bluuebunny/crossref_metadata_2025 huggingface dataset:
Design, implementation, and extension of thermal invisibility cloaks
Authors: Zhang Youming , Xu Hongyi , Zhang Baile
Published: March 2015

A thermal invisibility cloak, as inspired by optical invisibility cloaks, is a device which can steer the conductive heat flux around an isolated object without changing the ambient temperature distribution so that the object can be “invisible” to external thermal environment. While designs of thermal invisibility cloaks inherit previous theories from optical cloaks, the uniqueness of heat diffusion leads to more achievable implementations. Thermal invisibility cloaks, as well as the variations including thermal concentrator, rotator, and illusion devices, have potentials to be applied in thermal management, sensing and imaging applications. Here, we review the current knowledge of thermal invisibility cloaks in terms of their design and implementation in cloaking studies, and their extension as other functional devices.
Boldness and urban dwelling in little ravens
Authors: Vines Aaron , Lill Alan
Published: March 2015

Context To successfully inhabit urban environments, birds must cope with the presence of people and vehicles at high densities. One hypothesised component of such coping is a high level of boldness, which may be inherent in all, or a particular subset of, species’ members as the result of natural selection or achieved through phenotypic plasticity allowing rapid behavioural adjustment to human disturbance. Aims To determine how much bolder urban little ravens (Corvus mellori) are than exurban conspecifics. To determine whether urban little ravens vary in their boldness as a function of local pedestrian and vehicular traffic volume, an important issue with respect to adjusting to the urban environment that has received little attention. Methods We assessed the relative boldness of free-living urban and exurban little ravens using the Flight Initiation Distance (FID) paradigm. The boldness of urban little ravens was also tested by measuring the reaction of individuals in areas with varying traffic volumes to a potentially startling sound stimulus (PSS). Key results On average, exurban ravens approached by a researcher had FIDs nearly 6-fold longer, escaped 1.4 times more by flying and fled >10 m 3.4 times more than urban conspecifics. Urban ravens in areas with varying pedestrian and vehicular traffic volumes had similar FIDs and mostly reacted similarly to a PSS, although retreat behaviour from a human and the PSS was influenced by traffic volume. Conclusions Boldness seems to be important in facilitating urban dwelling by little ravens. Antipredator behaviour did not appear to be strongly adjusted to local variation in traffic volume within the urban environment, but the reason for this is unknown. Further research with more extensive traffic surveying could help to answer this question. Implications The results are consistent with little ravens’ urban boldness occurring through initial urban settlement by a bolder subset of individuals. The importance of boldness in coping with traffic should feature more prominently in urban boldness research.
A Sex‐Determining Gene (sdY) Assay Shows Discordance between Phenotypic and Genotypic Sex in Wild Populations of Chinook Salmon
Authors: Cavileer Timothy D. , Hunter Samuel S. , Olsen Jeffery , Wenburg John , Nagler James J.
Published: March 2015

Sex is determined genetically in most fishes, but the gene responsible for sex determination is not known for the vast majority of fish species, including Chinook Salmon Oncorhynchus tshawytscha. The purpose of this study was to characterize a putative sex‐determining gene (“sexually dimorphic on the Y‐chromosome” [sdY] gene) in Chinook Salmon and develop a method to test genomic DNA (gDNA) samples for genetic sex assignment. Using next‐generation sequencing and salmonid DNA sequence data from GenBank, the entire genomic organization of Chinook Salmon sdY was described. The corresponding full‐length complementary DNA (cDNA) sequence generated from total RNA was determined by using a combination of genomic‐based primers and “rapid amplification of cDNA ends” (RACE) PCR assays. A phylogenic analysis was conducted by comparing the Chinook Salmon sdY cDNA sequence with sdY sequences (GenBank) from 10 other teleost species. A multisequence alignment was performed, and a phylogenetic tree was inferred from the alignment, providing evidence for sdY identity. Based upon a TaqMan real‐time PCR assay, a genetic test for male sex using sdY was developed and tested on gDNA isolated from phenotypic female and male Chinook Salmon representing populations in Alaska, Idaho, and Washington. The results provide compelling evidence that sdY is the sex‐determining gene in Chinook Salmon. We developed a reliable assay for sdY that can be used for genetic sex assignment in this species. However, discordance between phenotype and genotype was noted in 13 of 107 phenotypic female Chinook Salmon from Alaska and Washington. Several explanations for this discordance are discussed.

