bluuebunny/crossref_metadata_2025_split huggingface dataset:
Was Everything Bigger in Texas? Characterization and Trends of a Land-Based Recreational Shark Fishery
Authors: Ajemian Matthew J. , Jose Philip D. , Froeschke John T. , Wildhaber Mark L. , Stunz Gregory W. 
Published: November 2016

Abstract
Although current assessments of shark population trends involve both fishery-independent and fishery-dependent data, the latter are generally limited to commercial landings that may neglect nearshore coastal habitats. Texas has supported the longest organized land-based recreational shark fishery in the United States, yet no studies have used this “non-traditional” data source to characterize the catch composition or trends in this multidecadal fishery. We analyzed catch records from two distinct periods straddling heavy commercial exploitation of sharks in the Gulf of Mexico (historical period = 1973–1986; modern period = 2008–2015) to highlight and make available the current status and historical trends in Texas’ land-based shark fishery. Catch records describing large coastal species (&gt;1,800 mm stretched total length [STL]) were examined using multivariate techniques to assess catch seasonality and potential temporal shifts in species composition. These fishery-dependent data revealed consistent seasonality that was independent of the data set examined, although distinct shark assemblages were evident between the two periods. Similarity percentage analysis suggested decreased contributions of Lemon Shark Negaprion brevirostris over time and a general shift toward the dominance of Bull Shark Carcharhinus leucas and Blacktip Shark C. limbatus. Comparisons of mean STL for species captured in historical and modern periods further identified significant decreases for both Bull Sharks and Lemon Sharks. Size structure analysis showed a distinct paucity of landed individuals over 2,000 mm STL in recent years. Although inherent biases in reporting and potential gear-related inconsistencies undoubtedly influenced this fishery-dependent data set, the patterns in our findings documented potential declines in the size and occurrence of select large coastal shark species off Texas, consistent with declines reported in the Gulf of Mexico. Future management efforts should consider the use of non-traditional fishery-dependent data sources, such as land-based records, as data streams in stock assessments.
Received January 8, 2016; accepted August 17, 2016
Tree invasions and biosecurity: eco-evolutionary dynamics of hitchhiking fungi
Authors: Burgess Treena I. , Crous Casparus J. , Slippers Bernard , Hantula Jarkko , Wingfield Michael J. 
Published: November 2016

AbstractWhen non-native plants reach novel environments, they typically arrive with hidden microbiomes. In general, most of these hitchhikers remain on their co-evolved hosts, some contribute to the invasiveness of their hosts, and a small number can undergo host shifts and move onto native hosts. Invasion success can vary depending upon the different categories of fungal associates. When an invader tree relies on a fungal mutualism to survive in the new environment, there is a fundamentally lower likelihood of either the tree, or the fungus, establishing novel associations. In contrast, parasitic hitchhikers could merely use their host plants to move through the landscape and to become established on new hosts (host shifts). Evidence suggests the frequency of these host shifts is low and depends upon the fungal functional group. However, epidemics caused by invasive pathogens in native ecosystems have occurred globally. Thus, elucidating the potential for hidden non-native fungi to form novel host associations in a new environment is important for biodiversity conservation.
The Utility of Red Cell Distribution Width as a Parameter for Calculating Indices of Allostatic Load
Authors: Bello Ghalib A , Dumancas Gerard G 
Published: November 2016

AbstractBackgroundAllostatic Load is a construct used to quantify the cumulative burden of exposure to stressors that, over the course of an individual’s life, exert a toll on the body’s physiological functions, increasing risks of various chronic ailments and conditions. Studies attempting to quantify allostatic load have used a variety of clinical biomarkers representing primary and secondary mediators. In this study, we demonstrate the value of including red blood cell distribution width (RDW) among the panel of clinical parameters used to calculate allostatic load.MethodsWe develop a novel formulation of allostatic load using RDW and other standard biomarkers. This index is computed using clinical laboratory data from the NHANES study. The predictive validity of the new index for tertiary outcomes (all-cause mortality and physician-assessed health status) is compared to that of the current formulation using Harrell’s C index, ROC analysis and regression-based goodness-of-fit measures.ResultsInclusion of RDW as an allostatic load biomarker yields a significantly improved index. It demonstrates a superior ability to predict mortality, health status and biological age than the standard formulation currently in use.ConclusionRDW has shown strong correlations with mortality and a broad spectrum of diseases. A review of the existing literature on allostatic load reveals its underutilization in this area, despite being a standard component of blood count panels. This study is the first to demonstrate its usefulness as a potential allostatic load biomarker.
A mathematical approach to correlating objective spectro-temporal features of environmental sounds with their subjective perceptions
Authors: Burns Thomas F , Rajan Ramesh 
Published: November 2016

