bluuebunny/crossref_metadata_2025_split huggingface dataset:
A scalable strategy for high-throughput GFP tagging of endogenous human proteins
Authors: Leonetti Manuel D. , Sekine Sayaka , Kamiyama Daichi , Weissman Jonathan S. , Huang Bo 
Published: June 2016

Significance
The function of a large fraction of the human proteome still remains poorly characterized. Tagging proteins with a functional sequence is a powerful way to access function, and inserting tags at endogenous genomic loci allows the preservation of a near-native cellular background. To characterize the cellular role of human proteins in a systematic manner and in a native context, we developed a method for tagging endogenous human proteins with GFP that is both rapid and readily applicable at a genome-wide scale. Our approach allows studying both localization and interaction partners of the protein target. Our results pave the way for the large-scale generation of endogenously tagged human cell lines for a systematic functional interrogation of the human proteome.
Microstructural evolution study of severely deformed commercial aluminium by transmission Kikuchi diffraction
Authors: Naghdy S. , Percq L. L. , Serret R. , Petrov R. , Hertelé S. , Kestens L. , Verleysen P. 
Published: June 2016

Commercially pure aluminium was selected as a model fcc material for a detailed investigation of the microstructural and textural evolution during processing by high pressure torsion (HPT). Vickers hardness measurements reveal that: the hardness is the lowest where the lowest strain is imposed and increases with increasing strain until saturation hardness is obtained. The microstructural evolution is investigated by means of electron backscattered diffraction and transmission Kikuchi diffraction. During HPT a grain fragmentation process takes place: within the original grains dislocations aggregate, resulting in the creation of very fine grains separated first by low and later by high angle grain boundaries. At a strain level of [Formula: see text] a simple shear texture of fcc structure was observed. This paper is part of a Themed Issue on Aluminium-based materials: processing, microstructure, properties, and recycling.
Comparing Stream Restoration Project Effectiveness Using a Programmatic Evaluation of Salmonid Habitat and Fish Response
Authors: O'Neal Jennifer S. , Roni Phil , Crawford Bruce , Ritchie Anna , Shelly Alice 
Published: June 2016

Abstract
Hundreds of millions of dollars have been spent on stream restoration projects to benefit salmonids and other aquatic species across the Pacific Northwest, though only a small percentage of these projects are monitored to evaluate effectiveness and far fewer are tracked for more than 1 or 2 years. The Washington State Salmon Recovery Board and the Oregon Watershed Enhancement Board have spent more than US$500 million on salmonid habitat restoration projects since 1999. We used a multiple before-after–control-impact design to programmatically evaluate the reach-scale physical and biological effectiveness of a subset of restoration actions. A total of 65 projects in six project categories (fish passage, instream habitat, riparian planting, livestock exclusion, floodplain enhancement, and habitat protection) were monitored over an 8-year period. We conducted habitat, fish, and macroinvertebrate surveys to calculate the following indicators: longitudinal pool cross section and depth, riparian shade and cover, large woody debris volumes, fish density, macroinvertebrate indices, and upland vegetation condition class. Results indicate that four categories (instream habitat, livestock exclusions, floodplain enhancements, and riparian plantings) have shown significant improvements in physical habitat after 5 years. Abundance of juvenile Coho Salmon Oncorhynchus kisutch increased significantly at fish passage projects and floodplain enhancement projects, but significant results were not detected for other fish species. Moreover, the biological response indicators of juvenile salmonid abundance and macroinvertebrate indices showed declines at instream habitat and habitat protection projects, respectively. Our results indicate that a subset of projects can be effectively evaluated programmatically, but power and sample size estimates indicate that two or more years of preproject data are necessary to adequately determine the effectiveness of many project types, particularly for fish. Programmatic evaluations of project effectiveness should include adequate preproject sampling and multiseason monitoring for fish species to address issues of variability that are likely to be encountered in large-scale monitoring programs.
Received September 16, 2015; accepted February 7, 2016 Published online June 6, 2016
What Can We Learn about the Effects of Food Stamps on Obesity in the Presence of Misreporting?
Authors: Almada Lorenzo , McCarthy Ian , Tchernis Rusty 
Published: June 2016

