bluuebunny/crossref_metadata_2025_split huggingface dataset:
The macrophage contribution to stress erythropoiesis: when less is enough
Authors: Ulyanova Tatiana , Phelps Susan R. , Papayannopoulou Thalia 
Published: August 2016

Key PointsSignificant expansion only of native splenic macrophages that are F4/80+/Cd11blo occurs in both post-Epo and post–hemolysis-induced stress. VCAM-1−/− mice, like Spi-C−/−, mice have significantly decreased macrophages but did not have a compromised E-stress response.
Improving feature selection performance using pairwise pre-evaluation
Authors: Li Songlu , Oh Sejong 
Published: August 2016

Abstract
Background
Biological data such as microarrays contain a huge number of features. Thus, it is necessary to select a small number of novel features to characterize the entire dataset. All combinations of the features subset must be evaluated to produce an ideal feature subset, but this is impossible using currently available computing power. Feature selection or feature subset selection provides a sub-optimal solution within a reasonable amount of time.

Results
In this study, we propose an improved feature selection method that uses information based on all the pairwise evaluations for a given dataset. We modify the original feature selection algorithms to use pre-evaluation information. The pre-evaluation captures the quality and interactions between two features. The feature subset should be improved by using the top ranking pairs for two features in the selection process.

Conclusions
Experimental results demonstrated that the proposed method improved the quality of the feature subset produced by modified feature selection algorithms. The proposed method can be applied to microarray and other high-dimensional data.
PI(3)P-p40phoxbinding regulates NADPH oxidase activation in mouse macrophages and magnitude of inflammatory responses in vivo
Authors: Bagaitkar Juhi , Barbu Emilia A , Perez-Zapata Lizet J , Austin Anthony , Huang Guangming , Pallat Sabine , Dinauer Mary C 
Published: August 2016

AbstractMutations in the leukocyte NADPH oxidase that abrogate superoxide production result in chronic granulomatous disease (CGD), an inherited immunodeficiency associated with recurrent infections and inflammatory complications. The cytosolic regulatory subunit p40phox plays a specialized role in stimulating NADPH oxidase activity on intracellular membranes via its phosphatidylinositol 3-phosphate [PI(3)P]-binding domain, as revealed by studies largely focused on neutrophils. Whether PI(3)P-p40phox-regulated superoxide production contributes to regulating inflammatory responses is not well understood. Here, we report that mice expressing p40phox R58A, which lacks PI(3)P binding, had impaired macrophage NADPH oxidase activity and increased sterile inflammation. p40phoxR58A/R58A macrophages exhibited diminished phagosome reactive oxygen species (ROS) in response to certain particulate and soluble ligands, including IgG-opsonized particles and a TLR2 agonist, along with unexpected defects in plasma membrane oxidase activity. Compared with wild-type (WT) mice, p40phoxR58A/R58A mice had elevated numbers of newly recruited neutrophils and monocytes in peritoneal inflammation elicited by zymosan, monosodium urate (MSU) crystals, or sodium periodate. At later time points, higher numbers of inflammatory macrophages in p40phoxR58A/R58A mice were consistent with delayed resolution. Our studies demonstrate a critical role of PI(3)P-p40phox binding for optimal activation of the NADPH oxidase in macrophages. Furthermore, selective loss of PI(3)P-regulated NADPH oxidase activity was sufficient to enhance significantly responses to inflammation and delay resolution.
Changes in fatty acid composition in the giant clamTridacna maximain response to thermal stress
Authors: Dubousquet Vaimiti , Gros Emmanuelle , Berteaux-Lecellier Véronique , Viguier Bruno , Raharivelomanana Phila , Bertrand Cédric , Lecellier Gaël J. 
Published: August 2016

ABSTRACTTemperature can modify membrane fluidity and thus affects cellular functions and physiological activities. This study examines lipid remodelling in the marine symbiotic organism, Tridacna maxima, during a time series of induced thermal stress, with an emphasis on the morphology of their symbiont Symbiodinium. First, we show that the French Polynesian giant clams harbour an important proportion of saturated fatty acids (SFA), which reflects their tropical location. Second, in contrast to most marine organisms, the total lipid content in giant clams remained constant under stress, though some changes in their composition were shown. Third, the stress-induced changes in fatty acid (FA) diversity were accompanied by an upregulation of genes involved in lipids and ROS pathways. Finally, our microscopic analysis revealed that for the giant clam's symbiont, Symbiodinium, thermal stress led to two sequential cell death processes. Our data suggests that the degradation of Symbiodinium cells could provide an additional source of energy to T. maxima in response to heat stress.
miR-20a regulates proliferation, differentiation and apoptosis in P19 cell model of cardiac differentiation by targeting Smoothened
Authors: Ai Feng , Zhang Yanwei , Peng Bangtian 
Published: August 2016

