bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fluorescence-Detected Linear Dichroism of Wood Cell Walls in Juvenile Serbian Spruce: Estimation of Compression Wood Severity
Authors: Savić Aleksandar , Mitrović Aleksandra , Donaldson Lloyd , Simonović Radosavljević Jasna , Bogdanović Pristov Jelena , Steinbach Gabor , Garab Győző , Radotić Ksenija 
Published: February 2016

AbstractFluorescence-detected linear dichroism (FDLD) microscopy provides observation of structural order in a microscopic sample and its expression in numerical terms, enabling both quantitative and qualitative comparison among different samples. We applied FDLD microscopy to compare the distribution and alignment of cellulose fibrils in cell walls of compression wood (CW) and normal wood (NW) on stem cross-sections of juvenile Picea omorika trees. Our data indicate a decrease in cellulose fibril order in CW compared with NW. Radial and tangential walls differ considerably in both NW and CW. In radial walls, cellulose fibril order shows a gradual decrease from NW to severe CW, in line with the increase in CW severity. This indicates that FDLD analysis of cellulose fibril order in radial cell walls is a valuable method for estimation of CW severity.
PPI in the PLEASANT trial: involving children with asthma and their parents in designing an intervention for a randomised controlled trial based within primary care
Authors: Boote Jonathan , Julious Steven , Horspool Michelle , Elphick Heather , Smithson W. Henry , Norman Paul 
Published: February 2016

AimsWe describe how patient and public involvement (PPI) was integrated into the design of an intervention for a randomised controlled trial (RCT) based within primary care. The RCT, known as the PLEASANT trial, aimed to reduce unscheduled medical contacts in children with asthma associated with start of the new school year in September with a simple postal intervention, highlighting the importance of maintaining asthma medication for helping to prevent increased asthma exacerbations.BackgroundPPI is a key feature of UK health research policy, and is often a requirement of funding from the National Institute for Health Research. There are few detailed accounts of PPI in the design and conduct of clinical trials in the PPI literature for researchers to learn from.MethodsWe held PPI consultation events to determine whether the proposed intervention for the trial was acceptable to children with asthma and their parents, and to ascertain whether enhancements should be made. Two PPI consultation events were held with children with asthma and their parents, prior to the research commencing. Detailed field notes were taken by the research team at each consultation event.FindingsAt the first consultation event, parents and children endorsed the trial’s rationale, made suggestions to the wording of the trial intervention letter, and made recommendations about to whom the letter should be sent out. At the second consultation event, parents discussed the timing of the intervention, commented on the lay summary of the Research Ethics Application, and were invited to join the trial’s steering committee, while the children selected a logo for the study. PPI has resulted in enhancements to the PLEASANT study’s intervention. A further PPI consultation event is scheduled for the end of the trial, in order for children with asthma and their parents to contribute to the trial’s dissemination strategy.
Understanding Agricultural Price Range Systems as Trade Restraints: Peru–Agricultural Products
Authors: SAGGI KAMAL , WU MARK 
Published: February 2016

AbstractAn agricultural price range system (PRS) aims to stabilize local prices in an open economy via the use of import duties that vary with international prices. The policy is inherently distortionary and welfare-reducing for a small open economy, at least according to the canonical economic model. We offer an explanation for why a government concerned with national welfare may nevertheless implement such a policy when faced with risk aversion and imperfect insurance markets. We also highlight open questions arising out of the Peru–Agricultural Products dispute for the WTO's Appellate Body to address in order to clarify how a PRS consistent with WTO rules could be designed. Finally, we discuss the possibility that a WTO member might resort to a free trade agreement (FTA) to preserve its flexibility to implement a PRS and how an FTA provision of this sort ought to be treated in WTO litigation.
The energetics of anabolism in natural settings
Authors: LaRowe Douglas E , Amend Jan P 
Published: February 2016