AbstractThere is an increasing perception among policy makers that food stamp benefits contribute positively to adult obesity rates. We show that these results are heavily dependent on one's assumptions regarding the accuracy of reported food stamp participation. When allowing for misreporting, we find no evidence that Supplemental Nutrition Assistance Program participation significantly increases the probability of being obese or overweight among adults. Our results also highlight the inherent bias and inconsistency of common point estimates when ignoring misreporting, with treatment effects from instrumental variable methods exceeding the nonparametric upper bounds by over 200% in some cases.
Who Really Benefits from Agricultural Subsidies? Evidence from Field‐level Data
Authors: Kirwan Barrett E. , Roberts Michael J. 
Published: June 2016

AbstractIf agricultural subsidies are largely capitalized into farmland values through their effect on rental rates, then expanding support for agriculture may not benefit farmers who rent the land they farm. Existing evidence on the incidence of subsidies on cash rental rates is mixed. Identification is obscured by unobserved or imprecisely measured factors that tend to be correlated with subsidies, especially land quality and time‐varying factors like commodity prices and adverse weather events. A problem that has received less attention is the fact that subsidies and land quality on rented land may differ from owned land. Since most farms possess both rented and owned acreage, farm‐level measures of subsidies, land values, and rental rates may bias estimated incidence. Using a new, field‐level data set that, for the first time, precisely links subsidies to land parcels, we show that this bias is considerable: where farm‐level estimates suggest an incidence of 42–49 cents of the marginal subsidy dollar, field‐level estimates from the same farms indicate that landlords capture just 20–28 cents. The size of the farm and the duration of the rental arrangement have substantial effects. Incidence falls by 5–15 cents when doubling total operated acres, and the incidence falls by 0.1–0.8 cents with each additional year of the rental arrangement. Low incidence of subsidies on rents combined with the farm‐size and duration effects suggest that farmers renting land have monopsony power.
MetalPredator: a web server to predict iron–sulfur cluster binding proteomes
Authors: Valasatava Yana , Rosato Antonio , Banci Lucia , Andreini Claudia 
Published: June 2016

Abstract
Motivation: The prediction of the iron–sulfur proteome is highly desirable for biomedical and biological research but a freely available tool to predict iron–sulfur proteins has not been developed yet.
Results: We developed a web server to predict iron–sulfur proteins from protein sequence(s). This tool, called MetalPredator, is able to process complete proteomes rapidly with high recall and precision.
Availability and Implementation: The web server is freely available at: http://metalweb.cerm.unifi.it/tools/metalpredator/.
Contact: andreini@cerm.unifi.it
Supplementary information: Supplementary data are available at Bioinformatics online.
Predicting regulatory variants with composite statistic
Authors: Li Mulin Jun , Pan Zhicheng , Liu Zipeng , Wu Jiexing , Wang Panwen , Zhu Yun , Xu Feng , Xia Zhengyuan , Sham Pak Chung , Kocher Jean-Pierre A. , Li Miaoxin , Liu Jun S. , Wang Junwen 
Published: June 2016

Abstract
Motivation: Prediction and prioritization of human non-coding regulatory variants is critical for understanding the regulatory mechanisms of disease pathogenesis and promoting personalized medicine. Existing tools utilize functional genomics data and evolutionary information to evaluate the pathogenicity or regulatory functions of non-coding variants. However, different algorithms lead to inconsistent and even conflicting predictions. Combining multiple methods may increase accuracy in regulatory variant prediction.
Results: Here, we compiled an integrative resource for predictions from eight different tools on functional annotation of non-coding variants. We further developed a composite strategy to integrate multiple predictions and computed the composite likelihood of a given variant being regulatory variant. Benchmarked by multiple independent causal variants datasets, we demonstrated that our composite model significantly improves the prediction performance.
Availability and Implementation: We implemented our model and scoring procedure as a tool, named PRVCS, which is freely available to academic and non-profit usage at http://jjwanglab.org/PRVCS.
Contact: wang.junwen@mayo.edu, jliu@stat.harvard.edu, or limx54@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Accurate self-correction of errors in long reads using de Bruijn graphs
Authors: Salmela Leena , Walve Riku , Rivals Eric , Ukkonen Esko 
Published: June 2016

