bluuebunny/crossref_metadata_2025_split huggingface dataset:
Negative regulatory roles of DE-ETIOLATED1 in flowering time inArabidopsis
Authors: Kang Min-Young , Yoo Soo-Cheul , Kwon Hye-Young , Lee Byoung-Doo , Cho Jung-Nam , Noh Yoo-Sun , Paek Nam-Chon 
Published: May 2015

AbstractArabidopsis flowers early under long days (LD) and late under short days (SD).The repressor of photomorphogenesis DE-ETIOLATED1 (DET1) delaysflowering; det1-1 mutants flower early, especially under SD, but themolecular mechanism of DET1 regulation remains unknown. Here we examine theregulatory function of DET1 in repression of flowering. Under SD, the det1-1mutation causes daytime expression of FKF1 and CO; however, theiraltered expression has only a small effect on early flowering in det1-1mutants. Notably, DET1 interacts with GI and binding of GI to the FT promoterincreases in det1-1 mutants, suggesting that DET1 mainly restricts GIfunction, directly promoting FT expression independent of COexpression. Moreover, DET1 interacts with MSI4/FVE, which epigenetically inhibitsFLC expression, indicating that the lack of FLC expression indet1-1 mutants likely involves altered histone modifications at theFLC locus. These data demonstrate that DET1 acts in both photoperiod andautonomous pathways to inhibit expression of FT and SOC1. Consistentwith this, the early flowering of det1-1 mutants disappears completely in theft-1 soc1-2 double mutant background. Thus, we propose that DET1 is astrong repressor of flowering and has a pivotal role in maintaining photoperiodsensitivity in the regulation of flowering time.
A point mutation in the extracellular domain of KIT promotes tumorigenesis of mastcells via ligand-independent auto-dimerization
Authors: Amagai Yosuke , Matsuda Akira , Jung Kyungsook , Oida Kumiko , Jang Hyosun , Ishizaka Saori , Matsuda Hiroshi , Tanaka Akane 
Published: May 2015

AbstractMutations in the juxtamembrane and tyrosine kinase domains of the KIT receptor havebeen implicated in several cancers and are known to promote tumorigenesis. However,the pathophysiological manifestations of mutations in the extracellular domainremain unknown. In this study, we examined the impact of a mutation in theextracellular domain of KIT on mast cell tumorigenesis. A KIT mutant with anAsn508Ile variation (N508I) in the extracellular domain derived from a canine mastcell tumor was introduced into IC-2 cells. The IC-2N508I cellsproliferated in a cytokine-independent manner and showed KIT auto-phosphorylation.Subcutaneous injection of IC-2N508I cells into the dorsal area ofimmunodeficient BALB/c-nu/nu mice resulted in the formation of solid tumors,but tumor progression was abrogated by treatment with a tyrosine kinase inhibitor(STI571). In addition, the N508I mutant KIT protein dimerized in the absence of thenatural ligand, stem cell factor. Structure modeling indicates that the increasedhydrophobicity of the mutant led to the stabilization of KIT dimers. These resultssuggest that this extracellular domain mutation confers a ligand-independenttumorigenic phenotype to mast cells by KIT auto-dimerization that isSTI571-sensitive. This is the first report demonstrating the tumorigenic potentialof a mutation in the extracellular domain of KIT.
A theoretical investigation of mixing thermodynamics, age-hardening potential and electronic structure of ternary M11–xM2xB2 alloys with AlB2 type structure
Authors: Alling B. , Högberg H. , Armiento R. , Rosen J. , Hultman L. 
Published: May 2015

AbstractTransition metal diborides are ceramic materials with potential applications as hard protective thin films and electrical contact materials. We investigate the possibility to obtain age hardening through isostructural clustering, including spinodal decomposition, or ordering-induced precipitation in ternary diboride alloys. By means of first-principles mixing thermodynamics calculations, 45 ternary M11–xM2xB2alloys comprising MiB2(Mi = Mg, Al, Sc, Y, Ti, Zr, Hf, V, Nb, Ta) with AlB2type structure are studied. In particular Al1–xTixB2is found to be of interest for coherent isostructural decomposition with a strong driving force for phase separation, while having almost concentration independentaandclattice parameters. The results are explained by revealing the nature of the electronic structure in these alloys and in particular, the origin of the pseudogap atEFin TiB2, ZrB2and HfB2.
Comparative analysis of the Dicer-like gene family reveals loss of miR162 target site in SmDCL1 from Salvia miltiorrhiza
Authors: Shao Fenjuan , Qiu Deyou , Lu Shanfa 
Published: May 2015