AbstractMany studies on the subjective perception of non-linguistic sounds have focused on only a single percept, e.g. pleasantness. In the present study, we have examined three different perception-related factors to also allow us to look at any inter-relationships between them that could be related to objective features. Objective features of the NLSs in this database were calculated and subjective perceptions were recorded from participants. These two elements - objective features and subjective perceptions - were then mapped together using various statistical and mathematical techniques. So as to ground our results in a meaningful context, we chose to map a set of objective features to human percepts which had been used in previous studies of NLS perception, but which had not yet been related back to objective features or combinations thereof.
Quark enables semi-reference-based compression of RNA-seq data
Authors: Sarkar Hirak , Patro Rob 
Published: November 2016

AbstractMotivationThe past decade has seen an exponential increase in biological sequencing capacity, and there has been a simultaneous effort to help organize and archive some of the vast quantities of sequencing data that are being generated. While these developments are tremendous from the perspective of maximizing the scientific utility of available data, they come with heavy costs. The storage and transmission of such vast amounts of sequencing data is expensive.ResultsWe presentQuark, a semi-reference-based compression tool designed for RNA-seq data.Quarkmakes use of a reference sequence when encoding reads, but produces a representation that can be decoded independently, without the need for a reference. This allowsQuarkto achieve markedly better compression rates than existing reference-free schemes, while still relieving the burden of assuming a specific, shared reference sequence between the encoder and decoder. We demonstrate thatQuarkachieves state-of-the-art compression rates, and that, typically, only a small fraction of the reference sequence must be encoded along with the reads to allow reference-free decompression.AvailabilityQuarkis implemented inC++11, and is available under a GPLv3 license atwww.github.com/COMBINE-lab/quark.Contactrob.patro@cs.stonybrook.edu
Verticillium dahliaeLysM effectors differentially contribute to virulence on plant hosts
Authors: Kombrink Anja , Rovenich Hanna , Shi-Kunne Xiaoqian , Rojas-Padilla Eduardo , van den Berg Grardy C.M. , Domazakis Emmanouil , de Jonge Ronnie , Valkenburg Dirk-Jan , Sánchez-Vallet Andrea , Seidl Michael F. , Thomma Bart P.H.J. 
Published: November 2016

SUMMARYChitin-binding LysM effectors contribute to virulence of various plant pathogenic fungi that are causal agents of foliar diseases. Here, we report on LysM effectors of the soil-borne fungal vascular wilt pathogenVerticillium dahliae. Comparative genomics revealed three core LysM effectors that are conserved in a collection ofV. dahliaestrains. Remarkably, and in contrast to the previously studied LysM effectors of other plant pathogens, no expression of core LysM effectors was monitoredin plantain a taxonomically diverse panel of host plants. Moreover, targeted deletion of the individual LysM effector genes inV. dahliaestrain JR2 did not compromise virulence in infections on Arabidopsis, tomato orNicotiana benthamiana. Interestingly, an additional lineage-specific LysM effector is encoded in the genome ofV. dahliaestrain VdLs17 but not in any otherV. dahliaestrain sequenced to date. Remarkably, this lineage-specific effector is expressedin plantaand contributes to virulence ofV. dahliaestrain VdLs17 on tomato, but not on Arabidopsis or onN. benthamiana. Functional analysis revealed that this LysM effector binds chitin, is able to suppress chitin-induced immune responses, and protects fungal hyphae against hydrolysis by plant hydrolytic enzymes. Thus, in contrast to the core LysM effectors ofV. dahliae, this lineage-specific LysM effector of strain VdLs17 contributes to virulencein planta.
Harnessing the lymphocyte meta-phenotype to optimize adoptive cell therapy
Authors: Mullinax John , O’Farrelly Cliona , Scott Jacob G. , Buttenschön Andreas , Elkenawi Asmaa E. , Moustaid Fadoua El , Fletcher Alexander G. , Grassberger Clemens , Kim Eunjung , Marusyk Andriy , McClelland Harry L.O. , Miroshnychenko Daria , Nichol Daniel 
Published: November 2016