ABSTRACT
MicroRNA (miR)-20a, a member of the miR-17-92 cluster related to cardiac development, was obviously downregulated in myocardially differentiated P19 cells compared with normal P19 cells. Smoothened (SMO) is a member of the Hh pathway. Hh signaling induces cardiac differentiation in P19 cells, and SMO mediates the Hh pathway during embryonic development. Using bioinformatic prediction software Targetscan (http://www.targetscan.org/), PicTar (http://pictar.bio.nyu.edu), and miRBase (http://microrna.sanger.ac.uk/), miR-20a and the 3′-untranslated region (3′-UTR) of SMO mRNA were predicted to have complementary binding regions. Accordingly, we inferred that miR-20a might act as a regulator of SMO, and regulate proliferation, differentiation and apoptosis in P19 cells. We determined the expression of miR-20a, SMO and marker proteins of cardiomyocytes (cTnT, GATA4 and desmin) by quantitative real-time PCR (qRT-PCR) and western blot assays, and found that P19 cells had differentiated into cardiomyocytes successfully at differentiation day 10, and downregulation of miR-20a and upregulation of SMO existed in myocardially differentiated P19 cells. Cell proliferation, differentiation and apoptosis detection showed that miR-20a upregulation inhibited proliferation and differentiation and enhanced apoptosis in P19 cells. Moreover, we verified that miR-20a directly targeted SMO and knockdown of SMO and miR-20a overexpression had similar effects on P19 cell proliferation, differentiation and apoptosis, which verified the speculation that miR-20a inhibits proliferation and differentiation and enhances apoptosis in P19 cells by directly targeting SMO. Our results suggest that miR-20a may be a potential target against congenital heart diseases.
Matriptase and prostasin are expressed in human skin in an inverse trend over the course of differentiation and are targeted to different regions of the plasma membrane
Authors: Lai Chih-Hsin , Chang Shun-Cheng , Chen Yen-Ju , Wang Yi-Jie J. , Lai Ying-Jun J. , Chang Hsiang-Hua D. , Berens Eric B. , Johnson Michael D. , Wang Jehng-Kang , Lin Chen-Yong 
Published: August 2016

ABSTRACT
Matriptase and prostasin, acting as a tightly coupled proteolytic cascade, were reported to be required for epidermal barrier formation in mouse skin. Here we show that, in human skin, matriptase and prostasin are expressed with an inverse pattern over the course of differentiation. Matriptase was detected primarily in epidermal basal keratinocytes and the basaloid cells in the outer root sheath of hair follicles and the sebaceous gland, where prostasin was not detected. In contrast, prostasin was detected primarily in differentiated cells in the epidermal granular layer, the inner root sheath of hair follicles, and the sebaceous gland, where matriptase expression is negligible. While co-expressed in the middle stage of differentiation, prostasin was detected as polarized patches, and matriptase at intercellular junctions. Targeting to different subcellular localizations is also observed in HaCaT human keratinocytes, in which matriptase was detected primarily at intercellular junctions, and prostasin primarily on membrane protrusion. Furthermore, upon induction of zymogen activation, free active prostasin remains cell-associated and free active matriptase is rapidly shed into the extracellular milieu. Our data suggest that matriptase and prostasin likely function as independent entities in human skin rather than as a tightly coupled proteolytic cascade as observed in mouse skin.
Maximum swimming speeds of sailfish and three other large marine predatory fish species based on muscle contraction time and stride length: a myth revisited
Authors: Svendsen Morten B. S. , Domenici Paolo , Marras Stefano , Krause Jens , Boswell Kevin M. , Rodriguez-Pinto Ivan , Wilson Alexander D. M. , Kurvers Ralf H. J. M. , Viblanc Paul E. , Finger Jean S. , Steffensen John F. 
Published: August 2016

