bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global evaluation of biofuel potential from microalgae
Authors: Moody Jeffrey W. , McGinty Christopher M. , Quinn Jason C. 
Published: May 2014

Significance
Research into microalgae as a feedstock for biofuels continues to increase because of the inherent potential advantages it holds over traditional terrestrial feedstocks. However, the true near-term large-scale productivity of microalgae remains uncertain. This study integrates a large-scale, outdoor growth model with historical meteorological data from 4,388 global locations to estimate the current near-term lipid and biomass productivity potential from microalgae cultivated in a photobioreactor architecture. Results show that previous life cycle, technoeconomic, and resource assessments dramatically overestimated lipid yields. A scalability assessment that leverages geographic information systems data to evaluate the current productivity potential from microalgae with global fuel consumption and land availability shows that microalgae can have a positive impact on the transportation energy portfolios of various countries.
Up-regulation of glycolytic metabolism is required for HIF1α-driven bone formation
Authors: Regan Jenna N. , Lim Joohyun , Shi Yu , Joeng Kyu Sang , Arbeit Jeffrey M. , Shohet Ralph V. , Long Fanxin 
Published: May 2014

Significance
Osteoblast precursors residing in the bone marrow experience hypoxia, which leads to stabilization and increased activity of hypoxia-inducible factor 1α (HIF1α). However, whether an increase in HIF1α activity directly impacts bone formation is not known. Two well-known functions of HIF1α are to promote angiogenesis and to stimulate glycolysis in the cell. Here, we demonstrate that HIF1α stabilization in osteoblast precursors of postnatal mice markedly increases osteoblast number and bone mass. Furthermore, the greater bone mass was not secondary to increased angiogenesis but rather dependent on the up-regulation of glycolysis in osteoblast precursors. These results provide strong evidence that alterations in cellular metabolism directly influence cell differentiation.
Yolk-sac–derived macrophages regulate fetal testis vascularization and morphogenesis
Authors: DeFalco Tony , Bhattacharya Indrashis , Williams Alyna V. , Sams Dustin M. , Capel Blanche 
Published: May 2014

SignificanceA main requisite for organogenesis is the integration of vascular networks, which not only deliver oxygen and nutrients but also serve instructive roles in organ patterning that determine how organs develop into their final structure and function in the adult. Our previous work showed that vascularization is essential to induce formation of the primitive cord structures that give rise to the seminiferous tubules of the adult testis. Here we show that fetal macrophages are required to remodel the vasculature and refine organ compartments during differentiation of the gonad. This study reveals an underappreciated and likely vital role for macrophages in fetal organogenesis that may be relevant to the development of many organs.
Impact of puberty on the evolution of cerebral perfusion during adolescence
Authors: Satterthwaite Theodore D. , Shinohara Russell T. , Wolf Daniel H. , Hopson Ryan D. , Elliott Mark A. , Vandekar Simon N. , Ruparel Kosha , Calkins Monica E. , Roalf David R. , Gennatas Efstathios D. , Jackson Chad , Erus Guray , Prabhakaran Karthik , Davatzikos Christos , Detre John A. , Hakonarson Hakon , Gur Ruben C. , Gur Raquel E. 
Published: May 2014

SignificanceBlood perfusion is a fundamental property of brain physiology and is known to be higher in adult females than in males. However, it is unknown when such a sex difference emerges during the lifespan, or what biological processes may cause it. In the largest study of brain perfusion yet reported, we establish for the first time to our knowledge that patterns of development of cerebral perfusion during adolescence are markedly different in males and females, and such differences are attributable in part to the effects of puberty. These results may have important implications for neuropsychiatric disorders with adolescent onset and strong gender disparities, such as mood disorders, anxiety disorders, and schizophrenia.
Reassessing the biogenicity of Earth’s oldest trace fossil with implications for biosignatures in the search for early life
Authors: Grosch Eugene G. , McLoughlin Nicola 
Published: May 2014