Received January 14, 2014; accepted November 25, 2014
Estimating Sturgeon Abundance in the Carolinas Using Side-Scan Sonar
Authors: Flowers H. Jared , Hightower Joseph E.
Published: March 2015

Sturgeons (Acipenseridae) are one of the most threatened taxa worldwide, including species in North Carolina and South Carolina. Populations of Atlantic Sturgeon Acipenser oxyrinchus in the Carolinas have been significantly reduced from historical levels by a combination of intense fishing and habitat loss. There is a need for estimates of current abundance, to describe status, and for estimates of historical abundance in order to provide realistic recovery goals. In this study we used N-mixture and distance models with data acquired from side-scan sonar surveys to estimate abundance of sturgeon in six major sturgeon rivers in North Carolina and South Carolina. Estimated abundances of sturgeon greater than 1 m TL in the Carolina distinct population segment (DPS) were 2,031 using the count model and 1,912 via the distance model. The Pee Dee River had the highest overall abundance of any river at 1,944 (count model) or 1,823 (distance model). These estimates do not account for sturgeon less than 1 m TL or occurring in riverine reaches not surveyed or in marine waters. Comparing the two models, the N-mixture model produced similar estimates using less data than the distance model with only a slight reduction of estimated precision.

Received May 3, 2014; accepted October 14, 2014
Franz Jägerstätter as social critic
Authors: Finn Peter D.
Published: March 2015

Alan Donagan's modern classic, A Theory of Morality, stands as an articulate and cogent apology for deontological ethics. Among its important contributions is the argument Donagan makes that this rationally anchored morality is the most reliable platform for social criticism – particularly in times of ethical ‘drift’. He rules out Hegel's alternative, developed in opposition to Kant, according to which to act morally simply means to comport oneself to the prevailing normative practices of one's community. In Donagan's view, this position risks dreadful ethical failure if such practices already are, or are gradually becoming, morally pernicious. To illustrate this point, Donagan considers the historical case of Franz Jägerstätter – a man whose conscientious objection to being conscripted to serve in the German Wehrmacht led eventually to his trial and execution. For Donagan, Jägerstätter's tragic case vividly and clearly illustrates the critical capacity of the deontological moral agent amidst a grotesquely malign ‘moral’ community. This essay argues that contrary to these conclusions, the Jägerstätter case, properly understood, affirms precisely the type of ethics Donagan thinks that it condemns.
Weakly coupled systems of the infinity Laplace equations
Authors: Mitake H. , Tran H.
Published: March 2015

We derive the weakly coupled systems of the infinity Laplace equations via a tug-of-war game introduced by Peres, Schramm, Sheffield, and Wilson (2009). We establish existence, uniqueness results of the solutions, and introduce a new notion of “generalized cones” for systems. By using “generalized cones” we analyze blow-up limits of solutions.
Video capture of crustacean fisheries data as an alternative to on-board observers
Authors: Hold Natalie , Murray Lee G. , Pantin Julia R. , Haig Jodie A. , Hinz Hilmar , Kaiser Michel J.
Published: March 2015

For EU member states to meet the requirements of the Marine Strategy Framework Directive and the reformed Common Fisheries Policy, it will be necessary to improve data collection related to many fisheries that are at present subject to relatively little monitoring or scientific research. This study evaluated the use of on-board camera systems to collect data from Cancer pagurus and Homarus gammarus fisheries. We evaluated the reliability of the hardware and its ability to collect images of sufficient accuracy and precision compared with using on-board observers. Fishers and on-board observers passed animals removed from traps across a defined area. The relationship between the in situ and predicted measurements of carapace length of lobsters or carapace width (CW) of crabs was investigated. The mean difference between the predicted and real crab measurements was −0.853 mm with a standard error of 0.378 mm. Suggesting that the model tends to underestimate the real CW slightly. The mean difference between predicted and real data for lobsters was 0.085 mm with a standard error of 0.208 mm. Sex allocation for crabs based on video images was 100% accurate. All male lobsters were correctly assigned. For lobsters >86 mm in length, the correct female sex allocation was 100% accurate. For smaller lobsters, the accuracy of sex allocation decreased to a low of 51% in lobsters <70 mm. Camera systems were found to be a suitable method for collecting data on the size and sex of crabs and lobsters. The error attributable to using video data rather than manual measurement was less than 3 mm, which is sufficient to detect growth increments in these species. The requirements to collect basic species data are increasing and the ability to do so without on-board observers will reduce the cost implications of these requirements. Future computer automation of image extraction and measurements will increase the application of video systems for data collection.
What's in a Name? A Method for Extracting Information about Ethnicity from Names
Authors: Andrew Harris J.
Published: March 2015

Questions about racial or ethnic group identity feature centrally in many social science theories, but detailed data on ethnic composition are often difficult to obtain, out of date, or otherwise unavailable. The proliferation of publicly available geocoded person names provides one potential source of such data'if researchers can effectively link names and group identity. This article examines that linkage and presents a methodology for estimating local ethnic or racial composition using the relationship between group membership and person names. Common approaches for linking names and identity groups perform poorly when estimating group proportions. I have developed a new method for estimating racial or ethnic composition from names which requires no classification of individual names. This method provides more accurate estimates than the standard approach and works in any context where person names contain information about group membership. Illustrations from two very different contexts are provided: the United States and the Republic of Kenya.
Prior Opioid Use Does Not Impact the Response to Pregabalin in Patients With Fibromyalgia
Authors: Argoff Charles E. , Clair Andrew , Emir Birol , Whalen Ed , Ortiz Marie , Pauer Lynne
Published: March 2015

Objective:

Fibromyalgia (FM) is a chronic pain disorder for which pregabalin is an approved treatment in the United States. Although opioids are not a recommended treatment option, they continue to be used by many FM patients. The impact of patients’ prior opioid use on their subsequent response to pregabalin has not been assessed.