ABSTRACTBillfishes are considered to be among the fastest swimmers in the oceans. Previous studies have estimated maximum speed of sailfish and black marlin at around 35 m s−1 but theoretical work on cavitation predicts that such extreme speed is unlikely. Here we investigated maximum speed of sailfish, and three other large marine pelagic predatory fish species, by measuring the twitch contraction time of anaerobic swimming muscle. The highest estimated maximum swimming speeds were found in sailfish (8.3±1.4 m s−1), followed by barracuda (6.2±1.0 m s−1), little tunny (5.6±0.2 m s−1) and dorado (4.0±0.9 m s−1); although size-corrected performance was highest in little tunny and lowest in sailfish. Contrary to previously reported estimates, our results suggest that sailfish are incapable of exceeding swimming speeds of 10-15 m s−1, which corresponds to the speed at which cavitation is predicted to occur, with destructive consequences for fin tissues.
Identification and characterization of a symbiotic alga from soil bryophyte for lipid profiles
Authors: Feng Jia , Guo Yuning , Zhang Xiujuan , Wang Guihua , Lv Junping , Liu Qi , Xie Shulian 
Published: August 2016

ABSTRACT
A symbiotic alga was successfully isolated from the soil moss Entodon obtusatus found in the Guandi Mountains, Shanxi Province, China, and cultivated under axenic conditions. Morphological observations showed that the symbiotic alga was similar to Chlorococcum. Based on phylogenetic analysis of 18S rRNA and rbcL genes and internal transcribed spacer (ITS) regions, Chlorococcum sp. GD was identified as Chlorococcum sphacosum. The three data sets were congruent for those aspects of the topologies that were relatively robust, and differed for those parts of the topologies that were not. This strain was cultured in BG11 medium to test its growth and biodiesel properties. It produced a lipid content of nearly 40%, and achieved biomass concentration of 410 mg l−1 and lipid productivity of 6.76 mg l−1 day−1, with favorable C16:0 (23.10%) and C18:1 (21.62%) fatty acid content. This alga appears to have potential for use in biodiesel production.
The decapping activator Edc3 and the Q/N-rich domain of Lsm4 function together to enhance mRNA stability and alter mRNA decay pathway dependence in Saccharomyces cerevisiae
Authors: Huch Susanne , Müller Maren , Muppavarapu Mridula , Gommlich Jessie , Balagopal Vidya , Nissan Tracy 
Published: August 2016

ABSTRACT
The rate and regulation of mRNA decay are major elements in the proper control of gene expression. Edc3 and Lsm4 are two decapping activator proteins that have previously been shown to function in the assembly of RNA granules termed P bodies. Here, we show that deletion of edc3, when combined with a removal of the glutamine/asparagine rich region of Lsm4 (edc3Δ lsm4ΔC) reduces mRNA stability and alters pathways of mRNA degradation. Multiple tested mRNAs exhibited reduced stability in the edc3Δ lsm4ΔC mutant. The destabilization was linked to an increased dependence on Ccr4-mediated deadenylation and mRNA decapping. Unlike characterized mutations in decapping factors that either are neutral or are able to stabilize mRNA, the combined edc3Δ lsm4ΔC mutant reduced mRNA stability. We characterized the growth and activity of the major mRNA decay systems and translation in double mutant and wild-type yeast. In the edc3Δ lsm4ΔC mutant, we observed alterations in the levels of specific mRNA decay factors as well as nuclear accumulation of the catalytic subunit of the decapping enzyme Dcp2. Hence, we suggest that the effects on mRNA stability in the edc3Δ lsm4ΔC mutant may originate from mRNA decay protein abundance or changes in mRNPs, or alternatively may imply a role for P bodies in mRNA stabilization.
The effect of problem based learning on 5th grades students’ energy literacy<p>Probleme dayalı öğrenme yaklaşımının 5. Sınıf öğrencilerinin enerji okuryazarlıkları üzerine etkisi
Authors: Göcük Aysun , Şahin Fatma 
Published: August 2016

