bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples
Authors: Brian Yu Feiqiao , Blainey Paul C. , Schulz Frederik , Woyke Tanja , Horowitz Mark A. , Quake Stephen R. 
Published: March 2017

AbstractMetagenomics and single-cell genomics have enabled the discovery of many new genomes from previously unknown branches of life. However, extracting novel genomes from complex mixtures of metagenomic data can still be challenging and in many respects represents an ill-posed problem which is generally approached with ad hoc methods. Here we present a microfluidic-based mini-metagenomic method which offers a statistically rigorous approach to extract novel microbial genomes from complex samples. In addition, by generating 96 sub-samples from each environmental sample, this method maintains high throughput, reduces sample complexity, and preserves single-cell resolution. We used this approach to analyze two hot spring samples from Yellowstone National Park and extracted 29 new genomes larger than 0.5 Mbps. These genomes represent novel lineages at different taxonomic levels, including three deeply branching lineages. Functional analysis revealed that these organisms utilize diverse pathways for energy metabolism. The resolution of this mini-metagenomic method enabled accurate quantification of genome abundance, even for genomes less than 1% in relative abundance. Our analyses also revealed a wide range of genome level single nucleotide polymorphism (SNP) distributions with nonsynonymous to synonymous ratio indicative of low to moderate environmental selection. The scale, resolution, and statistical power of microfluidic-based mini-metagenomic make it a powerful tool to dissect the genomic structure microbial communities while effectively preserving the fundamental unit of biology, the single cell.
TRPV1 activation relies on hydration/dehydration of nonpolar cavities
Authors: Kasimova Marina A. , Yazici Aysenur , Yudin Yevgen , Granata Daniele , Klein Michael L. , Rohacs Tibor , Carnevale Vincenzo 
Published: March 2017

ABSTRACTTRPV1 promotes cationic currents across cellular membranes in response to multiple stimuli such as increased temperature, binding of chemicals, low pH and voltage. The molecular underpinnings of TRPV1 gating, in particular the mechanism of temperature sensitivity, are still largely unknown. Here, we used molecular simulations and electrophysiology to shed light on the closed to open transition. Specifically, we found that gating of TRPV1 relies on the motion of an evolutionarily conserved amino acid (N676) in the middle of the S6 helix. On rotation, the side chain of this asparagine faces either the central pore or the S4-S5 linker. Only in the former case is the central pore hydrated and thus conductive. Interestingly, when N676 rotates toward the linker, we observe hydration of four so far unreported small nonpolar cavities. Based on these findings, we propose a model for TRPV1 gating involving the dynamic hydration of these four cavities. Free energy calculations indicate that this gating mechanisms is markedly temperature dependent favoring the open state at high temperature. On the basis of this model, which is able to rationalize a wealth of seemingly conflicting and/or unrelated experimental observations, we predicted the behavior of two single residue mutants, M572A and F580Y, the consequences of which we confirmed experimentally.
The interplay of demography and selection during maize domestication and expansion
Authors: Wang Li , Beissinger Timothy M. , Lorant Anne , Ross-Ibarra Claudia , Ross-Ibarra Jeffrey , Hufford Matthew B. 
Published: March 2017

AbstractThe history of maize has been characterized by major demographic events including changes in population size associated with domestication and range expansion as well as gene flow with wild relatives. The interplay between demographic history and selection has shaped diversity across maize populations and genomes. Here, we investigate these processes based on high-depth resequencing data from 31 maize landraces spanning the pre-Columbian distribution of maize as well as four wild progenitor individuals (Zea maysssp.parviglumis) from the Balsas River Valley in Mexico. Genome-wide demographic analyses reveal that maize domestication and spread resulted in pronounced declines in effective population size due to both a protracted bottleneck and serial founder effects, while, concurrently,parviglumisexperienced population growth. The cost of maize domestication and spread was an increase in deleterious alleles in the domesticate relative to its wild progenitor. This cost is particularly pronounced in Andean maize, which appears to have experienced a more dramatic founder event when compared to other maize populations. Introgression from the wild teosinteZea maysssp.mexicanainto maize in the highlands of Mexico and Guatemala is found found to decrease the prevalence of deleterious alleles, likely due to the higher long-term effective population size of wild maize. These findings underscore the strong interaction between historical demography and the efficiency of selection species- and genome-wide and suggest domesticated species with well-characterized histories may be particularly useful for understanding this interplay.
Coupling optogenetics and light-sheet microscopy, a method to study signal transductionin vivo
Authors: Kaur Prameet , Saunders Timothy E. , Tolwinski Nicholas S. 
Published: March 2017