Abstract

Motivation
New long read sequencing technologies, like PacBio SMRT and Oxford NanoPore, can produce sequencing reads up to 50 000 bp long but with an error rate of at least 15%. Reducing the error rate is necessary for subsequent utilization of the reads in, e.g. de novo genome assembly. The error correction problem has been tackled either by aligning the long reads against each other or by a hybrid approach that uses the more accurate short reads produced by second generation sequencing technologies to correct the long reads.

Results
We present an error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are further polished using long-distance dependencies that are found using multiple alignments. According to our experiments, the proposed method is the most accurate one relying on long reads only for read sets with high coverage. Furthermore, when the coverage of the read set is at least 75×, the throughput of the new method is at least 20% higher.

Availability and Implementation
LoRMA is freely available at http://www.cs.helsinki.fi/u/lmsalmel/LoRMA/.
Is Odette an Artist? Approaching Female Creativity in Proust’s
À la recherche du temps perdu
Authors: Hartley Julia Caterina 
Published: June 2016

Abstract

This article proposes to broaden our understanding of artistic activity in Proust’s
À la recherche du temps perdu
through the example of Odette Swann’s act of self-fashioning in the conclusion of ‘Autour de Mme Swann’. The article opens with an overview of the relationship between women and the arts in
À la recherche
: Proust’s female characters, apart from actresses, do not express themselves through the canonical arts. But Proust also depicts creative activities of a more domestic nature, not usually considered art forms. This article posits that
À la recherche
destabilizes hierarchical categorizations of what should be considered superior or inferior forms of creative expression. As a result, the passages concerned with Odette’s
toilettes
should be considered as integral parts of the novel’s exploration of the nature of art. Odette’s transformation from the Botticellian ‘pièce de musée’ desired by her husband into a new artefact of her own design is considered in dialogue with Charles Baudelaire’s essay ‘Le Peintre de la vie moderne’. Proust’s Odette can be viewed as a response both to Baudelaire’s suggestion that female adornment is an aesthetic endeavour and to the complex twofold temporality that Baudelaire finds behind both beauty and great art.
Towards Biopolitical Ecocriticism: The Example of the
Manifeste pour les ‘produits’ de haute nécessité
Authors: Hardwick Louise 
Published: June 2016

Abstract

This article undertakes a cultural and political examination of the
Manifeste pour les ‘produits’ de haute nécessité
, a manifesto co-authored by a collective of leading Martiniquan cultural figures, including Patrick Chamoiseau and Édouard Glissant, in response to the general strikes of 2009 in Guadeloupe, Martinique, French Guiana, and Réunion. These strikes focused metropolitan attention on the high cost of living or ‘la vie chère’. After a discussion of the aesthetics of the manifesto, with particular attention to the dichotomy it develops between
le prosaïque
and
le poétique
and the wider role of culture in challenging neo-liberalism’s global hold which is advanced by the
Manifesto
, this article introduces the new methodology of biopolitical ecocriticism. A biopolitical ecocritical reading of the manifesto, building on the biopolitical work of Foucault through reference to ecocriticism and the philosophical works of Edgar Morin and André Gorz, reveals the fundamental links between global governance and natural life, raising urgent questions about the relationship between language, life, the environment, history, and politics.
Weighted parallel contributions of binocular correlation and match signals to conscious perception of depth
Authors: Fujita Ichiro , Doi Takahiro 
Published: June 2016

