of external factors, including tropical sea surface temperatures, but the low also has a large locally driven intrinsic variability, suggesting that SIE in these areas is especially variable. Many of the current generation of coupled climate models have difficulty in simulating sea ice. However, output from the better-performing IPCC CMIP5 models suggests that the recent increase in Antarctic SIE may be within the bounds of intrinsic/internal variability.
OPERA-LG: Efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees
Authors: Gao Song , Bertrand Denis , Chia Burton KH , Nagarajan Niranjan 
Published: June 2015

AbstractThe assembly of large, repeat-rich eukaryotic genomes continues to represent a significant challenge in genomics. While long-read technologies have made the high-quality assembly of small, microbial genomes increasingly feasible, data generation can be prohibitively expensive for larger genomes. Advances in assembly algorithms are thus essential to exploit the characteristics of short and long-read sequencing technologies to consistently and reliably provide high-quality assemblies in a cost-efficient manner. OPERA-LG is a scalable, exact algorithm for the scaffold assembly of large, repeat-rich genomes, with consistent improvement over state-of-the-art programs for scaffold correctness and contiguity. It provides a rigorous framework for scaffolding of repetitive sequences and a systematic approach for combining data from different second-generation (Illumina, Ion Torrent) and third-generation (PacBio, ONT) sequencing technologies. OPERA-LG efficiently scaffolds large genomes with provable scaffold properties, providing an avenue for systematic augmentation and improvement of 1000s of existing draft eukaryotic genome assemblies.
Approximately independent linkage disequilibrium blocks in human populations
Authors: Berisa Tomaz , Pickrell Joseph K. 
Published: June 2015

AbstractWe present a method to identify approximately independent blocks of linkage disequilibrium (LD) in the human genome. These blocks enable automated analysis of multiple genome-wide association studies.Availability (code)http://bitbucket.org/nygcresearch/ldetectAvailability (data):http://bitbucket.org/nygcresearch/ldetect-data
Editorial
Authors: Ogliastri Enrique 
Published: June 2015

Abstract
This issue includes six research papers originating from ten different institutions across four countries: Chile, Spain, the USA and Portugal. The first paper deals with staff turnover in service companies. The second is a study into life-work interaction for executives who have to take short but frequent international trips as part of their job. The third paper investigates how being self-employed (or alternatively, a salaried employee) affects the relationship between life and job satisfaction. The fourth paper looks at the impact of information technology (IT) on hotel marketing. The fifth examines marketing strategies for the growing segment of people with high purchasing power. And the sixth and final paper studies the impact of IT on the relationship between environmental practices and companies’ actual environmental performance.

Resumen
Se incluyen seis artículos de investigación procedentes de diez instituciones en cuatro países: Chile, España, Estados Unidos y Portugal. El primero trata sobre la rotación de personal en empresas de servicios. El segundo es un estudio exploratorio sobre la interacción entre vida y trabajo de ejecutivos que deben realizar breves pero frecuentes viajes internacionales como parte de su trabajo. El tercero, estudia el efecto de trabajar por cuenta propia (o asalariado) en la relación entre la satisfacción con la vida y con el trabajo. El cuarto sobre el impacto de las tecnologías de información en el mercadeo de hoteles. El quinto sobre estrategias de mercadeo para el creciente segmento de personas en sectores de alto poder adquisitivo. El sexto estudia el impacto de la tecnología de información en la relación entre prácticas ambientales y el efectivo desempeño ambiental de las empresas.
Evolution of nutrient acquisition: when space matters
Authors: Barot Sébastien , Bornhofen Stefan , Boudsocq Simon , Raynaud Xavier , Loeuille Nicolas 
Published: June 2015

Summary

Evolution of nutrient acquisition by plants should depend on two forces: local competition is based on the capacity to exploit the local nutrient resource, and regional competition is based on the capacity to occupy the whole landscape through seed production and dispersal.

We build a spatially explicit simulation model where a limiting nutrient is recycled in each local patch of a lattice by individual plants. The model includes both local and regional competition.