Methods:

This was a pooled analysis of 4 clinical trials to assess the efficacy of pregabalin in FM patients both with and without prior opioid use. Patients were divided into those using opioids prior to the trial and those who were not. The change in least squares mean pain score (assessed by 0 to 10 numeric rating scale) with pregabalin compared with placebo was assessed together with FM symptoms, anxiety, and depression.

Results:

There were 2062 patients in the analysis set, including 371 patients with prior opioid use. Equal numbers of patients were treated with placebo, pregabalin 300 mg/d, and pregabalin 450 mg/d. Pregabalin significantly improved the least squares mean (95% confidence interval) difference in pain score compared with placebo in patients both with and without prior opioid use 0.87 (0.34-1.41) and 0.41 (0.17-0.65), respectively, at 300 mg/d and 0.91 (0.39-1.44) and 0.72 (0.48-0.96) at 450 mg/d (P≤0.001 for all). FM symptoms, anxiety, and depression were also improved with pregabalin compared with placebo, regardless of prior opioid use.

Discussion:

FM patients respond to treatment with pregabalin with significant improvements in pain scores irrespective of prior opioid use. These data could inform treatment decisions for FM patients with prior use of opioids.
Historical species losses in bumblebee evolution
Authors: Condamine Fabien L. , Hines Heather M.
Published: March 2015

Investigating how species coped with past environmental changes informs how modern species might face human-induced global changes, notably via the study of historical extinction, a dominant feature that has shaped current biodiversity patterns. The genus
Bombus
, which comprises 250 mostly cold-adapted species, is an iconic insect group sensitive to current global changes. Through a combination of habitat loss, pathogens and climate change, bumblebees have experienced major population declines, and several species are threatened with extinction. Using a time-calibrated tree of
Bombus
, we analyse their diversification dynamics and test hypotheses about the role of extinction during major environmental changes in their evolutionary history. These analyses support a history of fluctuating species dynamics with two periods of historical species loss in bumblebees. Dating estimates gauge that one of these events started after the middle Miocene climatic optimum and one during the early Pliocene. Both periods are coincident with global climate change that may have extirpated
Bombus
species. Interestingly, bumblebees experienced high diversification rates during the Plio-Pleistocene glaciations. We also found evidence for a major species loss in the past one million years that may be continuing today.
The importance of picking Porter: the Royal Institution, George Porter and the two cultures, 1959–64
Authors: Cole Rupert
Published: March 2015

This paper examines the cultural reasons why in 1964 the Royal Institution (RI) selected George Porter, who became the only person so far to have been Director of the Royal Institution (1966–85), President of the Royal Society (1985–90) and President of the British Association (1985–86) at the same time, to succeed William Lawrence Bragg as the institution's scientific director and resident professor. Porter was established as first choice by an inner group of RI Managers before the formal selection process began. In this article I argue that Porter won their favour by presenting himself, during his tenure as the RI's Professor of Chemistry (1963–66), as a candidate who fitted well with the Managers' ideas about the future role of the RI—ideas that were deeply influenced by the prevailing technocratic visions of ‘science and society’, particularly C. P. Snow's writings on the ‘two cultures’.
Expression of parasite genetic variation changes over the course of infection: implications of within-host dynamics for the evolution of virulence
Authors: Clerc Melanie , Ebert Dieter , Hall Matthew D.
Published: March 2015

How infectious disease agents interact with their host changes during the course of infection and can alter the expression of disease-related traits. Yet by measuring parasite life-history traits at one or few moments during infection, studies have overlooked the impact of variable parasite growth trajectories on disease evolution. Here we show that infection-age-specific estimates of host and parasite fitness components can reveal new insight into the evolution of parasites. We do so by characterizing the within-host dynamics over an entire infection period for five genotypes of the castrating bacterial parasite
Pasteuria ramosa
infecting the crustacean
Daphnia magna
. Our results reveal that genetic variation for parasite-induced gigantism, host castration and parasite spore loads increases with the age of infection. Driving these patterns appears to be variation in how well the parasite maintains control of host reproduction late in the infection process. We discuss the evolutionary consequences of this finding with regard to natural selection acting on different ages of infection and the mechanism underlying the maintenance of castration efficiency. Our results highlight how elucidating within-host dynamics can shed light on the selective forces that shape infection strategies and the evolution of virulence.
Evaluating the metapopulation consequences of ecological traps
Authors: Hale Robin , Treml Eric A. , Swearer Stephen E.
Published: March 2015