Significance
It has been argued that Archean subseafloor pillow lava sequences provide an environment in which to seek evidence for the earliest traces of life. Candidate titanite biosignatures of microbial activity have been reported in ∼3.45-Ga metavolcanic glass from the Barberton greenstone belt of South Africa. In this paper we present new in situ U–Pb age data, metamorphic constraints, and morphological observations on these titanite microtextures. Our data challenges a biological origin for these oldest purported trace fossils, with implications for the ecological niches where life may have first emerged. We therefore suggest alternative biosignatures and approaches should be considered in the search for subsurface life on early Earth and in extraterrestrial mafic–ultramafic rocks, for example, in martian basalts.
Membrane raft association is a determinant of plasma membrane localization
Authors: Diaz-Rohrer Blanca B. , Levental Kandice R. , Simons Kai , Levental Ilya 
Published: May 2014

Significance
The organization of metazoan membranes into functional domains is a key feature of their physiology. A subset of these domains, known as “membrane rafts,” has been implicated in a large variety of cellular processes; however, the molecular mechanisms by which raft domains regulate cell function remain elusive. Here, we demonstrate that membrane raft association is a necessary and sufficient sorting signal for cell-surface localization of a specific single-pass membrane protein, linker for activation of T-cells, and that this raft association is governed by the properties of the protein transmembrane domain. These results begin to define the physical bases for protein raft affinity and establish lateral membrane domains as mediators of protein sorting in mammalian cells.
Cognitive flexibility and long-term depression (LTD) are impaired following β-catenin stabilization in vivo
Authors: Mills Fergil , Bartlett Thomas E. , Dissing-Olesen Lasse , Wisniewska Marta B. , Kuznicki Jacek , Macvicar Brian A. , Wang Yu Tian , Bamji Shernaz X. 
Published: May 2014

Significance
Complex learning and memory are believed to require the weakening or elimination of synapses in the brain, a process mediated by adhesion molecules, which maintain synapse strength and stability. In the present study, we examine in vivo the effects of stabilization of β-catenin, an intracellular protein that is a component of the cadherin adhesion complex. We find that stabilization of β-catenin in the brain prevents normal activity-dependent downscaling of synapse strength, resulting in a striking impairment in cognitive flexibility. These results demonstrate that β-catenin plays an important role in learning and memory and that aberrant increases in synaptic adhesion can have detrimental effects on cognitive function.
Supplementation of Vitis thunbergii root extract alleviated high-fat diet-induced obesity in C57BL/6J mice
Authors: Hsu Hong-Ming , Chen Wen-Ying , Hu Tzer-Kuan , Mao Frank Chiahung 
Published: May 2014

Abstract
Vitis thunbergii root, widely used as folk medicine in Taiwan, has been found to contain polyphenolic compounds and resveratrol derivatives, which have been implicated in the prevention and treatment of obesity. Thus, we hypothesized it might show beneficial effects against obesity. C57BL/6JNarl mice fed with a high fat diet for 14 weeks increased body weight and epididymal fat pad weight, and accompanied by fatty liver, hyperglycemia, hyperinsulinemia, insulin resistance, hyperleptinemia, hypercholesterolemia, hyper-LDL-cholesterol, and high level of serum GPT, GOT, creatinine, and BUN. Supplementation of VTE in the last 7 weeks remarkably decreased body weight and epididymal fat pad weight, implying a potential anti-obesity effect. Mechanistic study showed that VTE supplementation increased energy expenditure-related CPT1 mRNA expression and AMPK phosphorylation, and decreased lipogenesis-related SREBP-1 expression in liver. In conclusion, Vitis thunbergii roots could alleviate high fat diet-induced obesity and its related complications by enhancing hepatic fatty acid oxidation and inhibitng lipogenesis.
Biochemical analyses of ppGpp effect on adenylosuccinate synthetases, key enzymes in purine biosynthesis in rice
Authors: Nomura Yuhta , Nozawa Akira , Tozawa Yuzuru 
Published: May 2014