Abstract
The environmental conditions that describe an ecosystem define the amount of energy available to the resident organisms and the amount of energy required to build biomass. Here, we quantify the amount of energy required to make biomass as a function of temperature, pressure, redox state, the sources of C, N and S, cell mass and the time that an organism requires to double or replace its biomass. Specifically, these energetics are calculated from 0 to 125 °C, 0.1 to 500 MPa and −0.38 to +0.86 V using CO2, acetate or CH4 for C, NO3− or NH4+ for N and SO42− or HS− for S. The amounts of energy associated with synthesizing the biomolecules that make up a cell, which varies over 39 kJ (g cell)−1, are then used to compute energy-based yield coefficients for a vast range of environmental conditions. Taken together, environmental variables and the range of cell sizes leads to a ~4 orders of magnitude difference between the number of microbial cells that can be made from a Joule of Gibbs energy under the most (5.06 × 1011 cells J−1) and least (5.21 × 107 cells J−1) ideal conditions. When doubling/replacement time is taken into account, the range of anabolism energies can expand even further.
Protistan community analysis: key findings of a large-scale molecular sampling
Authors: Grossmann Lars , Jensen Manfred , Heider Dominik , Jost Steffen , Glücksman Edvard , Hartikainen Hanna , Mahamdallie Shazia S , Gardner Michelle , Hoffmann Daniel , Bass David , Boenigk Jens 
Published: February 2016

Abstract
Protists are perhaps the most lineage-rich of microbial lifeforms, but remain largely unknown. High-throughput sequencing technologies provide opportunities to screen whole habitats in depth and enable detailed comparisons of different habitats to measure, compare and map protistan diversity. Such comparisons are often limited by low sample numbers within single studies and a lack of standardisation between studies. Here, we analysed 232 samples from 10 sampling campaigns using a standardised PCR protocol and bioinformatics pipeline. We show that protistan community patterns are highly consistent within habitat types and geographic regions, provided that sample processing is standardised. Community profiles are only weakly affected by fluctuations of the abundances of the most abundant taxa and, therefore, provide a sound basis for habitat comparison beyond random short-term fluctuations in the community composition. Further, we provide evidence that distribution patterns are not solely resulting from random processes. Distinct habitat types and distinct taxonomic groups are dominated by taxa with distinct distribution patterns that reflect their ecology with respect to dispersal and habitat colonisation. However, there is no systematic shift of the distribution pattern with taxon abundance.
Topographical pathways guide chemical microswimmers
Authors: Simmchen Juliane , Katuri Jaideep , Uspal William E. , Popescu Mihail N. , Tasinkevych Mykola , Sánchez Samuel 
Published: February 2016

AbstractAchieving control over the directionality of active colloids is essential for their use in practical applications such as cargo carriers in microfluidic devices. So far, guidance of spherical Janus colloids was mainly realized using specially engineered magnetic multilayer coatings combined with external magnetic fields. Here we demonstrate that step-like submicrometre topographical features can be used as reliable docking and guiding platforms for chemically active spherical Janus colloids. For various topographic features (stripes, squares or circular posts), docking of the colloid at the feature edge is robust and reliable. Furthermore, the colloids move along the edges for significantly long times, which systematically increase with fuel concentration. The observed phenomenology is qualitatively captured by a simple continuum model of self-diffusiophoresis near confining boundaries, indicating that the chemical activity and associated hydrodynamic interactions with the nearby topography are the main physical ingredients behind the observed behaviour.
De novo transcriptome sequencing and gene expression profiling of spinach (Spinacia oleracea L.) leaves under heat stress
Authors: Yan Jun , Yu Li , Xuan Jiping , Lu Ying , Lu Shijun , Zhu Weimin 
Published: February 2016

AbstractSpinach (Spinacia oleracea) has cold tolerant but heat sensitive characteristics. The spinach variety ‘Island,’ is suitable for summer periods. There is lack molecular information available for spinach in response to heat stress. In this study, high throughput de novo transcriptome sequencing and gene expression analyses were carried out at different spinach variety ‘Island’ leaves (grown at 24 °C (control), exposed to 35 °C for 30 min (S1) and 5 h (S2)). A total of 133,200,898 clean reads were assembled into 59,413 unigenes (average size 1259.55 bp). 33,573 unigenes could match to public databases. The DEG of controls vs S1 was 986, the DEG of control vs S2 was 1741 and the DEG of S1 vs S2 was 1587. Gene Ontology (GO) and pathway enrichment analysis indicated that a great deal of heat-responsive genes and other stress-responsive genes were identified in these DEGs, suggesting that the heat stress may have induced an extensive abiotic stress effect. Comparative transcriptome analysis found 896 unique genes in spinach heat response transcript. The expression patterns of 13 selected genes were verified by RT-qPCR (quantitative real-time PCR). Our study found a series of candidate genes and pathways that may be related to heat resistance in spinach.
Robotic lower limb prosthesis design through simultaneous computer optimizations of human and prosthesis costs
Authors: Handford Matthew L. , Srinivasan Manoj 
Published: February 2016