Ecological traps occur when environmental changes cause maladaptive habitat selection. Despite their relevance to metapopulations, ecological traps have been studied predominantly at local scales. How these local impacts scale up to affect the dynamics of spatially structured metapopulations in heterogeneous landscapes remains unexplored. We propose that assessing the metapopulation consequences of traps depends on a variety of factors that can be grouped into four categories: the probability of encounter, the likelihood of selection, the fitness costs of selection and species-specific vulnerability to these costs. We evaluate six hypotheses using a network-based metapopulation model to explore the relative importance of factors across these categories within a spatial context. Our model suggests (i) traps are most severe when they represent a large proportion of habitats, severely reduce fitness and are highly attractive, and (ii) species with high intrinsic fitness will be most susceptible. We provide the first evidence that (iii) traps may be beneficial for metapopulations in rare instances, and (iv) preferences for natal-like habitats can magnify the effects of traps. Our study provides important insight into the effects of traps at landscape scales, and highlights the need to explicitly consider spatial context to better understand and manage traps within metapopulations.
Fermentation characteristics of mulberry (Cudrania tricuspidata) fruit vinegar produced by acetic acid bacteria isolated from traditional fermented foods
Authors: Yim Eun-Jung , Jo Seung-Wha , Lee Eun-Sil , Park Hae-Suk , Ryu Myeong-Seon , Uhm Tai-Boong , Kim Hyoun-Young , Cho Sung-Ho
Published: March 2015

To raise the added value of the fruits of Cudrania tricuspidata, Cudrania tricuspidata vinegar was produced and examined for its fermentation conditions. Forty nine acetic acid bacteria with resistance against acetic acid, ethanol, and sulfide as high acetic acid producers were isolated from fermented foods and identified as Acetobacter indonesiensis, A. cerevisiae, A. orientalis, A. tropicalis, A. fabarum, A. pasteurianus, and A. syzygii based on the results of the analysis of the 16S rRNA gene sequences. Among them, two GRAS strains, A. pasteurianus SCMA5 and SCMA6, were finally selected for the production of acetic acid. Optimal vinegar productions were obtained from the medium containing 40% (v/v) fruit juice of Cudrania tricuspidata and 5% (v/v) ethanol at 25°Cfor 72 hr. The sensory panel preferred the vinegar fermented with the SCMA06 to that with the SCM05 strain. The radical scavenger capacity of DPPH was 53% higher than that of the control in the vinegar fermented with the SCMA06 strain. The α-glucosidase inhibitor activity as an index of the antidiabetic drug showed 91% inhibition, which is higher than that of acabose. This study will be helpful for the scale-up production of vinegar with the fruit of Cudrania tricuspidata.
Anti-diabetic effects of Allium tuberosum rottler extracts and lactic acid bacteria fermented extracts in type 2 diabetic mice model
Authors: Kim Bae Jin , Jo Seung Kyeung , Jeong Yoo Seok , Jung Hee Kyoung
Published: March 2015

The anti-diabetic effects of Allium tuberosum Rottler extracts (ATE) and ATE fermented with lactic acid bacteria in db/db mice were evaluated. The electron donating activity of ATE fermented with Lactobacillus plantarum, and Lactobacillus casei, respectively, increased compared to that of ATE, but the superoxide radical scavenging activity of the ATE incubated with L. plantarum decreased. The superoxide radical scavenging activity of the ATE fermented with both L. plantarum and L. casei was similar to that of the ATE. Therefore, fermented ATE (FATE) was prepared for in vivo testing by incubating it with both L. plantarum and L. casei. The db/db mice were divided into six groups: normal (non-diabetic mice), diabetic control (DM), and four experimental groups administered 200 or 400 mg/kg/day ATE (ATE200 and ATE400) and 200 or 400 mg/kg/day FATE (FATE200 and FATE400). Weight gain was significantly inhibited in the FATE200 group compared with that in the other db/db mice groups (p<0.05). The areas under the curve of the ATE400 and FATE400 groups were significantly smaller than that of the DM group in the glucose tolerance evaluation. The serum glucagon-like peptide-1 levels in the ATE400 and FATE400 groups increased. These results indicate that administering ATE and FATE may be effective against anti-hyperglycemia by regulating insulin resistance. In particular, FATE may be beneficial for controlling obesity in type 2 diabetes.
소화효소 저해 및 지방세포 분화 억제활성에 의한 상백피의 항비만 효능
Authors: Wu Yong-Xiang , Kim You-Jeong , Li Sha , Yun Myung-Chul , Yoon Jin-Mi , Kim Jin-Young , Cho Sung-Il , Son Kun-Ho , Kim Taewan
Published: March 2015