AbstractDCL1, the core component for miRNA biogenesis, is itself regulated by miR162 in Arabidopsis. MiRNA-mediated feedback regulation of AtDCL1 is important to maintain the proper level of DCL1 transcripts. However, it is unknown whether the miRNA-mediated regulation of DCL1 is conserved among plants. We analyzed the SmDCL gene family in Salvia miltiorrhiza, an emerging model plant for Traditional Chinese Medicine (TCM) studies, using a comprehensive approach integrating genome-wide prediction, molecular cloning, gene expression profiling and posttranscriptional regulation analysis. A total of five SmDCLs were identified. Comparative analysis of SmDCLs and AtDCLs showed an apparent enlargement of SmDCL introns in S. miltiorrhiza. The absence of miR162 in S. miltiorrhiza and the loss of miR162 target site in SmDCL1 were unexpectedly found. Further analysis showed that the miR162 target site was not present in DCL1 from ancient plants and was gained during plant evolution. The gained miR162 target site might be lost in a few modern plants through nucleotide mutations. Our results provide evidence for the gain and loss of miR162 and its target sites in Dicer-like genes during evolution. The data is useful for understanding the evolution of miRNA-mediated feedback regulation of DCLs in plants.
A systematic review and meta-analysis of the effect of statins on plasma asymmetric dimethylarginine concentrations
Authors: Serban Corina , Sahebkar Amirhossein , Ursoniu Sorin , Mikhailidis Dimitri P. , Rizzo Manfredi , Lip Gregory Y.H. , Kees Hovingh G. , Kastelein John J.P. , Kalinowski Leszek , Rysz Jacek , Banach Maciej 
Published: May 2015

AbstractThe impact of statin therapy on plasma asymmetric dimethylarginine (ADMA) levels has not been conclusively studied. Therefore the aim of the meta-analysis was to assess the effect of statins on circulating ADMA levels. We searched selected databases (up to August 2014) to identify randomized controlled trials (RCTs) that investigate the effect of statins on plasma ADMA concentrations. A weighted meta-regression (WMD) using unrestricted maximum likelihood model was performed to assess the impact of statin dose, duration of statin therapy and baseline ADMA concentrations as potential variables on the WMD between statin and placebo group. In total, 1134 participants in 9 selected RCTs were randomized; 568 were allocated to statin treatment and 566 were controls. There was a significant reduction in plasma ADMA concentrations following statin therapy compared with placebo (WMD: − 0.104 μM, 95% confidence interval: − 0.131 to − 0.077, Z = − 7.577, p < 0.0001). Subgroups analysis has shown a significant impact of hydrophilic statins (WMD: − 0.207 μM, 95%CI: − 0.427 to + 0.013, Z = − 7.250, p < .0001) and a non-significant effect of hydrophobic statins (WMD: − 0.101 μM, 95%CI: − 0.128 to − 0.074, Z = − 1.845, p = 0.065). In conclusion, this meta-analysis of available RCTs showed a significant reduction in plasma ADMA concentrations following therapy with hydrophilic statins.
Proteomic-based biotyping reveals hidden diversity within a microalgae culture collection: An example using Dunaliella
Authors: Emami Kaveh , Hack Ethan , Nelson Andrew , Brain Chelsea M. , Lyne Fern M. , Mesbahi Ehsan , Day John G. , Caldwell Gary S. 
Published: May 2015

AbstractAccurate and defendable taxonomic identification of microalgae strains is vital for culture collections, industry and academia; particularly when addressing issues of intellectual property. We demonstrate the remarkable effectiveness of Matrix Assisted Laser Desorption Ionisation Time of Flight Mass Spectrometry (MALDI-TOF-MS) biotyping to deliver rapid and accurate strain separation, even in situations where standard molecular tools prove ineffective. Highly distinctive MALDI spectra were obtained for thirty two biotechnologically interesting Dunaliella strains plus strains of Arthrospira, Chlorella, Isochrysis, Tetraselmis and a range of culturable co-occurring bacteria. Spectra were directly compared with genomic DNA sequences (internal transcribed spacer, ITS). Within individual Dunaliella isolates MALDI discriminated between strains with identical ITS sequences, thereby emphasising and enhancing knowledge of the diversity within microalgae culture collections. Further, MALDI spectra did not vary with culture age or growth stage during the course of the experiment; therefore MALDI presents stable and accurate strain-specific signature spectra. Bacterial contamination did not affect MALDI’s discriminating power. Biotyping by MALDI-TOF-MS will prove effective in situations wherein precise strain identification is vital, for example in cases involving intellectual property disputes and in monitoring and safeguarding biosecurity. MALDI should be accepted as a biotyping tool to complement and enhance standard molecular taxonomy for microalgae.
A method for human teratogen detection by geometrically confined cell differentiation and migration
Authors: Xing Jiangwa , Toh Yi-Chin , Xu Shuoyu , Yu Hanry 
Published: May 2015

