bluuebunny/crossref_metadata_2025_split huggingface dataset:
Steady, dynamic and structural deformation (three interval thixotropy test) characteristics of gluten‐free Tarhana soup prepared with different concentrations of quinoa flour
Authors: Demir M. Kürşat , Kutlu Gözde , Yilmaz Mustafa T. 
Published: July 2016

AbstractCeliac disease is among the most important health problems and the most important feature of this disease is its being the only lifelong food allergy. To overcome this problem, some gluten‐free and starch based food products have been generally introduced to the market; however, these products are starch based with low nutritive value. Therefore, it is important to enrich such products for individuals who are obliged to be nourished by gluten‐free diet. In this study, wheat flour was replaced with quinoa flour (QF) in the production of tarhana. The objective of this work was to investigate the steady shear, viscoelastic and deformation and recovery properties (applying three interval thixotropy test (3ITT)) of gluten‐free tarhana soups prepared with different concentrations of QF (40%, 50%, and 60%). It was found that the soups fitted well (R2 > 0.99) Ostwald de Waele model and exhibited shear thinning behavior. Besides, elastic properties dominated the viscous properties. Although the maximum deformation and recovery were determined at 40% concentration level, minimum deformation and recovery properties were specified at 60% concentration level. The results suggest that QF can be used in gluten‐free tarhana formulations to enhance rheological properties.Practical applicationsMalnutrition is currently widespread in many areas of the world. Therefore, it must be focused on the cheap, but nutritious plant protein and mineral sources, such as legume and cereals. Several recent studies have showed the successful formulation of pseudocereal containing cereal based products. Tarhana is a traditional fermented food made of mainly a mixture cereal and yoghurt. Tarhana or tarhana‐like products have been enriched or replaced with cereal and pseudocereal. In this research, the applicability of QF in traditional tarhana production were investigated. As a result, it is advisable to replace wheat flour with QF in products such as tarhana, couscous, noodle and pasta formulation for nutritional and sensory properties enrichment. The results suggest that QF can be used in gluten‐free tarhana formulations to enhance rheological properties.
The Embodied Narrative Nature of Learning: Nurture in School
Authors: Delafield‐Butt Jonathan T. , Adie Jillian 
Published: July 2016

ABSTRACTLearning is participatory and embodied. It requires active participation from both teacher and learner to come together to co‐create shared projects of discovery that allow meaning to unfold and develop between them. This article advances theory on the intersubjective and embodied nature of cognition and meaning‐making as constituted by co‐created narrative units. Learning within embodied narrative episodes incorporate affective, energetic, and intentional components to produce schemas of engagement that structure knowledge and become units held in memory. We examine two cases of nonverbal narrative patterns of engagement between teacher and child within Nurture Group practice, a special pedagogy that attunes to the affects and interests of children. Analysis of these cases reveal patterns that established shared rhythm, affect, and body movement between teacher and child, which, on completion, generated shared joy and learning. Thus, we identify an embodied, co‐created narrative structure of embodied cognition essential for learning and participatory meaning‐making.
Rapid adaptation to climate change
Authors: Hancock Angela M. 
Published: July 2016

In recent years, amid growing concerns that changing climate is affecting species distributions and ecosystems, predicting responses to rapid environmental change has become a major goal. In this issue, Franks and colleagues take a first step towards this objective (Franks et al. 2016). They examine genomewide signatures of selection in populations of Brassica rapa after a severe multiyear drought. Together with other authors, Franks had previously shown that flowering time was reduced after this particular drought and that the reduction was genetically encoded. Now, the authors have sequenced previously stored samples to compare allele frequencies before and after the drought and identify the loci with the most extreme shifts in frequencies. The loci they identify largely differ between populations, suggesting that different genetic variants may be responsible for reduction in flowering time in the two populations.
Synergistic targeted inhibition of MEK and dual PI3K/mTOR diminishes viability and inhibits tumor growth of canine melanoma underscoring its utility as a preclinical model for human mucosal melanoma
Authors: Wei Bih‐Rong , Michael Helen T. , Halsey Charles H.C. , Peer Cody J. , Adhikari Amit , Dwyer Jennifer E. , Hoover Shelley B. , El Meskini Rajaa , Kozlov Serguei , Weaver Ohler Zoe , Figg William. D. , Merlino Glenn , Simpson R. Mark 
Published: July 2016