Binocular disparity is detected in the primary visual cortex by a process similar to calculation of local cross-correlation between left and right retinal images. As a consequence, correlation-based neural signals convey information about false disparities as well as the true disparity. The false responses in the initial disparity detectors are eliminated at later stages in order to encode only disparities of the features correctly matched between the two eyes. For a simple stimulus configuration, a feed-forward nonlinear process can transform the correlation signal into the match signal. For human observers, depth judgement is determined by a weighted sum of the correlation and match signals rather than depending solely on the latter. The relative weight changes with spatial and temporal parameters of the stimuli, allowing adaptive recruitment of the two computations under different visual circumstances. A full transformation from correlation-based to match-based representation occurs at the neuronal population level in cortical area V4 and manifests in single-neuron responses of inferior temporal and posterior parietal cortices. Neurons in area V5/MT represent disparity in a manner intermediate between the correlation and match signals. We propose that the correlation and match signals in these areas contribute to depth perception in a weighted, parallel manner.
This article is part of the themed issue ‘Vision in our three-dimensional world’.
Defining the V5/MT neuronal pool for perceptual decisions in a visual stereo-motion task
Authors: Krug Kristine , Curnow Tamara L. , Parker Andrew J. 
Published: June 2016

In the primate visual cortex, neurons signal differences in the appearance of objects with high precision. However, not all activated neurons contribute directly to perception. We defined the perceptual pool in extrastriate visual area V5/MT for a stereo-motion task, based on trial-by-trial co-variation between perceptual decisions and neuronal firing (choice probability (CP)). Macaque monkeys were trained to discriminate the direction of rotation of a cylinder, using the binocular depth between the moving dots that form its front and rear surfaces. We manipulated the activity of single neurons trial-to-trial by introducing task-irrelevant stimulus changes: dot motion in cylinders was aligned with neuronal preference on only half the trials, so that neurons were strongly activated with high firing rates on some trials and considerably less activated on others. We show that single neurons maintain high neurometric sensitivity for binocular depth in the face of substantial changes in firing rate. CP was correlated with neurometric sensitivity, not level of activation. In contrast, for individual neurons, the correlation between perceptual choice and neuronal activity may be fundamentally different when responding to different stimulus versions. Therefore, neuronal pools supporting sensory discrimination must be structured flexibly and independently for each stimulus configuration to be discriminated.
This article is part of the themed issue ‘Vision in our three-dimensional world'.
Marine Ecosystems as Complex Adaptive Systems: Emergent Patterns, Critical Transitions, and Public Goods
Authors: Hagstrom George I. , Levin Simon A. 
Published: June 2016

AbstractComplex adaptive systems provides a unified framework for explaining ecosystem phenomena. In the past twenty years, complex adaptive systems has been sharpened from an abstract concept into a series of tools that can be used to solve concrete problems. These advances have been led by the development of new techniques for coupling ecological and evolutionary dynamics, for integrating dynamics across multiple scales of organization, and for using data to infer the complex interactions among different components of ecological systems. Focusing on the development and usage of these new methods, we explore how they have led to an improved understanding of three universal features of complex adaptive systems, emergent patterns; tipping points and critical phenomena; and cooperative behavior. We restrict our attention primarily to marine ecosystems, which provide numerous successful examples of the application of complex adaptive systems. Many of these are currently undergoing dramatic changes due to anthropogenic perturbations, and we take the opportunity to discuss how complex adaptive systems can be used to improve the management of public goods and to better preserve critical ecosystem services.
AFM-assisted investigation of conformal coatings in electronics
Authors: Szocinski Michal 
Published: June 2016

Purpose
This paper aims to presents a new method of investigation of local properties of conformal coatings utilized in microelectronics.

Design/methodology/approach
It is based on atomic force microscopy (AFM) technique supplemented with the ability of local electrical measurements, which apart from topography acquisition allows recording of local impedance spectra, impedance imaging and dc current mapping. Potentialities of the proposed AFM-assisted approach have been demonstrated on commercially available epoxy-coated electronic printed boards in as-received state and after six-year service.