AbstractOptogenetics allows precise, fast and reversible intervention in biological processes. Light-sheet microscopy allows observation of the full course of embryonic development from egg to larva. Bringing the two approaches together allows unparalleled precision into the temporal regulation of signaling pathways and cellular processesin vivo. To develop this method, we investigated the regulation of canonical Wnt signaling during anterior-posterior patterning of theDrosophilaembryonic epidermis. Cryptochrome 2 (CRY2) fromArabidopsis Thalianawas fused to mCherry fluorescent protein andDrosophilaβ–catenin to form an easy to visualize optogenetic switch. Blue light illumination caused oligomerization of the fusion protein and inhibited downstream Wnt signalingin vitroandin vivo. Temporal inactivation of β–catenin confirmed that Wnt signaling is required not only forDrosophilapattern formation, but also for maintenance later in development. We anticipate that this method will be easily extendable to other developmental signaling pathways and many other experimental systems.
Foresight for E-paper development in Taiwan
Authors: Hsieh Chih-Hung , Lin Chien-Huei , Huang Jia-Ling 
Published: March 2017

Purpose
This study aims to analyse the impact of e-paper on many existing industries including paper, publishing, book distribution, display, handheld device manufacturers and content service providers. Flexible display has been studied by many institutes, firms and market research companies. Some believe that e-paper is an exceptional application for flexible display, and the need for flexible display development for handheld devices and cloud-based e-book content is indisputable.

Design/methodology/approach
This study uses the Delphi technique and STEEP (Sociological, Technological, Economic, Environmental and Political aspects) with a panel to analyse a business model and the opportunity for the development of e-paper in Taiwan up to the year 2020.

Findings
The study concludes that e-paper content and customised digital services are an essential part of e-paper development, while hardware and cloud data are no more than a mechanism to show, compute and store data. Thus, whether the screen of a handheld device is flexible may not be of importance. Although e-paper will affect the display industry, it will not substitute for handheld devices and traditional bookstores.

Originality/value
This research can be used as a reference for government, academics, industry and international investors.
An analysis on the causal relationship between freight rate and newbuilding orders
Authors: Kim Chi Yeol , Park KwangSo 
Published: March 2017

Purpose
The purpose of this paper is to provide implications for forecasting export of Korean shipbuilding industry that is suffering from deadlock in newbuilding orders, by investigating the causal relationship between freight rate earnings and newbuilding orders in the shipbuilding market.

Design/methodology/approach
Using a sample of freight rate earnings and newbuilding orders (in various terms) over the period 1996-2016, Granger causality between the two variables are examined in a vector autoregressive (VAR) model. In addition, the potential asymmetry of the causal relationship according to bullish and bearish market conditions is also investigated using a combination of moving averages of different time spans.

Findings
The results indicate a uni-directional causality running from freight rate earnings to newbuilding orders. This finding implies that shipowners’ confidence in the shipping freight market is particularly important determinants in their newbuilding investment, which is consistent with the overconfidence hypothesis. However, the causality does not vary according to different market conditions.