Anti-obese effects of mulberry (Morus alba L.) root bark was investigated in vitro by measuring its inhibitory effect against 3T3-L1 preadipocyte differentiation and digestive enzymes such as α-amylase, α-glucosidase and pancreatic lipase. Ethanol extract of mulberry root bark (MRE) showed the potent inhibitory activities on α-amylase, α-glucosidase and pancreatic lipase with IC50 values of 7.86±0.36, 0.12±0.03 and 7.93±0.11 mg/mL, respectively. Furthermore, MRE significantly suppressed cellular lipid accumulation in 3T3-L1 cells in a dose-dependent manner. To elucidate the mechanism of MRE, we performed qRT-PCR and Western blotting for the expression of genes related with adipogenesis and lipogenesis. Treatment of MRE markedly suppressed the protein expression of PPARγ, C/EBPα and SREBP-1c, as well as FAS and ACC, which are the key transcription factors and metabolic enzymes in adipogenesis and lipogenesis. In addition, qRT-PCR analysis indicated that the anti-adipogenesis effect of MRE might be due to its inhibition at transcription levels. These results demonstrate that MRE can effectively suppress adipocyte differentiation and inhibit key enzymes related to obesity. Our findings suggest that mulberry root bark may have a potential benefit in preventing obesity.
Quality characteristics of Hijikia fusiforme extracts with different extraction method
Authors: Kwon Yu-Ri , Youn Kwang-Sup
Published: March 2015

The physiological properties of water extracts from Hizikia fusiformis extracted using different extraction methods
(water extraction, WE; autoclave extraction, AE; high pressure extraction, HPE) were investigated. The freeze-dried powder yields from HPE, AE and WE were 29.33, 27.84 and 23.63%, respectively. The L* and b* color values were higher in WE, while the a* color values were higher in WE and AE. The total sugar content of AE (60.14%) was higher than those of WE (47.10%), HPE (40.97%). The reducing sugar content (7.88%) and protein content (42.83%) of AE was higher than those of WE, and HPE. The uronic acid (5.04%), total free amino acid (785.19 mg/g), taurine (19.16 mg/g), aspartic acid (66.63 mg/g), asparagine (204.84 mg/g), alanine (188.87 mg/g) and ammonium chloride (243.91 mg/g) contents, however, were the highest in HPE. Additionally, the crude polysaccharide yield was higher in HPE (4.75%) than in AE and WE, and the crude saccharide (fucose, galactose, glucose, xylose and fucose) yields were higher in AE. It can be concluded that optimum conditions for the efficient extraction of Hizikia fusiformis depending on components are high pressure and a lower temperature than in the typical process.
svviz: a read viewer for validating structural variants
Authors: Spies Noah , Zook Justin M. , Salit Marc , Sidow Arend
Published: March 2015

Visualizing read alignments is the most effective way to validate candidate SVs with existing data. We present svviz, a sequencing read visualizer for structural variants (SVs) that sorts and displays only reads relevant to a candidate SV. svviz works by searching input bam(s) for potentially relevant reads, realigning them against the inferred sequence of the putative variant allele as well as the reference allele, and identifying reads that match one allele better than the other. Reads are assigned to the proper allele based on alignment score, read pair orientation and insert size. Separate views of the two alleles are then displayed in a scrollable web browser view, enabling a more intuitive visualization of each allele, compared to the single reference genome-based view common to most current read browsers. The web view facilitates examining the evidence for or against a putative variant, estimating zygosity, visualizing affected genomic annotations, and manual refinement of breakpoints. An optional command-line-only interface allows summary statistics and graphics to be exported directly to standard graphics file formats. svviz is open source and freely available from github, and requires as input only structural variant coordinates (called using any other software package), reads in bam format, and a reference genome. Reads from any high-throughput sequencing platform are supported, including Illumina short-read, mate-pair, synthetic long-read (assembled), Pacific Biosciences, and Oxford Nanopore. svviz is open source and freely available fromhttps://github.com/svviz/svviz.
Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads
Authors: Harry Chen Hung-I , Liu Yuanhang , Zou Yi , Lai Zhao , Sarkar Devanand , Huang Yufei , Chen Yidong
Published: March 2015

Background

RNA sequencing (RNA-seq) is a powerful tool for genome-wide expression profiling of biological samples with the advantage of high-throughput and high resolution. There are many existing algorithms nowadays for quantifying expression levels and detecting differential gene expression, but none of them takes the misaligned reads that are mapped to non-exonic regions into account. We developed a novel algorithm, XBSeq, where a statistical model was established based on the assumption that observed signals are the convolution of true expression signals and sequencing noises. The mapped reads in non-exonic regions are considered as sequencing noises, which follows a Poisson distribution. Given measureable observed and noise signals from RNA-seq data, true expression signals, assuming governed by the negative binomial distribution, can be delineated and thus the accurate detection of differential expressed genes.

Results

We implemented our novel XBSeq algorithm and evaluated it by using a set of simulated expression datasets under different conditions, using a combination of negative binomial and Poisson distributions with parameters derived from real RNA-seq data. We compared the performance of our method with other commonly used differential expression analysis algorithms. We also evaluated the changes in true and false positive rates with variations in biological replicates, differential fold changes, and expression levels in non-exonic regions. We also tested the algorithm on a set of real RNA-seq data where the common and different detection results from different algorithms were reported.