Findings
The technique proved to be capable of identification, spatial localization and characterization of conformal coating defects.

Practical implications
The proposed approach can be utilized for assessment of protective film state in such demanding fields as electronics or electrotechnics where the classical techniques of anticorrosion coatings investigation cannot be employed due to small element dimensions and relatively low coating thickness.

Originality/value
The approach adopted by the author is novel in the field of organic coatings investigation.
The corrosion behavior of Cu/Cr containing tube pile steel in half-immersion environment
Authors: Liu X.Q. , Liu Z.L. , Hu J.D. , Hou Z.G. , Tian Q.C. , Wang H.Z. 
Published: June 2016

Purpose
The purpose of this study is to explore the corrosion behaviors of tube pile steel with the addition of 0.2 per cent Cu and 0.2 per cent Cu-0.2 per cent Cr in half-immersion environment.

Design/methodology/approach
The electrochemical corrosion behaviors of tube pile steel with different alloy-elements addition were identified using the polarization curve method and electrochemical impedance spectroscopy technique. Corrosion product and its morphology were analyzed by X-ray diffraction, optical microscope and scanning electron microscopy.

Findings
Results indicate that the most serious corrosion occurred in the liquid-air interface zone due to the higher oxygen and water concentration. With the addition of Cu and Cu-Cr, pits were getting smaller and denser, transforming the corrosion type from pitting corrosion to uniform corrosion gradually. Rust layer containing Cu/Cr tended to compact and inhibited the anodic process, while the enrichment of Cu/Cr in rust layer decelerated the dissolution of substrate, thus the expanding of pits was suppressed.

Originality/value
This paper studied the corrosion behaviors of liquid-air interface zone of tube pile steel and verified the transformation of corrosion type with adding Cu, Cu/Cr elements.
Corrosion behaviors of weathering steel 09CuPCrNi welded joints in simulated marine atmospheric environment
Authors: Gong Lihua , Xing Qing , Wang Huihuang 
Published: June 2016

Purpose
The purpose of this paper is to investigate the effect of welding procedure on the corrosion behaviors of weathering steel 09CuPCrNi in marine atmospheric environment. The corrosion processes of weathering steel 09CuPCrNi and its welded joints in marine atmospheric environment were simulated by a salt spray dry-wet test.

Design/methodology/approach
The corrosion behaviors of the base metal and the welded joints at corrosion times of 2, 4, 8, 12, 24 weeks were investigated by weight loss test, electrochemical techniques, scanning electron microscope (SEM) and electron probe micro-analyzer (EPMA). The corrosion rates, as well as the morphologies and electrochemical characteristics of corrosion products, the distribution of major alloying elements in rust layer were obtained. The influence of welding on the atmospheric corrosion of 09CuPCrNi was studied.

Findings
The results indicate that the corrosion rate of the 09CuPCrNi welded joints decreases gradually with the corrosion time, and the major alloying elements are enriched in the inner rust layer, which are similar to that of the base metal. In the early stage during the corrosion process, the welded joints with inhomogeneous structure show the poorer corrosion resistance than that of the base metal. However, it looks the opposite way around in the late corrosion stage, when the uniform corrosion products with even thickness of the base metal tend to detach from the substrate easier and earlier and resulting in cracks, which increase the corrosion rate comparatively with that of the welded joints.

Originality/value
09CuPCrNi low alloy steel is a kind of typical weathering steel developed in China which is similar to Corten A developed by USA. Nowadays, 09CuPCrNi low alloy steel is widely adopted in many fields which require welding processes. In the past years, the research of weathering steel welded joints was mainly concentrated on the strength, toughness and weldability. Less work has been done to investigate the difference of corrosion evolution and characteristics between the base metal and its welded joints. Thus, the main objective of the present work was to analyze the influence of welding on the atmospheric corrosion.