SummaryHuman mucosal melanoma (MM), an uncommon, aggressive and diverse subtype, shares characteristics with spontaneous MM in dogs. Although BRAF and N‐RAS mutations are uncommon in MM in both species, the majority of human and canine MM evaluated exhibited RAS/ERK and/or PI3K/mTOR signaling pathway activation. Canine MM cell lines, with varying ERK and AKT/mTOR activation levels reflective of naturally occurring differences in dogs, were sensitive to the MEK inhibitor GSK1120212 and dual PI3K/mTOR inhibitor NVP‐BEZ235. The two‐drug combination synergistically decreased cell survival in association with caspase 3/7 activation, as well as altered expression of cell cycle regulatory proteins and Bcl‐2 family proteins. In combination, the two drugs targeted their respective signaling pathways, potentiating reduction of pathway mediators p‐ERK, p‐AKT, p‐S6, and 4E‐BP1 in vitro, and in association with significantly inhibited solid tumor growth in MM xenografts in mice. These findings provide evidence of synergistic therapeutic efficacy when simultaneously targeting multiple mediators in melanoma with Ras/ERK and PI3K/mTOR pathway activation.
Ultrasonography of the internal carotid artery during therapeutic hypothermia
Authors: Fukuda Sumio , Tanimura Tomoshige , Iwaki Toshihiko , Higuchi Machiko , Suyama Megumi , Goto Tomoki , Koide Wakato , Maki Kanemasa , Ushijima Katsumi , Ban Kyoko 
Published: July 2016

AbstractThe purpose of this study was to determine the accuracy of mean blood flow velocity (mean V) in the internal carotid artery (ICA) for prediction of outcome in infants with hypoxic–ischemic encephalopathy (HIE) exposed to therapeutic hypothermia (TH). Five newborns with HIE who met the criteria for TH were enrolled. Ultrasonography of the right and left ICA was performed before, during, and after TH. Mean V of the sampling point in each ICA was measured. Mean V was suppressed during TH and increased after rewarming in four infants with normal neurological development. In one infant with neurological disability, however, mean V increased during TH and decreased after therapy. In conclusion, cervical ultrasonography for ICA in infants during TH may be useful for the prediction of neurodevelopmental outcome.
Flavin Adenine Dinucleotide and N5,N10‐Methenyltetrahydrofolate are the in planta Cofactors of Arabidopsis thaliana Cryptochrome 3
Authors: Göbel Tanja , Reisbacher Stefan , Batschauer Alfred , Pokorny Richard 
Published: July 2016

AbstractMembers of the cryptochrome/photolyase family (CPF) of proteins utilize noncovalently bound light‐absorbing cofactors for their biological function. Usually, the identity of these cofactors is determined after expression in heterologous systems leaving the question unanswered whether these cofactors are identical to the indigenous ones. Here, cryptochrome 3 from Arabidopsis thaliana was expressed as a fusion with the green fluorescent protein in Arabidopsis plants. Besides the confirmation of the earlier report of its localization in chloroplasts, our data indicate that fractions of the fusion protein are present in the stroma and associated with thylakoids, respectively. Furthermore, it is shown that the fusion protein expressed in planta contains the same cofactors as the His6‐tagged protein expressed in Escherichia coli, that is, flavin adenine dinucleotide and N5,N10‐methenyltetrahydrofolate. This demonstrates that the heterologously expressed cryptochrome 3, characterized in a number of previous studies, is a valid surrogate of the corresponding protein expressed in plants. To our knowledge, this is also a first conclusive analysis of cofactors bound to an Arabidopsis protein belonging to the CPF and purified from plant tissue.
Environmental influence on the prevalence and pattern of airway dysfunction in elite athletes
Authors: Levai Irisz Karolina , Hull James H. , Loosemore Mike , Greenwell Jon , Whyte Greg , Dickinson John W. 
Published: July 2016