AbstractUnintended exposure to teratogenic compounds can lead to various birth defects; however current animal-based testing is limited by time, cost and high inter-species variability. Here, we developed a human-relevantin vitromodel, which recapitulated two cellular events characteristic of embryogenesis, to identify potentially teratogenic compounds. We spatially directed mesoendoderm differentiation, epithelial-mesenchymal transition and the ensuing cell migration in micropatterned human pluripotent stem cell (hPSC) colonies to collectively form an annular mesoendoderm pattern. Teratogens could disrupt the two cellular processes to alter the morphology of the mesoendoderm pattern. Image processing and statistical algorithms were developed to quantify and classify the compounds’ teratogenic potential. We not only could measure dose-dependent effects but also correctly classify species-specific drug (Thalidomide) and false negative drug (D-penicillamine) in the conventional mouse embryonic stem cell test. This model offers a scalable screening platform to mitigate the risks of teratogen exposures in human.
Skin Rejuvenation with Non-Invasive Pulsed Electric Fields
Authors: Golberg Alexander , Khan Saiqa , Belov Vasily , Quinn Kyle P. , Albadawi Hassan , Felix Broelsch G. , Watkins Michael T. , Georgakoudi Irene , Papisov Mikhail , Mihm Martin C. , Austen William G. , Yarmush Martin L. 
Published: May 2015

AbstractDegenerative skin diseases affect one third of individuals over the age of sixty. Current therapies use various physical and chemical methods to rejuvenate skin; but since the therapies affect many tissue components including cells and extracellular matrix, they may also induce significant side effects, such as scarring. Here we report on a new, non-invasive, non-thermal technique to rejuvenate skin with pulsed electric fields. The fields destroy cells while simultaneously completely preserving the extracellular matrix architecture and releasing multiple growth factors locally that induce new cells and tissue growth. We have identified the specific pulsed electric field parameters in rats that lead to prominent proliferation of the epidermis, formation of microvasculature and secretion of new collagen at treated areas without scarring. Our results suggest that pulsed electric fields can improve skin function and thus can potentially serve as a novel non-invasive skin therapy for multiple degenerative skin diseases.
A hybrid-membrane migration method to isolate high-purity adipose-derived stem cells from fat tissues
Authors: Higuchi Akon , Wang Ching-Tang , Ling Qing-Dong , Lee Henry Hsin-chung , Kumar S. Suresh , Chang Yung , Alarfaj Abdullah A. , Munusamy Murugan A. , Hsu Shih-Tien , Wu Gwo-Jang , Umezawa Akihiko 
Published: May 2015

AbstractHuman adipose-derived stem cells (hADSCs) exhibit heterogeneous characteristics, indicating various genotypes and differentiation abilities. The isolated hADSCs can possess different purity levels and divergent properties depending on the purification methods used. We developed a hybrid-membrane migration method that purifies hADSCs from a fat tissue solution with extremely high purity and pluripotency. A primary fat-tissue solution was permeated through the porous membranes with a pore size from 8 to 25 μm and the membranes were incubated in cell culture medium for 15-18 days. The hADSCs that migrated from the membranes contained an extremely high percentage (e.g., >98%) of cells positive for mesenchymal stem cell markers and showed almost one order of magnitude higher expression of some pluripotency genes (Oct4, Sox2, Klf4 and Nanog) compared with cells isolated using the conventional culture method.
The focal adhesion kinase Pyk2 links Ca2+ signalling to Src family kinase activation and protein tyrosine phosphorylation in thrombin-stimulated platelets
Authors: Canobbio Ilaria , Cipolla Lina , Guidetti Gianni F. , Manganaro Daria , Visconte Caterina , Kim Soochong , Okigaki Mitsuhiko , Falasca Marco , Kunapuli Satya P. , Torti Mauro 
Published: May 2015