Conclusions

In this paper, we proposed a novel XBSeq, a differential expression analysis algorithm for RNA-seq data that takes non-exonic mapped reads into consideration. When background noise is at baseline level, the performance of XBSeq and DESeq are mostly equivalent. However, our method surpasses DESeq and other algorithms with the increase of non-exonic mapped reads. Only in very low read count condition XBSeq had a slightly higher false discovery rate, which may be improved by adjusting the background noise effect in this situation. Taken together, by considering non-exonic mapped reads, XBSeq can provide accurate expression measurement and thus detect differential expressed genes even in noisy conditions.
Mutational oncogenic signatures on structurally resolved protein interacting interfaces
Authors: Garcia-Alonso Luz , Dopazo Joaquin
Published: March 2015

The importance of the context of interactions in the proteins mutated in cancer is long known. However, our knowledge on how mutations affecting to protein-protein interactions (PPIs) are related to cancer occurrence and progression is still poor. Here, we extracted the missense somatic mutations from 5920 cancer patients of 33 different cancer types, taken from the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), and mapped them onto a structurally resolved interactome, which integrates three-dimensional atomic-level models of domain-domain interactions with experimentally determined PPIs, involving a total of 7580 unique interacting domains that participate in 13160 interactions connecting 4996 proteins. We observed that somatic nonsynonymous mutations tend to concentrate in ordered regions of the affected proteins and, within these, they have a clear preference for the interacting interfaces. Also, we have identified more than 250 interacting interfaces candidate to drive cancer. Examples demonstrate how mutations in the interacting interfaces are strongly associated with patient survival time, while similar mutations in other areas of the same proteins lack this association. Our results suggest that the perturbation caused by cancer mutations in protein interactions is an important factor in explaining the heterogeneity between cancer patients.
Different Coupling Modes Mediate Cortical Cross-Frequency Interactions
Authors: Helfrich Randolph F. , Herrmann Christoph S. , Engel Andreas K. , Schneider Till R.
Published: March 2015

Cross-frequency coupling (CFC) has been suggested to constitute a highly flexible mechanism for cortical information gating and processing, giving rise to conscious perception and various higher cognitive functions in humans. In particular, it might provide an elegant tool for information integration across several spatiotemporal scales within nested or coupled neuronal networks. However, it is currently unknown whether low frequency (theta/alpha) or high frequency gamma oscillations orchestrate cross-frequency interactions, raising the question of who is master and who is slave. While correlative evidence suggested that at least two distinct CFC modes exist, namely phase-amplitude-coupling (PAC) and amplitude-envelope-correlations (AEC), it is currently unknown whether they subserve distinct cortical functions. Novel non-invasive brain stimulation tools, such as transcranial alternating current stimulation (tACS), now provide the unique opportunity to selectively entrain the low or high frequency component and study subsequent effects on CFC. Here, we demonstrate the differential modulation of CFC during selective entrainment of alpha or gamma oscillations. Our results reveal that entrainment of the low frequency component increased PAC, where gamma power became preferentially locked to the trough of the alpha oscillation, while gamma-band entrainment reduced alpha power through enhanced AECs. These results provide causal evidence for the functional role of coupled alpha and gamma oscillations for visual processing.
Versatile sample environments and automation for biological solution X-ray scattering experiments at the P12 beamline (PETRA III, DESY)
Authors: Blanchet Clement E. , Spilotros Alessandro , Schwemmer Frank , Graewert Melissa A. , Kikhney Alexey , Jeffries Cy M. , Franke Daniel , Mark Daniel , Zengerle Roland , Cipriani Florent , Fiedler Stefan , Roessle Manfred , Svergun Dmitri I.
Published: March 2015

A high-brilliance synchrotron P12 beamline of the EMBL located at the PETRA III storage ring (DESY, Hamburg) is dedicated to biological small-angle X-ray scattering (SAXS) and has been designed and optimized for scattering experiments on macromolecular solutions. Scatterless slits reduce the parasitic scattering, a custom-designed miniature active beamstop ensures accurate data normalization and the photon-counting PILATUS 2M detector enables the background-free detection of weak scattering signals. The high flux and small beam size allow for rapid experiments with exposure time down to 30–50 ms covering the resolution range from about 300 to 0.5 nm. P12 possesses a versatile and flexible sample environment system that caters for the diverse experimental needs required to study macromolecular solutions. These include an in-vacuum capillary mode for standard batch sample analyses with robotic sample delivery and for continuous-flow in-line sample purification and characterization, as well as an in-air capillary time-resolved stopped-flow setup. A novel microfluidic centrifugal mixing device (SAXS disc) is developed for a high-throughput screening mode using sub-microlitre sample volumes. Automation is a key feature of P12; it is controlled by a beamline meta server, which coordinates and schedules experiments from either standard or nonstandard operational setups. The integrated SASFLOW pipeline automatically checks for consistency, and processes and analyses the data, providing near real-time assessments of overall parameters and the generation of low-resolution models within minutes of data collection. These advances, combined with a remote access option, allow for rapid high-throughput analysis, as well as time-resolved and screening experiments for novice and expert biological SAXS users.
The effects of second screen use on sponsor brand awareness: a dual coding theory perspective
Authors: Jensen Jonathan A. , Walsh Patrick , Cobbs Joe , Turner Brian A.
Published: March 2015

Purpose

– The purpose of this paper is to investigate how simultaneous use of devices such as personal computers, tablets and smartphones impacts the sponsors that receive brand integration during the broadcasts. Advances in technology now allow fans to consume broadcasts of televised events almost anywhere via personal computers, tablets and smartphones. These devices are also frequently utilized as “second screens” to communicate with fellow consumers on social media, access additional content or otherwise multitask during televised consumption.