AbstractRobotic lower limb prostheses can improve the quality of life for amputees. Development of such devices, currently dominated by long prototyping periods, could be sped up by predictive simulations. In contrast to some amputee simulations which track experimentally determined non-amputee walking kinematics, here, we explicitly model the human-prosthesis interaction to produce a prediction of the user’s walking kinematics. We obtain simulations of an amputee using an ankle-foot prosthesis by simultaneously optimizing human movements and prosthesis actuation, minimizing a weighted sum of human metabolic and prosthesis costs. The resulting Pareto optimal solutions predict that increasing prosthesis energy cost, decreasing prosthesis mass and allowing asymmetric gaits all decrease human metabolic rate for a given speed and alter human kinematics. The metabolic rates increase monotonically with speed. Remarkably, by performing an analogous optimization for a non-amputee human, we predict that an amputee walking with an appropriately optimized robotic prosthesis can have a lower metabolic cost – even lower than assuming that the non-amputee’s ankle torques are cost-free.
Crystal structure of SEL1L: Insight into the roles of SLR motifs in ERAD pathway
Authors: Jeong Hanbin , Sim Hyo Jung , Song Eun Kyung , Lee Hakbong , Ha Sung Chul , Jun Youngsoo , Park Tae Joo , Lee Changwook 
Published: February 2016

AbstractTerminally misfolded proteins are selectively recognized and cleared by the endoplasmic reticulum-associated degradation (ERAD) pathway. SEL1L, a component of the ERAD machinery, plays an important role in selecting and transporting ERAD substrates for degradation. We have determined the crystal structure of the mouse SEL1L central domain comprising five Sel1-Like Repeats (SLR motifs 5 to 9; hereafter called SEL1Lcent). Strikingly, SEL1Lcent forms a homodimer with two-fold symmetry in a head-to-tail manner. Particularly, the SLR motif 9 plays an important role in dimer formation by adopting a domain-swapped structure and providing an extensive dimeric interface. We identified that the full-length SEL1L forms a self-oligomer through the SEL1Lcent domain in mammalian cells. Furthermore, we discovered that the SLR-C, comprising SLR motifs 10 and 11, of SEL1L directly interacts with the N-terminus luminal loops of HRD1. Therefore, we propose that certain SLR motifs of SEL1L play a unique role in membrane bound ERAD machinery.
Bif-1 deficiency impairs lipid homeostasis and causes obesity accompanied by insulin resistance
Authors: Liu Ying , Takahashi Yoshinori , Desai Neelam , Zhang Jun , Serfass Jacob M. , Shi Yu-Guang , Lynch Christopher J. , Wang Hong-Gang 
Published: February 2016

AbstractBif-1 is a membrane-curvature inducing protein that is implicated in the regulation of autophagy and tumorigenesis. Here, we report that Bif-1 plays a critical role in regulating lipid catabolism to control the size of lipid droplets and prevent the development of obesity and insulin resistance upon aging or dietary challenge. Our data show that Bif-1 deficiency promotes the expansion of adipose tissue mass without altering food intake or physical activities. While Bif-1 is dispensable for adipose tissue development, its deficiency reduces the basal rate of adipose tissue lipolysis and results in adipocyte hypertrophy upon aging. The importance of Bif-1 in lipid turnover is not limited to adipose tissue since fasting and refeeding-induced lipid droplet clearance is also attenuated by Bif-1 loss in the liver. Interestingly, obesity induced by a high fat-diet or Bif-1 deficiency downregulates the expression of proteins involved in the autophagy-lysosomal pathway, including Atg9a and Lamp1 in the adipose tissue. These findings thus identify Bif-1 as a novel regulator of lipid homeostasis to prevent the pathogenesis of obesity and its associated metabolic complications.
The distinct clinical features and prognosis of the CD10+MUM1+ and CD10−Bcl6−MUM1− diffuse large B-cell lymphoma
Authors: Lu Ting-Xun , Miao Yi , Wu Jia-Zhu , Gong Qi-Xing , Liang Jin-Hua , Wang Zhen , Wang Li , Fan Lei , Hua Dong , Chen Yao-Yu , Xu Wei , Zhang Zhi-Hong , Li Jian-Yong 
Published: February 2016