ABSTRACTThere is an urgent need for reliable effective therapy for patients with metastatic sarcoma. Approaches that manipulate the immune system have shown promise for patients with advanced, widely disseminated malignancies. One of these approaches is adoptive cell therapy (ACT), where tumor-infiltrating lymphocytes (TIL) are isolated from the tumor, expandedex vivo, and then transferred back to the patient. This approach has shown great promise in melanoma, leading to an objective response in approximately half of treated patients [14]. Standard protocols involve characterization of TIL populations with respect to adaptive CD4+ and CD8+ T-lymphocytes, but neglect the possible role of the innate lymphoid repertoire. Due to toxicity and the high cost associated with ACT, the IFN-γ release assay is currently used as a proxy to identify suitable TIL isolates for ACT. Efforts in TIL-ACT for sarcoma, which are pre-clinical and pioneered at Moffitt Cancer Center, have shown that only a minority of the TIL cultures show tumor specific activity in ex vivo IFN-γ assays. Surprisingly, internal melanoma trial data reveal a lack of correlation between IFN-γ assay and clinical outcomes, highlighting the need for a more reliable proxy. We hypothesize the existence of a predictable TIL meta-phenotype that leads to optimal tumor response. Here, we describe preliminary efforts to integrate prospective and existing patient data with mathematical models to optimize the TIL meta-phenotype prior to re-injection.
Stable multi-level social structure is maintained by habitat geometry in a wild bird population
Authors: Farine Damien R. , Sheldon Ben C. 
Published: November 2016

ABSTRACTSocial structure can have profound evolutionary and ecological implications for animal populations. Structure can arise and be maintained via social preferences or be indirectly shaped by habitat structure. Understanding how social structure emerges is important for understanding the potential links between social structure and evolutionary and ecological processes. Here, we study a large community of wild birds fitted with uniquely-coded passive integrated transponder (PIT) tags and recorded on a grid of automated feeders fitted with radio frequency identification (RFID) antennae. We show that both large-scale and fine-scale network communities are consistent across years in this population, despite high generational turn-over. Studying the process that generates community structure, here the movement of individual birds across the woodland, suggests an important role of habitat geometry in shaping population-level social community structure. Our study highlights how relatively simple factors can produce apparent emergent social structure at the population scale, which has widespread implications for understanding eco-evolutionary dynamics.
A network-based approach to eQTL interpretation and SNP functional characterization
Authors: Fagny M. , Paulson J.N. , Kuijjer M.L. , Sonawane A.R. , Chen C.-Y. , Lopes-Ramos C.M. , Glass K. , Quackenbush J. , Platig J. 
Published: November 2016

SummaryExpression quantitative trait locus (eQTL) analysis associates genotype with gene expression, but most eQTL studies only includecis-acting variants and generally examine a single tissue. We used data from 13 tissues obtained by the Genotype-Tissue Expression (GTEx) project v6.0 and, in each tissue, identified bothcis- andtrans-eQTLs. For each tissue, we represented significant associations between single nucleotide polymorphisms (SNPs) and genes as edges in a bipartite network. These networks are organized into dense, highly modular communities often representing coherent biological processes. Global network hubs are enriched in distal gene regulatory regions such as enhancers, but are devoid of disease-associated SNPs from genome wide association studies. In contrast, local, community-specific network hubs (core SNPs) are preferentially located in regulatory regions such as promoters and enhancers and highly enriched for trait and disease associations. These results provide help explain how many weak-effect SNPs might together influence cellular function and phenotype.
Complete mapping of viral escape from neutralizing antibodies
Authors: Doud Michael B. , Hensley Scott E. , Bloom Jesse D. 
Published: November 2016