In blood platelets, stimulation of G protein-coupled receptors (GPCRs) by thrombin triggers the activation of Src family kinases (SFKs), resulting in the tyrosine-phosphorylation of multiple substrates, but the mechanism underlying this process is still poorly understood. In the present study, we show that the time-dependent protein-tyrosine phosphorylation triggered by thrombin in human or murine platelets was totally suppressed only upon concomitant chelation of intracellular Ca2+ and inhibition of SFKs. Thrombin-induced activation of SFKs was regulated by intracellular Ca2+ and accordingly the Ca2+ ionophore A23187 was sufficient to stimulate SFKs. A23187 also triggered the phosphorylation and activation of the Ca2+-dependent focal adhesion kinase Pyk2 and Pyk2 activation by thrombin was Ca2+-dependent. Stimulation of SFKs by thrombin or A23187 was strongly reduced in platelets from Pyk2 knockout (KO) mice, as was the overall pattern of protein-tyrosine phosphorylation. By immunoprecipitation experiments, we demonstrate that Lyn and Fyn, but not Src, were activated by Pyk2. Inhibition of SFKs by PP2 also reduced the phosphorylation of Pyk2 in thrombin or A23187-stimulated platelets. Analysis of KO mice demonstrated that Fyn, but not Lyn, was required for complete Pyk2 phosphorylation by thrombin. Finally, PP2 reduced aggregation of murine platelets to a level comparable to that of Pyk2-deficient platelets, but did not have further effects in the absence of Pyk2. These results indicate that in thrombin-stimulated platelets, stimulation of Pyk2 by intracellular Ca2+ initiates SFK activation, establishing a positive loop that reinforces the Pyk2/SFK axis and allows the subsequent massive tyrosine phosphorylation of multiple substrates required for platelet aggregation.
Crop rotations in the sea: Increasing returns and reducing risk of collapse in sea cucumber fisheries
Authors: Plagányi Éva Elizabeth , Skewes Timothy , Murphy Nicole , Pascual Ricardo , Fischer Mibu 
Published: May 2015

Significance
Rotating the harvest of natural resources is a management strategy that humans have used on land for centuries, but it is less commonly applied to marine resources. Marine animals, such as sea cucumbers, scallops, and abalone, may be particularly suited for this form of management. Although highly important to many communities worldwide, they are often severely overexploited, underlining the need for effective and easy to manage harvest strategies. We modeled the rotational zone strategy applied to the multispecies sea cucumber fishery in Australia’s Great Barrier Reef Marine Park and show a substantial reduction in the risk of localized depletion, higher long-term yields, and improved economic performance. Hence, our results support the use of rotational harvests to better manage these marine resources.
Superficial white matter fiber systems impede detection of long-range cortical connections in diffusion MR tractography
Authors: Reveley Colin , Seth Anil K. , Pierpaoli Carlo , Silva Afonso C. , Yu David , Saunders Richard C. , Leopold David A. , Ye Frank Q. 
Published: May 2015

Significance
It is widely recognized that studying the detailed anatomy of the human brain is of great importance for neuroscience and medicine. The principal means for achieving this goal is presently diffusion magnetic resonance imaging (dMRI) tractography, which uses the local diffusion of water throughout the brain to estimate the course of long-range anatomical projections. Such projections connect gray matter regions through axons that travel in the deep white matter. The present study combines dMRI tractography with histological analysis to investigate where in the brain this method succeeds and fails. We conclude that certain superficial white matter systems pose challenges for measuring cortical connections that must be overcome for accurate determination of detailed neuroanatomy in humans.
Random coil negative control reproduces the discrepancy between scattering and FRET measurements of denatured protein dimensions
Authors: Watkins Herschel M. , Simon Anna J. , Sosnick Tobin R. , Lipman Everett A. , Hjelm Rex P. , Plaxco Kevin W. 
Published: May 2015