Design/methodology/approach

– An initial study served to test the applicability of the theoretical framework of a dual coding theory in this new context, followed by a 3 × 2 between-subjects design utilized to advance understanding of the influence of second screens on brand awareness of the sponsors of televised events.

Findings

– Results demonstrated that both brand recognition and recall were reduced by second screen activity across nearly all audio or visual consumption experiences. Further, while second screen use in an audiovisual setting did not interfere with consumers’ ability to recognize brands, indicating they were able to multitask and were not distracted, it inhibited their ability to recall brands from memory. This result provides evidence that second screen use may interfere with elaborative rehearsal and reduce cognitive capacity.

Practical implications

– Given that marketers are investing more resources than ever to achieve brand integration during televised events, these findings suggest that brands face challenges in achieving a requisite return on their investments.

Originality/value

– This study represents the first empirical investigation of the impact of consumers’ use of second screens in the academic literature, and has important implications for the sponsors of televised events.
Impact of consumers’ effort investments on buying decisions
Authors: Lala Vishal , Chakraborty Goutam
Published: March 2015

Purpose

– This study aims to explore the effect of amount of effort invested by consumers toward the purchase of a product on the amount they will spend on the product. Authors argue that greater effort on the part of the consumer will lead to an irrational focus on sunk effort causing them to spend more.

Design/methodology/approach

– To explore the effect of amount of effort invested by consumers toward the purchase of a product on the amount they will spend on the product. Authors argue that greater effort on the part of the consumer will lead to an irrational focus on sunk effort, causing them to spend more.

Findings

– Consumers who invest more effort in buying, spend more on the product in a bid to justify their decision to invest effort in the first place. This effect is stronger in the presence of decisional control.

Originality/value

– Much academic research has examined adverse effects of effort spent by consumers and has sought to make things easier for consumers. This research shows that making it harder rather than easier, can make consumers willing to spend more money, particularly when they view themselves in control.
Consumer attitude and behavioural intention towards Internet banking adoption in India
Authors: Bashir Irfan , Madhavaiah Chendragiri
Published: March 2015

Purpose

– The purpose of this paper is to provide an insight into the determinants of the customers’ attitude and behavioural intention to use Internet banking services, paying special attention to the role of perceived risk, trust, enjoyment, website design and social influence.

Design/methodology/approach

– A research model grounded on the technology acceptance model (TAM) reflecting the effects of trust, perceived risk, perceived enjoyment, perceived website design and social influence on TAM constructs is proposed. The structural equation modelling technique is used to analyse a sample of 697 individual Internet banking users in India through an online survey.

Findings

– The results of data analysis confirm some of the hypotheses drawn from the literature. Consistent with some of the other studies, perceived usefulness, perceived ease of use, trust and perceived enjoyment are found to be immediate direct determinants of customers’ attitude towards using Internet banking. Attitude, perceived risk, perceived enjoyment and trust determine the customers’ behavioural intentions to use Internet banking. Although the direct effect of perceived website design is significant only on perceived ease of use, its indirect effects are significant on perceived usefulness, attitude and behavioural intentions. Furthermore, perceived enjoyment exerts both direct and indirect effects on perceived usefulness but exerts only direct effect on perceived ease of use.

Research limitations/implications

– Generalizability of the research is a practical limitation in consumer research studies and the present study is not an exception to that. The current study focused only on some technological, behavioural and attitudinal factors, and many customer-specific factors and other psychographic and behavioural factors such as cost, perceived value, service quality and satisfaction, which can provide more significant insight into the adoption process, are not a part of the scope of the study.

Practical implications

– This research specifies the implications in three perspectives, viz., theoretical, methodological and managerial. Furthermore, this study provides the practical recommendations to enhance customer trust and guidelines to reduce perceived risk. The most significant implication for the banking sector is that apart from offering useful and user-friendly services, they need to build a trusting relationship with customers.

Originality/value

– This study extends existing body of Internet banking literature by incorporating trust and risk perceptions. The effects of website design and perceived enjoyment on Internet banking acceptance have been examined and were found to be significant in the Indian context. In addition, it enables us to contribute to the current literature on the emerging Indian Internet banking services (IBS) market, which is largely under-researched.
Daily environmental conditions determine the competition–facilitation balance for plant water status
Authors: Wright Alexandra , Schnitzer Stefan A. , Reich Peter B.
Published: March 2015

Plants compete with their neighbours for a finite set of limiting resources, and this decreases individual plant performance, growth and survival. However, neighbouring plants also affect each other in positive ways.