Heterogeneity in nutrient availability and dispersal limitation mitigate the effect of competition for the local nutrient resource and allow the evolution of lower rates of nutrient uptake. Our spatially explicit model suggests that evolution in richer ecosystems selects ‘expensive’ strategies (high acquisition, low conservation of resources) compared to poor ecosystems.

Low rates of nutrient acquisition can be considered as a form of altruism because they leave more resource available for other individuals. Our model thus suggests that the influence of spatial processes on the evolution of altruism is pervasive and is linked to key aspects of ecosystem functioning.

Because our model includes both regional and local competition, evolution does not minimize the availability of mineral nutrient, although evolution or species replacement is often thought to minimize the availability of nutrient. Taken together, our work confirms that the interplay between local and regional competition is critical for the evolution of plant nutrient strategies and its effect on ecosystem properties.
Tougher and thornier: general patterns in the induction of physical defence traits
Authors: Barton Kasey E. 
Published: June 2015

Summary

Most plants rely at least in part on physical defence traits to deter herbivores, and yet, very little is known about the inducibility of these traits.

A meta‐analysis was conducted on data extracted from 57 publications from 1982 to 2014, including 53 species in 20 plant families in which the induction of physical defence traits was examined. Log response ratio effect sizes were calculated for 112 separate responses and analysed to characterize general patterns and test whether induction differed between physical and chemical defence traits (in the same study), among defence traits, and in response to the damage type (artificial, herbivore, jasmonates).

Physical defence traits are generally inducible, showing a mean increase of 52% in damaged compared to control plants. The magnitude of increase did not differ between physical and chemical defence traits measured within the same experiments, and nutrients showed no overall response. Physical defence traits varied significantly in their responses, with non‐glandular trichomes showing the greatest magnitude of increase, and no induction detected for leaf toughness. Responses induced by real herbivores or by jasmonate application were significantly greater than responses elicited by mechanical damage alone. This suggests that specificity in physical trait induction in response to different kinds of damage may occur.

Induction of physical defence traits is common and widespread, but the ecological and evolutionary consequences of this response remain unknown. Future studies examining genetic variation in the inducibility of physical defence traits and their fitness consequences for plants would be particularly informative.
Facilitation and sustainable agriculture: a mechanistic approach to reconciling crop production and conservation
Authors: Brooker Rob W. , Karley Alison J. , Newton Adrian C. , Pakeman Robin J. , Schöb Christian 
Published: June 2015

Summary

Food security is currently considered a major global problem. However, increasing intensity of food production in agricultural systems has driven reductions in farmland biodiversity. A major challenge is to enable biodiversity conservation whilst addressing the problem of food security.

Here we describe how facilitative plant–plant interactions in crop systems could be used to help strike this balance. An obvious example is that of intercropping systems, where combinations of crop species can – under some circumstances – deliver reduced inputs of agrochemicals (fertilizers, pesticides) per unit yield, with potential knock‐on benefits for biodiversity conservation.

Other facilitative processes can also play a role in biodiversity conservation. Increased intraspecific crop genetic diversity can help protect crops from pests and diseases. Although overlooked in facilitation research, we argue that the mechanisms operate in a manner which is directly analogous to associational defence against herbivores, a process well recognized in the facilitation literature. As with intercropping, the benefits to nature conservation arise from reduced pesticide use per unit harvested crop.

Crops may have facilitative effects on some arable weed species, particularly those that are currently considered rare in intensive farming systems. Work is in its early stages to understand the underlying mechanisms, but it appears that crops might create niche space to which some weed species are adapted. Increasing plant species diversity through niche space creation may then have cascading benefits for other components of farmland biodiversity.

Our new understanding of facilitative processes arising from work on crop systems has lessons for the study of facilitative interactions in natural and semi‐natural communities. We argue that, although easier to identify and quantify in crop systems, some of these facilitative processes have to date been overlooked in studies of non‐crop systems and certainly deserve further consideration.

Finally, we discuss what steps may be needed to move from our understanding of the role of facilitation to the development of new agricultural practice. In some cases the challenge may be one of the encouraging uptake of existing practices, and in others more research is needed to understand how new ecological understanding might deliver more sustainable agricultural practice.