Research limitations/implications
This study offers several importation contributions. First, the authors provide evidence that newbuilding orders are positively associated with increase in freight rate earnings. Second, the authors document a causality running from changes in freight rate earnings to the volume of newbuilding orders. These findings support the theoretical expectation of the overconfidence hypothesis. Third, contrary to the findings in the financial market, there is no asymmetric response of the volume of newbuilding orders in bullish and bearish markets. Fourth, this study provide implications for management of Korean shipyards by providing evidence on driving force of newbuilding investment decisions of their customers (shipowners).

Practical implications
The findings in this study suggest implications for management of Korean shipyards by providing evidence on driving force of newbuilding investment decisions of their customers, as well as determinants of shipbuilding export, an important source of Korea’ national income.

Social implications
The analysing the major determinants of shipbuilding exports, the findings in this study presents understanding of market cycles in shipbuilding, an important source of Korea’s national income and balance of payment.

Originality/value
This study is the first attempt to analyse the relationship between freight rate earnings and newbuilding investment in the context of the behavioural theory in economics.
The effects of applying alternative discounting methods on the economic feasibility test of Free Trade Zone development project
Authors: Kyum Kim Sang 
Published: March 2017

Purpose
The purpose of this paper is to examine the applicability of the alternative way of discounting, such as the hyperbolic discount method, for the economic feasibility test on Free Trade Zone development project that needs intergenerational analysis.

Design/methodology/approach
To analyze the effects of applying alternative discounting method in the cost-benefit analysis, this paper uses the hyperbolic discount method and HM-Treasury’s method (Britain), as well as the traditional exponential discount method. Also, this study uses benefit and cost data from the actual feasibility test of the Free Trade Zone development project in Korea, to obtain better policy implication.

Findings
For the case of long-term analysis, using the exponential discounting method in the benefit-cost analysis could not give us balanced analytic results, because it discounts too much on future generation’s benefits. In contrast, if we use the hyperbolic discounting method, we could obtain better balanced results since it can control the generational effects. This paper also finds that for the results to be valid, the analysis period must be expanded long enough (a minimum of 100 years).

Originality/value
The major findings of this paper confirm the results of previous studies regarding long-term benefit-cost analysis. Also, the result of this paper is properly compatible with the findings of behavioral economics, such as the time inconsistency of preferences. However, no research has been done with the proper length of analytic periods for using hyperbolic discounting yet. To examine this matter, this paper performs benefit-cost analysis with actual data from the feasibility studies in Korea. To the best of the author’s knowledge, this is the first study to find the proper length of analytic periods that can be compatible with the hyperbolic discount method.
Sentiment analysis of virtual brand communities for effective tribal marketing
Authors: Pathak Xema , Pathak-Shelat Manisha 
Published: March 2017

Purpose
By doing sentiment analysis of netnographic data, this study aims to explain the need to give special attention to negative sentiments expressed in virtual tribes, as they play a significant role in translating the informational mode of conversation to the relational mode of conversation. The overall purpose is to aid brand managers in the process of brand co-creation by articulating brand communication targeted to specific audiences based on their shared passions and interests.

Design/methodology/approach
The study adopts a mixed-methods approach. The primary data were collected from two virtual brand communities through qualitative net-based ethnographic methods. Semantria Excel plug-in was used to categorize the extracted consumer statements based on positive, neutral and negative sentiments.

Findings
Managing the negative interactions in the virtual communities and relationship development with members through non-commercial conversations should be the two main priorities for effective brand management. Sentiment analysis specifically helps to identify pain points and consumer sentiments at each stage of the shopper journey. The findings of the study endorse the importance of offering and supporting communities as a valid marketing.

Research limitations/implications
This paper shows how systematic attention to user interactions on virtual brand communities can be used for tribal marketing, which in turn will impact the intangible aspects of the business, such as increasing brand value and loyalty. By engaging the consumers, the social ties among the target audience can be nurtured and strengthened.