Positive facilitative effects can occur when neighbouring plants ameliorate harsh abiotic conditions (temperature, wind and high irradiation). Thus, when environmental conditions are severe, the importance of facilitation may increase. The co‐occurrence and masking effects of competition and facilitation among neighbouring plants have made it difficult to tease them apart in the past.

We planted bur oak acorns (Quercus macrocarpa) into an experimental diversity gradient in a centralMNgrassland that provided a gradient in plant biomass. We predicted that greater biomass of neighbours would increase both competition and facilitation as measured by impacts on the minimum leaf water potential reached on any given day. Under moderate conditions, competition should predominate, but under hot/dry conditions, facilitation should become more important. We measured temperature, humidity and soil moisture in these plots for two growing seasons, as well as oak seedling leaf water potential across a range of daily conditions.

On cool/humid days, plant interactions were dominated by competition for soil water: leaf water potentials of juvenile oaks were lower in plots with greater herbaceous biomass (and higher diversity). Conversely, on hot/dry days, facilitation of the microclimate determined the net effect of plants on their neighbours: leaf water potentials of juvenile oaks were higher in plots with higher herbaceous diversity and biomass.

Synthesis. In terms of plant water status, plant interactions among neighbours can flip from net negative (competition) to net positive (facilitation) depending on daily abiotic conditions. The relative importance of both positive and negative interactions for plant water status may affect the overall performance of plants over time.
The role of SES in Chinese (L1) and English (L2) word reading in Chinese‐speaking kindergarteners
Authors: Liu Duo , Chung Kevin K. H. , McBride Catherine
Published: March 2015

The present study investigated the relationships between socioeconomic status (SES) and word reading in both Chinese (L1) and English (L2), with children's cognitive/linguistic skills considered as mediators and/or moderators. One hundred ninety‐nine Chinese kindergarteners in Hong Kong with diverse SES backgrounds participated in this study. SES explained unique variance in English word reading even after age, phonological processing, vocabulary and working memory were controlled. However, the effect of SES on Chinese word reading became nonsignificant when these control variables were included. Moreover, phonological awareness showed a full mediating effect on the relationship between SES and Chinese word reading. Both phonological awareness and vocabulary were found to partially mediate the association between SES and English word reading. These findings complement our understanding of the relation between SES and reading development in Chinese societies and may have policy or intervention development implications.
Where You Live Matters: Quality and Racial/Ethnic Disparities in Schizophrenia Care in Four State Medicaid Programs
Authors: Horvitz‐Lennon Marcela , Volya Rita , Garfield Rachel , Donohue Julie M. , Lave Judith R. , Normand Sharon‐Lise T.
Published: March 2015

Objective

To determine whether (a) quality in schizophrenia care varies by race/ethnicity and over time and (b) these patterns differ across counties within states.

Data Sources

Medicaid claims data from California, Florida, New York, and North Carolina during 2002–2008.

Study Design

We studied black, Latino, and white Medicaid beneficiaries with schizophrenia. Hierarchical regression models, by state, quantified person and county effects of race/ethnicity and year on a composite quality measure, adjusting for person‐level characteristics.

Principal Findings

Overall, our cohort included 164,014 person‐years (41–61 percent non‐whites), corresponding to 98,400 beneficiaries. Relative to whites, quality was lower for blacks in every state and also lower for Latinos except in North Carolina. Temporal improvements were observed in California and North Carolina only. Within each state, counties differed in quality and disparities. Between‐county variation in the black disparity was larger than between‐county variation in the Latino disparity in California, and smaller in North Carolina; Latino disparities did not vary by county in Florida. In every state, counties differed in annual changes in quality; by 2008, no county had narrowed the initial disparities.

Conclusions

For Medicaid beneficiaries living in the same state, quality and disparities in schizophrenia care are influenced by county of residence for reasons beyond patients’ characteristics.
RACIALLY HOMOPHILOUS SOCIAL TIES AND INFORMAL SOCIAL CONTROL
Authors: WARNER BARBARA D. , SWARTZ KRISTIN , HAWK SHILA RENÉ
Published: March 2015

Social disorganization theory argues that racial/ethnic heterogeneity is a key neighborhood characteristic leading to social disorganization and, consequently, higher levels of crime. Heterogeneity's effect is argued to be a result of its fragmentation of social ties along racial/ethnic lines, which creates racially homophilous social networks with few ties bridging racial/ethnic groups. Most studies of social ties in social disorganization models, however, have examined their quantity and left unaddressed the extent to which ties are within or across different racial groups. This study goes beyond previous studies by examining the effects of both racially homophilous and interracial friendship networks on informal social control. Using multilevel models and data from 66 neighborhoods with approximately 2,300 respondents, we found that heterogeneity actually increased the average percentage of residents with interracial friendship networks, but the percentage of residents with interracial networks decreased the likelihood of informal social control. In contrast, the percentage of residents with White racially homophilous networks increased the likelihood of informal social control. Examining the microcontext of individuals’ networks, however, we found residents with interracial ties reported higher likelihoods of informal social control and that this effect was enhanced in neighborhoods with higher percentages of non‐White racially homophilous networks.