AbstractIdentifying viral mutations that confer escape from antibodies is crucial for understanding the interplay between immunity and viral evolution. Here we quantify how every amino-acid mutation to influenza hemagglutinin affects neutralization by monoclonal antibodies targeting several antigenic regions. Our approach involves creating all replication-competent protein variants of the virus, selecting these variants with antibody, and using deep sequencing to identify enriched mutations. These high-throughput measurements are predictive of the effects of individual mutations in traditional neutralization assays. At many residues, only some of the possible mutations escape from an antibody. For instance, at a single residue targeted by two different antibodies, we identify some mutations that escape both antibodies and other mutations that escape only one or the other. Therefore, our approach maps how viruses can escape antibodies with mutation-level sensitivity, and shows that only some mutations at antigenic residues actually alter antigenicity.
Balance of microtubule stiffness and cortical tension determines the size of blood cells with marginal band across species
Authors: Dmitrieff Serge , Alsina Adolfo , Mathur Aastha , Nedéléc François 
Published: November 2016

The fast blood stream of animals is associated with large shear stresses. Consequently, blood cells have evolved a special morphology and a specific internal architecture allowing them to maintain their integrity over several weeks. For instance, non-mammalian red blood cells, mammalian erythroblasts and platelets have a peripheral ring of microtubules, called the marginal band, that flattens the overall cell morphology by pushing on the cell cortex. In this article, we model how the shape of these cells stems from the balance between marginal band elasticity and cortical tension. We predict that the diameter of the cell scales with the total microtubule polymer, and verify the predicted law across a wide range of species. Our analysis also shows that the combination of the marginal band rigidity and cortical tension increases the ability of the cell to withstand forces without deformation. Finally, we model the marginal band coiling that occurs during the disc-to-sphere transition observed for instance at the onset of blood platelet activation. We show that when cortical tension increases faster than crosslinkers can unbind, the marginal band will coil, whereas if the tension increases slower, the marginal band may shorten as microtubules slide relative to each other.Significance StatementMany blood cells have a discoidal shape, which is essential for them to function properly within the organism. For some cells, such as blood platelets, this shape is due to the interplay between the elasticity of the marginal band, which is a closed ring of stiff filaments called microtubules, and the tension of the cell cortex, a polymer scaffold associated with the plasma membrane. Dmitrieff et al. examined how cell size is determined by the mechanical balance between these two components. Remarkably, the theory is confirmed over nearly three orders of magnitudes, by data collected from 25 species. The theory also shows how the composite structure is adapted to resist transient mechanical challenges, as encountered in the blood stream.
Low toxic polymeric surfactant as a corrosion inhibitor for mild steel in hydrochloric acid medium
Authors: de Souza Paulo Renato , Ferrari Jean Vicente , Guedes Isabel Correia 
Published: November 2016

PurposeSurfactants have been reported to have high inhibition efficiencies for corrosion of steel. This paper aims to study the performance of a low toxic copolymer of polydimethylsiloxane and polyoxyalkylene (POA) surfactant named as POPS, as a corrosion inhibitor for mild steel (ASTM 1005) in hydrochloric acid (HCl) solution at 25°C.Design/methodology/approachTo evaluate POPS efficiency as a corrosion inhibitor, the following techniques were used: surface tension measurements, weight loss measurements, open circuit potential monitoring, potentiodynamic polarization curves, electrochemical impedance spectroscopy (EIS), scanning electron microscopy and contact angle measurements.FindingsResults indicated that POPS acted as a mixed corrosion inhibitor and led to a hydrophobic protector film on the metal surface. The adsorption process obeyed the Langmuir adsorption isotherm by chemisorption. The maximum efficiency of the surfactant studied was achieved in a concentration around the critical micelle concentration.Originality/valueSurfactant (POPS) of low level of toxicity acts as a mixed corrosion inhibitor in HCl medium. Inhibitor film formation was characterized by EIS results. A mechanism for corrosion inhibition is proposed.
Price promotions and products with low consumer ratings
Authors: Kuo Hsiao-Ching , Nakhata Chinintorn 
Published: November 2016

Purpose
Previous research indicates the aversive effect of low consumer ratings on consumers’ purchasing decisions. This paper aims to apply decision justifiability theory to investigate how price promotions – price discount and price bundling – can reduce this effect.