Originality/value
This paper focuses on decoding their behavior by unpeeling the consumer statements rather than tangible aspects of the business, such as sales of products or services. It contributes to development of a theoretical framework that outlines how the interactions in virtual brand communities can aid in formulating the functional and communicational strategies for a brand.
Harvesting wildlife affected by climate change: a modelling and management approach for polar bears
Authors: Regehr Eric V. , Wilson Ryan R. , Rode Karyn D. , Runge Michael C. , Stern Harry L. 
Published: March 2017

SummaryThe conservation of many wildlife species requires understanding the demographic effects of climate change, including interactions between climate change and harvest, which can provide cultural, nutritional or economic value to humans.We present a demographic model that is based on the polar bearUrsus maritimuslife cycle and includes density‐dependent relationships linking vital rates to environmental carrying capacity (K). Using this model, we develop a state‐dependent management framework to calculate a harvest level that (i) maintains a population above its maximum net productivity level (MNPL; the population size that produces the greatest net increment in abundance) relative to a changingK, and (ii) has a limited negative effect on population persistence.Our density‐dependent relationships suggest thatMNPLfor polar bears occurs at approximately 0·69 (95%CI = 0·63–0·74) ofK. Population growth rate atMNPLwas approximately 0·82 (95%CI = 0·79–0·84) of the maximum intrinsic growth rate, suggesting relatively strong compensation for human‐caused mortality.Our findings indicate that it is possible to minimize the demographic risks of harvest under climate change, including the risk that harvest will accelerate population declines driven by loss of the polar bear's sea‐ice habitat. This requires that (i) the harvest rate – which could be 0 in some situations – accounts for a population's intrinsic growth rate, (ii) the harvest rate accounts for the quality of population data (e.g. lower harvest when uncertainty is large), and (iii) the harvest level is obtained by multiplying the harvest rate by an updated estimate of population size. Environmental variability, the sex and age of removed animals and risk tolerance can also affect the harvest rate.Synthesis and applications. We present a coupled modelling and management approach for wildlife that accounts for climate change and can be used to balance trade‐offs among multiple conservation goals. In our example application to polar bears experiencing sea‐ice loss, the goals are to maintain population viability while providing continued opportunities for subsistence harvest. Our approach may be relevant to other species for which near‐term management is focused on human factors that directly influence population dynamics within the broader context of climate‐induced habitat degradation.
Climate, soil and plant functional types as drivers of global fine‐root trait variation
Authors: Freschet Grégoire T. , Valverde‐Barrantes Oscar J. , Tucker Caroline M. , Craine Joseph M. , McCormack M. Luke , Violle Cyrille , Fort Florian , Blackwood Christopher B. , Urban‐Mead Katherine R. , Iversen Colleen M. , Bonis Anne , Comas Louise H. , Cornelissen Johannes H. C. , Dong Ming , Guo Dali , Hobbie Sarah E. , Holdaway Robert J. , Kembel Steven W. , Makita Naoki , Onipchenko Vladimir G. , Picon‐Cochard Catherine , Reich Peter B. , de la Riva Enrique G. , Smith Stuart W. , Soudzilovskaia Nadejda A. , Tjoelker Mark G. , Wardle David A. , Roumet Catherine 
Published: March 2017

Summary

Ecosystem functioning relies heavily on below‐ground processes, which are largely regulated by plant fine‐roots and their functional traits. However, our knowledge of fine‐root trait distribution relies to date on local‐ and regional‐scale studies with limited numbers of species, growth forms and environmental variation.

We compiled a world‐wide fine‐root trait dataset, featuring 1115 species from contrasting climatic areas, phylogeny and growth forms to test a series of hypotheses pertaining to the influence of plant functional types, soil and climate variables, and the degree of manipulation of plant growing conditions on species fine‐root trait variation. Most particularly, we tested the competing hypotheses that fine‐root traits typical of faster return on investment would be most strongly associated with conditions of limiting versus favourable soil resource availability. We accounted for both data source and species phylogenetic relatedness.