Abstract
The ppGpp-signaling system functions in plant chloroplasts. In bacteria, a negative effect of ppGpp on adenylosuccinate synthetase (AdSS) has been suggested. Our biochemical analysis also revealed rice AdSS homologs are apparently sensitive to ppGpp. However, further investigation clarified that this phenomenon is cancelled by the high substrate affinity to the enzymes, leading to a limited effect of ppGpp on adenylosuccinate synthesis.
A protocol for in vitro production of microtubers in Chinese yam (Dioscorea opposita)
Authors: Li Mingjun , Li Junhua , Liu Wen , Liu Luying , Lu Jie , Niu Jia , Liu Xinying , Yang Qingxiang 
Published: May 2014

Abstract
Chinese yam (Dioscorea opposita) is an important tuberous crop owing to its dual use as a food as well as a medicine. Tissue culture techniques allow the rapid multiplication of virus-free plant materials. The use of microtubers offers an attractive alternative to in vitro-grown plantlets for the micropropagation and exchange of healthy Chinese yam materials. A protocol for the in vitro production of Chinese yam microtubers was developed in this study. Though we tested both one-step and two-step procedures, only the two-step procedure showed favorable results for tuberization. Media with 60 g L−1 sucrose yielded the highest microtuber index. We demonstrate that table sugar was an efficient and economical alternative to analytical grade sucrose for microtuber production. Using an orthogonal experimental design, we determined the optimal growth regulator combination for microtuber induction and development. The microtubers obtained from our protocol sprouted readily both in vitro and in soil.
Chromophores in photoproteins of a glowing squid and mollusk
Authors: Kuse Masaki 
Published: May 2014

Abstract
Bioluminescence is a chemical reaction process for light emission in vivo. An organic substance is normally oxidized in the protein to obtain the energy required for the light emission. Determination of the structure of the substance is one of the most important parts of bioluminescent research. Photoproteins of a flying squid and a mollusk contain chromophores that are formed by connecting an apo-protein and dehydrocoelenterazine. The chromophore has a chemical structure that can emit light in a photoprotein. The structural analysis of the chromophores in the photoproteins is described.
Different profile of transcriptome between wheat Yunong 201 and its high-yield mutant Yunong 3114
Authors: Chen Feng , Dong Zhongdong , Ning Zhang , Xiangfen Zhang , Cui Dangqun 
Published: May 2014

AbstractWheat is one of the most important crops in the world. With the exponentially increasing population and the need for ever increased food and feed production, an increased yield of wheat grain (as well as rice, maize and other grains) will be critical. Modern technologies are utilized to assist breeding programs. Such as the transcriptome sequencing, which greatly improves our genetic understanding, provides a platform for functional genomics research on crops. Herein, to get an overview of transcriptome characteristics of Yunong 3114, which is screened from the EMS mutagenized population of, a high quality Chinese winter noodle wheat, due to its different plant architecture as well as larger kernel size and higher grain weight, a high-throughput RNA sequencing based on next generation sequencing technology (Illumina) were performed. These unigenes were annotated by Blastx alignment against the NCBI non-redundant (nr), Clusters of orthologous groups (COG), gene orthology (GO), and the Kyoto Encyclopedia of Genesand Genomes (KEGG) databases. The 90.96% of the unigenes matched with protein in the NCBI nr database. Functional analysis identified that changes in several GO categories, including recognition of pollen, apoptotic process, defense response, receptor activity, protein kinase activity, DNA integration and so forth, played crucial roles in the high-yield characteristics of the mutant. Real-time PCR analysis revealed that the recognition of pollen related gene GsSRK is significantly up-regulated in Yunong 3114. In addition, alternative splicing (AS) analysis results indicated that mutation influence AS ratio, especially the retained introns, including the pollen related genes. Furthermore, the digital gene expression spectrum (DGE) profiling data provides comprehensive information at the transcriptional level that facilitates our understanding of the molecular mechanisms of various physiological aspects including development and high-yield of wheat. Together, these studies substantially increase our knowledge of potential genes and pathways for the genetic improvement of wheat and provide new insights into the yield and breeding strategies.
Lighter: fast and memory-efficient error correction without counting
Authors: Song Li , Florea Liliana , Langmead Ben 
Published: May 2014