ABSTRACTBackground and objectiveElite swimming and boxing require athletes to achieve relatively high minute ventilation. The combination of a sustained high ventilation and provocative training environment may impact the susceptibility of athletes to exercise‐induced bronchoconstriction (EIB). The purpose of this study was to evaluate the prevalence of EIB in elite Great British (GB) boxers and swimmers.MethodsBoxers (n = 38, mean age: 22.1 ± 3.1 years) and swimmers (n = 44, mean age: 21.1 ± 2.6 years) volunteered for the study. Athletes completed an exercise‐induced respiratory symptom questionnaire, baseline assessment of fraction of exhaled nitric oxide (FeNO), maximal spirometry manoeuvres and a eucapnic voluntary hyperpnoea (EVH) challenge. EIB was confirmed if forced expiratory volume in 1 s (FEV1
) reduced by ≥10% from baseline at two time points post‐EVH challenge.ResultsThe prevalence of EIB was greater in elite swimmers (30 of 44; 68%) than in boxers (3 of 38; 8%) (P < 0.001). Twenty‐two out of the 33 (67%) EVH‐positive athletes had no prior diagnosis of asthma/EIB. Moreover, 12% (6 of 49) of the EVH‐negative athletes had a previous diagnosis of asthma/EIB. We found a correlation between FeNO and FEV1
change in lung function post‐EVH challenge in swimmers (r = 0.32; P = 0.04) but not in boxers (r = 0.24; P = 0.15).ConclusionThe prevalence of EIB was ninefold greater in swimmers when compared with boxers. Athletes who train and compete in provocative environments at sustained high ventilation may have an increased susceptibility to EIB. It is not entirely clear whether increased susceptibility to EIB affects elite sporting performance and long‐term airway health in elite athletes.
Heterogeneity of incidence and outcome of acute exacerbation in idiopathic interstitial pneumonia
Authors: Arai Toru , Kagawa Tomoko , Sasaki Yumiko , Sugawara Reiko , Sugimoto Chikatoshi , Tachibana Kazunobu , Kitaichi Masanori , Akira Masanori , Hayashi Seiji , Inoue Yoshikazu 
Published: July 2016

ABSTRACT
Background and objectiveAcute exacerbations (AEs) of idiopathic pulmonary fibrosis (IPF) and other idiopathic interstitial pneumonia (IIP) have a poor prognosis. This study aims to clarify the incidence and prognosis of AE in IPF and the other IIP.MethodsA total of 229 patients were enrolled, of whom 92 had IPF and 137 had ‘IIP other than IPF’ based on the American Thoracic Society/European Respiratory Society/Japanese Respiratory Society/Latin American Thoracic Association (ATS/ERS/JRS/ALAT) 2011 IPF Guidelines. IIP other than IPF included 11 patients with a surgical lung biopsy (SLB) and the remainder without such a biopsy. IIP other than IPF was further classified into IIP with a ‘possible usual interstitial pneumonia (UIP)’ pattern on HRCT (n = 75) and IIP with ‘inconsistent with UIP’ pattern (n = 62) based on published guidelines. Predictors of AE and the prognosis after AE were examined in these groups.ResultsThe 1‐year incidence of AE in IPF, IIP with possible UIP HRCT patterns and IIP with inconsistent with UIP HRCT patterns was 16.5%, 8.9% and 4.0%, respectively. AE occurred significantly more frequently in IPF than in IIP with possible UIP and inconsistent with UIP HRCT patterns after adjustment for BMI, modified Medical Research Council score and %forced vital capacity. Prognosis of AE‐IIP with possible UIP HRCT pattern was significantly worse than that of AE‐IPF.ConclusionAlthough AE occurred significantly less frequently in IIP with possible UIP and inconsistent with UIP HRCT patterns than in IPF, the prognosis of AE‐IIP with possible UIP HRCT patterns might be worse than that of AE‐IPF.
Getting along or ahead: Effects of gender identity threat on communal and agentic self‐presentations
Authors: Sinclair Samantha , Carlsson Rickard , Björklund Fredrik 
Published: July 2016

When faced with a threat to gender identity, people may try to restore their gender status by acting in a more gender‐typical manner. The present research investigated effects of gender identity threat on self‐presentations of agentic and communal traits in a Swedish and an Argentine sample (N = 242). Under threat (vs. affirmation), Swedish women deemphasized agentic traits (d [95% CI] = −0.41 [−0.93, 0.11]), Argentine women increased their emphasis on communal traits (d = 0.44 [−0.08, 0.97]), and Argentine men increased their emphasis on agentic traits (d = 0.49 [−0.03, 1.01]). However, Swedish men did not appear to be affected by the threat regarding agentic (d = 0.04 [−0.47, 0.55]) or communal traits (d = 0.23 [−0.29, 0.74]). The findings are to be considered tentative. Implications for identity threat research are discussed.
Use of intravenous immunoglobulin in neonates at a tertiary academic hospital: a retrospective 11‐year study
Authors: Lieberman Lani , Spradbrow Jordan , Keir Amy , Dunn Michael , Lin Yulia , Callum Jeannie 
Published: July 2016