The need for energy is increasing. If fossil fuels continue to be consumed at this rate, they will disappear after a short period of time. Therefore, it is essential to use limited energy resources consciously. How early students wins this awareness, positive outcomes will be much more. The main purpose of the study is to make students aware of the problems from early ages and the object of this study is to find out how Problem Based Learning (PBL) affect the 5th grade students literacy improvement by using knowledge tests. It is an experimental study with a controlled group applied pre-test and final- test. It was carried out with the 5th grade students on 2013-2014 education year. A total of 36 students participated in the study. The involved in the experiment and control group were selected randomly. In the experiment group, the students were taught using activities prepared by Problem Based Learning and in control group, the students were taught using traditional methods. The duration for each group was 10 lesson hours. Data of search was derived using energy literacy knowledge test (ELKT). When researched the effect of Problem Based Learning method carried out on experiment group and traditional method carried out on control group, a significant distinction in favor of Problem Based Learning method was found out. ÖzetEnerjiye olan ihtiyaç giderek artmaktadır. Fosil yakıtlar bu hızla tüketilmeye devam ederse, kısa bir süre sonra yok olacaklar. Bu yüzden, sınırlı olan enerji kaynaklarını bilinçli kullanmak şarttır. Öğrenciler bu bilinci ne kadar erken kazanırlarsa, olumlu sonuçları o kadar fazla olacaktır. Bu çalışmanın temel amacı öğrencilerin erken yaşta problemin farkına varmasını sağlamaktır ve bu çalışmayla Probleme Dayalı Öğrenme (PDÖ) yaklaşımının 5. sınıf öğrencilerinin enerji okuryazarlığı üzerine etkisini bilgi testi kullanarak incelemek amaçlanmıştır. Çalışma ön test – son test kontrol gruplu deneysel bir çalışma olarak planlanmıştır. Araştırmanın çalışma grubunu 2013-2014 Eğitim Öğretim yılı içerisinde 5. sınıfta eğitim gören toplam 36 öğrenci oluşturmuştur. Deney ve kontrol grubunu oluşturan öğrenciler şans (random) yoluyla belirlenmiştir. Deney grubunda dersler PDÖ yöntemiyle hazırlanan ders etkinlikleriyle işlenirken, kontrol grubunda dersler mevcut programdaki etkinlikler ile işlenmiştir. Her iki grup için de çalışmanın süresi 10 ders saatidir. Araştırmanın verileri enerji okuryazarlığı bilgi testi (EOBT) ile toplanmıştır. Deney grubunda uygulanan PDÖ yöntemin mevcut programdaki etkinliklere göre enerji okuryazarlığında daha etkili olduğu tespit edilmiştir.
Visual drainage assessment: A standardised visual soil assessment method for use in land drainage design in Ireland
Authors: Tuohy P. , Humphreys J. , Holden N.M. , O’Loughlin J. , Reidy B. , Fenton O. 
Published: August 2016

AbstractThe implementation of site-specific land drainage system designs is usually disregarded by landowners in favour of locally established ‘standard practice’ land drainage designs. This is due to a number of factors such as a limited understanding of soil–water interactions, lack of facilities for the measurement of soil’s physical or hydrological parameters and perceived time wastage and high costs. Hence there is a need for a site-specific drainage system design methodology that does not rely on inaccessible, time-consuming and/or expensive measurements of soil physical or hydrological properties. This requires a standardised process for deciphering the drainage characteristics of a given soil in the field. As an initial step, a new visual soil assessment method, referred to as visual drainage assessment (VDA), is presented whereby an approximation of the permeability of specific soil horizons is made using seven indicators (water seepage, pan layers, texture, porosity, consistence, stone content and root development) to provide a basis for the design of a site-specific drainage system. Across six poorly drained sites (1.3 ha to 2.6 ha in size) in south-west Ireland a VDA-based design was compared with (i) an ideal design (utilising soil physical measurements to elucidate soil hydraulic parameters) and (ii) a standard design (0.8 m deep drains at a 15 m spacing) by model estimate of water table control and rainfall recharge/drain discharge capacity. The VDA method, unlike standard design equivalents, provided a good approximation of an ideal (from measured hydrological properties) design and prescribed an equivalent land drainage system in the field. Mean modelled rainfall recharge/drain discharge capacity for the VDA (13.3 mm/day) and ideal (12.0 mm/day) designs were significantly higher (P< 0.001, s.e. 1.42 mm/day) than for the standard designs (0.5 mm/day), when assuming a design minimum water table depth of 0.45 m.
Mathematical study of multispecies dynamics modeling predator–prey spatial interactions
Authors: Owolabi Kolade M. 
Published: August 2016