AbstractLighter is a fast, memory-efficient tool for correcting sequencing errors. Lighter avoids countingk-mers. Instead, it uses a pair of Bloom filters, one holding a sample of the inputk-mers and the other holdingk-mers likely to be correct. As long as the sampling fraction is adjusted in inverse proportion to the depth of sequencing, Bloom filter size can be held constant while maintaining near-constant accuracy. Lighter is parallelized, uses no secondary storage, and is both faster and more memory-efficient than competing approaches while achieving comparable accuracy.
Identifying Restrictions in the Order of Accumulation of Mutations during Tumor Progression: Effects of Passengers, Evolutionary Models, and Sampling
Authors: Diaz-Uriarte Ramon 
Published: May 2014

AbstractCancer progression is caused by the sequential accumulation of mutations, but not all orders of accumulation of mutations are equally likely. When the fixation of some mutations depends on the presence of previous ones, identifying restrictions in the order of accumulation of mutations can lead to the discovery of therapeutic targets and diagnostic markers. Using simulated data sets, I conducted a comprehensive comparison of the performance of all available methods to identify these restrictions from cross-sectional data. In contrast to previous work, I embedded restrictions within evolutionary models of tumor progression that included passengers (mutations not responsible for the development of cancer, known to be very common). This allowed me to asses the effects of having to filter out passengers, of sampling schemes, and of deviations from order restrictions. Poor choices of method, filtering, and sampling lead to large errors in all performance metrics. Having to filter passengers lead to decreased performance, especially because true restrictions were missed. Overall, the best method for identifying order restrictions were Oncogenetic Trees, a fast and easy to use method that, although unable to recover dependencies of mutations on more than one mutation, showed good performance in most scenarios, superior to Conjunctive Bayesian Networks and Progression Networks. Single cell sampling provided no advantage, but sampling in the final stages of the disease vs. sampling at different stages had severe effects. Evolutionary model and deviations from order restrictions had major, and sometimes counterintuitive, interactions with other factors that affected performance. This paper provides practical recommendations for using these methods with experimental data. Moreover, it shows that it is both possible and necessary to embed assumptions about order restrictions and the nature of driver status within evolutionary models of cancer progression to evaluate the performance of inferential approaches.
OPT3 Is a Phloem-Specific Iron Transporter That Is Essential for Systemic Iron Signaling and Redistribution of Iron and Cadmium inArabidopsis
Authors: Zhai Zhiyang , Gayomba Sheena R. , Jung Ha-il , Vimalakumari Nanditha K. , Piñeros Miguel , Craft Eric , Rutzke Michael A. , Danku John , Lahner Brett , Punshon Tracy , Guerinot Mary Lou , Salt David E. , Kochian Leon V. , Vatamaniuk Olena K. 
Published: May 2014

AbstractIron is essential for both plant growth and human health and nutrition. Knowledge of the signaling mechanisms that communicate iron demand from shoots to roots to regulate iron uptake as well as the transport systems mediating iron partitioning into edible plant tissues is critical for the development of crop biofortification strategies. Here, we report that OPT3, previously classified as an oligopeptide transporter, is a plasma membrane transporter capable of transporting transition ions in vitro. Studies in Arabidopsis thaliana show that OPT3 loads iron into the phloem, facilitates iron recirculation from the xylem to the phloem, and regulates both shoot-to-root iron signaling and iron redistribution from mature to developing tissues. We also uncovered an aspect of crosstalk between iron homeostasis and cadmium partitioning that is mediated by OPT3. Together, these discoveries provide promising avenues for targeted strategies directed at increasing iron while decreasing cadmium density in the edible portions of crops and improving agricultural productivity in iron deficient soils.
A novel particle swarm optimization based robust H-infinity control for rotorcrafts
Authors: Dai Jiyang , Ying Jin , Tan Chang 
Published: May 2014