AbstractUsing an immunohistochemistry (IHC) based method, diffuse large B-cell lymphoma (DLBCL) can be classified into germinal center B-cell (GCB) and non-GCB subtypes. However, the prognostic value of Hans algorithm was contradictory in the literature. Using IHC and fluorescence in situ hybridization, we analyzed the antibodies applied in Hans algorithm and other genetic factors in 601 DLBCL patients and prognostic value of Hans algorithm in 306 cases who were treated with chemoimmunotherapy. The results showed that patients with GCB subtype have better overall survival (OS) and progression-free survival (PFS) than non-GCB cases. However, to some extent, double positive (CD10+MUM1+, DP) and triple negative (CD10−Bcl6−MUM−, TN) showed different clinical characteristics and prognosis to others that were assigned to the same cell-of-origin group. The DP group showed similar OS (median OS: both not reached, P = 0.3650) and PFS (median PFS: 47.0 vs. 32.7 months, P = 0.0878) with the non-GCB group while the TN group showed similar OS (median OS: both not reached, P = 0.9278) and PFS (median PFS: both not reached, P = 0.9420) with the GCB group. In conclusion, Recognition of specific entities in Hans algorithm could help us to accurately predict outcome of the patients and choose the best clinical management for them.
Clostridium butyricum in combination with specific immunotherapy converts antigen-specific B cells to regulatory B cells in asthmatic patients
Authors: Liao Hong-Ying , Tao Li , Zhao Jian , Qin Jie , Zeng Gu-Cheng , Cai Song-Wang , Li Yun , Zhang Jian , Chen Hui-Guo 
Published: February 2016

AbstractThe effect of antigen specific immunotherapy (SIT) on asthma is supposed to be improved. Published data indicate that administration of probiotics alleviates allergic diseases. B cells play important roles in the pathogenesis of allergic diseases. This study aims to modulate antigen specific B cell property by the administration of Clostridium butyrate (CB) in combination with SIT. The results showed that after a 3-month treatment, the total asthma clinical score and serum specific IgE were improved in the patients treated with SIT, which was further improved in those treated with both SIT and CB, but not in those treated with CB alone. Treatment with SIT and CB increased p300 and STAT3 activation, up regulated the IL-10 gene transcription and increased the frequency of peripheral antigen specific B cells. In conclusion, administration with SIT in combination with CB converts Der p 1 specific B cells to regulatory B cells in asthma patients allergic to Der p 1. The data suggest a potential therapeutic remedy in the treatment of allergic diseases.
Co-activation of AKT and c-Met triggers rapid hepatocellular carcinoma development via the mTORC1/FASN pathway in mice
Authors: Hu Junjie , Che Li , Li Lei , Pilo Maria G. , Cigliano Antonio , Ribback Silvia , Li Xiaolei , Latte Gavinella , Mela Marta , Evert Matthias , Dombrowski Frank , Zheng Guohua , Chen Xin , Calvisi Diego F. 
Published: February 2016

AbstractActivation of the AKT/mTOR cascade and overexpression of c-Met have been implicated in the development of human hepatocellular carcinoma (HCC). To elucidate the functional crosstalk between the two pathways, we generated a model characterized by the combined expression of activated AKT and c-Met in the mouse liver. Co-expression of AKT and c-Met triggered rapid liver tumor development and mice required to be euthanized within 8 weeks after hydrodynamic injection. At the molecular level, liver tumors induced by AKT/c-Met display activation of AKT/mTOR and Ras/MAPK cascades as well as increased lipogenesis and glycolysis. Since a remarkable lipogenic phenotype characterizes liver lesions from AKT/c-Met mice, we determined the requirement of lipogenesis in AKT/c-Met driven hepatocarcinogenesis using conditional Fatty Acid Synthase (FASN) knockout mice. Of note, hepatocarcinogenesis induced by AKT/c-Met was fully inhibited by FASN ablation. In human HCC samples, coordinated expression of FASN, activated AKT and c-Met proteins was detected in a subgroup of biologically aggressive tumors. Altogether, our study demonstrates that co-activation of AKT and c-Met induces HCC development that depends on the mTORC1/FASN pathway. Suppression of mTORC1 and/or FASN might be highly detrimental for the growth of human HCC subsets characterized by concomitant induction of the AKT and c-Met cascades.
Enhanced electrostatic force microscopy reveals higher-order DNA looping mediated by the telomeric protein TRF2
Authors: Kaur Parminder , Wu Dong , Lin Jiangguo , Countryman Preston , Bradford Kira C. , Erie Dorothy A. , Riehn Robert , Opresko Patricia L. , Wang Hong 
Published: February 2016

