bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resolving molecule-specific information in dynamic lipid membrane processes with multi-resonant infrared metasurfaces
Authors: Rodrigo Daniel , Tittl Andreas , Ait-Bouziad Nadine , John-Herpin Aurelian , Limaj Odeta , Kelly Christopher , Yoo Daehan , Wittenberg Nathan J. , Oh Sang-Hyun , Lashuel Hilal A. , Altug Hatice 
Published: May 2018

AbstractA multitude of biological processes are enabled by complex interactions between lipid membranes and proteins. To understand such dynamic processes, it is crucial to differentiate the constituent biomolecular species and track their individual time evolution without invasive labels. Here, we present a label-free mid-infrared biosensor capable of distinguishing multiple analytes in heterogeneous biological samples with high sensitivity. Our technology leverages a multi-resonant metasurface to simultaneously enhance the different vibrational fingerprints of multiple biomolecules. By providing up to 1000-fold near-field intensity enhancement over both amide and methylene bands, our sensor resolves the interactions of lipid membranes with different polypeptides in real time. Significantly, we demonstrate that our label-free chemically specific sensor can analyze peptide-induced neurotransmitter cargo release from synaptic vesicle mimics. Our sensor opens up exciting possibilities for gaining new insights into biological processes such as signaling or transport in basic research as well as provides a valuable toolkit for bioanalytical and pharmaceutical applications.
Pancharatnam–Berry phase in condensate of indirect excitons
Authors: Leonard J. R. , High A. A. , Hammack A. T. , Fogler M. M. , Butov L. V. , Campman K. L. , Gossard A. C. 
Published: May 2018

AbstractThe Pancharatnam–Berry phase is a geometric phase acquired over a cycle of parameters in the Hamiltonian governing the evolution of the system. Here, we report on the observation of the Pancharatnam–Berry phase in a condensate of indirect excitons (IXs) in a GaAs-coupled quantum well structure. The Pancharatnam–Berry phase is directly measured by detecting phase shifts of interference fringes in IX interference patterns. Correlations are found between the phase shifts, polarization pattern of IX emission, and onset of IX spontaneous coherence. The evolving Pancharatnam–Berry phase is acquired due to coherent spin precession in IX condensate and is observed with no decay over lengths exceeding 10 μm indicating long-range coherent spin transport.
Precipitation and ectoparasitism reduce reproductive success in an arctic-nesting top-predator
Authors: Lamarre Vincent , Legagneux Pierre , Franke Alastair , Casajus Nicolas , Currie Douglas C. , Berteaux Dominique , Bêty Joël 
Published: May 2018

AbstractIndirect impacts of climate change, mediated by new species interactions (including pathogens or parasites) will likely be key drivers of biodiversity reorganization. In addition, direct effects of extreme weather events remain understudied. Simultaneous investigation of the significance of ectoparasites on host populations and extreme weather events is lacking, especially in the Arctic. Here we document the consequences of recent black fly outbreaks and extreme precipitation events on the reproductive output of an arctic top predator, the peregrine falcon (Falco peregrinus tundrius) nesting at the northern range limit of ornithophilic black flies in Nunavut, Canada. Overall, black fly outbreaks and heavy rain reduced annual nestling survival by up to 30% and 50% respectively. High mortality caused by ectoparasites followed record-breaking spring snow precipitation, which likely increased stream discharge and nutrient runoff, two key parameters involved in growth and survival of black fly larvae. Using the RCP4.5 intermediate climate scenario run under the Canadian Global Climate Model, we anticipate a northward expansion of black fly distribution in Arctic regions. Our case study demonstrates that, in the context of climate change, extreme weather events can have substantial direct and indirect effects on reproductive output of an arctic top-predator population.
Seasonal variation in a diverse beetle assemblage along two elevational gradients in the Australian Wet Tropics
Authors: Wardhaugh C. W. , Stone M. J. , Stork N. E. 
Published: May 2018