Abstract
In this work, we present analysis of a scaled time-dependent reaction–diffusion system modeling three competitive species dynamics that is of Lotka–Volterra type for coexistence, permanence and stability. The linear analysis is based on the application of qualitative theory of ordinary differential equations and dynamical systems. We consider two notable spatial discretization methods in conjunction with an adaptive time stepping method to verify the biological wave phenomena of the solutions and present the numerical results in one dimensional space. Adequate numerical resulting are provided in one and two dimensions to justify theoretical investigations. In addition, efficiency of the proposed numerical schemes are justified.
The lexicon in Functional Discourse Grammar: Theory, typology, description
Authors: Genee Inge , Keizer Evelien , García Velasco Daniel 
Published: August 2016

AbstractThis paper discusses the treatment of the lexicon in Functional Discourse Grammar (FDG) and serves to provide a general introduction to the theoretical framework and its formalizations, in particular for readers who may not be intimately familiar with it. After outlining the general architecture of the model, we discuss the position, content and function of the FDG lexicon in more detail. The FDG lexicon is often called the Fund, as it contains more than just a collection of lexemes. The Fund is conceived of as a storehouse containing all unpredictable linguistic knowledge in the form of various types of primitives. In addition to a lexicon proper this includes structural and grammatical primitives that feed the grammar, such as: pragmatic and semantic frames, functions and operators; morphosyntactic and phonological templates and operators; and suppletive forms. The “lexicon proper” contains grammatical morphemes and suppletive forms in addition to lexemes; the collection of frames and templates is sometimes called the “structicon”; and operators and functions constitute what may be called the “grammaticon”. The division of labor between the Fund and the Grammar is illustrated by showing how FDG treats lexeme, word and frame formation: lexeme formation is located in the Fund, word formation is located in the Grammar, and frame formation may be located in either, depending on the particular frame or the approach of the analyst. We then discuss the form and content of lexical entries. This has been a topic of some discussion recently, and several of the contributions to this special issue contain proposals in this area. The central question here is how best to capture the existence of common or even default associations between primitives at different levels of representation while still allowing for the occurrence of mismatches. Mismatches allow us to account for phenomena like coercion and other creative uses of the linguistic apparatus available to the language user. Next we address the construction of lexical meaning, showing where FDG draws the line between semantics on the one hand and pragmatics, contextual factors, and conceptualization on the other hand. Here again, different points of view coexist and several contributions contain proposals for how to represent lexical meaning. Our final section briefly introduces the other contributions to this special issue.
Lexical auxiliaries in Spanish: How and why?
Authors: Olbertz Hella 
Published: August 2016

AbstractDeparting from a proposal by Keizer on how to bridge the gap between the grammar and the lexicon in Functional Discourse Grammar (FDG), this article deals with three aspectual verbal periphrases in Spanish, which are, in the order of their degrees of grammaticalization, (i) weakly grammaticalized resultative
Idiomatic expressions in Functional Discourse Grammar
Authors: Keizer Evelien 
Published: August 2016

AbstractThis article addresses the question of how the theory of Functional Discourse Grammar (FDG), with its clear distinction between lexicon and grammar, can deal with semi-fixed constructions by proposing a consistent and cognitively plausible account of idiomatic expressions that can not only deal with the partly unpredictable and partly productive character of these expressions, but also with the variation within the class of idioms. It is argued that, on the basis of both semantic and syntactic criteria, three major types of idiom can be distinguished. Subsequently, an FDG analysis is provided which shows that the syntactic behavior of these types is not entirely arbitrary and unpredictable, but that it can to a large extent be accounted for by the specific functional properties of each of these types. Finally, the article addresses the question of how to represent idioms in the FDG lexicon. It is suggested that the lexical entry of an idiom should take the form of a meaning definition which is associated with a semi-fixed combination of interpersonal and representation frames and morphosyntactic templates specifying the functional and formal constraints on individual idioms, while at the same time accounting for the (different degrees of) syntactic flexibility exhibited by the three major types of idiom. All that is needed for idioms to be integrated in the theory of FDG, it is concluded, is the introduction of a new primitive, the so-called ComPIF (Combination of Partially Instantiated Frames).