AbstractShelterin protein TRF2 modulates telomere structures by promoting dsDNA compaction and T-loop formation. Advancement of our understanding of the mechanism underlying TRF2-mediated DNA compaction requires additional information regarding DNA paths in TRF2-DNA complexes. To uncover the location of DNA inside protein-DNA complexes, we recently developed the Dual-Resonance-frequency-Enhanced Electrostatic force Microscopy (DREEM) imaging technique. DREEM imaging shows that in contrast to chromatin with DNA wrapping around histones, large TRF2-DNA complexes (with volumes larger than TRF2 tetramers) compact DNA inside TRF2 with portions of folded DNA appearing at the edge of these complexes. Supporting coarse-grained molecular dynamics simulations uncover the structural requirement and sequential steps during TRF2-mediated DNA compaction and result in folded DNA structures with protruding DNA loops as seen in DREEM imaging. Revealing DNA paths in TRF2 complexes provides new mechanistic insights into structure-function relationships underlying telomere maintenance pathways.
Precise AuxPt1−x Alloy Nanoparticle Array of Tunable Composition for Catalytic Applications
Authors: Jahn Sarah , Lechner Sebastian J. , Freichels Helene , Möller Martin , Spatz Joachim P. 
Published: February 2016

AbstractA 3-dimensional Block Copolymer Micellar nanoLithography (BCML) process was used to prepare AuxPt1−x alloy nanoparticles (NPs) monodisperse in size and composition, strongly anchored onto SiO2-particles (0.2 wt.% AuxPt1−x/SiO2). The particles possess a face-centered cubic (fcc) crystal structure and their size could be varied from 3–12 nm. We demonstrate the uniformity of the Au/Pt composition by analyzing individual NPs by energy-dispersive X-ray spectroscopy. The strongly bound AuxPt1−x NPs catalyzed the oxidation of CO with high activity. Thermal ageing experiments in pure CO2 as well as in ambient atmosphere demonstrated stability of the size distribution for times as long as 22 h.
Computational studies of the binding profile of phosphoinositide PtdIns (3,4,5) P3 with the pleckstrin homology domain of an oomycete cellulose synthase
Authors: Kuang Guanglin , Bulone Vincent , Tu Yaoquan 
Published: February 2016

AbstractSaprolegnia monoicais a model organism to investigateSaprolegnia parasitica, an important oomycete which causes considerable loss in aquaculture every year.S. monoicacontains cellulose synthases vital for oomycete growth. However, the molecular mechanism of the cellulose biosynthesis process in the oomycete growth is still poorly understood. Some cellulose synthases ofS. monoica, such as SmCesA2, are found to contain a plecsktrin homology (PH) domain, which is a protein module widely found in nature and known to bind to phosphoinositides, a class of signaling compounds involved in many biological processes. Understanding the molecular interactions between the PH domain and phosphoinositides would help to unravel the cellulose biosynthesis process of oomycetes. In this work, the binding profile of PtdIns (3,4,5) P3, a typical phosphoinositide, with SmCesA2-PH was studied by molecular docking, molecular dynamics and metadynamics simulations. PtdIns (3,4,5) P3is found to bind at a specific site located at β1, β2 and β1-β2 loop of SmCesA2-PH. The high affinity of PtdIns (3,4,5) P3to SmCesA2-PH is contributed by the free phosphate groups, which have electrostatic and hydrogen-bond interactions with Lys88, Lys100 and Arg102 in the binding site.
Specific cell surface labeling of GPCRs using split GFP
Authors: Jiang Wen-Xue , Dong Xu , Jiang Jing , Yang Yu-Hong , Yang Ju , Lu Yun-Bi , Fang San-Hua , Wei Er-Qing , Tang Chun , Zhang Wei-Ping 
Published: February 2016

AbstractSpecific cell surface labeling is essential for visualizing the internalization processes of G-protein coupled receptors (GPCRs) and for gaining mechanistic insight of GPCR functions. Here we present a rapid, specific and versatile labeling scheme for GPCRs at living-cell membrane with the use of a split green fluorescent protein (GFP). Demonstrated with two GPCRs, GPR17 and CysLT2R, we show that two β-stands (β-stands 10 and 11) derived from a superfolder GFP (sfGFP) can be engineered to one of the three extracellular loop of a GPCR. The complementary fragment of sfGFP has nine β-strands (β-stands 1-9) that carries the mature fluorophore and can be proteolytically derived from the full-length sfGFP. Separately the GFP fragments are non-fluorescent, but become fluorescent upon assembly, thus allowing specific labeling of the target proteins. The two GFP fragments rapidly assemble and the resulting complex is extremely tight under non-denaturing conditions, which allows real-time and quantitative assessment of the internalized GPCRs. We envision that this labeling scheme will be of great use for labeling other membrane proteins in various biological and pharmacological applications.