We demonstrate that: (i) Climate conditions promoting soil fertility relate negatively to fine‐root traits favouring fast soil resource acquisition, with a particularly strong positive effect of temperature on fine‐root diameter and negative effect on specific root length (SRL), and a negative effect of rainfall on root nitrogen concentration; (ii) Soil bulk density strongly influences species fine‐root morphology, by favouring thicker, denser fine‐roots; (iii) Fine‐roots from herbaceous species are on average finer and have higher SRL than those of woody species, and N2‐fixing capacity positively relates to root nitrogen; and (iv) Plants growing in pots have higher SRL than those grown in the field.

Synthesis. This study reveals both the large variation in fine‐root traits encountered globally and the relevance of several key plant functional types and soil and climate variables for explaining a substantial part of this variation. Climate, particularly temperature, and plant functional types were the two strongest predictors of fine‐root trait variation. High trait variation occurred at local scales, suggesting that wide‐ranging below‐ground resource economics strategies are viable within most climatic areas and soil conditions.
Soil carbon response to woody plant encroachment: importance of spatial heterogeneity and deep soil storage
Authors: Zhou Yong , Boutton Thomas W. , Wu X. Ben 
Published: March 2017

Summary

Recent global trends of increasing woody plant abundance in grass‐dominated ecosystems may substantially enhance soil organic carbon (SOC) storage and could represent a strong carbon (C) sink in the terrestrial environment. However, few studies have quantitatively addressed the influence of spatial heterogeneity of vegetation and soil properties on SOC storage at the landscape scale. In addition, most studies assessing SOC response to woody encroachment consider only surface soils, and have not explicitly assessed the extent to which deeper portions of the soil profile may be sequestering C.

We quantified the direction, magnitude and pattern of spatial heterogeneity of SOC in the upper 1·2 m of the profile following woody encroachment via spatially specific intensive soil sampling across a landscape in a subtropical savanna in the Rio Grande Plains, USA, that has undergone woody proliferation during the past century.

Increased SOC accumulation following woody encroachment was observed to considerable depth, albeit at reduced magnitudes in deeper portions of the profile. Overall, woody clusters and groves accumulated 12·87 and 18·67 Mg C ha−1 more SOC compared to grasslands to a depth of 1·2 m.

Woody encroachment significantly altered the pattern of spatial heterogeneity of SOC to a depth of 5 cm, with marginal effect at 5–15 cm, and no significant impact on soils below 15 cm. Fine root density explained greater variability of SOC in the upper 15 cm, while a combination of fine root density and soil clay content accounted for more of the variation in SOC in soils below 15 cm across this landscape.

Synthesis. Substantial soil organic carbon sequestration can occur in deeper portions of the soil profile following woody encroachment. Furthermore, vegetation patterns and soil properties influenced the spatial heterogeneity and uncertainty of soil organic carbon in this landscape, highlighting the need for spatially specific sampling that can characterize this variability and enable scaling and modelling. Given the geographic extent of woody encroachment on a global scale, this undocumented deep soil carbon sequestration suggests this vegetation change may play a more significant role in regional and global carbon sequestration than previously thought.
Gastric cancer management: Kinases as a target therapy
Authors: Farran Batoul , Müller Susanne , Montenegro Raquel C 
Published: March 2017

SummaryThe molecular diagnostics revolution has reshaped the practice of oncology by facilitating the identification of genetic, epigenetic and proteomic modifications correlated with cancer, thus delineating ‘oncomaps’ for various cancer types. These advances have enhanced our understanding of gastric cancer, one of the most fatal diseases worldwide, and culminated in the approval of novel molecular therapies such as trastuzumab. Gastric tumours display recurrent aberrations in key kinase oncogenes such as Her2, epidermal growth factor receptor (EGFR), PI3K, mTOR or c‐Met, suggesting that these receptors are amenable to inhibition using specific drug agents. In this review, we examine the mutational landscape of gastric cancer, the use of kinase inhibitors as targeted therapies in gastric tumours and the clinical trials underway for novel inhibitors, highlighting successes, failures and future directions.