AbstractAltered abiotic conditions resulting from human-induced climate change are already driving changes in the spatial and temporal distributions of many organisms. For insects, how species are distributed across elevations is relatively well known, but data on their seasonality at different elevations are lacking. Here we show seasonal variation in beetle abundance and species richness along two spatially-distinct elevational transects (350–1000 m and 100–1000 m asl) in the rainforests of northern Australia. Temperature was the best predictor of temporal abundance and species richness patterns, while rainfall had little influence. Elevation had little effect on seasonal changes in abundance or diversity. Adults of most beetle species exhibited long season-lengths (>6 months of the year) with distinct peaks in abundance during the summer wet-season. We found evidence of phenotypic variation among the more widespread species, with seasonal peaks in abundance often not coinciding across elevations or transects. Due to the wide elevational range of most species, and the lack of consistency in the seasonality of wide-spread individual species, we suggest that many beetles inhabiting the low to mid-elevation mountains in the Wet Tropics, and potentially other tropical rainforests, are not as vulnerable to extinction due to climate change as many other organisms.
Protein kinase Cε regulates nuclear translocation of extracellular signal-regulated kinase, which contributes to bradykinin-induced cyclooxygenase-2 expression
Authors: Nakano Rei , Kitanaka Taku , Namba Shinichi , Kitanaka Nanako , Sugiya Hiroshi 
Published: May 2018

AbstractThe proinflammatory mediator bradykinin stimulated cyclooxygenase-2 (COX-2) expression and subsequently prostaglandin E2 synthesis in dermal fibroblasts. The involvement of B2 receptors and Gαq in the role of bradykinin was suggested by using pharmacological inhibitors. The PKC activator PMA stimulated COX-2 mRNA expression. Bradykinin failed to induce COX-2 mRNA expression in the presence of PKC inhibitors, whereas the effect of bradykinin was observed in the absence of extracellular Ca2+. Bradykinin-induced COX-2 mRNA expression was inhibited in cells transfected with PKCε siRNA. These observations suggest that the novel PKCε is concerned with bradykinin-induced COX-2 expression. Bradykinin-induced PKCε phosphorylation and COX-2 mRNA expression were inhibited by an inhibitor of 3-phosphoinositide-dependent protein kinase-1 (PDK-1), and bradykinin-induced PDK-1 phosphorylation was inhibited by phospholipase D (PLD) inhibitors, suggesting that PLD/PDK-1 pathway contributes to bradykinin-induced PKCε activation. Pharmacological and knockdown studies suggest that the extracellular signal-regulated kinase 1 (ERK1) MAPK signaling is involved in bradykinin-induced COX-2 expression. Bradykinin-induced ERK phosphorylation was attenuated in the cells pretreated with PKC inhibitors or transfected with PKCε siRNA. We observed the interaction between PKCε and ERK by co-immunoprecipitation experiments. These observations suggest that PKCε activation contributes to the regulation of ERK1 activation. Bradykinin stimulated the accumulation of phosphorylated ERK in the nuclear fraction, that was inhibited in the cells treated with PKC inhibitors or transfected with PKCε siRNA. Consequently, we concluded that bradykinin activates PKCε via the PLD/PDK-1 pathway, which subsequently induces activation and translocation of ERK1 into the nucleus, and contributes to COX-2 expression for prostaglandin E2 synthesis in dermal fibroblasts.
Characterisation of tree vibrations based on the model of orthogonal oscillations
Authors: Kovacic Ivana , Radomirovic Dragi , Zukovic Miodrag , Pavel Benka , Nikolic Milutin 
Published: May 2018

AbstractThis study presents quantitative and qualitative insights into the analysis of data obtained by tracking the motion of reflective markers arranged along the trunk of a pole-like potted tree, which was recorded by a state-of-the-art infrared motion-tracking system. The experimental results showed in-plane damped trajectories of the markers with lateral displacements, i.e. out-of-plane vibrations of the tree under consideration. To explain such response and to determine the corresponding oscillatory characteristics, a completely new and original utilisation of the recorded in-plane damped trajectories is presented. The quantitative insight gained is based on the mechanical model that consists of two orthogonal springs and dampers placed in the plane where the motion takes place, and it is then directed towards the determination of the characteristics of the related orthogonal oscillations: two natural frequencies, the position of the principal axes to which they correspond, and two damping ratios. The qualitative insight gained involves analysing the shape and narrowness of the trajectory to assess how close-valued two natural frequencies are, and how small the overall damping is. The quantitative and qualitative methodologies presented herein are seen as beneficial for arboriculture, forestry and botany, but given the fact that orthogonal oscillations appears in many natural and engineering systems, they are also expected to be useful for specialists in other fields of science and engineering as well.
Synthetic Rhamnolipid Bolaforms trigger an innate immune response in Arabidopsis thaliana
Authors: Luzuriaga-Loaiza W. Patricio , Schellenberger Romain , De Gaetano Yannick , Obounou Akong Firmin , Villaume Sandra , Crouzet Jérôme , Haudrechy Arnaud , Baillieul Fabienne , Clément Christophe , Lins Laurence , Allais Florent , Ongena Marc , Bouquillon Sandrine , Deleu Magali , Dorey Stephan 
Published: May 2018