Purpose– The purpose of this paper is to present a novel optimization approach to design a robust H-infinity controller.Design/methodology/approach– To use a modified particle swarm optimization (PSO) algorithm and to search for the optimal parameters of the weighting functions under the circumstance of the given structures of three weighting matrices in the H-infinity mixed sensitivity design.Findings– This constrained multi-objective optimization is a non-convex, non-smooth problem which is solved by a modified PSO algorithm. An adaptive mutation-based PSO (AMBPSO) algorithm is proposed to improve the search accuracy and convergence of the standard PSO algorithm. In the AMBPSO algorithm, the inertia weights are modified as a function with the gradient descent and the velocities and positions of the particles.Originality/value– The AMBPSO algorithm can efficiently solve such an optimization problem that a satisfactory robust H-infinity control performance can be obtained.
Collaborative application of the Adaptive Mentorship© model
Authors: Godden Lorraine , Tregunna Leigha , Kutsyuruba Benjamin 
Published: May 2014

Purpose– The purpose of this paper is to describe a qualitative action research study into the collective experiences of establishing a mentoring culture within a research triad consisting of a university professor together with a doctoral student and a master's level student who served as research assistants (RAs). This paper documents a process of ongoing reflection, which was used to gain insight about the personal selves, the professional selves, the role of being a RA, and concepts, ideas, and frameworks that might be useful in fulfilling the work inside and outside of the collaborative research project.Design/methodology/approach– A Faculty of Education within a Canadian university provided the context for the study. A large-scale, pan-Canadian document analysis research project served as the context for mentorship activities. The Adaptive Mentorship© model (Ralph and Walker, 2010) was the tool used to document and analyze experiences of working on the research project. Completion of individual mentoring session reflections, as recommended by the Adaptive Mentorship© model, provided a means for documenting the process and experiences within the triad.Findings– Findings indicated that the enhancement of working environment and the professional growth of all three members of the research triad were primarily achieved as a result of the commitment to collaborative mentoring for the duration of this project rather than as a direct result of application of the model. Nonetheless, the application of the Adaptive Mentorship© model within the research project triad proved to be a valuable tool for supporting the social competence-based and experiential needs.Originality/value– In the context of this study, collaborative mentoring led to professional growth and an enhancement of the working environment due to multiple contact-points and exposures to specific tasks or skill-sets. The establishment of the mentoring culture and continued identification of individual needs within the triad allowed for adaptive support, appropriate skills development, and an increase in confidence necessary for both students to be successful in their RA positions and in turn, successfully support the university professor to complete the project. The experience suggests that the Adaptive Mentorship© model, if further refined, could be applied to graduate RAships with multiple participants, increasing the potential to enhance research experiences through its focus on one or several specific tasks or skill-sets around which the work is organized.
Freshwater conservation planning under climate change: demonstrating proactive approaches for Australian Odonata
Authors: Bush Alex , Hermoso Virgilio , Linke Simon , Nipperess David , Turak Eren , Hughes Lesley 
Published: May 2014

SummaryClimate change represents a major challenge for conservation in the future and undermines protection within reserve boundaries. Freshwater biodiversity is still under‐represented within reserves world‐wide, and connectivity among reserves will become increasingly crucial if species are to persist under climate change.We tested the likely benefits of including predicted species distributions in systematic reserve design for rivers under climate change and the impact of varying connectivity requirements on future representation.We used the modelled distribution of 126 east Australian Odonata to identify reserve networks using data for current or future (2055 and 2085) distributions either by filling gaps additively, or as separate targets in a single solution. We then assessed the potential improvements to species representation in the future using different types of connectivity penalties that emphasized either longitudinal riverine connections or connections to all neighbouring subcatchments.Solutions that did not include future distributions in the planning stages were 16 to 30% less likely to protect the same species by 2055 and 2085, respectively. Inclusion of species' future distributions in the design phase leads to short‐term increases in cost, but in the longer term fewer additional areas are required to meet targets and this strategy is likely to be significantly more efficient than implementing systematic design in stages. In addition, solely targeting riverine connectivity was significantly less likely to protect current species in the future than if cross‐catchment connections were included.Synthesis and applications. Where protected areas can be expanded to assist species adaptation to climate change, significant gains in efficiency are possible if longer term goals are considered when selecting sites. Furthermore, to improve the representation of species under future climates, reserve selection should consider inter‐catchment connectivity, although the nature of optimal solutions will depend heavily on the range of taxa included, their dispersal capacity, and the availability of climatic refugia.