BACKGROUNDIntravenous immunoglobulin (IVIG) is used to treat a variety of diseases in the neonatal intensive care unit (NICU). Although audits have reported on the spectrum of IVIG use in adults, the indications and utilization in neonates has not been investigated. The objectives of this study were to describe the usage pattern of and indications for IVIG in a tertiary care NICU.STUDY DESIGN AND METHODSA retrospective chart review was performed of all neonates who received IVIG in the NICU from January 2003 to December 2013. Data collected included patient demographic features, antenatal maternal details, neonatal laboratory results, treatment details, adverse events, and patient outcome.RESULTSThirty‐seven neonates received IVIG over the 11‐year period. Twenty‐three (67%) were treated for hemolytic disease of the newborn (HDN); 13 treatments were ABO related, six were anti‐D related, and four were for clinically significant antibodies. Fourteen (33%) were treated for non‐HDN causes, including eight for septic neonates, two for neonates with necrotizing enterocolitis, two for neonates with a clinically significant antibody but without evidence of hemolysis, and two for neonates with glucose 6‐phosphate dehydrogenase deficiency. A complete hemolytic workup was not performed consistently before the receipt of IVIG.CONCLUSIONSThis novel assessment of IVIG use in the NICU revealed the spectrum of disease for which IVIG is ordered. This study also found that key diagnostic tests needed to confirm an immune etiology for idiopathic jaundice are not performed routinely before IVIG receipt. Neonatal transfusion‐related databases are needed to carry out pragmatic clinical trials to establish better evidence‐based guidelines for IVIG therapy in the NICU.
Endocannabinoids control vesicle release mode at midbrain periaqueductal grey inhibitory synapses
Authors: Aubrey Karin R. , Drew Geoffrey M. , Jeong Hyo‐Jin , Lau Benjamin K. , Vaughan Christopher W. 
Published: July 2016

Key points
The midbrain periaqueductal grey (PAG) forms part of an endogenous analgesic system which is tightly regulated by the neurotransmitter GABA.
The role of endocannabinoids in regulating GABAergic control of this system was examined in rat PAG slices.
Under basal conditions GABAergic neurotransmission onto PAG output neurons was multivesicular.
Activation of the endocannabinoid system reduced GABAergic inhibition by reducing the probability of release and by shifting release to a univesicular mode.
Blockade of endocannabinoid system unmasked a tonic control over the probability and mode of GABA release.
These findings provides a mechanistic foundation for the control of the PAG analgesic system by disinhibition.
AbstractThe midbrain periaqueductal grey (PAG) has a crucial role in coordinating endogenous analgesic responses to physiological and psychological stressors. Endocannabinoids are thought to mediate a form of stress‐induced analgesia within the PAG by relieving GABAergic inhibition of output neurons, a process known as disinhibition. This disinhibition is thought to be achieved by a presynaptic reduction in GABA release probability. We examined whether other mechanisms have a role in endocannabinoid modulation of GABAergic synaptic transmission within the rat PAG. The group I mGluR agonist DHPG ((R,S)‐3,5‐dihydroxyphenylglycine) inhibited evoked IPSCs and increased their paired pulse ratio in normal external Ca2+, and when release probability was reduced by lowering Ca2+. However, the effect of DHPG on the coefficient of variation and kinetics of evoked IPSCs differed between normal and low Ca2+. Lowering external Ca2+ had a similar effect on evoked IPSCs to that observed for DHPG in normal external Ca2+. The low affinity GABAA receptor antagonist TPMPA ((1,2,5,6‐tetrahydropyridin‐4‐yl)methylphosphinic acid) inhibited evoked IPSCs to a greater extent in low than in normal Ca2+. Together these findings indicate that the normal mode of GABA release is multivesicular within the PAG, and that DHPG and lowering external Ca2+ switch this to a univesicular mode. The effects of DHPG were mediated by mGlu5 receptor engagement of the retrograde endocannabinoid system. Blockade of endocannabinoid breakdown produced a similar shift in the mode of release. We conclude that endocannabinoids control both the mode and the probability of GABA release within the PAG.
Genomes of Abundant and Widespread Viruses from the Deep Ocean
Authors: Mizuno Carolina Megumi , Ghai Rohit , Saghaï Aurélien , López-García Purificación , Rodriguez-Valera Francisco 
Published: July 2016