AbstractStimulation of plant innate immunity by natural and synthetic elicitors is a promising alternative to conventional pesticides for a more sustainable agriculture. Sugar-based bolaamphiphiles are known for their biocompatibility, biodegradability and low toxicity. In this work, we show that Synthetic Rhamnolipid Bolaforms (SRBs) that have been synthesized by green chemistry trigger Arabidopsis innate immunity. Using structure-function analysis, we demonstrate that SRBs, depending on the acyl chain length, differentially activate early and late immunity-related plant defense responses and provide local increase in resistance to plant pathogenic bacteria. Our biophysical data suggest that SRBs can interact with plant biomimetic plasma membrane and open the possibility of a lipid driven process for plant-triggered immunity by SRBs.
Impairment of photoreceptor ribbon synapses in a novel Pomt1 conditional knockout mouse model of dystroglycanopathy
Authors: Rubio-Fernández Marcos , Uribe Mary Luz , Vicente-Tejedor Javier , Germain Francisco , Susín-Lara Cristina , Quereda Cristina , Montoliu Lluis , de la Villa Pedro , Martín-Nieto José , Cruces Jesús 
Published: May 2018

AbstractHypoglycosylation of α-dystroglycan (α-DG) resulting from deficiency of protein O-mannosyltransferase 1 (POMT1) may cause severe neuromuscular dystrophies with brain and eye anomalies, named dystroglycanopathies. The retinal involvement of these disorders motivated us to generate a conditional knockout (cKO) mouse experiencing a Pomt1 intragenic deletion (exons 3–4) during the development of photoreceptors, mediated by the Cre recombinase expressed from the cone-rod homeobox (Crx) gene promoter. In this mouse, retinal α-DG was unglycosylated and incapable of binding laminin. Retinal POMT1 deficiency caused significant impairments in both electroretinographic recordings and optokinetic reflex in Pomt1 cKO mice, and immunohistochemical analyses revealed the absence of β-DG and of the α-DG-interacting protein, pikachurin, in the outer plexiform layer (OPL). At the ultrastructural level, noticeable alterations were observed in the ribbon synapses established between photoreceptors and bipolar cells. Therefore, O-mannosylation of α-DG in the retina carried out by POMT1 is crucial for the establishment of proper synapses at the OPL and transmission of visual information from cones and rods to their postsynaptic neurons.
A gender specific improved survival related to stromal miR-143 and miR-145 expression in non-small cell lung cancer
Authors: Skjefstad Kaja , Johannessen Charles , Grindstad Thea , Kilvaer Thomas , Paulsen Erna-Elise , Pedersen Mona , Donnem Tom , Andersen Sigve , Bremnes Roy , Richardsen Elin , Al-Saad Samer , Busund Lill-Tove 
Published: May 2018

AbstractMicro RNAs (miRNA) are small non-coding RNAs that post-transcriptionally regulate gene expression. Dysregulation of miRNA cluster 143/145 has been reported in several malignancies, but their role in non-small cell lung cancer (NSCLC) remains elusive. This study investigates the prognostic impact of miR-143 and miR-145 in primary tumors and metastatic lymph nodes in NSCLC tissue. Tissue from 553 primary tumors and 143 matched metastatic lymph nodes were collected and tissue microarrays were constructed. In situ hybridization was used to evaluate miR-143 and miR-145 expression in tumor epithelial cells and stromal cells in the primary tumors and lymph nodes. In vivo data was supplemented with functional studies of cell lines in vitro to evaluate the role of miR-143 and miR-145 in NSCLC tumorigenesis. In our cohort, stromal miR-143 (S-miR-143) and miR-145 (S-miR-145) expression in primary tumor tissue were independent prognosticators of improved disease-specific survival (DSS) in female (S-miR-143, HR: 0.53, p = 0.019) and male patients (S-miR-145, HR: 0.58, p = 0.021), respectively. Interesting correlations between the miR cluster 143/145 and previously investigated steroid hormone receptors from the same cohort were identified, substantiating their gender dependent significance.
The impact of using BARCIST 1.0 criteria on quantification of BAT volume and activity in three independent cohorts of adults
Authors: Martinez-Tellez Borja , Nahon Kimberly J. , Sanchez-Delgado Guillermo , Abreu-Vieira Gustavo , Llamas-Elvira Jose M. , van Velden Floris H. P. , Pereira Arias-Bouda Lenka M. , Rensen Patrick C. N. , Boon Mariëtte R. , Ruiz Jonatan R. 
Published: May 2018