Design/methodology/approach
Two scenario-based experiments were administered among college students (Experiment 1) and online consumer panels (Experiment 2) to test the research hypotheses.

Findings
When time-to-purchase is long (vs short), a large discount is more effective in alleviating consumers’ negative responses toward products with low consumer ratings. However, when a price discount is presented as a bundle rather than a separate deal, a small discount size becomes as attractive as a large discount size for consumers with a longer time-to-purchase.

Practical implications
This paper identifies two controllable factors, price discounts and price bundling, that could help to alleviate the negative impact of low consumer ratings. Marketing managers can apply the findings of this paper as guidelines to deal with the aversive effect of low consumer ratings.

Originality/value
This paper makes an initial attempt to examine situations where consumers would be less averse to products with low consumer ratings. It identifies the roles of two price promotions (i.e. price discount size and price bundling) and an important contextual factor (i.e. time-to-purchase) that influence consumers’ decision justifiability and, subsequently, alter consumers’ online purchase decisions for such products.
The Suburb as a Space of Capital Accumulation: The Development of New Towns in Shanghai, China
Authors: Shen Jie , Wu Fulong 
Published: November 2016

AbstractDrawing attention to the governing role of capital accumulation and its interaction with the state, this study examines the dynamics of the new wave of suburbanization in China, which is characterized by the development of new towns. New towns essentially function as a spatial fix in China's contemporary accumulation regime. Rather than resulting from capital switching from the primary to the secondary circuits, new towns help to collect funds for the leverage of industrial capital and thus simultaneously sustain both circuits. Meanwhile, the development of new towns is also a process of territorial development, in which municipal governments expand the space of accumulation under strengthened fiscal and land controls and develop a metropolitan structure. Underlying the specific form and dynamics, however, is the worldwide trend of capital switching from declining manufacturing industries in developed countries to the new investment frontier in developing countries.
Influence of topography on long‐term successional trajectories in canyon grasslands
Authors: Bernards Samantha J. , Morris Lesley R. 
Published: November 2016

AbstractQuestionSome of the last remaining grassland communities of the Pacific Northwest Bunchgrass Region (PNWBR) in North America are found in canyon grasslands, primarily because the rugged topography has left many of these associations untouched by agricultural development. However, there have been no prior examinations into how canyon grassland communities change over the long term or how topography relates to these changes. In this study, we examined how successional stages changed over a 33‐yr time period and which topographical variables were most related to these long‐term outcomes (elevation, aspect or slope). We predicted that areas with more gentle slopes (<20%) would have changed the most because they have seen a higher concentration of historical land uses (e.g. livestock grazing, wildlife herbivory, and cultivation).LocationCanyon grasslands of Hells Canyon National Recreation Area, northwest USA.MethodsWe looked at how the canyon grasslands have changed over the long term by repeating a vegetation survey of plant species cover and frequency that was completed in 1981 and comparing the results after a 33‐yr time period.ResultsWe found that 58% of our plots stayed in the same seral stage or transitioned into later ones. As predicted, the plots that remained in early seral condition or transitioned from later to early seral stages were found on more shallow slopes. In addition, drier aspects within all plant associations appeared to be less resistant and resilient to change, particularly invasion by exotic species.ConclusionsThe results of this resurvey suggest that topographic patterns may not only be related to the distribution of plant associations across the canyon grasslands, but may also influence which sites change most over time. Our findings are consistent with other studies of the relationships between topography and land uses through time in other grasslands, and are highly relevant to conservation management where unique vegetation communities develop within heterogeneous topographic areas.