ABSTRACT

The deep sea is a massive, largely oligotrophic ecosystem, stretched over nearly 65% of the planet’s surface. Deep-sea planktonic communities are almost completely dependent upon organic carbon sinking from the productive surface, forming a vital component of global biogeochemical cycles. However, despite their importance, viruses from the deep ocean remain largely unknown. Here, we describe the first complete genomes of deep-sea viruses assembled from metagenomic fosmid libraries. “
Candidatus
Pelagibacter” (SAR11) phage HTVC010P and
Puniceispirillum
phage HMO-2011 are considered the most abundant cultured marine viruses known to date. Remarkably, some of the viruses described here recruited as many reads from deep waters as these viruses do in the photic zone, and, considering the gigantic scale of the bathypelagic habitat, these genomes provide information about what could be some of the most abundant viruses in the world at large. Their role in the viral shunt in the global ocean could be very significant. Despite the challenges encountered in inferring the identity of their hosts, we identified one virus predicted to infect members of the globally distributed SAR11 cluster. We also identified a number of putative proviruses from diverse taxa, including deltaproteobacteria, bacteroidetes, SAR11, and gammaproteobacteria. Moreover, our findings also indicate that lysogeny is the preferred mode of existence for deep-sea viruses inhabiting an energy-limited environment, in sharp contrast to the predominantly lytic lifestyle of their photic-zone counterparts. Some of the viruses show a widespread distribution, supporting the tenet “everything is everywhere” for the deep-ocean virome.

IMPORTANCE
The deep sea is among the largest known habitats and a critical cog in biogeochemical cycling but remains underexplored in its microbiology. Even more than is the case for its prokaryotic community, our knowledge of its viral component has remained limited by the paucity of information provided by studies dependent upon short sequence fragments. In this work, we attempt to fill this existing gap by using a combination of classical fosmid libraries with next-generation sequencing and assembly to recover long viral genomic fragments. We have sequenced ca. 6,000 fosmids from two metagenomics libraries made from prokaryotic biomass from the deep Mediterranean Sea and recovered twenty-eight complete viral genomes, all of them novel and quite distinct from all previously described viral genomes. They are preferentially found in deeper waters and are widely distributed all over the oceans. To our knowledge, this is the first report on complete and cosmopolitan viral genomes from the bathypelagic habitat.
Unlocking the Constraints of Cyanobacterial Productivity: Acclimations Enabling Ultrafast Growth
Authors: Bernstein Hans C. , McClure Ryan S. , Hill Eric A. , Markillie Lye Meng , Chrisler William B. , Romine Margie F. , McDermott Jason E. , Posewitz Matthew C. , Bryant Donald A. , Konopka Allan E. , Fredrickson James K. , Beliaev Alexander S. 
Published: July 2016

ABSTRACT

Harnessing the metabolic potential of photosynthetic microbes for next-generation biotechnology objectives requires detailed scientific understanding of the physiological constraints and regulatory controls affecting carbon partitioning between biomass, metabolite storage pools, and bioproduct synthesis. We dissected the cellular mechanisms underlying the remarkable physiological robustness of the euryhaline unicellular cyanobacterium
Synechococcus
sp. strain PCC 7002 (
Synechococcus
7002) and identify key mechanisms that allow cyanobacteria to achieve unprecedented photoautotrophic productivities (~2.5-h doubling time). Ultrafast growth of
Synechococcus
7002 was supported by high rates of photosynthetic electron transfer and linked to significantly elevated transcription of precursor biosynthesis and protein translation machinery. Notably, no growth or photosynthesis inhibition signatures were observed under any of the tested experimental conditions. Finally, the ultrafast growth in
Synechococcus
7002 was also linked to a 300% expansion of average cell volume. We hypothesize that this cellular adaptation is required at high irradiances to support higher cell division rates and reduce deleterious effects, corresponding to high light, through increased carbon and reductant sequestration.

IMPORTANCE
Efficient coupling between photosynthesis and productivity is central to the development of biotechnology based on solar energy. Therefore, understanding the factors constraining maximum rates of carbon processing is necessary to identify regulatory mechanisms and devise strategies to overcome productivity constraints. Here, we interrogate the molecular mechanisms that operate at a systems level to allow cyanobacteria to achieve ultrafast growth. This was done by considering growth and photosynthetic kinetics with global transcription patterns. We have delineated putative biological principles that allow unicellular cyanobacteria to achieve ultrahigh growth rates through photophysiological acclimation and effective management of cellular resource under different growth regimes.