AbstractHuman brown adipose tissue (BAT) is commonly assessed by cold-induced 18F-fluorodeoxyglucose (FDG) PET-CT using several quantification criteria. Uniform criteria for data analysis became available recently (BARCIST 1.0). We compared BAT volume and activity following BARCIST 1.0 criteria against the most commonly used criteria [Hounsfield Units (HU):-250, -50, standardized uptake value (SUV):2.0; HU: Not applied, SUV:2.0 and HU:-180, -10, SUV:1.5] in a prospective study using three independent cohorts of men including young lean adults, young overweight/obese adults and middle-aged overweight/obese adults. BAT volume was the most variable outcome between criteria. While BAT volume calculated using the HU: NA; SUV: 2.0 criteria was up to 207% higher than the BAT volume calculated based on BARCIST 1.0 criteria, it was up to 57% lower using the HU: -250, -50; SUV: 2.0 criteria compared to the BARCIST 1.0. Similarly, BAT activity (expressed as SUVmean) also differed between different thresholds mainly because SUVmean depends on BAT volume. SUVpeak was the most consistent BAT outcome across the four study criteria. Of note, we replicated these findings in three independent cohorts. In conclusion, BAT volume and activity as determined by 18F-FDG-PET/CT highly depend on the quantification criteria used. Future human BAT studies should conduct sensitivity analysis with different thresholds in order to understand whether results are driven by the selected HU and/or SUV thresholds. The design of the present study precludes providing any conclusive threshold, but before more definitive thresholds for HU and SUV are available, we support the use of BARCIST 1.0 criteria to facilitate interpretation of BAT characteristics between research groups.
Cell-free protein synthesis as a novel tool for directed glycoengineering of active erythropoietin
Authors: Zemella Anne , Thoring Lena , Hoffmeister Christian , Šamalíková Mária , Ehren Patricia , Wüstenhagen Doreen A. , Kubick Stefan 
Published: May 2018

AbstractAs one of the most complex post-translational modification, glycosylation is widely involved in cell adhesion, cell proliferation and immune response. Nevertheless glycoproteins with an identical polypeptide backbone mostly differ in their glycosylation patterns. Due to this heterogeneity, the mapping of different glycosylation patterns to their associated function is nearly impossible. In the last years, glycoengineering tools including cell line engineering, chemoenzymatic remodeling and site-specific glycosylation have attracted increasing interest. The therapeutic hormone erythropoietin (EPO) has been investigated in particular by various groups to establish a production process resulting in a defined glycosylation pattern. However commercially available recombinant human EPO shows batch-to-batch variations in its glycoforms. Therefore we present an alternative method for the synthesis of active glycosylated EPO with an engineered O-glycosylation site by combining eukaryotic cell-free protein synthesis and site-directed incorporation of non-canonical amino acids with subsequent chemoselective modifications.
Effective thresholds for reporting suspicions and improve early detection of avian influenza outbreaks in layer chickens
Authors: Gonzales Jose L. , Elbers Armin R. W. 
Published: May 2018