Significance
The relationship between proteins unfolded under physiological conditions and those unfolded by chemical denaturation remains controversial. Specifically, although FRET studies suggest that unfolded proteins invariably contract with falling denaturant levels, scattering studies argue that they do not. Here, we explore the origins of this discrepancy using PEG as a negative control. Scattering indicates that, as expected, the polymer’s dimensions are denaturant-independent. The dye-labeled polymer, nevertheless, exhibits denaturant-dependent changes in measured transfer efficiency similar to those seen for unfolded proteins. This similarity raises questions regarding the interpretation of such changes as being indicative of hydrophobic or hydrogen bond-driven collapse.
Identifying personal microbiomes using metagenomic codes
Authors: Franzosa Eric A. , Huang Katherine , Meadow James F. , Gevers Dirk , Lemon Katherine P. , Bohannan Brendan J. M. , Huttenhower Curtis 
Published: May 2015

Significance
Recent surveys of the microbial communities living on and in the human body—the human microbiome—have revealed strong variation in community membership between individuals. Some of this variation is stable over time, leading to speculation that individuals might possess unique microbial “fingerprints” that distinguish them from the population. We rigorously evaluated this idea by combining concepts from microbial ecology and computer science. Our results demonstrated that individuals could be uniquely identified among populations of 100s based on their microbiomes alone. In the case of the gut microbiome, >80% of individuals could still be uniquely identified up to a year later—a result that raises potential privacy concerns for subjects enrolled in human microbiome research projects.
Protein aggregation in salt solutions
Authors: Kastelic Miha , Kalyuzhnyi Yurij V. , Hribar-Lee Barbara , Dill Ken A. , Vlachy Vojko 
Published: May 2015

Significance
Protein aggregation is a problem in amyloid and other diseases, and it is a challenge when formulating solutions of biological drugs, such as monoclonal antibodies. The physical processes of aggregation, especially in salt solutions, are not well understood. We model a protein as having multiple binding sites to other proteins, leading to orientational variations, dependent on salt. With few parameters and with knowledge of the cloud-point temperatures as a function of added salt, the model gives good predictions for properties including the liquid–liquid coexistence curves, the second virial coefficients, and others for lysozyme and gamma-crystallin.
Lactobionic and cellobionic acid production profiles of the resting cells of acetic acid bacteria
Authors: Kiryu Takaaki , Kiso Taro , Nakano Hirofumi , Murakami Hiromi 
Published: May 2015

Abstract
Lactobionic acid was produced by acetic acid bacteria to oxidize lactose. Gluconobacter spp. and Gluconacetobacter spp. showed higher lactose-oxidizing activities than Acetobacter spp. Gluconobacter frateurii NBRC3285 produced the highest amount of lactobionic acid per cell, among the strains tested. This bacterium assimilated neither lactose nor lactobionic acid. At high lactose concentration (30%), resting cells of the bacterium showed sufficient oxidizing activity for efficient production of lactobionic acid. These properties may contribute to industrial production of lactobionic acid by the bacterium. The bacterium showed higher oxidizing activity on cellobiose than that on lactose and produced cellobionic acid.
A spring-clean of Michael Porter’s Attic
Authors: Gould Anthony M. , Desjardins Guillaume 
Published: May 2015

Purpose– This paper views the phenomenon of offering/user interface complexity as having competitive strategy-related consequences. Porter’s conception of generic management strategy was created in the 1980s. It is not well adapted to industries which have proliferated in the Internet age. Accordingly, the conception presented in this article offers a modified version of Porter’s generic strategy framework. The new view incorporates the dimension of complexity alongside the original dimensions of “target market” and “type of advantage”. The article uses an analysis of the contemporary Canadian Telco sector to prosecute its case.Design/methodology/approach– The project uses an analysis of the stated competitive positioning orientations of firms operating in the contemporary Canadian Telecommunications sector to build a case about the changed nature of generic strategy in the digital age. It uses inductive reasoning to generalise findings about the Telco sector to other recently emerged (digital-age) industries.Findings– A revised view of Porter’s generic strategy grid is presented and defended.Research limitations/implications– The study analyses only one sector, but draws many broad conclusions. It uses inductive reasoning which is limited by the extent to which the exemplar case (telecommunications) may be compared to other cases within the same category (other digital age industries). The study does not use an extensive analysis of strategic planning documents of individual firms; however, this is not a limitation unless and until a critique challenges the claims made about generic strategies being pursued.Practical implications– The new conceptualisation may be used as a planning tool for digital-age firms.Originality/value– The project is a genuinely new attempt to update Porter’s view of generic strategy. It overcomes the problems which have been associated with previous attempts at such revision.