AbstractThe objective of this study was to identify effective reporting thresholds for suspicions of both highly pathogenic (HPAI) and low pathogenic avian influenza (LPAI) outbreaks in layer farms. Daily mortality and egg-production data from 30 Dutch farms with no record of AI infection were analysed and thresholds set. Mortality rates above or egg-production below these thresholds for two consecutive days would trigger an alarm sign. The following thresholds were identified for mortality: (i) A mortality threshold of 0.08% or 0.13% for layers kept indoors or with free-range access respectively, (ii) a 2.9 times higher mortality than the average weekly mortality of the previous week, and iii) a moving-average threshold that could be implemented for each specific farm. For egg-production: (i) a weekly ratio lower than 0.94 in egg-production drop, and (ii) a moving-average threshold. The accuracy of these thresholds was assessed by quantifying their sensitivity, specificity and time to trigger disease detection using data from 15 infected and 31 non-infected farms. New thresholds were more sensitive and signalled infection two to six days earlier than the presently used thresholds. A high Specificity (97–100%) was obtained by combining mortality and egg production thresholds in a serial approach to trigger an alarm.
Biphasic regulation of tumorigenesis by PTK7 expression level in esophageal squamous cell carcinoma
Authors: Shin Won-Sik , Gim Jungsoo , Won Sungho , Lee Seung-Taek 
Published: May 2018

AbstractProtein tyrosine kinase 7 (PTK7), also known as colon carcinoma kinase 4 (CCK-4), is a member of the catalytically defective receptor protein tyrosine kinase family and is upregulated in various cancers, where it is known to act as either an oncoprotein or a tumor suppressor. To understand the contrasting roles of PTK7 in tumorigenesis, we analyzed the tumorigenic characteristics of esophageal squamous cell carcinoma (ESCC) cells with low levels of endogenous PTK7 expression (TE-5 and TE-14 cells) and high levels of expression (TE-6 and TE-10 cells) after transfections with a PTK7 expression vector. PTK7 overexpression increased the proliferation of TE-5 and TE-14 cells but decreased the proliferation of TE-6 and TE-10 cells. In the ESCC cells, proliferation, migration, and invasion were initially increased and then decreased according to PTK7 expression levels, which were mirrored by initial increases and then decreases in the tyrosine phosphorylation of cellular proteins and phosphorylation of Src, Akt, and ERK. In ESCC patients included in The Cancer Genome Atlas database, those with higher PTK7 mRNA levels had a longer overall survival and lower relative risk than those with lower PTK7 mRNA levels. These results demonstrate that PTK7 biphasically regulates tumorigenesis in ESCC.
Modelling The Combined Effects Of Collagen and Cyclic Strain On Cellular Orientation In Collagenous Tissues
Authors: Ristori T. , Notermans T. M. W. , Foolen J. , Kurniawan N. A. , Bouten C. V. C. , Baaijens F. P. T. , Loerakker S. 
Published: May 2018

AbstractAdherent cells are generally able to reorient in response to cyclic strain. In three-dimensional tissues, however, extracellular collagen can affect this cellular response. In this study, a computational model able to predict the combined effects of mechanical stimuli and collagen on cellular (re)orientation was developed. In particular, a recently proposed computational model (which only accounts for mechanical stimuli) was extended by considering two hypotheses on how collagen influences cellular (re)orientation: collagen contributes to cell alignment by providing topographical cues (contact guidance); or collagen causes a spatial obstruction for cellular reorientation (steric hindrance). In addition, we developed an evolution law to predict cell-induced collagen realignment. The hypotheses were tested by simulating bi- or uniaxially constrained cell-populated collagen gels with different collagen densities, subjected to immediate or delayed uniaxial cyclic strain with varying strain amplitudes. The simulation outcomes are in agreement with previous experimental reports. Taken together, our computational approach is a promising tool to understand and predict the remodeling of collagenous tissues, such as native or tissue-engineered arteries and heart valves.
Micro-computed tomography reconstructions of tibiae of stem cell transplanted osteogenesis imperfecta mice
Authors: Ranzoni Anna M. , Corcelli Michelangelo , Arnett Timothy R. , Guillot Pascale V. 
Published: May 2018

AbstractMicro-computed tomography (micro-CT) is commonly used to assess bone quality and to evaluate the outcome of experimental therapies in animal models of bone diseases. Generating large datasets is however challenging and data are rarely made publicly available through shared repositories. Here we describe a dataset of micro-CT reconstructed scans of the proximal part of 21 tibiae from wild-type mice, osteogenesis imperfecta mice (homozygous oim/oim) and oim/oim mice transplanted with human amniotic fluid stem cells. The dataset contains, for each sample, 991 8-bit Bitmap reconstructed images and a 3D reconstruction of the bone in the PLY format, available at the online repository Figshare. In line with the increasing effort to make scientific datasets open-access, our data can be downloaded and used by other researchers to compare their observations with ours and to directly test scientific questions on osteogenesis imperfecta bones without the need to generate complete datasets.